tag:blogger.com,1999:blog-71275263344194234992024-02-21T08:00:02.719-08:00Here Be Dragons A Biology BlogUnknownnoreply@blogger.comBlogger53125tag:blogger.com,1999:blog-7127526334419423499.post-89021972997680102672019-07-29T21:30:00.001-07:002019-07-29T21:34:34.478-07:00Novel Insights on the Biochemistry of Immune Activation<div dir="ltr" style="text-align: left;" trbidi="on">
<i>Maliha Tanjum Chowdhury Deneb</i><br />
<i>Junior</i><br />
<i>School of Life Sciences</i><br />
<i>Independent University, Bangladesh</i><br />
<i><br /></i>
<i>July 30th, 2019</i><br />
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The remarkable ability of immune cells to alter their functions upon activation is a phenomenon that is well known to most biologists. When we think of cellular differentiation or activation, our minds typically drift to the explanation that it is due to changes in gene expression. While it is true that the systematic reprogramming of gene expression is key to transitioning between cellular states, some exciting recent studies times have added another layer of understanding by showing that phenotypic changes in the context of immune cells are also often accompanied by metabolic changes. But before we dive into some of this recent work, some context is necessary.<br />
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Innate immune cells constantly patrolling our tissues recognize threats on the basis of special structures that are unique to various classes of pathogens, collectively known as pathogen-associated molecular patterns (PAMPs). For instance, lipopolysaccharide serves as a signature of Gram-negative bacteria. This recognition is mediated by receptors on innate immune cells called pattern recognition receptors (PRRs). In contrast, adaptive immune cells, (B and T cells), upon initial activation, take a few days to learn to recognize antigens - unique signatures associated with specific pathogens - via B cell receptors (antibodies), and T cell receptors (TCRs). These cells retain memory and act rapidly upon reinfection.<br />
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<tr><td class="tr-caption" style="text-align: center;">Immune cells chasing down microbes.<i> Ilora Shabnam Kheya</i></td></tr>
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It is increasingly evident that specific metabolic pathways are more suited to support different immune states. A well-established example is that of macrophages [1] - innate immune cells which are among the first responders during infection. Macrophages have multiple, mainly two, activated states. An initial activation by pathogens results in M1 or classically activated macrophages, which ramp up inflammation. Inflammation refers to the migration of immune cells to an infected site and the accompanying release of various chemicals to target pathogens. As part of this process, M1 macrophages metabolize the amino acid arginine to produce nitric oxide – a toxic product to kill pathogens – via the enzyme nitric oxide synthase. However, as the infection progresses and the pathogens are cleared, the macrophages switch to M2 or alternatively activated macrophages, which are dedicated to repair collateral damage caused by inflammation, and these cells now metabolize arginine using the enzyme arginase 1 to produce ornithine – an amino acid that is used for tissue re-modelling. Such interplay between immunity and metabolism is now being referred to as immunometabolism. Let us now delve into three recent studies which deal with exciting findings in the field of immunometabolism.<br />
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The first of these studies explored changes in metabolic states of immune cells in the context of Mycobacterium tuberculosis infections [2]. Previous research had shown that most immune cell types, upon activation, adopt an alternative metabolic pathway known as aerobic glycolysis to generate energy over the conventional TCA cycle and oxidative phosphorylation. This alternative pathway, which produces lactate even in the presence of oxygen, is much more effective at producing a substantial amount of energy in a short time, even though the amount of energy produced per glucose molecule is less than what is produced via the conventional route. Immune effector cells appear to favor speed over efficiency in order to meet the towering demands of quickly producing signals, mediating downstream activation of other immune cells, and killing pathogens.<br />
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The study first established that M. tuberculosis infection induces a shift to the aerobic glycolytic pathway in human peripheral blood mononuclear cells (PBMCs, which include lymphocytes). They then showed that M. tuberculosis infection activates the AKT-mTOR pathway, a cell signaling pathway known to trigger glucose metabolism, among other cellular processes, in response to signals like growth factors and oxidative stress. Chemical inhibition of this pathway resulted in low lactate levels and poor inflammatory cytokine release to fight the infection both in mice and in human PBMCs, thereby establishing a role for the AKT-mTOR pathway in aerobic glycolysis induction as well as immune activation. They also showed that glycolysis induction by M. tuberculosis is dependent on a receptor called TLR2, which recognizes components of the bacterial cell wall. These results indicate that enzymes that are part of this metabolic pathway could perhaps be targeted to bring about a stronger host immune response while fighting tuberculosis, if needed.<br />
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A more recent study, published in 2018 [3] explored metabolic rewiring of an adaptive immune cell type called T cells. They were using human cells. T cells have a wide-range of functions, and numerous sub-types which facilitate these functions. Some T cell types contribute to inflammation, and/or killing of infected cells upon detection of pathogens, while others, broadly grouped together as T regulatory (Treg) cells suppress the production of, and activation by inflammatory signals. The Treg cells are important because they prevent the system from going overboard and causing damage to organs and tissues of the body. Differentiation into Treg cells is known to be dependent on a transcription factor called Foxp3, and individuals with defects in Foxp3 are poorly tolerized to a range of self-antigens, giving rise to several types of autoimmune disorders.<br />
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Now, a large proportion of Treg cells belong to a larger class of T cells called CD4 positive T cells. CD4 positive T cells exhibit phenotypic plasticity, meaning that they can interchange between different states that are suited to fighting different classes of pathogens, as well as regulatory states. In the 2018 study, the authors reported the transformation of an inflammatory T cell type called T helper type 1 cells to Treg-like cells (dubbed TH1reg cells) by resting the cells in the absence of activation of their T cell receptors before activating the receptors in the presence of TGF-β (a growth factor involved in the normal development of Treg cells from progenitors, and in wound healing). This makes physiological sense, as the progressive clearance of pathogens and their associated antigens after an infection would be expected to result in less frequent T cell receptor stimulation, and TGF-β levels may increase due to tissue damage from inflammation.<br />
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The authors went on to find that the treatment elevated Foxp3 expression through a change in metabolic regulation, leading to the Treg-like phenotype. In the absence of receptor activation, there is reduced mTOR signaling in the T cells, and this allows TGF-β-mediated elevation of Foxp3 expression while also making the cells switch from glycolysis to oxidative phosphorylation as the mode of energy generation. While the molecular mechanism connecting the metabolic switch and TGF-β-mediated expression of Foxp3 needs to be further explored, this study again points to the possibility of targeting metabolic or signaling pathways, in this case to curb inflammatory T cells implicated in autoimmune disorders and immunopathologies.<br />
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Our third and final recent study [4], published just this year, deals with a very interesting twist on the role of innate immunity in battling cancer. Cancer cells arise from unwanted mutations occuring in normal cells and causing them to divide uncontrollably. Therefore, by default, they express most if not all of the normal cell surface proteins that are known in the body as self-antigens. One such antigen, which acts as a “don’t-eat-me” signal is the CD47 protein. “Don’t-eat-me” implies that these proteins inhibit macrophages from phagocytizing (eating) the individual’s own cells. Recall that macrophages are phagocytic cells that have two distinct phenotypes – either the pro-inflammatory M1, or the anti-inflammatory M2. M1 macrophages have ways of detecting and killing cancer cells despite the “don’t-eat-me” signal. But in the case of many tumors, macrophages surrounding the tumor take on an M2-like phenotype, and produce cell proliferation signals that may assist both tumor progression and immunosuppression.<br />
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In this regard, this study shows that stimulation of the PRR, the Toll-like receptor 9 (TLR 9), by CpG oligonucleotide (a DAMP produced due to cell damage and cancerous growth) causes a shift in the central carbon metabolism of mouse macrophages to a state requiring fatty acid oxidation. This allows overriding of the “don’t-eat-me” signal and phagocytosis of the cancer cells expressing CD47. Interestingly, this does not require differentiation into an M1 state. Fatty acid oxidation, and the accompanying rewiring of the TCA cycle to support this oxidative state, somehow facilitate the anti-tumor activity of the macrophages. Therefore, manipulation of the carbon metabolism pathway of the macrophages is highlighted as a possible therapeutic mechanism to fight cancer. However, the problem is that human macrophages lack the TLR 9 receptor, and so the challenge of inducing such changes in mode and implementing them clinically in humans remains and is demanding of further research.<br />
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In the papers discussed in this piece, the scientists triggered and recorded metabolic changes in immune cells simply by using the right kinds of receptor stimulation and cytokines, but these findings barely scratch the surface. In the future, it might be possible to manipulate immune phenotypes by directly targeting metabolic pathways through enzymes and enzyme blockers.<br />
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<b>References:</b><br />
<br />
[1] K. Ley, “M1 Means Kill; M2 Means Heal,” J. Immunol., vol. 199, no. 7, p. 2191, Oct. 2017.<br />
[2] E. Lachmandas et al., “Rewiring cellular metabolism via the AKT/mTOR pathway contributes to host defence against Mycobacterium tuberculosis in human and murine cells,” Eur. J. Immunol., vol. 46, no. 11, pp. 2574–2586, Nov. 2016.<br />
[3] M. Kanamori, H. Nakatsukasa, M. Ito, S. Chikuma, and A. Yoshimura, “Reprogramming of Th1 cells into regulatory T cells through rewiring of the metabolic status,” Int. Immunol., vol. 30, no. 8, pp. 357–373, Jul. 2018.<br />
[4] M. Liu, R. S. O’Connor, S. Trefely, K. Graham, N. W. Snyder, and G. L. Beatty, “Metabolic rewiring of macrophages by CpG potentiates clearance of cancer cells and overcomes tumor-expressed CD47−mediated ‘don’t-eat-me’ signal,” Nat. Immunol., vol. 20, no. 3, pp. 265–275, Mar. 2019.<br />
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<i>Maliha is a weirdo who somehow believes she's from a different planet. But she likes Earth just fine, and is fascinated by the science and beauty of life and has made it her purpose to explore it. Besides this, her most burning desires include becoming a synthetic biologist/ genetic engineer and running away with a heavy metal band.</i><br />
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-74202681475984601462019-04-03T00:55:00.002-07:002019-04-06T02:32:43.576-07:00Leading the Next Medical Revolution: Dr. Nazneen Aziz on Her Work in Genomics and Precision Medicine<div dir="ltr" style="text-align: left;" trbidi="on">
<i>This interview was conducted on February 13th, 2019, by:</i><br />
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<i>Tahsin Tabassum, Tasmin Tabassum, Ridwan Hossain, Maliha Tanjum Chowdhury, and Jabale Rahmat</i></div>
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<i>Juniors at the Schools of Life Sciences</i></div>
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<i>Independent University, Bangladesh</i></div>
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<i>Published on April 3rd, 2019</i></div>
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Dr. Nazneen Aziz, Ph.D., the
President and CEO of Variant Genomics, Inc. Variant Genomics provides expert
advice and guidance for implementing clinical genomic testing and precision
medicine research in the community health care systems in the US as well as in
developing nations. She is the former Executive Director of the Kaiser
Permanente Research Bank and Senior Vice President and Chief Research Officer
at Phoenix Children’s Hospital and the Director of Molecular Medicine at the
College of American Pathologists (CAP). Dr.
Aziz has held executive leadership positions in the biotech/biopharma industry.
In her industry career, Dr. Aziz focused on personalized medicine, biomarkers,
genetic tests, and development of drugs for cancer and diabetes. Prior to
joining the biotechnology industry, Dr. Aziz was an Assistant Professor at
Harvard Medical School and Boston Children's Hospital where she discovered new genes
and their role in polycystic kidney disease. She currently holds Adjunct
Professorships in the School of Life Sciences at Arizona State University and
in the Department of Child Health at University of Arizona College of Medicine.<br />
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Dr. Aziz received her
Ph.D. in Molecular Genetics and MS in Biochemistry at the Massachusetts</div>
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Institute of Technology
(MIT) and her BA (Honors) in Biological Sciences from Wellesley College.<o:p></o:p></div>
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She has several issued
and pending patents. Her publications have been cited extensively in the<o:p></o:p></div>
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medical and scientific
literature and she has been invited to speak at numerous national and<o:p></o:p></div>
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international
conferences.<o:p></o:p></div>
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During a visit to IUB to conduct a highly informative and engaging seminar on precision medicine, Dr. Aziz graciously agreed to be interviewed by some of the students from the School of Life Sciences for the <i>HERE BE DRAGONS </i>blog<i>.</i> The following transcript of her interview contains amazing advice for students and early career scientists thinking about going into industry, as well as numerous insights on genomics and precision medicine, and the prospect of using such technology in Bangladesh.</div>
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<b>Maliha: <i>For
someone who was in academia, how was the transition into industry? What are the
similarities and differences you experienced between the two?</i><o:p></o:p></b></div>
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<b>Dr. Aziz:</b> A very
good question. In my experience, as a faculty at Harvard Medical School for 8
years, I was completely independent. I had my own funding and my own lab while conducting
research in discovering new genes and their functions in polycystic kidney
disease. I loved interacting with my lab team – students, technicians,
post-doctoral and medical fellows. We were one team and working the course of
action that were my labs research objectives. <span style="mso-spacerun: yes;"> </span>I loved that independence, the thrill of discovery
research from large victories to small successes. <span style="mso-spacerun: yes;"> </span>For example, the euphoria that comes with
discovering a new gene associated with a devastating disease to the simple joy
of running a successful electrophoresis gel. So really, there is great
satisfaction and contentment in academic research. However I realized that if I
stayed in academia for a very long period of time my focus would become too
narrowed into my own specialized field. I <span style="mso-spacerun: yes;"> </span>wanted to make a contribution to healthcare
and not just be highly focused on getting another publication that may or may
not translated into products or that would impact human health in the near term.
This area of research is called translational research and it had a strong
appeal for me. <span style="mso-spacerun: yes;"> </span>I decided to move into
the biotechnology industry which was growing rapidly in Cambridge, MA in early
2000 with spin-off companies being created from MIT and Harvard.<br />
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The biggest difference between the two worlds- academics and
biotechnology- is that the research that you conduct in biotech is not solely
determined by you but it follows the company’s greater goals and objectives. However,
because I was in a leadership role in my biotech/biopharma career, I did have
the authority to delineate the scientific and technical strategy of the company
and the research direction. And I really think that my industry career has helped
shape my strategic thinking and built my business acumen. I think the biotech
industry experience has broadened my horizons as well. My discoveries and
publications of my academic research <span style="mso-spacerun: yes;"> </span>were
certainly important contributions to the scientific community. However, the
products that you create whether it is a drug or a genetic test ---things in
the research and development realm or in the translational research realm in biotech
have a more immediate impact on human health. <span style="mso-spacerun: yes;"> </span>It is a gratifying experience.<br />
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<b>Maliha: <i>Students
completing undergraduate and Master’s programs in fields like Biochemistry and
Microbiology often want to go on to do basic science research in academia. How
do you attract or recruit such people into the industry instead? And if you
have to convince them, what advice would you have for them to succeed?</i></b><br />
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<b>Dr. Aziz: </b>I think
academic research is a great choice for some but others may choose to go into
biotechnology/biopharmaceutical industry to develop medical devices, medicine,
genetic tests or consider a healthcare profession that could range from being a
medical doctor to a medical technologist, genetic counseling etc.<span style="mso-spacerun: yes;"> </span>However, the opportunities for these
alternative careers has to be readily available. In Bangladesh, I am not sure
how developed the biotech and health technology industry has become.<span style="mso-spacerun: yes;"> </span>Industry leaders should open up internships
in their organizations for students. Graduates of the life sciences should
certain try to do internships in these alternative career paths<span style="mso-spacerun: yes;"> </span>to see if that line of work appeals to them
or not.<br />
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<b>Maliha: <i>Does your
company currently have any collaborations with any academic institutions?</i></b><br />
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<b>Dr. Aziz:</b> Yes,
indeed. <span style="mso-spacerun: yes;"> </span>Variant Genomics’ business is to
advice and provide guidance to help community healthcare organizations in the
USA to implement precision medicine in the care of patients. That involves keeping
very deep connections with numerous academic professionals as well as the
biotech/genomic healthcare industry. My company uses a number of consultants in
these different sectors for various projects. <span style="mso-spacerun: yes;"> </span>Precision medicine also referred to as genomic
medicine has been growing and evolving at a rapid pace. This excitement has
attracted many from the academic sector to seek opportunities in the precision
medicine industry. <span style="mso-spacerun: yes;"> </span>There is an intense
appeal of this burgeoning and cutting-edge diagnostic technology that requires
a merging of research and clinical care. In the USA, <span style="mso-spacerun: yes;"> </span>there are many examples of how academics,
healthcare and genomic industries are working closely as there has been a keen awareness
that it takes diverse skillsets to deliver the benefits of genomic technologies
for patient care.<br />
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<b>Maliha: <i>How much
experience would a student who completed their Master’s degree in biological
sciences need in order to work in companies like yours?</i></b><br />
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<b>Dr. Aziz:</b> It
really depends on the position you want to hold in those companies. For
example, if you want to be a medical technologist, you would need to learn how
to operate cutting-edge instruments such next generation sequencing machines.
The same is true for bioinformaticians who would need to be proficient in next
generation data analysis. Interpretation scientists to understand and create
knowledge databases. <span style="mso-spacerun: yes;"> </span>Therefore, I would
say that for these entry level jobs, one would not need too much previous
experience other than internships and learnings through coursework in the
Master’s degree since they would receive comprehensive training on the job.<br />
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<b>Jabale: <i>Doctors have not traditionally been trained in genomics. How might doctors and medical professionals in Bangladesh and similar countries be trained on the use of genomics and precision medicine?</i></b><br />
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<b>Dr. Aziz:</b> This is one of the bottlenecks in the implementation of
precision medicine. Even in the US, doctors do not get intensive education or
training in medical genetics in their medical curriculum even though in recent
years that has changed. With genomics bursting into the clinical care scene
around 2010 it is a bit overwhelming for doctors everywhere, not just in
Bangladesh, to understand how to approach it. As you know, genomics is based on the concept
of genetics except that it involves a much greater volume of data. Most physicians do understand that this new field
is coming close to home and yet they don’t have the time to learn a whole new
science which leads to certain level of fear of the unknown. Therefore, there
is a great need for companies like Variant Genomics and other genomic companies
to develop tools, services and products to make it seamless and easy for
doctors. All physicians need to do is to understand the power of genomics in
patient care by educating themselves. They do not need to learn the
complexities of next generation sequencing, data analysis and interpretation
but that they should be aware of where to order genomic tests for the care of
their patients.<br />
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In the USA, there is the
requirement for medical doctors to take Continuing Medical Education (CME). CME
can be fulfilled in a variety of ways, for example, attending a medical or
scientific conference, taking an online course. It is important for Bangladesh
to consider something of this nature so that doctors can keep up with the new
research and new advancements in medical knowledge and how they can implement these
new advancement in healthcare in patient care.<br />
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<b>Jabale: <i>How often do you find Single Nucleotide Polymorphisms
(SNPs) in non-coding DNA regions like satellite DNA or any other repetitive DNA
that actually are associated with disease?</i></b><br />
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<b>Dr. Aziz: </b>There are 3 to 4 million variants within individual
genomes. The majority of the SNVs are in non-coding areas. The monogenic diseases
(more serious types) are due to<i style="mso-bidi-font-style: normal;"> SNVs</i> <i style="mso-bidi-font-style: normal;">or structural variants</i> that are
generally found in the coding regions of the genes. These SNVs tend to disrupt
the protein code and so they are rarer in frequency in the human
population.<br />
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Many of the variants in the
non-coding regions are benign. Recently, there is a greater appreciation
regarding the role of noncoding SNVs in complex genetic diseases, e.g.,
hypertension and type 2 diabetes. <span style="mso-spacerun: yes;"> </span>Complex
genetic diseases are a different category of genetic disease than the monogenic
(Mendelian) types. More and more research is leading to our understanding that SNVs
in non-coding regions of our genome are associated with complex genetic
diseases. For example, if a SNV happens to alter a gene regulatory motif in the
promoter region, or in enhancers within introns and in intergenic spaces they
can aberrantly regulate the expression of the gene which can lead to disease. <span style="mso-spacerun: yes;"> </span>ENCODE was a big project funded by the NIH that
investigated the function of non-coding regions of the human genome. <o:p></o:p></div>
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<b>Tahsin: <i>Do you expect there to be challenges to setting up
precision medicine in a country like Bangladesh?</i></b><br />
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<b>Dr. Aziz:</b> Perhaps it is important to emphasize that precision medicine
is not as difficult as the name suggests. A simple way to think of the field of
precision medicine is to call it genomic medicine-- a specialized field that
utilizes a new high throughput and cost effective DNA sequencing technology,
called next generation sequencing to analyze a patient’s DNA. The DNA analysis
provides insights in to the patient’s disease and how they should be managed
based on their genetic profile. There
are molecular diagnostic labs in Bangladesh that does simple genotyping and PCR
tests. Precision medicine or genomic testing is just a much large scale version
of singe gene analysis.<br />
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Certainly, there will be some challenges in the initial
phases of setting up clinical genomics in Bangladesh, especially since the
higher education in the new field of human genomics in this country is somewhat
lagging behind other developing nations. However, a challenge is always an
opportunity. I would find it exceedingly satisfying if my efforts can help pave
the first steps towards implementing precision medicine in healthcare. What my
company, Variant Genomics, intends to do is to make genomic tests easily
available for patients in Bangladesh. These tests are being used in many
aspects of clinical care. For example, in cancer, NGS tests can identify and
match targeted drugs for patients. In pharmacogenomics, tests can identify if
patients will have adverse reactions to certain medications. In inherited
disease, NGS identify the genetic causes of diseases.<br />
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Bangladeshi healthcare systems have implemented very complex
technologies such as MRI, CAT scans, PET scans including complex surgical
procedures and therefore it would be a natural evolution for Bangladesh to develop
the field of precision medicine next. It would give patients access to genomic
tests that are routinely being used elsewhere in the world. I do not think it
would be enormously challenging to bring this genomic testing technology to
Bangladesh especially since India, Thailand, and other developing nations have
already implemented genomic testing in healthcare.<br />
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<b>Tahsin: <i>Do you
think doctors attending seminars and conferences are enough to help them
understand and execute precision medicine?</i></b><br />
<b><i><br /></i></b></div>
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<b>Dr. Aziz:</b> It is
not enough, but it creates awareness. <span style="mso-spacerun: yes;"> </span>The
physician will be aware that there are better options than chemo and radiation
for their cancer patients. <span style="mso-spacerun: yes;"> </span>They will
know the right questions to ask when they come across patients who are
suffering from genetic diseases or patients who respond adversely to many
medicines. Doctor don’t need to understand how to conduct the genomic test but
just be aware that this new technology exists and where to order the test. The
reports for these tests lay out the interpretation of the results and guides
the physicians with knowledge available on how to manage the patient based on
their genetic profile.<br />
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By going to conferences and seminars, physicians become aware
of the latest advances in medicine and diagnostics. <span style="mso-spacerun: yes;"> </span>Wouldn’t you want your doctor to provide you
the most effective medicine or the best test available in case you were the
patient being treated in Bangladesh?<br />
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<b>Tasmin: <i>Is there
anything related to genomics that you are working on currently in Bangladesh?</i></b><br />
<b><i><br /></i></b></div>
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<b>Dr. Aziz:</b> I want
to start with bringing awareness that genomic testing labs are needed in
Bangladesh. Hospitals and diagnostic
labs are well aware that patient samples are being sent abroad for testing in
large numbers.<br />
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My goal is to bring this technology to Bangladesh and to
spread awareness that inherited diseases and cancers can be due to ethnicity
specific mutations. Therefore, there is a huge need to bring this technology to
this country in order to look at patient’s genetic profile from the context of ethnicity.<br />
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<b>Ridwan: <i>If
precision medicine was to become the norm, that could lead to a contraction in
the market for individual drugs. How will pharmaceutical companies handle this?
Will the drugs become more expensive because they are for specific people and
not everyone can use it? In the long term, will it become a problem?</i></b><br />
<b><i><br /></i></b></div>
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<b>Dr. Aziz:</b> This
argument of shrinking market size for a drug is now proving to be without merit
and had raised concerns for the pharma industry initially. <span style="mso-spacerun: yes;"> </span>Pharmaceutical companies have traditionally
tried to create blockbuster drugs which will make them $1 billion annually
called “block buster drugs”. They have had very little success in marketing
blockbuster drugs in recent years, so the industry is becoming very aware that
they need to adopt a different approach.<br />
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I look at the
precision medicine area with <i style="mso-bidi-font-style: normal;">optimism</i>.
<span style="mso-spacerun: yes;"> </span>Incorporating precision medicine will
allow pharmaceutical companies to manufacture and sell <i style="mso-bidi-font-style: normal;">many more classes of</i> medicine.<span style="mso-spacerun: yes;">
</span>There will be subgroups of patients who will match medications because
these drugs <i style="mso-bidi-font-style: normal;">will actually work in that
group of patients</i> <span style="mso-spacerun: yes;"> </span>and a simple
genomic test can find that match. Wouldn’t we want to know if the drug is
actually helping the patient or that it can harm the patient?<span style="mso-spacerun: yes;"> </span>Pharmaceutical companies actually do want
their drugs to be efficacious and to lead to fewer adverse events. In the US
and in Europe, they are now doing clinical trials and investing genetic markers
of people who respond or don’t respond to new investigational drugs during the
development phase.<br />
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Regarding the price of these targeted drugs for cancer,
there are over 200 or more that have been approved by the FDA and over 650
drugs listed that have a pharmacogenetic associations and it has not led to any
significant increase in pricing or availability. It is just a safer and effective
use of drugs for patient care.<br />
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<b>Ridwan: <i>Will the
availability of these drugs all around the world be an issue?</i></b><br />
<b><i><br /></i></b></div>
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<b>Dr. Aziz:</b> Targeted
oncology drugs are becoming available all around the world. Pharmaceutical
companies market their drugs all over the world. If an effective medication is
there it will ultimately make it to patients around the world.<br />
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<b>Ridwan: <i>What are
you currently finding out about the possibility of using precision medicine in
this country?</i></b><br />
<b><i><br /></i></b></div>
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<b>Dr. Aziz:</b> I am
exploring whether healthcare and academic leaders understand what precision
medicine is all about. I am actually happily surprised to see how receptive
they are to implementing this technology. I think Bangladesh has gone through
some remarkable achievements in recent years and has now been classified as a
middle income nation. With the expanding middle class there is also greater
expectation of the population of access to better healthcare– drugs that are
efficacious and diagnostics that can precisely identify the cause of the
disease.<span style="mso-spacerun: yes;"> </span>Therefore, Bangladesh is poised
to implement this powerful technology <i style="mso-bidi-font-style: normal;">because
it is cost effective in the overall scheme</i>.<br />
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<b>Ridwan: <i>A recent population
genomics study showed that African-Americans showed more elevated inflammatory
responses to pathogens than European-Americans as a result of differences in
their genomes. Can you explain to our readers how precision medicine can help
to more effectively treat diseases that occur differently between populations?</i></b><br />
<b><i><br /></i></b></div>
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<b>Dr. Aziz: </b>I am
not aware of this particular study you mention.<span style="mso-spacerun: yes;">
</span>In general the more we understand about genetic differences in health
and disease in different ethnic groups, the better prepared we are with that
knowledge to manage patients of different ethnic groups.<br />
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<b>Ridwan: <i>Could
studying the differences between different ethnicities lead to more
discrimination?</i></b><br />
<b><i><br /></i></b></div>
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<b>Dr. Aziz:</b> It is
good to study genetic diversity. It shouldn’t lead to racial discrimination
with the proper regulatory framework in place. In the USA, there is a law
called GINA (Genetic Information Nondiscrimination Act) which was passed in
2003. <span style="mso-spacerun: yes;"> </span>Every new technology needs
appropriate policies in place. Genetic differences among patients with
different ethnicities should only be used <span style="mso-spacerun: yes;"> </span>for maximizing its benefits in their medical
care. In the USA and Europe researchers have focused
genetic studies heavily with European Caucasians recruits and therefore at this
time we have realized that we do not fully understand genetic diseases in
minority populations. Therefore much effort is being expended for equitable
health access and in studying the minority populations in the USA through the <i style="mso-bidi-font-style: normal;">All of Us</i> program initiated by President
Obama. It is just as important to develop understanding here in Bangladesh of
the genetics of the Bengali populations. <o:p></o:p></div>
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-25846961570007769852019-03-23T12:30:00.007-07:002021-03-18T00:47:19.307-07:00Bacteria in the Atmosphere Bring Snow and Lightning<div dir="ltr" style="text-align: left;" trbidi="on">
<i>Ridwan Hossain</i><br />
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<i>Junior</i></div>
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<i>School of Life Sciences</i></div>
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<i>Independent University, Bangladesh</i></div>
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<i>March 23rd, 2019</i></div>
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We know that our planet is infested with bacteria and that they play major roles in the earth’s ecosystem. For instance, nitrogen-fixing bacteria enable the nitrogen cycle that is essential for the protein-based life forms on earth, while cyanobacteria in the ocean are responsible for a large proportion of atmospheric carbon fixation. Fascinatingly, thanks to a string of studies over the past decade, we are learning that bacteria play a part in our weather system as well.<br />
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To understand how that works we need to think about how precipitation occurs. In our planet’s water cycle, water is taken up into the atmosphere by evaporation, and this in turn later comes down as rain, hail, or snow. Scientists have realized that a huge number of bacteria is also taken up into the atmosphere along with the water. And it turns out that while they are up there, the bacteria play an important role in precipitation.<br />
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Some specific types of bacteria, found largely among Gammaproteobacteria, act as ice nuclei. Ice nucleation is when something acts as the nucleus for the formation of ice around it. Such bacteria have specific proteins on their surfaces which result in the formation of ice a lot more rapidly and at higher temperatures than would otherwise occur. This often damages plants by promoting the formation of frost, but when these ice-nucleating bacteria are present in the atmosphere, the water in the atmosphere becomes rapidly condensed into ice. When they become too heavy to keep floating in the sky, they fall as rain, snow or hail, depending on temperatures closer to the surface.</div>
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<span style="font-size: x-small;">Ice-nucleating bacteria promote frost formation on plants. <i>ASM</i></span></div>
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Just how much more rain is produced by these ice-nucleating bacteria? A 2012 study tried to tackle this question using a modeling approach [1]. The authors of the study employed the BRAMS (Brazilian Regional Atmospheric Model System) model, which is typically used for simulating weather conditions based on environmental parameters like pressure, temperature, and humidity. They ran simulations using atmospheric data collected using a radiosonde on a typical summer day in Sao Paulo City to predict ice crystal formation, precipitable ice mass, and rainfall, among other variables under different varying environmental conditions. In these simulations, they incorporated estimates of the concentration of the ice-nucleating bacteria <i>Pseudomonas syringae</i> from previous studies, to see to what extent their presence would affect precipitation. According to their simulations, ice-nucleating bacteria being present would be expected to reduce the percentage of rainfall by about 8%. The amount of hail and snow, on the other hand, would see massive increases. Snow, for instance, showed an increase of over 200% in most of the simulations.<br />
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As ice-containing structures and the friction between them in the clouds play an important role in the making of lightning they also wanted to find out if the presence of ice-nucleating bacteria may increase the amount of lightning being generated. Unsurprisingly, they saw a massive increase in the lightning rate due to the presence of ice-nucleating bacteria in their simulations. While this study exclusively used simulations, the results are consistent with data from experimental cloud chambers. But the simulations are limited by the use of estimates for the numbers of only one type of ice-nucleating bacteria.<br />
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Other studies since then have tried to quantify the diversity of bacteria, ice-nucleating or not, in the atmosphere. A 2013 study [2] attempted to do this for the upper troposphere, and also sought to find associations with weather patterns. The authors of the study collected bacterial samples from the upper troposphere before and after two hurricanes. Sequencing of pre-hurricane samples showed the presence of many more types of bacteria than previously estimated, with many appearing to be well-adapted to the upper troposphere. The majority of the bacteria in the upper troposphere appeared to be aquatic, and the hurricanes resulted in the introduction of a large number of new bacterial species.<br />
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The bacterial particles were found to be a major constituent of atmospheric aerosols, which suggests that the dynamic microbiome of the atmosphere may have major roles to play in weather cycles.<br />
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A more recent study [3] attempted to quantify ice-nucleating bacteria in precipitation. Previous studies had shown that ice-nucleating bacteria mostly belong to the Gammaproteobacteria class of bacteria, but in this study they identified additional groups of bacteria acting as ice-nucleating agents. Notably, they identified the first known ice-nucleating Gram-positive bacteria. These bacteria are distantly related to the Gram-negative Gammaproteobacteria, suggesting that ice nucleation evolved at least twice in the evolutionary history of bacteria. This leads to speculation over whether this trait was adaptive. It is not inconceivable that the bacteria evolved to nucleate ice to rapidly exit the harsh conditions of the atmosphere as precipitation.<br />
<br />
While this field is still in its infancy, these and other studies have established that bacteria are abundant in the atmosphere, and they are likely to play a significant role in the precipitation system. With climate change affecting the diversity of organisms from all branches of life, it is important to understand what roles bacteria in the atmosphere play, which bacteria are mainly involved, and how these functions may be affected by disruption of the atmospheric microbiome.</div>
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<b>Bibliography:</b><o:p></o:p></div>
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<span style="background-color: #cccccc; color: #990000; display: inline; float: none; font-family: inherit; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: normal; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">1. Gonçalves, F. L. T., Martins, J. A., Albrecht, R. I.,
Morales, C. A., Silva Dias, M. A., & Morris, C. E. (2012). Effect of
bacterial ice nuclei on the frequency and intensity of lightning activity
inferred by the BRAMS model. Atmospheric Chemistry and Physics, 12(13),
5677–5689. https://doi.org/10.5194/acp-12-5677-2012</span><b></b><i></i><u></u><sub></sub><sup></sup><strike></strike><br />
<b></b><i></i><u></u><sub></sub><sup></sup><strike></strike><br />
2. DeLeon-Rodriguez, N., Lathem, T. L., Rodriguez-R, L. M.,
Barazesh, J. M., Anderson, B. E., Beyersdorf, A. J., … Konstantinidis, K. T.
(2013). Microbiome of the upper troposphere: species composition and
prevalence, effects of tropical storms, and atmospheric implications.
Proceedings of the National Academy of Sciences of the United States of
America, 110(7), 2575–2580. https://doi.org/10.1073/pnas.1212089110<o:p></o:p></div>
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3. Failor, K. C., Schmale, D. G., Vinatzer, B. A., &
Monteil, C. L. (2017). Ice nucleation active bacteria in precipitation are
genetically diverse and nucleate ice by employing different mechanisms. ISME
Journal, 11(12), 2740–2753. https://doi.org/10.1038/ismej.2017.124<o:p></o:p></div>
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<i>Ridwan is a junior at IUB whose
dream is to be a renowned mad scientist. He will be a Nobel laureate.</i><br />
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-19165184790689877192019-03-23T12:30:00.003-07:002019-09-13T09:54:52.572-07:00Conflict and Cooperation in the Phage World<div dir="ltr" style="text-align: left;" trbidi="on">
<i>Shaheera Rahman</i><br />
<i>Junior</i><br />
<i>School of Life Sciences</i><br />
<i>Independent University, Bangladesh</i><br />
<i><br /></i>
<i>March 23rd, 2019</i><br />
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<br />Viruses are the ultimate survivors. They have existed since the dawn of life on earth (if not before), and no matter what evolution has thrown at them, these obligate parasites have collectively continued to survive against seemingly much stronger hosts. Recent research on bacteriophages – viruses that infect bacteria – illuminates the variety of ways in which viruses interact with and exploit their environment.<br />
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Much is made of the battle for supremacy between bacteria and phages. But bacteria are not the only enemies that phages have to encounter; they also have to deal with other phages. A recent study on bacteriophages that infect <i>Mycobacterium smegmatis</i> showed that certain phages do not take kindly to the idea of sharing their host and like to keep their host to themselves [1]. They prevent other phages, both of the same and different types, from infecting the same host by various means. They can block the entrance of other phages, or bring the growth of the bacterial cell to a halt, which would also put a stop to the replication of lytic phages. Lytic phages rapidly replicate and ultimately lyse the host cell to leave; lysogenic phages, which incorporate themselves into the host genome, would clearly benefit from not having their long-term home (the host) destroyed! To regulate the bacterial cell growth, one of the phages studied appears to encode its own ppGpp synthetase. This enzyme synthesizes the molecule ppGpp, an alarmone which is normally involved in the transition of bacteria into the non-growing stationary phase when they run out of nutrients. The phage, therefore, deceives the bacterial cell into not growing. Unsurprisingly, another phage the authors looked at encodes a protein that inhibits ppGpp synthesis, which acts as an effective counter defense.<br />
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<span style="font-size: x-small;">Electron micrographs of some mycobacteriophages from Dedrick et al.</span></div>
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But bacteriophages do not always fight among themselves. In the face of adversity, certain phages stop fighting among themselves and come together to defeat the greater evil, that is, the bacterial defense system. Bacteria naturally do not like being preyed upon, and have evolved numerous defenses to counter the threat posed by phages. Among them, CRISPR (clustered regularly interspersed short palindromic repeats) provides a strikingly effective example.</div>
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In many bacteria, CRISPR-based systems allow bacterial cells to recognize and target foreign DNA. If the bacteria survive the first infection, they retain a piece of the viral DNA which serves as memory when the same virus attempts to infect the bacteria again. The response in the second instance is much faster and potent as the retained viral DNA encodes an RNA molecule that directs a caspase to cut the DNA of the infecting virus. This is how bacterial CRISPR/Cas immunity works. This is a very effective form of immunity and poses a great threat to the phages. However, phages have evolved to find ways to circumvent this system. Some phages encode anti-CRISPR (Acr) proteins that antagonize bacterial CRISPR-Cas immunity by binding components of its machinery. Another recent study, conducted on <i>Pseudomonas aeruginosa</i> and its phages, demonstrated that bacteria with CRISPR-Cas remain partially immune to Acr-encoding phages during single-phage infections [2]. In order to survive, the phages must cooperate. </div>
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The first infecting batch of the Acr-encoding phage blocks the CRISPR-Cas system, allowing subsequent infecting batches to replicate efficiently. The initial density of Acr-encoding phages that infect bacteria determines whether the phage population will go extinct or amplify.</div>
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Other bacteriophages deal with bacterial weaponry as lone wolves. In order to be self-sufficient, certain phages that infect <i>Vibrio cholerae</i> have now evolved to have mechanisms that can single-handedly defeat bacterial defenses. This was first demonstrated in a study published in 2013 [3]. Vibrio cholerae contain phage inducible chromosomal islands (PICI) which identify phage sequences and prevent the phages from replicating. However, some phages have managed to acquire from previous bacterial PICI-like elements in bacteria, rendering this defense useless. Demonstrating a vicious knack for manipulating aspects of their ecological environment to their advantage, these phages have acquired and coopted one of the defense systems that had evolved to kill them. </div>
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The vicissitudes of their existence as obligate parasites drive bacteriophages (and all viruses) to endlessly creative strategies to ensure their survival. We can marvel at their prowess, but perhaps we could also learn a lesson or two from these bacteriophages, as we wage an increasingly hopeless war against multidrug bacterial pathogens.</div>
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<b>Bibliography:<o:p></o:p></b></div>
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1. Dedrick RM, Jacobs-Sera D, Bustamante CAG, et al.
Prophage-mediated defence against viral attack and viral counter-defence. Nat
Microbiol. 2017;2(3):16251. doi:10.1038/nmicrobiol.2016.251<o:p></o:p></div>
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<br /></div>
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2. Landsberger M, Gandon S, Meaden S, et al. Anti-CRISPR
Phages Cooperate to Overcome CRISPR-Cas Immunity. Cell.
2018;174(4):908-916.e12. doi:10.1016/j.cell.2018.05.058<o:p></o:p></div>
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3. Seed KD, Lazinski DW, Calderwood SB, Camilli A. A
bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate
immunity. Nature. 2013;494(7438):489-491. doi:10.1038/nature11927<o:p></o:p><br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBNLP75H2kA1Bx2bkA9tjUphkourqzUhYoLfxRHGTSQhKpVPbkB23Dm9HR2LQLH1l_0n2seayc39dOK5k96Hcj0yqX_Fx_HlBdGjMmQpkAOd4vnZ7tzFFLM_-poQtN251yUcpkKzbfC9E/s1600/55719247_395514790999847_1702671756512198656_n.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="1024" data-original-width="828" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBNLP75H2kA1Bx2bkA9tjUphkourqzUhYoLfxRHGTSQhKpVPbkB23Dm9HR2LQLH1l_0n2seayc39dOK5k96Hcj0yqX_Fx_HlBdGjMmQpkAOd4vnZ7tzFFLM_-poQtN251yUcpkKzbfC9E/s200/55719247_395514790999847_1702671756512198656_n.jpg" width="161" /></a></div>
<i>Shaheera plans to go into biomedical research to figure out all the cures. Her hobbies include reading and eating.</i></div>
<br /></div>
Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-62679317099913789852019-03-23T12:30:00.002-07:002019-03-22T02:53:34.405-07:00Adaptive Introgression of Neanderthal Genes<div dir="ltr" style="text-align: left;" trbidi="on">
<i>Samara Tawziat Choudhury</i><br />
<i>Graduated student (now a Master's student at North Dakota State University)</i><br />
<i>School of Life Sciences</i><br />
<i>Independent University, Bangladesh</i><br />
<i><br /></i>
<i>March 23rd, 2019</i><br />
<br />
<br />
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You might think that this (pictured) is a
human skull, but is, in fact, a replica of a Neanderthal skull.
<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgUoK_Mf1Q4UkEejmVbJTovhymS3oa3KzyMuZPdxIcDrXNfNvCYOAeuNBj2G86htGtv-bZJkR52V7hztd9TK3sykTAHwMv5IzATFaQasjGIZ5kzsBl9yBHGI_eY6cwY9aIDoY-6rQ5LDN8/s1600/neandertal1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="300" data-original-width="250" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgUoK_Mf1Q4UkEejmVbJTovhymS3oa3KzyMuZPdxIcDrXNfNvCYOAeuNBj2G86htGtv-bZJkR52V7hztd9TK3sykTAHwMv5IzATFaQasjGIZ5kzsBl9yBHGI_eY6cwY9aIDoY-6rQ5LDN8/s1600/neandertal1.jpg" /></a></div>
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<span style="font-size: x-small;">Image from <a href="https://www.dinosaurcorporation.com/neandertal1.html" target="_blank"><span style="color: orange;">Dinosaur Corporation</span></a></span></div>
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Neanderthals were a human-like
species-- not humans, mind you, that went extinct about 24,000 years ago. So
did we get to meet them?<o:p></o:p></div>
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Well, I’m going to tell you a
story. More than a hundred thousand years ago in Africa, where all humans were
born, a particularly daring group decided it was time to venture out into the
world. <o:p></o:p></div>
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More humans followed them and
before you knew it, we were everywhere, all over the world.<span style="mso-spacerun: yes;"> </span>On one of these expeditions around 70,000
years ago, we met the Neanderthals.<span style="mso-spacerun: yes;"> </span>In
fact, not only did we meet them, we fell in love with them.<o:p></o:p></div>
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Neanderthals and humans coexisted
and mated and consequently, exchanged genes. Genes are the biological material
that we inherit from our both of our parents that make each of us who we
are.<span style="mso-spacerun: yes;"> </span>Our genes will determine whether we
have black eyes or blue, are short or tall, have dimples or not, and
importantly, whether we are more likely to get a certain disease or not.<span style="mso-spacerun: yes;"> </span><o:p></o:p></div>
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<span style="mso-spacerun: yes;"><br /></span></div>
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Humans have their own set of
genes, and Neanderthals have their own. Neanderthals have gone extinct since we
met, but the genes that they gave us are still in our genome, which is referred to as an introgression. Why?<o:p></o:p></div>
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Recently, a study looked at one
such set of genes, and showed that it is very impropable that they should
remain in us for so many years.<span style="mso-spacerun: yes;"> </span>But,
they have.<span style="mso-spacerun: yes;"> </span>As with everything else, if
we hang on to something, then it’s probably something important.<span style="mso-spacerun: yes;"> </span>So why are Neanderthal genes important for us
to keep in our bodies even after all these thousands of years?<o:p></o:p></div>
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It turns out that some of these genes are
involved in keeping us safe from viruses that cause disease. The study showed
that the Neanderthal version of some immune genes found in Europeans and Asians differ in function from the human version.<span style="mso-spacerun: yes;"> </span>So, as we moved from one place to another, we may have kept the Neanderthal genes within us to keep us safe from diseases we were likely to encounter in new and unknown places. Thus, these introgressions had an adaptive benefit.<o:p></o:p></div>
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Ladies and gentlemen, I would like
to leave you all with a simple thought: that somewhere in us is a small part of
a long-forgotten species, the Neanderthals.<span style="mso-spacerun: yes;">
</span>And that they have probably protected us more times than we can
count.<span style="mso-spacerun: yes;"> </span>Now that is truly amazing.<span style="mso-spacerun: yes;"> </span>Thank you.<o:p></o:p><br />
<br />
Source to explore:<br />
Original <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1098-6" target="_blank"><span style="color: orange;">study</span></a><br />
<a href="https://www.the-scientist.com/daily-news/natural-selection-kept-neanderthal-dna-in-modern-humans-32295" target="_blank"><span style="color: orange;">Report</span></a> on the original study<br />
More recent <a href="https://www.nytimes.com/2018/10/04/science/neanderthal-genes-viruses.html" target="_blank"><span style="color: orange;">work</span></a></div>
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<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2mamDONZ3daEcSHvhi8clTAm86v4LyQHBVxjb0SXiDRsHg1bVV-NW_FRIY7UuqMhlUps-w8Oysa_lFQ4O6IfxpFFMXCv424LLZY5WSKxcSeQ_pgMXt1dtnxZo83td97KXAbijc51vziw/s1600/Cropped.PNG" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="373" data-original-width="267" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2mamDONZ3daEcSHvhi8clTAm86v4LyQHBVxjb0SXiDRsHg1bVV-NW_FRIY7UuqMhlUps-w8Oysa_lFQ4O6IfxpFFMXCv424LLZY5WSKxcSeQ_pgMXt1dtnxZo83td97KXAbijc51vziw/s200/Cropped.PNG" width="143" /></a></div>
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<i>Samara dreams of curing diseases
and working for the WHO. She also loves to cook, and has a weird wish to be
buried in a library so that her soul can read books for eternity.</i><o:p></o:p></div>
<br /></div>
Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-20158702915682454232019-03-23T12:30:00.001-07:002019-03-24T01:40:08.657-07:00Quorum Sensing and Viral Espionage<div dir="ltr" style="text-align: left;" trbidi="on">
<i>Shaheera Rahman</i><br />
<i>Junior</i><br />
<i>School of Life Sciences</i><br />
<i>Independent University, Bangladesh</i><br />
<i><br /></i>
<i>March 23rd, 2019</i><br />
<br />
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Do you know how communities
develop and civilizations come to be? It has taken thousands of years for human civilization to reach
where it is today. This would not have been possible without communication.
Communication is the vital thing that enabled us to grow as a species. However,
we are not only the species that inhabits this giant planet. All other species
similarly rely on communication, for survival if not for civilization as we
define it. Among these other species, many are visible to the naked eye and countless others are not. <o:p></o:p></div>
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Bacteria are superstars among
these unseen forms of life, at least for their sheer numbers and diversity.
Could bacteria, that have existed for almost the entire span of life on earth,
have been so successful without the ability to communicate among themselves?
Of course not. While they do not call each other up and say, “Hey, what’s up?”,
they do have their unique way of communicating and their language is known to
scientists and bacterial communication enthusiasts as quorum sensing. For
bacteria to use quorum sensing effectively, they need to be able to do three
things: produce signals, detect the
level of those signals in the environment, and produce different
responses as a result of sensing the signals. If an individual bacterium
picks up a lot of these signals from the environment, it immediately knows that
it is in a high-density population, and starts behaving accordingly.<o:p></o:p><br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWQpI9ugo_m74zBB1kGlQMvzPn0lo0XKLoMYWFs8gZuT_Aio27iOcW6c_oHEsILjzX75OjArBq6WoAzHza-F437tbah7Ahc3UpTK9NEtFzpN2KqbesZQQjOr8-qbDko6w6J2W18bc01xk/s1600/6a00d8341c5e1453ef01bb09453318970d-600wi.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="356" data-original-width="600" height="236" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWQpI9ugo_m74zBB1kGlQMvzPn0lo0XKLoMYWFs8gZuT_Aio27iOcW6c_oHEsILjzX75OjArBq6WoAzHza-F437tbah7Ahc3UpTK9NEtFzpN2KqbesZQQjOr8-qbDko6w6J2W18bc01xk/s400/6a00d8341c5e1453ef01bb09453318970d-600wi.png" width="400" /></a></div>
<div style="text-align: center;">
<span style="font-size: x-small;">Quorum sensing relies on the detection of autoinducer signals at high cell densities. <i>Small Things Considered</i></span></div>
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Now, history without war seems a
bit unrealistic, doesn’t it? War has raged between us and microorganisms for
millions of years but do these microorganisms not fight with each other? Of
course they do. Bacteria, despite often being infectious and dangerous
themselves, are at risk of getting infected themselves. By viruses! Considering
the small size of viruses, one might think they are insignificant but that
couldn’t be further from the truth. Viruses that infect us often cause disease,
and the ones that infect bacteria, the bacteriophages, are no less devastating.
Bacteriophages can cause infections in two pathways: in the first kind of infection, they
activate Hulk mode and destroy everything; in more scientific terms, they infect the host cells,
keep on replicating, and break apart the host cell to release all their
offspring into the surroundings to infect new bacteria. In the second pathway,
the virus enters stealth mode where they incorporate their genetic material
into the host chromosome in such a way that every time the bacteria multiplies,
the virus multiplies as well. However, in this pathway, the virus does not
break apart the bacterial cell and keeps on living inside it undetected. Many
bacteriophages are capable of switching between hulk mode and stealth mode.<o:p></o:p></div>
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Now, we must always remember that
where there is war, there are spies as well. You know who the best spies in the
world have been? Viruses! How? Allow me to explain. Certain viruses have
evolved a way of tapping into the bacterial communication system in order to
determine whether it would be more beneficial to use Hulk mode or
stealth mode. You see, if the bacterial population is large and dense, these bacteriophages can detect this by eavesdropping on the bacterial quorum sensing
system, and go into Hulk mode to infect the large pool of possible hosts. They can
similarly go into stealth mode when the bacterial population is sparse as it would not be very nice to break out of a host and find no new bacteria to infect. Viruses, by definition, cannot survive for long or reproduce outside their hosts. Being
tuned in to bacterial communication therefore helps these bacteriophages choose the best
lifestyle for their continued survival.<o:p></o:p></div>
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Sources to explore:</div>
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<a href="https://www.theatlantic.com/science/archive/2018/12/some-viruses-can-eavesdrop-their-hosts/578071/" target="_blank"><span style="color: orange;">Ed Yong article</span></a> on a study demonstrating the phenomenon in a vibriophage<br />
The original <a href="https://www.cell.com/cell/fulltext/S0092-8674(18)31458-2" target="_blank"><span style="color: orange;">study</span></a></div>
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<a href="https://schaechter.asmblog.org/schaechter/2016/10/quorum-sensing-for-the-mutes.html" target="_blank"><span style="color: orange;">More</span></a> fun research if you are interested in quorum sensing<br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBNLP75H2kA1Bx2bkA9tjUphkourqzUhYoLfxRHGTSQhKpVPbkB23Dm9HR2LQLH1l_0n2seayc39dOK5k96Hcj0yqX_Fx_HlBdGjMmQpkAOd4vnZ7tzFFLM_-poQtN251yUcpkKzbfC9E/s1600/55719247_395514790999847_1702671756512198656_n.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="1024" data-original-width="828" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBNLP75H2kA1Bx2bkA9tjUphkourqzUhYoLfxRHGTSQhKpVPbkB23Dm9HR2LQLH1l_0n2seayc39dOK5k96Hcj0yqX_Fx_HlBdGjMmQpkAOd4vnZ7tzFFLM_-poQtN251yUcpkKzbfC9E/s200/55719247_395514790999847_1702671756512198656_n.jpg" width="161" /></a></div>
<i>Shaheera
plans to go into biomedical research to figure out all the cures. Her hobbies
include reading and eating.</i><br />
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<o:p></o:p></div>
</div>
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-20236670640127335242019-03-22T22:35:00.001-07:002019-03-24T01:36:43.067-07:00The Science of Eliminating Aging<div dir="ltr" style="text-align: left;" trbidi="on">
<i>Shalizma Khandaker Orni</i><br />
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<i>Sophomore</i></div>
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<i>School of Life Sciences</i></div>
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<i>Independent University, Bangladesh</i><br />
<i><br /></i></div>
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<i>March 23rd, 2019</i><o:p></o:p></div>
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Aging is a fairly normal physiological process that occurs
in almost all living organisms. It is part of the fundamental cycle of life as
we think of it. However, there are some species in this world that have somehow
avoided this aging process completely. These biologically “immortal” animals,
such as hydras, jellyfish, and possibly some lobsters, pose an interesting
question: could it be possible to eliminate aging? To answer that question, we
have to understand what brings about aging in the first place.</div>
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<o:p></o:p></div>
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All cells in our body go through cell division, during which
DNA replicates. Due to the nature of DNA replication, every time a chromosome
is replicated, it loses some DNA at the very ends. This is where protective
sequences of DNA called telomeres, come into play. The telomeres at the ends of
chromosomes protect the chromosomal DNA (which harbors functionally important
DNA sequences called genes, among others).<span style="mso-spacerun: yes;">
</span>After each successful cell division, the telomeres get shorter and
shorter until they are gone, and the cells stop dividing and are said to become
senescent. These senescent cells can often persist without being replaced,
leading to the tissue degeneration associated with aging, among other outcomes.
Interestingly, stem cells and cancer cells produce an enzyme called telomerase
which can lengthen the telomeres, allowing the cells to continue growing
indefinitely. This enzyme helps lengthen the telomeres, and increased
telomerase activity is associated with cancer.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8UX6Wg9l1yzMQfB32-IwMNXlmjp7JpyyC7GJ7-DBL0CjshGNu2Ovs2DJHidHOeks08l0PirV9s9j1MP4nmXENAw6FEfwpTb0tRO1HSiairCzQI4jwqrer1CS6m8UNXM5QKNyz9CW9ghI/s1600/curious_case_of_benjamin_button_ver10.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="755" data-original-width="465" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8UX6Wg9l1yzMQfB32-IwMNXlmjp7JpyyC7GJ7-DBL0CjshGNu2Ovs2DJHidHOeks08l0PirV9s9j1MP4nmXENAw6FEfwpTb0tRO1HSiairCzQI4jwqrer1CS6m8UNXM5QKNyz9CW9ghI/s320/curious_case_of_benjamin_button_ver10.jpg" width="197" /></a></div>
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<div style="text-align: center;">
<span style="font-size: x-small;"><i>IMDb</i></span></div>
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Another factor that accounts for aging is metabolism.
Metabolism enables life itself, but toxic byproducts of respiration, such as
reactive oxygen species, can damage and wear down cells. When this damage
eventually builds up, it is associated with some the pathology that we see in
aging individuals. The damages can be in the form of cellular atrophy, nuclear
mutations, mitochondrial mutations and others.<br />
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Now that we have some understanding regarding the aging
process, we can focus our attention on ways to possibly eliminate it. One idea
that has persisted for a while now is to eliminate the senescent cells that
characterize aging tissue. To that end, researchers at the Mayo Clinic in
Rochester and the Scripps Research Institute in Jupiter, Florida, among other
places, first identified six signaling pathways that various types of senescent
cells rely on to prevent cell death and continue to persist. In early 2015, the
team identified the first senolytic (drugs which kill senescent cells) based on
inhibiting a pathway that senescent cells need for survival. Dasatinib, an
FDA-approved chemotherapy drug, was found to eliminate human fat-cell
progenitors that have turned senescent, while quercetin, a health-food
supplement, was found to target senescent human endothelial cells. Many other
senolytics have since been discovered.. The major difficulty right now is that
these senolytic compounds only target particular cell types. Combination
therapies are currently being considered and investigated.<o:p></o:p></div>
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Another method to prevent aging, that scientists at Harvard
University, among other institutions, are researching have to do with a
molecule called NAD+ (nicotinamide adenine dinucleotide). An important cofactor
in several metabolic pathways for its ability to transfer electrons, NAD+ has been
compared to a fountain of youth. As the body ages, the supply of NAD+ in the
mitochondria diminishes, and this leads to oxidative damage of DNA and other
cellular components by reactive oxygen species. The Harvard scientists are
developing an “anti-aging” pill containing precursors for NAD+ synthesis in
cells. NAD+ has been demonstrated to reverse signs of aging in mice, and a
company called Elysium already sells an NAD+ boosting pill as a supplement,
although they are now going through clinical trials in humans in order to be
able to market it as an actual drug.<o:p></o:p></div>
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One final method (that we will talk about) that scientists
are looking into is the concept of stem cells. Stem cells are the rejuvenating
blocks of life, and have the ability to grow indefinitely and replace other
cell types. Some types of stem cells persist in adults. For instance,
hematopoietic stem cells found in our bone marrow continually replenish our
blood cell populations. As we age, the regenerative ability of stem cells
deteriorates, and the body becomes less capable of repair and recovery.
Scientists are now considering implanting stem cells into aging individuals to
restore their ability to heal or replace old tissue. This has been already been
demonstrated to produce great results in mice, but clinical trials in humans
are still pending.<o:p></o:p></div>
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In conclusion, as technology advances, we are getting closer
and closer to achieving a state of longevity that far exceed any previous human
generations. But the prospect of eliminating aging leaves us with a few
existential questions. Firstly, would elimination of aging lead to an
overwhelming overpopulation that far exceeds the carrying capacity of the
planet? And if so, what measures can be taken in order to prevent that from
happening? Should we even attempt trying to eliminate aging because of the possible
complications that can arise from it? How would this affect culture, religious
beliefs, and society? While there is only a thin chance that this will actually
happen, we should still proceed with caution and awareness.<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEivEdJVee6jDN2R1Th7WsRT_f1jxlIYQtQ90HAlmrIYhJuo8mr2scvdJWkeIJTmxjWVwV05SliEvP9iEvFKhApkhZql2RHBL5w9GmdUpzLX0FRyxcnxEoeeP0vilIgAS79JaTuerfBB7Ss/s1600/2019-03-22-17-39-59-488.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="496" data-original-width="424" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEivEdJVee6jDN2R1Th7WsRT_f1jxlIYQtQ90HAlmrIYhJuo8mr2scvdJWkeIJTmxjWVwV05SliEvP9iEvFKhApkhZql2RHBL5w9GmdUpzLX0FRyxcnxEoeeP0vilIgAS79JaTuerfBB7Ss/s200/2019-03-22-17-39-59-488.jpg" width="170" /></a></div>
<i>Shalizma is a sophomore in Biochemistry who wants to be a
researcher and help humanity with my work. She is always open to trying new
things and challenges which help her get out of her comfort zone. In short, she
is just a girl chasing her dreams and having an amazing adventure while doing
it.</i></div>
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<o:p></o:p></div>
<br /></div>
Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-40451413741548182872019-03-22T12:30:00.001-07:002019-03-24T01:41:25.155-07:00When Cancer Becomes a SCANDAL<div dir="ltr" style="text-align: left;" trbidi="on">
<i>Jabale Rahmat</i><br />
<i>Junior</i><br />
<i>School of Life Sciences</i><br />
<i>Independent University, Bangladesh</i><br />
<i><br /></i>
<i>March 23rd, 2019</i><br />
<br />
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Have you ever heard of a bacterium afflicted by cancer? Of
course not. Cancer is an accidental consequence of multicellularity.
Multicellular organisms, like animals, have tightly regulated numbers and
distributions of many different types of cells that cooperate as a functional
whole. Cancer occurs when some of these cells decide to go rebel and keep
dividing even at the expense of the organism. We could think of cancers as
cellular parasites.<o:p></o:p></div>
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Actual parasites are transmitted from host to host, but we
obviously do not see cancers being transmitted between humans. There are,
however, transmissible cancers that have been discovered in other animals,
leading to some fascinating speculation on what actually distinguishes these
cancers from parasites.<o:p></o:p></div>
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Metzger et al, in their 2016 paper [1], reported that
mussels, cockles, and golden carpet shell clams are afflicted by independent
lineages of leukemia-like transmissible cancers, adding to three other kinds of
transmissible cancers that had been previously known (in dogs, Tasmanian
devils, and soft-shell clams, respectively). In these bivalve species,
cancerous hemocytes (the equivalent of blood cells in invertebrates) get
transmitted between individuals of the same species through the water as they
breathe by filtering oxygen directly from the water. In all three cases, while
cancer may be occurring spontaneously with some frequency, the transmissible
forms appear to be responsible for most of the cases in natural populations.
Interestingly, they discovered that the golden carpet shell clams got their
cancer from another clam species, the pullet carpet shell clams, suggesting a
cross-transmissible event of cancer. But the pullet carpet shell clams are
resistant to the cancer. This suggests that they may have evolved resistance to
this transmissible cancer, owing to strong selection pressures exerted by the
cancer. Adaptation like this would mirror the dynamics of host-pathogen
coevolution.<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7TIm3e3VAwLtPxjaMdDYt4fYfPrTe0B4QjSLTZXSETPdGB4QeYgNfVvjC0J_5fVdvtuhKVcDGzEmch2LL8Zd9yabJ2A17Qjli2TQuFDvlnKs64v4OnTLn8uh7KvpJu9hIHz6rIVOWrcE/s1600/utas.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="600" data-original-width="1200" height="160" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7TIm3e3VAwLtPxjaMdDYt4fYfPrTe0B4QjSLTZXSETPdGB4QeYgNfVvjC0J_5fVdvtuhKVcDGzEmch2LL8Zd9yabJ2A17Qjli2TQuFDvlnKs64v4OnTLn8uh7KvpJu9hIHz6rIVOWrcE/s320/utas.jpg" width="320" /></a></div>
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<span style="font-size: x-small;">A healthy Tasmanian devil. <i>University of Tasmania</i></span></div>
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While it is difficult to know whether this was indeed an
adaptation,<span style="mso-spacerun: yes;"> </span>Epstein et al. [2] were able
to ask a similar question about a transmissible cancer in Tasmanian devils in a
2016 study. The devil facial tumor disease (DFTD), the transmissible cancer
found in Tasmanian devils, had been discovered in the Tasmanian island of
Australia in 1996. The disease, which is lethal in virtually all cases, has
since been devastating Tasmanian devil populations. The cancer is able to
spread between individuals by evading and suppressing immune responses. But
against all odds, the Tasmanian devils have successfully avoided extinction and
managed to persist. Epstein and colleagues, in the 2016 study, investigated
whether the Tasmanian devils had evolved resistance to DFTD. Using tissue
samples from Tasmanian devils that were collected before and after DFTD ravaged
the populations, they were able to show different populations of Tasmanian
devils had undergone rapid evolution in regions of the genome containing genes
related to immune function and cancer risk. This suggests that strong selection
pressure imposed by the DFTD has resulted in evolution of improved defenses
against the cancer in Tasmanian devils. An arms race could ensue, leading to
the evolution of DFTD to avoid these new defenses. <o:p></o:p></div>
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If these transmissible cancers are genetically distinct and
act essentially like parasites, why do we not think of them as distinct
species? Could they perhaps represent the origin of new species? Recently,
Panchin et al. proposed the SCANDAL (Speciated by CANcer Development Animal)
hypothesis, which posits that speciation may sometimes arise from transmissible
cancers [3]. <o:p></o:p></div>
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By using bioinformatic approaches, they showed that one form
of obligate parasites of fish called Myxosporea may have arisen in this manner.
They provide evidence that its ancestor was a free-living cnidarian that had
lost a large number of genes involved in apoptosis and tumor-suppression. They
hypothesized that this loss of genes may have taken in a single somatic cell,
leading to cancer, which was followed by the spread of the cancer cells to
fish. This may have ultimately led to the parasitic relationship we observe
today. While an attractive hypothesis, the loss of these genes may also have
occurred as part of an overall simplification of the genome of the free-living
cnidarian as it adapted to a parasitic lifestyle, much like how obligate
intracellular bacteria tend to have reduced genome sizes.<o:p></o:p></div>
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Mechanisms of speciation remain mired in mysteries, but we
can at least state with some certainty that there have been several different
mechanisms at work in the evolutionary history of life on earth. Whether or not
the SCANDAL hypothesis finds more support, the Tasmanian devil study points to
an essential truth. If it spreads like a parasite, and if it drives adaptation
like a parasite, it may as well be one. <o:p></o:p><br />
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<b>Bibliography</b>:<o:p></o:p></div>
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1. Metzger MJ, Villalba A, Carballal MJ, et al. Widespread
transmission of independent cancer lineages within multiple bivalve species.
Nature. 2016;534(7609):705-709. doi:10.1038/nature18599<o:p></o:p></div>
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2. Epstein B, Jones M, Hamede R, et al. Rapid evolutionary
response to a transmissible cancer in Tasmanian devils. 2016.
doi:10.1038/ncomms12684<o:p></o:p></div>
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3. Panchin AY, Aleoshin V V, Panchin Y V. From tumors to
species : a SCANDAL hypothesis. 2019:1-10.<o:p></o:p></div>
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<o:p><br /></o:p></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXjZDWVYo5S-0rGdSNbAdmeqVUlYo511TbjiXGtooIlVHWFYllVL63Z4F5KyqRltS_FmyWL3c7KzT9r2lC1tW0npSirJA0stz41Eo9KNYZz-idi8mmPk5t7Dklkzd5RZncy1_feH6Pi_I/s1600/Picture.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="960" data-original-width="720" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXjZDWVYo5S-0rGdSNbAdmeqVUlYo511TbjiXGtooIlVHWFYllVL63Z4F5KyqRltS_FmyWL3c7KzT9r2lC1tW0npSirJA0stz41Eo9KNYZz-idi8mmPk5t7Dklkzd5RZncy1_feH6Pi_I/s200/Picture.jpg" width="150" /></a></div>
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<o:p></o:p></div>
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<i>Jabale is a Junior in the School of Life Sciences at IUB
majoring in Biochemistry. He is a future scientist who is crazy about
everything related to biology, especially genetics.</i><o:p></o:p></div>
<br /></div>
Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-24854021607251126132019-03-22T12:30:00.000-07:002019-03-24T01:40:43.816-07:00Modern Alchemy: Using Cacao Extract in the Synthesis of Gold Nanoparticles<div dir="ltr" style="text-align: left;" trbidi="on">
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<span style="font-family: "times new roman" , serif;"><i>Samira Hussein</i></span></div>
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<span style="font-family: "times new roman" , serif;"><i>Sophomore (transferred to University of Missouri)</i></span></div>
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<span style="font-family: "times new roman" , serif;"><i>School of Sciences</i></span></div>
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<span style="font-family: "times new roman" , serif;"><i>Independent University, Bangladesh</i></span></div>
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<span style="font-family: "times new roman" , serif;"><i><br /></i></span></div>
<div class="MsoNormal" style="margin-bottom: .0001pt; margin-bottom: 0in; mso-layout-grid-align: none; text-autospace: none;">
<i>March 23rd, 2019</i></div>
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Gold is associated by most people with jewelry, and in
regions like South Asia, it remains a regular item of gift exchange. Cacao on
the other hand is known to us as the source of chocolate. Who would have
thought that cacao powder could help in the synthesis of gold nanoparticles? It
sounds a bit strange, but a group of scientists have managed to make it happen.<o:p></o:p></div>
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To begin with, we ought to know about nanoparticles; these
are extremely tiny particles, about 1 to 100nm in size. Nanoparticles of gold
(AuNPs), which form a colloidal suspension in water and other fluids, have been
shown to have unique electronic and optical properties, making them useful in a
number of applications. AuNPs enhance contrast and thereby enable better
visualization of cells and tissues for spotting signs of inflammation, cancer,
or other diseases. The large surface area-to-volume ratio of the nanoparticles
allows hundreds of molecules of a drug (alongside antibodies that target the
particles to the right tissues) to be coated onto their surfaces for efficient
delivery. In photodynamic therapy, gold nanoparticles delivered to a specific
site, such as a tumor, can be excited by light of specific wavelengths to
produce heat (to kill the tumor cells, in this instance).<o:p></o:p></div>
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Traditional methods of synthesizing AuNPs have been plagued
by challenging limitations such as toxic byproducts and complex reaction
parameters. A recent study published in the journal Nanoparticles by Roy
Chowdhury et al. tried to overcome these problems by using cacao extract, that
has both reducing and stabilizing properties, in the synthesis of AuNPs.
Previous work had demonstrated a key advantage of using plant extracts and
microbes for biosynthesis over older approaches using inorganic chemicals: the
biological agents and their byproducts are generally not toxic to human and
other mammalian cells, as well as the environment. <o:p></o:p></div>
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<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisEBQGiTygt_1zEIrpz_5BFkj6Jav3xe9VxHX2kVsiASe6ODQK8faAYOA53PeswDYSbQHoSiz_o53CtsGrf4OcHbEL63QOm8gTCZZV-n4plOsKpj1oBtr5PKEwWjWqPzblpvaqA5mrd0I/s1600/goldnano.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="283" data-original-width="636" height="177" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisEBQGiTygt_1zEIrpz_5BFkj6Jav3xe9VxHX2kVsiASe6ODQK8faAYOA53PeswDYSbQHoSiz_o53CtsGrf4OcHbEL63QOm8gTCZZV-n4plOsKpj1oBtr5PKEwWjWqPzblpvaqA5mrd0I/s400/goldnano.JPG" width="400" /></a></div>
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<span style="font-size: x-small;">Schematic of the process provided in the paper</span></div>
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In their experiments, the scientists incubated hydrogen
tetrachloroaurate, (HAuCl4), a gold-containing compound, with different
concentrations of cacao extract at 100 ̊C. UV-visible spectroscopy was used to
monitor the progress of the synthesized AuNPs, alongside other characterization
methods. UV-visible spectroscopy measures the absorbance of molecules when hit
with light of the ultraviolet and visible electromagnetic spectra, and
different structures produce different absorbance peaks. They determined that
increasing the concentration of cacao extract beyond a certain point promoted
aggregation in the suspension.</div>
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Following the determination of the appropriate concentration
of cacao extract, they employed a technique called dynamic light scattering
(DLS) to measure the diameters of the particles produced. In this technique,
light, usually a laser, is shot through a suspension of particles in a solvent,
and the resulting scatter indicates what sizes of particles are present in the
suspension. They also measured the zeta potential of the products, which was
the potential difference the surface of the particles and the water they were
immersed in. The zeta potential is predictive of the colloidal stability;
nanoparticles with zeta potential values greater than +25 mV or less than -25
mV typically have high degrees of stability. The zeta potential of
non-aggregated AuNPs (which were produced at the lower concentrations of cacao
extract) were between -11mV to -17mV, indicating the stability of the
suspensions. Indeed, these suspensions were so stable that even after a month,
no particle agglomeration was observed.<o:p></o:p></div>
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The scientists then used transmission electron microscopy
(TEM) to observe the morphology, and measure the size of the particles. In TEM,
electrons are blasted through the specimen. The specimen scatters the
electrons, and an image of the specimen is interpreted from the pattern of
scattering of the electrons by the specimen. The morphology results indicated
that most of the AuNPs were spherical and crystalline, and confirmed that there
was no aggregation in the samples. The numerical values of the measured sizes
obtained from DLS and TEM showed some differences owing to the different
principles employed in the techniques, but this did not change the essential
conclusion that this method of synthesis was successfully producing
non-aggregating gold nanoparticles. Lastly, to detect the presence of any toxic
byproducts, the synthesized gold nanoparticles were administered to cultured
human dermal fibroblasts, which are normally present in a layer of skin. The
cells were not adversely affected. <o:p></o:p></div>
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The one-pot synthesis of biocompatible, spherical, and crystalline
AuNPs is a promising breakthrough in the field. So, why does cacao work for
this? Cacao contains a chemical called oxalic acid, which reduces the Au3+ in
hydrogen tetrachloroaurate to metallic gold, and subsequently stabilizes the
product by preventing agglomeration. This simple yet elegant biosynthesis could
be part of a revolution in the production of nanoparticles.<o:p></o:p><br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMTUS8FGUu8rXQ4ALseLJZdJM2xvz2vCC1VRV_JD1WLBRIlXu79VILRJkk9EfkqpiZRwDxB2urrdbcA9-boucFlUGaaBRNRb55k4PZnemE_xjxHkRpf-D05Q5TWC1LUJLB7wFNDbAUWbI/s1600/54514181_434589933970463_3507435950802206720_n.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="1600" data-original-width="1057" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMTUS8FGUu8rXQ4ALseLJZdJM2xvz2vCC1VRV_JD1WLBRIlXu79VILRJkk9EfkqpiZRwDxB2urrdbcA9-boucFlUGaaBRNRb55k4PZnemE_xjxHkRpf-D05Q5TWC1LUJLB7wFNDbAUWbI/s200/54514181_434589933970463_3507435950802206720_n.jpg" width="131" /></a></div>
<i>Samira writes:</i><br />
<i><br /></i>
<br />
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<i>"Completing two semesters in IUB, I realized my passion for
knowing the unknown in the biological sciences. It excites my nerves high way beyond the
threshold level. I like to read biomedical papers, and hope to join the medical field or go into research in the biomedical sciences."</i></div>
<br /></div>
<br /></div>
Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-38192397963458442392019-02-27T01:09:00.002-08:002019-03-30T01:57:16.773-07:00Endogenous Retroviruses<div dir="ltr" style="text-align: left;" trbidi="on">
<i>Maliha Tanjum Chowdhury</i><br />
<i>Junior</i><br />
<i>School of Life Sciences</i><br />
<i>Independent University, Bangladesh</i><br />
<br />
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“I am terrified by this dark thing<o:p></o:p></div>
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That sleeps in me;<o:p></o:p></div>
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All day I feel its soft, feathery turnings, its malignity.”<o:p></o:p></div>
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Like the poetess Sylvia Plath who wrote these lines, men of
wisdom have always recited one thing time and time again: that there are
monsters living inside us. I, for one, am sure that I am haunted. Every cell in
me, in fact, is haunted… But before I go any further, I must ask – how many of
you here believe in things such as monsters, ghosts or demons? Can you please
raise your hand? Hmm, not many I see. But that’s alright, because in the span of the next three minutes, I am sure I will have made believers out of all of you. And
so begins my story.<o:p></o:p></div>
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Let me take you back to a time around 500 million years ago. Down
below in earth’s seven seas, life is flourishing without bounds. Several types
of complex, multicellular animals have already evolved. But, while the realm of
the living thrives, an enemy lurks in every corner of this vast kingdom. A
creature that stands as an exclusion to life itself, as it does not eat,
digest, or excrete like any of the living creatures. It is a tiny vessel of
protein holding in its genetic material with just one purpose – to invade and
multiply. These tiny yet monstrous entities are called viruses. </div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiERTZV-n6QH-b5rjyp6TsJfHPYsb3fAubgaSSOl6zsxn_GhQAa6wkqS3BqWh6UB9sUseH0_Ks2cSuSDgtUn5PvsxVoSoUPUquEMnQJpCqXu-QFslxYHte4snMMRWQ2UtDSbiMm4O39ijk/s1600/great-white-shark-398276_1280.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="960" data-original-width="1280" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiERTZV-n6QH-b5rjyp6TsJfHPYsb3fAubgaSSOl6zsxn_GhQAa6wkqS3BqWh6UB9sUseH0_Ks2cSuSDgtUn5PvsxVoSoUPUquEMnQJpCqXu-QFslxYHte4snMMRWQ2UtDSbiMm4O39ijk/s320/great-white-shark-398276_1280.jpg" width="320" /></a></div>
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<span style="font-size: x-small;">Endogenous retroviruses in sharks, the oldest surviving jawed vertebrates, and other existing organisms helped determine the time of origin of retroviruses</span></div>
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Now, around the
time of our story, a special new kind of virus came into being. In their war
against animal cells, viruses typically employ an explosive battle strategy
where they invade and pillage the cells, and then leave it to die. But these new viruses, called retroviruses, refrained from taking such a crude approach. Retroviruses, which still persist, incorporate their genetic material right into the host DNA, hiding in
plain sight. The cell is now "possessed" by this monster, which slowly but often surely consumes its host instead of killing it right away. The most-well known
retrovirus, HIV, does this to our immune cells, rendering them non-functional,
and giving people AIDS.<o:p></o:p></div>
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Things look bleak for the poor besieged cell, but it is
about to get much worse. Retroviruses which get woven into the DNA of germline
cells, which include sperm and egg cells, gain the ability to be transferred
into the animal’s babies as well – and thus, family curses are born. Animals do
not sit idle, and have evolved to harbor defenses to deactivate these
retroviruses, but remnants of the viral genetic material linger on in the host.
Millions of years down the line, these invading genes are just specters. But
specters need not remain silent. The descendants of the ancient infected hosts
have unwittingly crafted quite the revenge. In a human cell, the pieces of DNA
that were once invaders now assist the cell in obliterating other viruses that
try to infect us.<o:p></o:p></div>
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The story of the ancient battle between the living realm and
the unliving viruses will never truly reach an end<span style="mso-spacerun: yes;"> </span>But these ghosts from the past have helped us
get where we stand today. Embrace your inner monster, because in the
end, it has only made you stronger.<o:p></o:p></div>
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<br /></div>
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Sources to explore more:</div>
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<a href="https://www.scientificamerican.com/article/ancient-retroviruses-emerged-half-a-billion-years-ago/" target="_blank"><span style="color: orange;">Article on origin of retroviruses</span></a></div>
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<a href="https://www.theatlantic.com/science/archive/2016/03/how-we-repurposed-viruses-to-defend-ourselves-from-viruses/471702/" target="_blank"><span style="color: orange;">Ed Yong article on cooption of endogenous retroviruses for immune function</span></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeZtu7jedoR3X2dDbJ5z1Pkkoycb99ztRIG4P0tLVRSt5_8MyTSbnp2qQPrVhVwB_mx8w7wL6VkCOqynWvnDiMpphgpPnq1XW-lkXDbrIAGwCR9GNNIOcBLwx8zp3yNfV2NSdmylZsjtc/s1600/Picture.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="960" data-original-width="720" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeZtu7jedoR3X2dDbJ5z1Pkkoycb99ztRIG4P0tLVRSt5_8MyTSbnp2qQPrVhVwB_mx8w7wL6VkCOqynWvnDiMpphgpPnq1XW-lkXDbrIAGwCR9GNNIOcBLwx8zp3yNfV2NSdmylZsjtc/s200/Picture.jpg" width="150" /></a></div>
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<i>Maliha is a weirdo who somehow
believes she's from a different planet. But she likes Earth just fine, and is
fascinated by the science and beauty of life and has made it her purpose to
explore it. Besides this, her most burning desires include becoming a synthetic
biologist/ genetic engineer and running away with a heavy metal band.</i><o:p></o:p></div>
<br /></div>
Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-65572894559637376632019-02-27T00:12:00.002-08:002019-02-27T00:19:30.992-08:00Exaptations<div dir="ltr" style="text-align: left;" trbidi="on">
<i>Humaira Marzia Alam</i><br />
<i>Junior</i><br />
<i>School of Life Sciences</i><br />
<i>Independent University, Bangladesh</i><br />
<br />
Lucy is my best friend, but I am jealous of her. I envy the way she flies from one part of the sky to another using her feathered wings. Oh! Lucy, she is a bird and she is blue in color. One day while sharing how envious I am about Lucy's flight with my uncle asked me a question: where do feathers come from? It actually made me wonder, and led me to read the latest research papers on the subject. Since you're also probably wondering the same now, let me tell you how feathers came about.<br />
<br />
To understand the evolution of feathers, we need to go millions of years back when dinosaurs used to dominate this world. Fossils tell us that many dinosaurs had feathers but could not fly. What were these terrestrial animals doing with feathers? Current research indicates that their primary purpose in the beginning was insulation. Feathers have pockets where air can be stored, and could have protected cold-blooded dinosaurs from heat loss. Some scientists believe feathers could even have served as ornamentation to attract mates. With time, these animals evolved increased feather cover throughout their bodies, perhaps for better insulation. It’s the same reason that mammals have fur or hair!<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiESxXNpJbvro35VTnbBj7Ssbcla_y513WDIUgZWESPH4RTo2GtnYSV-8XdBfPEbBQbeSUesBo4fqRcgA6cQCQukLL7WIKh624OLz2FqK3Pewoo7AR6UwjcHcoPIiqEMKkBFL3svmAULcs/s1600/dino-reconstruction.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="363" data-original-width="655" height="177" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiESxXNpJbvro35VTnbBj7Ssbcla_y513WDIUgZWESPH4RTo2GtnYSV-8XdBfPEbBQbeSUesBo4fqRcgA6cQCQukLL7WIKh624OLz2FqK3Pewoo7AR6UwjcHcoPIiqEMKkBFL3svmAULcs/s320/dino-reconstruction.jpg" width="320" /></a></div>
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<span style="font-size: x-small;">Reconstruction of a feathered dinosaur. <i>Chung-tat Cheung and
Yi Liu</i></span><o:p></o:p></div>
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One day, while chasing its prey, a dinosaur with feathers raised it arms and the action not only increased its speed but also allowed it to glide through the air. Now, having such feathers equipped these dinosaurs with a distinct advantage over less-feathered competitors while catching prey! Over millions of years, natural selection optimized the feathers for gliding, ultimately allowing the animals to completely take off from the ground and fly!<br />
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This example of transformation of the function of feathers from insulation to flight is known as exaptation, a theme in evolutionary biology where a tool or structure that had evolved for a specific function became coopted for a completely different function by chance or accident. The dinosaurs as we think of them no longer exist. Some combination of asteroids, supervolcanoes, and infections wiped most of them off from the face of the earth, but their innovation still thrives in our world through a few surviving lineages. Due to the exaptation of feathers for flight, Lucy the bird, a descendant of the dinosaurs, is able to roam our skies.<br />
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Sources to explore more:<br />
<br />
<a href="https://carlzimmer.com/evolution-of-feathers-274/" target="_blank"><span style="color: orange;">Carl Zimmer article on the evolution of feathers</span></a><br />
<a href="https://www.quantamagazine.org/evolutionary-modeling-study-provides-new-evidence-for-exaptation-20130904/" target="_blank"><span style="color: orange;">Quanta article on exaptations</span></a><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEij0N_SEwmxCp5-JoKXLFbuTyQWFuNB26dWE8RO3Vq_I4w0z2GGac-glCTPsvE0dwZVXzxZtk9feR8rmG0Ff1Dwp1BaXB8hrFIU0jpyOS0A_4HcL_6oEkeTjncUDi_ctprdJMUI0lTsWjk/s1600/Photo.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="767" data-original-width="767" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEij0N_SEwmxCp5-JoKXLFbuTyQWFuNB26dWE8RO3Vq_I4w0z2GGac-glCTPsvE0dwZVXzxZtk9feR8rmG0Ff1Dwp1BaXB8hrFIU0jpyOS0A_4HcL_6oEkeTjncUDi_ctprdJMUI0lTsWjk/s200/Photo.jpg" width="200" /></a></div>
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<i>Humaira writes: </i></div>
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<i>"I just want to get lost in my own world where I will live my
life riding a bicycle and with undying enthusiasm that I have for life science.
I wish to create the best in myself as a biochemist. Besides my passion in
biochemistry I like writing, reading and sports!"<o:p></o:p></i></div>
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-61719353496248072672018-11-24T05:25:00.001-08:002019-03-22T07:46:53.843-07:00Biotechnology: A Promising Investment Opportunity<div dir="ltr" style="text-align: left;" trbidi="on">
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<span style="background-color: black; text-align: start;"><span style="font-family: inherit;"><i>A.B.M. Mushfiq-Uz-Zaman</i></span></span></div>
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<span style="font-family: inherit;"><i style="background-color: black;">Senior</i></span></div>
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<span style="font-family: inherit;"><i style="background-color: black;">Department of Marketing</i></span></div>
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<span style="font-family: inherit;"><i style="background-color: black;">School of Business</i></span></div>
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<span style="font-family: inherit;"><i style="background-color: black;">Independent University, Bangladesh</i></span></div>
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<span style="line-height: 148%;"><span style="font-family: inherit;">Are you already intrigued because the term “biotechnology” seems
apocalyptic to you, as if this tech is a mad scientist’s brainchild with which
they want to take over the world? Assuming the readers are somewhat equally
divided between “I have no idea what I am reading” and “This is 2018, I know
stuff”, I shall try to enlighten both stakeholders by defining biotechnology in
simple terms.<o:p></o:p></span></span></div>
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<span style="line-height: 149%;"><span style="font-family: inherit;">Biotechnology in a nutshell means creating products using living systems
and organisms. How do they do it? Well, it is done without altering Mother
Nature’s usual flow of getting things done. Today’s world comprises of too many
chemically aided goods, disrupting the natural balance of our eco system and
resulting in pure havoc. Biotechnology can alter this scenario and a gradual
development in different fields of biotechnology, such as biomedical
engineering, bioengineering, bio manufacturing, molecular engineering and etc.
can eventually lead to a more sustainable future for mother Earth.<o:p></o:p></span></span></div>
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<span style="line-height: 147%;"><span style="font-family: inherit;">To figure out the prospects of these promising fields and their probable
growth through sufficient investment, we need to dig deeper into the science of
biology and see how a combination of science and business can change the world
both ethically and profitably.<o:p></o:p></span></span></div>
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<b style="mso-bidi-font-weight: normal;"><u><span style="font-family: inherit;">Gene Therapy<o:p></o:p></span></u></b></div>
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<span style="line-height: 148%;"><span style="font-family: inherit;">Human gene transfer or gene therapy is a form of treatment for diseases
where a patient undergoes therapy as nucleic acid is delivered into their cell.
Nucleic acids are small biomolecules essential to all forms of life. Two
principal nucleic acids are RNA and DNA which are found in abundance in all
living things, where they function to create and encode and then store
information in the nucleus of every living cell of every life-form organism on
Earth.<o:p></o:p></span></span></div>
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<span style="line-height: 156%;"><span style="font-family: inherit;">On experimental basis, gene therapy was used to treat complex diseases
such as acute lymphocytic leukemia, Parkinson’s disease and etc. where US
companies invested over $600 million between 2013 and 2014 in the field. In
2013, the first commercial gene therapy was approved in China which was used to
treat certain cancers. The following years have seen growth in gene therapy
acceptance as Russia in 2011 treated peripheral artery disease whilst in 2012, “Glybera”,
a treatment for a rare inherited disorder, became the first treatment to be
approved for clinical use in either Europe or the United States after its
endorsement by the European Commission.</span></span><br />
<span style="font-family: inherit;"><br /></span>
<span style="font-family: inherit;">It is not like gene transfer can only happen in humans to cure diseases
since the same can also happen for plant life forms. Genetically modified crops
have been popular in our own country, Bangladesh, where in 2013, “Bt”, i.e.
biotech brinjal was successfully released as the country’s first commercially
released biotech crop. The following success led to the testing and development
of three more crops; Late blight resistant potato, Bt cotton and vitamin – A
enriched golden rice.</span></div>
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<span style="line-height: 147%;"><span style="font-family: inherit;">Once released, late blight resistant potatoes will save farmers from
spending a fortune in fungicides. Bt cotton will turn out to be a boost for the
profitable cotton/textile industry of the country whilst golden rice could
address the prevalent Vitamin A deficiency in the country.<o:p></o:p></span></span></div>
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<b style="mso-bidi-font-weight: normal;"><u><span style="font-family: inherit;">The Fusion of the Unlikely and Its Consequences:<o:p></o:p></span></u></b></div>
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<span style="line-height: 149%;"><span style="font-family: inherit;">Proper investment, calculated risk and handsome return is the goal of all
businesses and investment in vague ideas would be unlikely for any investor.
Since science and its prospects plus business and its effective return cannot
be vivid for both parties, an unlikely fusion is the only option we are left
with. However, the end result can be beneficial for both. If investors show
interest, more research and development can be carried out which can facilitate
more development of biotechnology as a result of which, the number of end
consumer will increase. This means, the current market gap can be fulfilled
efficiently through economies of scale.<o:p></o:p></span></span></div>
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<span style="line-height: 156%;"><span style="font-family: inherit;">Gradually, we can hope to see a prosperous industry being built from
scratch and boom as a whole. Our annual brain drain will be minimized
substantially with opportunities for foreign students and researchers to
contribute if offers remain lucrative which can enrich our international
prestige.<o:p></o:p></span></span></div>
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<span style="line-height: 148%;"><span style="font-family: inherit;">The concept of biotechnology is immense by itself. Firstly, both parties
involved needs to understand the best possible sector to invest in and research
on. Even biogas as a form of renewable energy can be a promising sector to
invest in if marketed correctly. Waste management, use of plastic and
biodegradable products are gradually becoming popular with wide scope for first
movers.<o:p></o:p></span></span></div>
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<span style="line-height: 148%;"><span style="font-family: inherit;">Therefore, the transition and the trend of accepting change needs to
develop among everyone if we are to see sustainable growth in the following
arena. Change is crucial but if done ethically while keeping it profitable, it
can affect the lives of the mass positively and cater to a better version of
the world tomorrow.<o:p></o:p></span></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjq6OhgFmy218sI2M8c0Jm_zPY9-NBfgzsT5-EemOKOVaHMand983ydbNAIolk0vVV2UVpYaLM1Me-cU10Z62-C12Dnja92r9P6hcPMr4Db0fxmDY-ijoAgqPHfra4jGIcGaHkqDHuTtjM/s1600/Mushfiq.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="960" data-original-width="960" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjq6OhgFmy218sI2M8c0Jm_zPY9-NBfgzsT5-EemOKOVaHMand983ydbNAIolk0vVV2UVpYaLM1Me-cU10Z62-C12Dnja92r9P6hcPMr4Db0fxmDY-ijoAgqPHfra4jGIcGaHkqDHuTtjM/s200/Mushfiq.jpg" width="200" /></a></div>
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<span style="font-family: inherit;"><i>Mushfiq writes,</i></span></div>
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<span style="font-family: inherit;"><i><br /></i></span></div>
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<span style="font-family: inherit;"><i>"<span style="line-height: 107%;">Plain,
simple and ordinary.</span></i></span></div>
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<span style="line-height: 107%;"><span style="font-family: inherit;"><i>
A marketer in the making, driven by coffee and dreams! <br />
Favorite quote: '30 years from now, it won’t matter what jeans you wore or how
your hair looked. What would matter is the things you have learned and how you
have used it.'<o:p></o:p></i></span></span></div>
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<span style="line-height: 107%;"><span style="font-family: inherit;"><i><br /></i></span></span></div>
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<span style="line-height: 107%;"><span style="font-family: inherit;"><i>Last
but not the least, I am a car enthusiast who loves everything about cars,
literally!"<o:p></o:p></i></span></span></div>
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-91896003178528763102018-10-17T23:54:00.000-07:002018-11-24T05:44:29.884-08:00The School of Life Sciences Celebrates Life Sciences in the 2018 Nobels<div dir="ltr" style="text-align: left;" trbidi="on">
<span style="font-size: small;"><span style="font-family: "trebuchet ms" , sans-serif;">
</span></span><br />
For members of the global scientific community, the Nobel Prizes bring special excitement every year in anticipating just which of the many breakthroughs in biology, chemistry, and physics would be celebrated and publicly recognized this time around. As a life sciences school, we particularly look forward to the announcement of the prize for Physiology or Medicine, which often serves to reignite our passion, validate our choices, and stimulate interest in areas of research and thinking that we may not have paid the most attention to before. However, going by this year’s Nobel Prizes, we should spare more than an ear for the announcement of the prizes awarded in Chemistry and Physics as well.<br />
<div>
<br /></div>
<div>
All three of the Nobel Prizes in the sciences this year share deep connections with biology and biological research. James P. Allison and Tasuku Honjo shared the prize in Physiology or Medicine for their work on discovering negative regulators of immune cells and inhibiting them in order to unleash the substantial firepower of the immune system to act against cancer cells. Frances H. Arnold won half of the prize in Chemistry for employing principles from evolution to develop enzymes with improved and novel functions for industrial and biomedical applications, while the other half went to George P. Smith and Sir Gregory P. Winter for developing the phage display, a protein screening method that is often used in the directed evolution of proteins. The Nobel Prize in Physics was split between Arthur Ashkin, who developed optical tweezers from lasers and has used them to understand biological systems, and Gerard Mourou and Donna Strickland for developing high-intensity, ultra-short optical pulses that enabled laser surgeries among other applications. Alongside their ties to the life sciences, the three Nobel Prizes share a common theme of taking a known concept or principle far beyond its usual application. They harness our understanding of complex phenomena such as evolution, adaptive immunity, and electromagnetic radiation to unlock new avenues of innovation and application. </div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_7jhtVRykWz8ymrEQ9TsBEr3AvvJc0B9fLQqcH8gEBXabXq_pBe8bL4KYXjfL_LYDvOQPtg7u6H4sRK9rFyfxwQvBPnfkCj2DwnrGZ7pR81R2TXTN_GnUhaElV57hH08i4PmfknSgyl0/s1600/nobel+1.png" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_7jhtVRykWz8ymrEQ9TsBEr3AvvJc0B9fLQqcH8gEBXabXq_pBe8bL4KYXjfL_LYDvOQPtg7u6H4sRK9rFyfxwQvBPnfkCj2DwnrGZ7pR81R2TXTN_GnUhaElV57hH08i4PmfknSgyl0/s320/nobel+1.png" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">James P. Allison Tasuku Honjo</td></tr>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0-y1_GIoEcFwV5DF7WcWfuU5lkZ8z5eypXOcohWAiL4WdicD0-IobCuObDxDtbp2ef5dPpMesfq53wNZ68jJP7wX7qCV7aK-7rEeLuqbWxTAtUEpZBVLIy_Fz6eWe6GbWzfYfcy88meo/s1600/nobel+2.png" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0-y1_GIoEcFwV5DF7WcWfuU5lkZ8z5eypXOcohWAiL4WdicD0-IobCuObDxDtbp2ef5dPpMesfq53wNZ68jJP7wX7qCV7aK-7rEeLuqbWxTAtUEpZBVLIy_Fz6eWe6GbWzfYfcy88meo/s320/nobel+2.png" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"> Frances H. Arnold George P. Smith Sir Gregory P. Winter</td></tr>
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As is always the case, the Nobels also serve as key reminders of the value of basic science research. Years of research by hundreds of scientists on understanding evolutionary principles and the structure of biomolecules reached a zenith in the work of Frances H. Arnold. Phages – viruses that infect bacteria and a classic model system in genetics research – remain the gift that keeps on giving, finding new life as a tool that allows proteins to be displayed on structures that house the DNA encoding each protein. George P. Smith and Sir Gregory P. Winter realized that the rapid identification of the DNA sequence encoding a protein after selection of the protein for function or affinity could accelerate the screening and production process for commercial proteins such as antibodies. James P. Allison and Tasuku Honjo’s discoveries demonstrate that no basic science research is ever very far from application to cancer. On a more serious note, inhibition of negative immune regulation builds on decades of work describing the minutiae of the seemingly endlessly complex vertebrate immune system. And while we are discussing the magic of basic science research, it is worth noting that Arthur Ashkin’s optical tweezers have allowed us to trap and follow RNA polymerase as it adds individual nucleotides while synthesizing the mRNA strand during transcription, and the ribosome as it moves along the mRNA strand during translation. Applications in delivering cargo to cells for treatment and sorting infected cells from healthy ones only add to the glory of this invention.<br />
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That all three of this year’s scientific Nobels have gone to developments born out of, or that led to major applications in biological research is probably not a coincidence. It is reflective of the exciting transitions and innovations that have been revolutionizing the field with increasing frequency since the birth of molecular biology. Knowledge begets knowledge, and draws the attention of other fields to employ or develop tools for further exploration. Many would have touted the gene-editing technology called CRISPR or the novel cancer immunotherapy of CAR-T cells, which trains one’s own immune cells to directly target cancer cells, as candidates for this year’s prize in Physiology or Medicine. But it seems like revolutions in biological research now occur often enough to warrant a waiting list. And sometimes, these innovations extend to or emerge from the other basic sciences.<br />
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<i>The School of Life Sciences<br />Independent University, Bangladesh </i><br />
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-50414024084789219562018-09-10T01:47:00.001-07:002019-09-13T10:37:04.366-07:00Moths Hold Their Own in an Acoustic Evolutionary Arms Race<div dir="ltr" style="text-align: left;" trbidi="on">
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<i><span style="font-family: inherit;">Jabale Rahmat</span></i></div>
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<i><span style="font-family: inherit;">Junior</span></i></div>
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<i><span style="font-family: inherit;">School of Life Sciences</span></i></div>
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<i><span style="font-family: inherit;">Independent University, Bangladesh</span></i></div>
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<i><span style="font-family: inherit;">September 10th, 2018</span></i></div>
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<span style="font-family: inherit;">Many of us are familiar with the scene of a speedy chase between a cheetah and its prey, for example, a deer, from runs on National Geographic. Cheetahs can reach up speeds up to 96.5 kilometers per hour in a few seconds, but this speed lasts for less than a minute. With this lung-busting speed, a cheetah can make sharp turns and catch its prey by surprise. None of its cousin species can achieve this speed let alone make such turns. This turning for the cheetah is stabilized or balanced by its muscular long tail. Alongside its speed and unique tail, cheetahs have numerous other adaptations that arose to keep up with the prey in their habitat. Similarly, prey species do not sit back and resolve to get outmaneuvered forever; they also adapt to avoid or evade predators, resulting in an adaptive arms race between predators and prey over evolutionary time.</span></div>
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<span style="font-family: inherit;">Rubin et al., in a recent paper [1], describes some interactions between predator and prey where the prey appears to be a step ahead its predator. The predator is the famous nocturnal animal, the bat, which locates its prey by echolocation. With this technique, the bats produce ultrasound that rebounds from various objects including its prey and by reading the reflected ultrasound waves, bats can deduce the location of its prey. The prey is the moth.</span></span><span style="font-family: inherit;"><br /></span></div>
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<span style="font-family: inherit;">Bats and moths offer interesting perspectives on coevolution. Several adaptations have been reported on either side. There are moths that produce clicks to confuse the bats by interfering with their echoes. There is a species of bat that has been shown to lower the intensity of its echolocation calls as it approaches its moth prey, helping to provide an illusion of increased distance from the prey. A recent study reported greater absorption of echolocation calls by the wings of nocturnal moths (that tend to be hunted by bats) compared to diurnal moths, providing support for the idea of adaptation to avoid predation.</span></div>
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<span style="font-family: inherit; font-size: x-small;">A long-tailed wild silk moth. <i>Focus on Boise State</i></span></div>
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<span style="font-family: inherit;">In the paper from Rubin et al., the authors demonstrate that wild silk moth species with specific hindwing shapes and morphologies more effectively escape bat attacks. It built upon previous studies showing that spinning hindwing limbs are able to deflect sonar.</span></div>
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<span style="font-family: inherit;">The researchers first utilized a dataset of several hundred genes found across species of wild silk moths to create a phylogenetic tree to identify patterns of relatedness. They discovered four shapes that have convergently evolved multiple times – twisted and cupped long hindwing tails (tails are extensions that emerge from the hindwing), a short hindwing tail, and a long hindwing lobe (a longer lobe means the entire hindwing structure is longer; think droopy earlobes). This was consistent with modification of the hindwing being adaptive or beneficial.</span></span></div>
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<span style="font-family: inherit;">They became interested in how the length of the hindwing tail or lobe impacted escape from bat attacks. To that end, they pit big brown bats against the moths with different types of hindwings (that were tethered using strings) and observed how well the moths escaped attacks. They pit the bats against intact moths, sham moths that they experimentally created by cutting part of the hindwing and regluing it with the moth (this is a control to show that the cutting procedure itself does not bias results), and moths with experimentally increased or decreased hindwing tail and lobe lengths.</span></span></div>
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<span style="font-family: inherit;">By analyzing the data from these experiments – collected using slow motion camera – they discovered that moths with longer hindwing tails or lobes, whether or not they were natural or experimentally manipulated, had the highest chances of escape.</span></span></div>
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<span style="font-family: inherit;">To elucidate how the hindwing helps the moth to avert bat attacks, the authors carried out further tests. By looking at what parts of the moth the bats were being able to strike, they were able to conclude that that the hindwing structures very likely create an illusion of multiple targets, prompting the bats to aim for the lower end of the moths rather than the center. The hindwings of moths are disposable for flight, so it is plausible that moths would present them as alternative targets to allow escape.</span></span></div>
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<span style="font-family: inherit;">This paper presents evidence of a powerful form of convergent evolution that arose several times in different species of moths, indicating a strong selection pressure. Much, however, remains to be done. Besides big brown bats, each moth may be attacked by other or more bats in their natural habitats. Could it be possible to find evidence for coevolution between specific species of bats and moths? This research must be put in context with other known adaptations undergone by bats and moths in their increasingly well-documented evolutionary arms race.</span></span></div>
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<span style="font-family: inherit;"><b>Bibliography:</b></span></span></div>
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<span style="font-family: inherit;">[1] J. J. Rubin, C. A. Hamilton, C. J. W. McClure, B. A. Chadwell, A. Y. Kawahara, and J. R. Barber, “The evolution of anti-bat sensory illusions in moths,” Sci. Adv., vol. 4, no. 7, pp. eaar7428–eaar7428, Jul. 201</span></span></div>
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<i><span style="font-family: inherit;">Jabale is a Junior in the School of Life Sciences at IUB, majoring in biochemistry. He is a future scientist who is crazy about everything related to biology, especially genetics.</span></i></div>
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-51594251505897008032018-06-13T01:50:00.001-07:002020-02-28T10:20:53.191-08:00The Age of Optogenetics: Lighting Up Neurons to Explore Brain Function<div dir="ltr" style="text-align: left;" trbidi="on">
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<span style="line-height: 107%;"><i><span style="font-family: inherit;">Jabale Rahmat</span></i></span></div>
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<span style="line-height: 107%;"><i><span style="font-family: inherit;">Sophomore</span></i></span></div>
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<span style="line-height: 107%;"><i><span style="font-family: inherit;">School of Life Sciences</span></i></span></div>
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<span style="line-height: 107%;"><i><span style="font-family: inherit;">Independent University, Bangladesh</span></i></span></div>
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<span style="line-height: 107%;"><i><span style="font-family: inherit;">June 13th, 2018</span></i></span></div>
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<span style="line-height: 107%;"><span style="font-family: inherit;"></span></span><span style="line-height: 107%;"><span style="font-family: inherit;"><br />“Tubelight”. We do not restrain ourselves from assigning our friends with this euphemistic word for dimwit. It indicates that their brain needs time to turn on and comprehend something. But lighting up the brain has a new and completely literal meaning today, and it is helping us address hitherto unanswerable questions about how the brain works.</span></span><br />
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<span style="line-height: 107%;"><span style="font-family: inherit;">The human brain is a labyrinth of neurons: thousands of nerve cells residing in a complex network. For decades, scientists have been working to elucidate how this labyrinth is compartmentalized to perform different functions and have made enormous strides in discovering which regions of the brain are involved in movement, sensation, memory, emotion, and other hallmarks of cognitive function. But it has been much harder until recently to get to the much finer resolution of the role of specific neurons in processes such as memory formation and retrieval.</span></span><br />
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<span style="line-height: 107%;"><span style="font-family: inherit;">Neurons in the brain work in synergistic or antagonistic ways for different processes that are occurring in the body. It is difficult to make associations between specific neuronal activity and cognitive functions. Classical ways to study neuron function include stimulating neurons with electrodes and identifying the effects of stimulation. But this is physically invasive, can lack specificity, and does not allow fine-scale control of neurons. To study the function of specific sets of neurons, one would ideally be able to turn them on and off at will and see how they affect different aspects of cognitive function.</span></span><br />
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<span style="line-height: 107%;"><span style="font-family: inherit;">To solve this problem, neuroscientists have developed a method known as optogenetics that uses light-sensitive proteins to turn neurons on and off. Before describing how optogenetics works let us work through the necessary background on how neurons work.</span></span><br />
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<span style="line-height: 107%;"><span style="font-family: inherit; font-size: x-small;">Light being shone onto the brain of a mouse. <i>Britannica</i></span></span></div>
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<span style="line-height: 107%;"><span style="line-height: 107%;"><span style="color: #990000; font-family: inherit;">Neurons carry electrical signals, much like electrical wires. These signals are transmitted through creating changes in the charge carried inside the membrane along the length of the neuron. Charge is manipulated by moving ions (which carry charge) in and out of neurons using molecular pumps and ion channel proteins that span the membrane and transport ions through it. Each kind of ion (sodium, potassium, chloride etc.) has its own specific channel protein.</span></span></span><br />
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<span style="color: #990000;"><span style="line-height: 107%;"><span style="font-family: inherit;">When a neuron or part of a neuron is at a resting or inactive stage, the sodium-potassium pump maintains a constant resting charge inside the membrane relative to the outside due to the unbalanced share of ions inside and outside the neurons. The sodium-potassium pump transports three sodium ions out for every two potassium ions brought in, regardless of concentration or charge gradient. Both of these carry a single positive charge, so this makes the inside of the neurons less positive. </span></span></span><br />
<span style="color: #990000;"><span style="line-height: 107%;"><span style="font-family: inherit;"><br /></span></span><span style="line-height: 107%;"><span style="font-family: inherit;">Upon receiving a sufficiently strong signal, for example from pressure receptors that are present under the skin, specific ion channels for sodium are activated, allowing sodium to flow down the concentration gradient into the region of the neuron that is closest to the signal, resulting in a positive charge inside the membrane. This sudden change activates sodium ion channels adjacent to the initial site of activation, and the signal is passed along neurons to be processed by the central nervous system. Once the stimulating signal is removed, activated regions are returned to their resting state via other ion channel proteins. When our brain responds to a stimulus, it activates a different set of neurons that carry signals to muscles and other effector organs. In a nutshell, neurons can be excited by activating specific ion channel proteins.</span></span></span><br />
<span style="color: #990000;"><span style="line-height: 107%;"><span style="font-family: inherit;"><br /></span></span><span style="line-height: 107%;"><span style="font-family: inherit;">Optogenetics utilizes certain light-sensitive ion channel proteins isolated from microorganisms like unicellular algae and archaea that open in response to light. Channelrhodopsin-2, a blue light-sensitive channel protein from algae, allows the transport of positively charged ions into cells upon activation by blue light. Halorhodopsins, isolated from archaea, become activated by specific wavelengths of light to move negatively charged chloride ions into the cell, thereby making the inside of the membrane less positive and inhibiting neuronal activation.</span></span></span><br />
<span style="color: #990000;"><span style="line-height: 107%;"><span style="font-family: inherit;"><br /></span></span><span style="line-height: 107%;"><span style="font-family: inherit;">But these proteins molecules are obviously not typically produced by the nerve cells of mammals. So how do we use them to turn neurons on and off? Well, specific neurons are genetically engineered to express the genes encoding the light-sensitive channel proteins. While we cannot experimentally manipulate humans in this manner, extensive research is being conducted in model organisms such as mice. One particularly interesting line of work using optogenetics has discovered that different neurons are involved in memory formation and recall. Picture one of the experiments conducted for this discovery: you turn off a set of neurons after teaching mice to be afraid of a stimulus. The mice no longer seem to remember the fear. But if you turn off those neurons while the fear is being taught, and later turn on the neurons and expose them to the stimulus, the mice do exhibit fear. This suggests that the memory had formed through a different pathway but could only be recalled upon activation of this specific set of neurons [1].</span></span></span><br />
<span style="color: #990000;"><span style="line-height: 107%;"><span style="font-family: inherit;"><br /></span></span><span style="line-height: 107%;"><span style="font-family: inherit;">Optogenetics can also utilize light-emitting proteins to light up neurons engaged in specific activities. If you tie the expression of a light-emitting protein to genes that are turned on during learning, you can watch memories form by observing which parts of the brain glow while the organism is being exposed to novel stimuli.</span></span></span><br />
<span style="color: #990000;"><span style="line-height: 107%;"><span style="font-family: inherit;"><br /></span></span><span style="line-height: 107%;"><span style="font-family: inherit;">Optogenetics can helps us answer central questions surrounding how the brain processes information. It holds great promise in understanding neurogenerative disorders such as Parkinson’s and Alzheimer’s through the study of the brains of model organisms. Although developed to study neurons, optogenetics is also being adapted to manipulate other cell types using light. </span></span></span><br />
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<span style="line-height: 107%;"><span style="color: #990000; font-family: inherit;"><b>Further Reading:</b></span></span></div>
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<span style="line-height: 107%;"><span style="color: #990000; font-family: inherit;">[1] D. S. Roy et al., “Distinct Neural Circuits for the Formation and Retrieval of Episodic Memories,” Cell, vol. 170, no. 5, pp. 1000-1012.e19, Aug. 2017.</span></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXjZDWVYo5S-0rGdSNbAdmeqVUlYo511TbjiXGtooIlVHWFYllVL63Z4F5KyqRltS_FmyWL3c7KzT9r2lC1tW0npSirJA0stz41Eo9KNYZz-idi8mmPk5t7Dklkzd5RZncy1_feH6Pi_I/s1600/Picture.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><span style="clear: left; float: left; font-family: inherit; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="960" data-original-width="720" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXjZDWVYo5S-0rGdSNbAdmeqVUlYo511TbjiXGtooIlVHWFYllVL63Z4F5KyqRltS_FmyWL3c7KzT9r2lC1tW0npSirJA0stz41Eo9KNYZz-idi8mmPk5t7Dklkzd5RZncy1_feH6Pi_I/s200/Picture.jpg" width="150" /></span></a><br />
<i style="text-align: justify;"><span style="font-family: inherit;">Jabale is a Sophomore in the School of Life Sciences at IUB majoring in Biochemistry. He is a future scientist who is crazy about everything related to biology, especially genetics.</span></i><br />
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-45751089799272051832018-04-23T00:04:00.003-07:002019-05-06T12:02:49.753-07:00Vaccines and the Bizarre Hounding of an Established Science<div dir="ltr" style="text-align: left;" trbidi="on">
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<i><span style="font-family: inherit;">Iffat Ara Sharmeen</span></i><br />
<i><span style="font-family: inherit;">Former Student</span></i><br />
<i><span style="font-family: inherit;">School of Life Sciences</span></i><br />
<i><span style="font-family: inherit;">Independent University, Bangladesh</span></i><br />
<i><span style="font-family: inherit;"><br /></span></i>
<i><span style="font-family: inherit;">April 23, 2018</span></i><br />
<span style="font-family: inherit;"><br /></span>
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<span style="font-family: inherit; line-height: 107%;">The idea behind vaccines originated
in China during the 10<sup>th</sup> century. The Chinese prevented smallpox by
blowing powdered smallpox scabs through the nostrils, i.e., literally breathing
in the smallpox virus through the nose. It was Edward Jenner in the 17<sup>th</sup>
century that popularized such peculiar ways of inoculation in Britain. He
observed how milkmaids never contracted smallpox, because they were previously
infected with cowpox. Curious, he took cowpox pus from a milkmaid and scratched
it onto a young boy. A few weeks later, he inoculated the boy with smallpox and
observed that the boy did not get smallpox. He introduced the term “vaccine”. <o:p></o:p></span></div>
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<span style="font-family: inherit; line-height: 107%;"><br /></span></div>
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<span style="font-family: inherit; line-height: 107%;">Vaccines began to enter the
mainstream after Louis Pasteur created vaccines for chicken cholera and anthrax
during the 18<sup>th</sup> century. Laws on compulsory vaccination began to get
established. Vaccines against diphtheria, measles, mumps and rubella became
revolutionary. Discovery of polio vaccine in the 1950s and eradication of
smallpox were major accomplishments in medical science. Till now, vaccines
remain one of the most heavily-researched and thoroughly debated topic among
scientists worldwide. <o:p></o:p></span></div>
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<b><span style="font-family: inherit; line-height: 107%;">Currently Used Vaccines<o:p></o:p></span></b></div>
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<b><span style="font-family: inherit; line-height: 107%;"><br /></span></b></div>
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<span style="font-family: inherit; line-height: 107%;">Until 15 months after a baby is
born, a number of vaccines are recommended, even compulsory in many countries.
The list includes vaccines against hepatitis B, BCG, rotavirus, diphtheria,
tetanus, pertussis, influenza, polio, measles, mumps, rubella, varicella,
hepatitis A, pneumococcal conjugate and polysaccharide, meningococcus and human
papilloma virus. Many of these vaccines are followed up in later years, until
18 years of age. Unfortunately, there have been many vocal concerns from
parents about the dangers of vaccination in recent years.<o:p></o:p></span></div>
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<b><span style="font-family: inherit; line-height: 107%;">The Science Behind Vaccines<o:p></o:p></span></b></div>
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<b><span style="font-family: inherit; line-height: 107%;"><br /></span></b></div>
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<span style="font-family: inherit; line-height: 107%;">Vaccines might sound scary, but
they are a proven way of protecting us against some very horrible diseases. So
what exactly are vaccines made of. Some vaccines may be preparations of
micro-organisms that were once active but have been killed or inactivated. Some
vaccines may contain live, virulent particles that have been weakened to be
safe. Still others contain deactivated toxic compounds derived from organisms,
which are the main causes of disease rather than the organisms themselves. One
recent innovation is the protein subunit vaccine against human papilloma virus
which contains the viral capsid without the genome inside. One might wonder,
why inject such harmful substances in our body? Wouldn’t it cause more harm
rather than do good? Actually, it is quite the contrary.<o:p></o:p></span></div>
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<span style="font-family: inherit; line-height: 107%;">When viruses or bacteria enter the
human body, the immune system responds by identifying the virus or bacteria as “foreign”.
Parts that are specifically recognized and subsequently targeted as markers of
infection are called antigens. During the first encounter with a pathogen, it
takes a while for the specific immune response to develop (four to seven days)
and produce antibodies to target the antigens. By this time, many pathogens can
cause disease. However, if the host is able to survive, and the immune system
is able to mount an immune response and produce antibodies to control the infection,
it also retains memory of the antigen and the response. This means that the
next time the antigen attacks, the immune system is prepared to immediately
take it on. Vaccines work by deceiving the immune system into mounting an immune
response against specific antigens, so that during infection by the real pathogens
carrying those antigens, the host is ready. But the vaccines themselves do not
cause disease as they are dead or weakened forms of the pathogens.<o:p></o:p></span></div>
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<b><span style="font-family: inherit; line-height: 107%;">How Vaccines Came to Be Considered As
Harmful<o:p></o:p></span></b></div>
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<span style="font-family: inherit; line-height: 107%;">Worryingly, a very small but increasingly
significant number of the population believe and depict vaccines to be harmful.
They argue that vaccines may be responsible for conditions like autism or argue
that there has not been enough research done to ensure vaccines are completely
safe. However, these are not well-researched opinions, since decades of medical
research has indeed shown vaccines to be completely safe. The anti-vaccination
movement can be traced back to a 1998 study that showed a link between the MMR
(Measles, Mumps, Rubella) vaccine and autism. The study has since been
discredited and retracted from its journal of publication for containing fabricated
data, but the author Andrew Wakefield continues to fan the flames it set off.
In addition to the autism scare, some parents are concerned about how large pharma
companies and public health organizations earn huge profits by selling
vaccines, that are shown to be effective, but are actually not. They also feel
that vaccines are expensive and too numerous. None of this is based on fact.<o:p></o:p></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_zC_223paJzHz1CBLpzTDy-3AuVNVRpiuB1z6yf8sTbTl51SlFILWVodCQkz0_GdGnUcpNpeFY3oLNBfT3jGem_EKBewDslgQjzDpaynydXNMtt-szCWS1ZHTI3aRCatxC2X3g4P0ytU/s1600/vaccine-awareness.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1536" data-original-width="1190" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_zC_223paJzHz1CBLpzTDy-3AuVNVRpiuB1z6yf8sTbTl51SlFILWVodCQkz0_GdGnUcpNpeFY3oLNBfT3jGem_EKBewDslgQjzDpaynydXNMtt-szCWS1ZHTI3aRCatxC2X3g4P0ytU/s640/vaccine-awareness.jpg" width="494" /></a></div>
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<span style="font-family: inherit; font-size: x-small; line-height: 107%;">A Vaccine Awareness Poster</span></div>
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<b><span style="font-family: inherit; line-height: 107%;"><br />Not vaccinating? Think Again<o:p></o:p></span></b></div>
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<b><span style="font-family: inherit; line-height: 107%;"><br /></span></b></div>
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<span style="font-family: inherit; line-height: 107%;">Parents make decisions for their
children, keeping in mind their healthy and safe future. However, what if some
of these choices end up endangering their lives, the very thing they wanted to
protect their children from? The MMR vaccine scare has had real consequences. Measles
is coming back around the world from the verge of eradication. A study that
looked at the incidence of measles in the US between 2000 and 2015 showed that
it has doubled in this time span, although the overall incidence is still quite
low (so far). There have been more outbreaks of more than 20 after 2010,
suggesting a rising trend. People have also evidently forgotten the harsh realities
of diseases such as measles and whooping cough, leading them to downplay the risk.
In an important act of science communication and creating public awareness,
this was addressed in an episode of the famous medical drama, House MD.<o:p></o:p></span></div>
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<span style="font-family: inherit; line-height: 107%;">Dr. House comes across a teenaged
patient who has been experiencing double vision, sleeplessness, and night
terrors. After going through and eliminating several possibilities, including PTSD
(from sexual abuse, for instance), and concussion, Dr. House is initially
stumped. He observes the patient’s leg is exhibiting a myoclonic jerk, which occurs
due to sudden muscle contractions. Dr. House gets even more intrigued after results
from MRI showed a blockage in the corpus collosum of the brain due to excess
cerebrospinal fluid (CSF). As the condition progresses, the patient starts to
have auditory hallucinations and violent shaking. After much drama, Dr. House
realizes that the patient’s biological mother had not been vaccinated. She <span style="mso-spacerun: yes;"> </span>had also never had measles. During the first
few months of a child’s life, the child relies on anti-measles antibodies that
it gets from the mother during breastfeeding as the MMR vaccine is administered
at nine months. In this case, since the unvaccinated mother left the patient
vulnerable, and the observed symptoms match up a rare (1 in 100,000 cases) form
of persistent measles: sub-acute sclerosing pan-encephalitis. This is an
extremely rare consequence of persistent measles infection (1 in 10,000
thousand cases of measles). The virus hid inside the patient’s brain and ultimately led to severe inflammation there,
resulting in the symptoms describe<o:p></o:p>d.</span></div>
<span style="font-family: inherit;"><span style="mso-bookmark: _Hlk510618983;"></span>
</span><br />
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<span style="font-family: inherit; line-height: 107%;">If the biological mother had been
vaccinated, none of this would happen. Vaccines are not as expensive, if
long-term thought is given. The patient, fictional but relevant, required
various tests, including MRI scans, and two surgeries, which are individually
and collectively far more expensive compared to vaccines. Many argue about
pharmaceuticals and public health organizations profiting vastly from vaccines
which might not be even as effective as they advertise to be. However, a 2015
statistics report showed that the top 20 pharmaceutical drugs with the biggest profit
were not even vaccines. If what they sold were not effective, and if years of
research and history were wrong about vaccines, there would have been large
epidemics of preventable diseases by now. But that is not the case. During the
1950s, 3-4 million people in the USA got measles. Vaccination until now has
reduced chances of measles by 95%. Similar decreases have been seen for
numerous other diseases such as polio, whooping cough, diphtheria, and tetanus.
By accusing vaccines of causing autism, birth defects and other conditions
without solid statistical proof, parents are depriving children from their
ability to fight diseases that have been prevented by millions of people in
this century. France points us toward a possible solution: it is a criminal
offence there for a parent to not vaccine children. <o:p></o:p></span></div>
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<b><span style="font-family: inherit; line-height: 107%;">The Future of Vaccines<o:p></o:p></span></b></div>
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<b><span style="font-family: inherit; line-height: 107%;"><br /></span></b></div>
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<span style="font-family: inherit; line-height: 107%;">Research on vaccines is still at
large, as there are no established vaccines for HIV, hepatitis C, Ebola,
respiratory syncytial virus, cytomegalovirus and malaria, although there are many
experimental candidates, and there have been several trials. Several new
approaches to vaccinations are being tested. For instance, DNA vaccines, which have
been in the works for several years, use the concept of inserting
viral/bacterial DNA into the body for the DNA to be expressed as proteins in host
cells, and the immune system to then respond to them as antigens. But continued
progress relies on public funding which in turn ultimately depends on public
opinion. Therefore, for preventing preventable diseases, and generating novel
vaccines against emerging pathogens, the importance of vaccines cannot be
overstated. <o:p></o:p></span><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiIhF7CqjwU3P3E1JG79xTpfKRMG3MfPJddeCkMxpYw4XZpumIoV7lvcVNnWT0SBuWK2vIpwu87jSg77hqG4kFqnfCV9n6lFaiS1WC0NQ9C-L958Nu_znW-CkVbEUqhv0jWDM-QB4a8lLg/s1600/Capture.PNG" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="250" data-original-width="229" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiIhF7CqjwU3P3E1JG79xTpfKRMG3MfPJddeCkMxpYw4XZpumIoV7lvcVNnWT0SBuWK2vIpwu87jSg77hqG4kFqnfCV9n6lFaiS1WC0NQ9C-L958Nu_znW-CkVbEUqhv0jWDM-QB4a8lLg/s200/Capture.PNG" width="182" /></a></div>
<span style="font-family: inherit; line-height: 107%;"></span><br />
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<span style="font-family: inherit; line-height: 107%;"><i>Sharmeen is a recent Biochemistry graduate from IUB. She loves to explore the real world and her inner
self through science and logic.</i></span></div>
</div>
</div>
Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-66655123746010299842018-03-07T23:49:00.005-08:002018-04-22T23:54:27.876-07:00Grow Your Fetuses Outside Your Body in the Biobag<div dir="ltr" style="text-align: left;" trbidi="on">
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<i>Zebedia R. Quader</i></div>
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<i>Freshman</i></div>
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<i>School of Life Sciences</i></div>
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<i>Independent University, Bangladesh</i></div>
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<i>March 8th, 2018</i></div>
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We all have heard about Mary and her little lamb, but have
you heard that Mary can now watch her little lambs grow in front of her own
eyes? Some researchers at the Children’s Hospital of Philadelphia (CHOP)
located in Pennsylvania, recently came up with what they have dubbed as the
biobag. In this biobag, they saw eight little lambs grow just like they would
in their mother’s uterus or womb. What is this biobag? It is a transparent plastic bag
filled with artificial amniotic fluid and blood just like a natural womb. <o:p></o:p></div>
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The CHOP team, collected surplus materials from hospitals,
such as those required for extracorporeal membrane oxygenation (ECMO) which
oxygenates the blood of very ill infants. The ECMO equipment was collected to
attempt to provide oxygen to the lambs just like it would in a baby. <o:p></o:p></div>
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To ease into the process, the researchers first placed the
lambs into early biobag prototypes only a little before they should be
delivered naturally. These early versions made use of circulating artificial
amniotic fluid with infused electrolytes, and were connected to an oxygenator.
Only one animal lived for 108 hours, and that too with complications. This was
not enough.<o:p></o:p></div>
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Over the next few months, they worked on refining their
technique with the additional help of surgeons. A major change that they
settled on involved using non-circulating artificial amniotic fluid; this
basically meant that the fluid would enter through one tube and leave through
another, and the exiting fluid would not reenter. They also connected the oxygenation
unit to the fetus lamb directly via the umbilical cord, allowing the fetus’s
heart to control the circulation.<o:p></o:p></div>
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The completed version of the biobag was able to allow
development of premature fetuses (eight of them) for four weeks, until they
were ready for “delivery”. Sheep pregnancies last around five months, so being
able to facilitate the final month of development of the fetus outside the
mother’s womb is a ground-breaking advancement. These lambs look, behave, eat,
and respond like naturally born lambs, short of some minor side-effects in a
few of them.<span style="mso-spacerun: yes;"> </span>It is nothing short of a
miracle that a little piece of plastic could replicate the function of a womb.<o:p></o:p></div>
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<o:p><span style="font-size: x-small;">Schematic diagram of the set-up. <i>Nature Communications</i></span></o:p></div>
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<o:p><br /></o:p></div>
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When the results of this study were published, the science
world raged into a storm. Lots of praises resounded, but there were more
critical voices as well, mostly surrounding ethical implications of the
study.<span style="mso-spacerun: yes;"> </span>People were concerned about how
being able to develop babies outside the womb could erode the mother-baby
relationship, or allow experimentation. The researchers responded that the
biobag is for premature animals and babies only, and could not support embryos
from inception. And even if it were possible, one might argue that surrogacy
already exists, and there are regulations for conducting research on embryos.
The biobag in its current state, and if perfected for human babies, would only
reduce the mortality rate of premature babies, which often suffer from serious,
life-threatening complications. Who could oppose that?<o:p></o:p></div>
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Now, lambs and human babies are not the same but the
researchers expect the process to be ready for human trials by 2019. If
successful, it could revolutionize maternal-fetal medicine. But it is going to
be a lot of work.<o:p></o:p></div>
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Flake, the head researcher for the study, has said in an
interview, “I’m still blown away, whenever I’m down looking at our lamb. I
think it’s just an amazing thing to sit there and watch the fetus on this
support acting like it normally acts in the womb... It’s a really awe-inspiring
endeavor to be able to continue normal gestation outside of the mom.”<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWhBNSLDC_S8Wz6ni6rOgi0ojVZhU4m1x2-dZsYzIT7bTQG0hQfYfhhhj3VX5DbzEpOamU9H8DRa95r_s1VcXfD16R0LmLy_cjgLrXnjyMhVqEmSHt07Kh8Y7UBHa245AZSXV4vLUP37g/s1600/Blog+photo.JPG" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="177" data-original-width="167" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWhBNSLDC_S8Wz6ni6rOgi0ojVZhU4m1x2-dZsYzIT7bTQG0hQfYfhhhj3VX5DbzEpOamU9H8DRa95r_s1VcXfD16R0LmLy_cjgLrXnjyMhVqEmSHt07Kh8Y7UBHa245AZSXV4vLUP37g/s1600/Blog+photo.JPG" /></a></div>
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<i>Zebedia writes,</i></div>
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<i><br /></i></div>
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<i>"With a curious mind, microbiology has provided me with the ultimate source of entertainment, perhaps for life."</i></div>
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-33185825798933225192018-02-09T14:22:00.002-08:002018-09-10T01:08:20.950-07:00Examining a Lesser Known Side of Cystic Fibrosis<div dir="ltr" style="text-align: left;" trbidi="on">
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<i>Nuzhat Faizah<br />
Sophomore<br />
School of Life Sciences<br />
Independent University, Bangladesh<br />
<br />
February 10th, 2018</i><br />
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For Raima’s family, that sweltering April summer not only brought the flares of
the scorching sun, and the kath golap and krishnochura blooms, but also new
hope of the arrival of a new member. Elation spread through the house after
Farhan (Raima's husband) received the news that finally, the joy of parenthood
was about to knock at their door because the doctors had found a surrogate
mother who was ready to help the couple conceive a child.<br />
<br />
Raima was then 35 years old. She had been diagnosed with cystic fibrosis (CF)
when she was in her teen years. The signs and symptoms were not very prominent
until she suddenly could not breathe properly and began to suffer from
continuous coughing. While going through puberty, she suffered from
malnutrition and could not gain weight despite having good meals, had issues
with bowel movements, and repeatedly got lung infections. In addition, she
experienced irregular menstrual cycles, and ovulatory disorders that would
later lead to fertility problems.<br />
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After getting married, a gynecologist she consulted with explained that
pregnancy might be deferred for female patients of CF. To understand the
possible ways in which CF causes this and its other symptoms, let us delve a
little into the mechanism of the disease.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiuvuhO_RJtzrAob2jsAa0QOsfhb3LxVskX4QupG3nvlQCRe3OZwgdsXgx25zfXMdkrwFNxlnUdkyxAEEAb5npCVUzwNdlfOxLxDhQ7aRangkq8gYMQoTyd2HdE5KFRS3jyphkcODsgUvA/s1600/cf-channel.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="516" data-original-width="704" height="234" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiuvuhO_RJtzrAob2jsAa0QOsfhb3LxVskX4QupG3nvlQCRe3OZwgdsXgx25zfXMdkrwFNxlnUdkyxAEEAb5npCVUzwNdlfOxLxDhQ7aRangkq8gYMQoTyd2HdE5KFRS3jyphkcODsgUvA/s320/cf-channel.jpg" width="320" /></a></div>
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<span style="font-size: x-small;">Impeded chloride ion transport leads to mucus buildup. <i>University of Utah</i></span></div>
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CF arises from mutations (changes in the genetic code) in a gene called CFTR
(cystic fibrosis transmembrane conductance regulator). The gene is named after
the disease, but its normal function is in fact to make a protein (also named
CFTR) which acts as a channel across cell membranes to transport chloride ions
into and out of the cells which helps to regulate the movement of water in
tissues. This is important for maintain a certain thin consistency of mucus (a
slippery substance whose function is to lubricate and shield the lining of the
airways, tissues, organs and organ systems; basically, what clogs your airways
when you have a cold).<br />
<br />
Certain mutations in the CFTR gene result in changes in the structure of the
membrane-spanning chloride channel, and the changes impede its normal
functioning. The movement of chloride ions, and the subsequent movement of
water are impeded, resulting in the production of very thick and sticky mucus
in various organs. This leads to the typical symptoms of breathing difficulties
by clogging up the airways with thick mucus, and malnutrition from impaired
absorption of food in the bowels due to the presence of thicker mucus. Problems
with nutrition and increased energy needs for dealing with the thick mucus also
contribute to the irregular menstrual cycles and ovulatory issues. A lesser
known consequence of CF is thicker cervical mucus. This reduces the likelihood
of sperm cells successfully penetrating the cervix. These are thought to have
converged in Raima’s case.<br />
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It is worth noting that the majority of women with CF are able to conceive and
give live birth, but as Raima’s case demonstrates, symptoms arising from CF can
seriously impede conception. Interestingly, CF’s impact on fertility is far
more devastating in men; more than 90% of men with CF are infertile. These
cases are due to the absence or incompleteness of a certain canal (the vas
deferens) that transports sperm prior to ejaculation. The canal fails to
develop properly as a result of the defective CFTR gene. To conclude on a
broader note, the diverse set of symptoms resulting from a single defective
gene is a neat demonstration of the pleiotropic effects of genes, which refers
to the ability of many genes to affect two or more different phenotypes.<o:p></o:p><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAK-Hn6tuvKOh_f2ICPZIwcCf6Nhs89nWegu-KEE8BmK2v6nHxpbRDBvTOg-2Rag9CEn5b1tznBCvzLxDjzy3oTZ_78J8tHnDztTRgVyb1pRQW1m3J67ftkUY1u8Uk7iXmshnZRQKccXA/s1600/Picture%252C+NF.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="640" data-original-width="557" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAK-Hn6tuvKOh_f2ICPZIwcCf6Nhs89nWegu-KEE8BmK2v6nHxpbRDBvTOg-2Rag9CEn5b1tznBCvzLxDjzy3oTZ_78J8tHnDztTRgVyb1pRQW1m3J67ftkUY1u8Uk7iXmshnZRQKccXA/s200/Picture%252C+NF.jpg" width="172" /></a></div>
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<i>Nuzhat Faizah is a Biochemistry second-year with a never-ending passion for photography and birds. She likes to study about mental health and reproductive disorders.</i></div>
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com1tag:blogger.com,1999:blog-7127526334419423499.post-81291300063248959422018-01-04T07:41:00.000-08:002018-02-09T14:09:26.199-08:00Designer Babies: A Bioethics Perspective<div dir="ltr" style="text-align: left;" trbidi="on">
<i>Abrar Hamim Fayz</i><br />
<i>Sophomore</i><br />
<i>School of Life Sciences</i><br />
<i>Independent University, Bangladesh</i><br />
<i><br /></i>
<i>January 4th, 2018</i><br />
<br />
Humans often customize things that they possess, use, or consume to align them to their tastes. We do it with cars, houses, clothes, food, and many other things. But what about babies? Yes, modern biology has brought us to a point where we could very soon have babies with characteristics we desire. Sounds intriguing, doesn’t it?<br />
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We know genes control the features of an organism. It is possible to manipulate the characteristics of a baby before it develops by altering its genes when it is still an embryo. This can be done through genetic engineering, which has seen widespread application in other animals as well as plants and microbes. Current advances in this technology, led by the CRISPR-cas9 gene editing system, could allow safe and efficient manipulation of human embryos sooner rather than later.<br />
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One of the main potential advantages of editing embryos is to remove or fix genes that are responsible for hereditary genetic disorders like cystic fibrosis, sickle cell anemia and Huntington’s disease. Already this year, human embryos were edited to remove genetic defects underlying a hereditary heart condition. Even though this was experimental, and the embryos were not implanted for development, early results on the accuracy of the edits are promising. The technology would also allow people to produce what are often referred to as designer babies, with characteristics they consider desirable such as blue eyes, blonde hair, athletic build, and intelligence, creating what they perceive to be the perfect human.<br />
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But is it ethical? “Aren’t we trying to outsmart God’s creation?” Many already ask. It is illegal in many countries to even experiment on human embryos. There are no simple answers. If it is possible to preemptively fix cystic fibrosis, wouldn’t it be cruel not to? But it is conceivable that large numbers of people will prioritize good looks and intelligence to produce the aforementioned designer babies. The downstream consequences of this need to be considered. How would such trends affect the gene pool? Would we see a decline in genetic diversity? Designer babies could create a difference between normal humans and near-perfect ones, which would probably reflect economic differences between individuals who can and cannot afford the technology.<br />
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For any of this to be possible, the technology still needs to be perfected. Off target changes in gene sequences must be reliably avoided, for instance. Time will reveal whether one day we are going to be surrounded by near-perfect humans, but a little foresight may go a long way in tackling many of the ethical quandaries that will predictably arise.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKtZY41dk7SK6t8vwlOAkNCIrbVuN0s4NJpk6_lpcj8zusRMr1F3dpwyGjM-2B7jHlLgA_ioP11xxsBRcsGNJfPigVADHINQsysIyFJahXTjzb0RCfhva3sbajufmRBCkYkims6ATwVg8/s1600/Blog+picture.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="1204" data-original-width="1203" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKtZY41dk7SK6t8vwlOAkNCIrbVuN0s4NJpk6_lpcj8zusRMr1F3dpwyGjM-2B7jHlLgA_ioP11xxsBRcsGNJfPigVADHINQsysIyFJahXTjzb0RCfhva3sbajufmRBCkYkims6ATwVg8/s200/Blog+picture.jpg" width="198" /></a></div>
<span style="font-family: inherit; font-size: 12.0pt; line-height: 115%;"><i>Abrar is a second-year student in Microbiology. He writes:</i></span><br />
<span style="font-family: inherit;"><span style="font-size: 12.0pt; line-height: 115%;"><i><br /></i></span>
</span><span style="font-size: 12.0pt; line-height: 115%;"><i><span style="font-family: inherit;">"I love to play football, read books, and travel to gain more knowledge. I want to do something with genetics, as it is the most interesting topic I have known since I was a child."</span>
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-48870286778901729122017-12-21T10:56:00.001-08:002017-12-21T10:58:05.346-08:00Infecting the Infectious: Viruses vs. Bacteria<div dir="ltr" style="text-align: left;" trbidi="on">
<i><span style="font-family: inherit;">Ramisa Maliha</span></i><br />
<i><span style="font-family: inherit;">Sophomore</span></i><br />
<i><span style="font-family: inherit;">School of Life Sciences</span></i><br />
<i><span style="font-family: inherit;">Independent University, Bangladesh</span></i><br />
<i><span style="font-family: inherit;"><br /></span></i>
<i><span style="font-family: inherit;">December 23, 2017</span></i><br />
<span style="font-family: inherit;"><br /></span>
<span style="font-family: inherit;">To be fair, bacteria are mostly our friends. The human body holds about 100 trillion commensal bacteria, that is, bacteria that do not harm us, and often benefit us. We can therefore think of them as part of our team. But not all bacteria are team players, as we are all very well aware. Disease-causing or pathogenic bacteria look to harm us in various ways, and many have even become resistant to multiple antibiotics, making treatment very difficult. But behold! Where there is life, there is predation. There is an entity on earth that outnumbers every living thing combined that most people are not even aware of: Bacteriophages (or phages, in short).</span><br />
<span style="font-family: inherit;"><br /></span>
<span style="font-family: inherit;">No, it’s not an insect nor some fantastic devourer of bacteria. These organisms, which are so simple that many do not label them as organisms at all, are even smaller than bacteria. Bacteriophages are viruses that infect bacteria. Bacteriophages that go through a certain kind of lifecycle end up rapidly killing the bacterial host. Because of their impressive action, bacteriophages have been employed as bacterial agents for 90 years to treat bacterial infections in humans and other species, and are prescribed to this day in places like Georgia and Russia. After all, the enemy of our enemy is our friend.</span><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhYLHikalj9s3M4TIO1o57_5WnAGcMpZ_3puQ6HgW5vHnx0b8nuFDTi2uu7gUjD7qKrD6dc3hIKcPQZGC5kW037Cr1HrArN7Ql1SsliHgu4BlwFwi-6ldBxVL_isGxqQ2TGBBJ8aHVPnE/s1600/ehp.121-a48.g001.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="625" data-original-width="800" height="311" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhYLHikalj9s3M4TIO1o57_5WnAGcMpZ_3puQ6HgW5vHnx0b8nuFDTi2uu7gUjD7qKrD6dc3hIKcPQZGC5kW037Cr1HrArN7Ql1SsliHgu4BlwFwi-6ldBxVL_isGxqQ2TGBBJ8aHVPnE/s400/ehp.121-a48.g001.png" width="400" /></a></div>
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<span style="font-family: inherit; font-size: x-small;"><span style="background-color: black;"><span style="color: white;">Phages on the surface of an <em style="margin: 0px; padding: 0px;">Escherichia coli</em> cell inject genetic material into the bacterium.</span></span><em style="background-color: black; margin: 0px; padding: 0px;">© Eye of Science/Science Source</em></span></div>
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<span style="font-family: inherit;">Bacteriophages first attach themselves to the surface of bacterial cells, and insert their genetic material (which can be DNA or RNA) into the bacteria by a syringe-like mechanism. The viral shell remains outside the bacterium. The injected viral genetic material utilizes the bacterium's resources and produces viral enzymes, as well as more viral genetic material. With the new viral proteins and enzymes, many new phage particles are assembled inside the host bacterium. Eventually the bacterium bursts (lyses), releasing the phage particles to infect neighboring bacteria after destroying the original host. Bacteriophages tend to be very specific to different hosts via surface binding interactions. For instance, a phage that infects Vibrio cholerae (the causative agent of cholera) would not affect Mycobacterium tuberculosis (the causative agent of tuberculosis). This property greatly accentuated their potential for use against specific pathogenic bacteria.</span><br />
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<span style="font-family: inherit;">Frederick Twort, a bacteriologist from England is thought to be the first to suggest that phages could be used for killing bacteria in 1915. Later, Felix d'Herelle, a microbiologist at the Institute Pasteur in Paris, anticipated the use of phages to treat bacterial infection in humans, that is, phage therapy. In 1919 the first recorded phage therapy occurred when d'Herelle prescribed a mixture of phages to a 12-year-old boy with severe dysentery. At that time human trials were not as strictly regulated as we see today and the only method of knowing any side effects was for d’Herelle and his team to ingest the concoction themselves before prescribing it! According to the records, the boy’s symptoms cleared up after a single dose and he fully recovered within a few days.</span><br />
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<span style="font-family: inherit;">Most of the results of the early research for phages to treat bacterial infections were published in non-English journals, and thus did not greatly influence research and therapy in Western Europe and the U.S. Having said that, bacteriophages were sold as a form of medication to treat a range of bacterial infections by a pharmaceutical company in the U.S called Eli Lilly as early as the 1940s. It was meant for treatment of wounds and upper respiratory infections. At that time phage therapy was not prevalent and efficient as there were no proper storage and purification methods. Also, it was not known that bacteriophages were very specific to the bacteria they attack. On top of that, the dawn of antibiotics (which were much faster and better understood) swept people off their feet and phage therapy fell out of use in most places.</span><br />
<span style="font-family: inherit;"><br /></span>
<span style="font-family: inherit;">Bacteriophages, as a form of therapy, have pros and cons. Most traditionally used antibiotics are broad spectrum, so along with destroying the pathogenic species of bacteria, they also destroy many beneficial bacteria making up a person’s microbiome. On the other hand, bacteriophages are very specific, which is ideal for treatment. However, bacteria can become resistant to the virus too. This problem is tackled by using phage cocktails, which incorporate many different phages targeting the same bacteria, making it very difficult for the bacteria to evolve resistance.</span><br />
<span style="font-family: inherit;"><br /></span>
<span style="font-family: inherit;">In the 1980s, the growing threat of antibiotic-resistant bacterial strains lead to Western scientists “re-discovering” phage therapy as a potential alternative. In the 2000s, human experiments began again, and data from the first phase I clinical trial in the U.S. was published in 2009. It is hoped that phage therapy will be an approved therapeutic option for bacterial infections throughout the world in the near future. In 2006 the Food and Drug Administration allowed the use of bacteriophages that attack strains of Listeria as a food additive on ready-to-eat meat products. This contribution of bacteriophages in the food treatment sector could be a peek into the future; replacing antibiotics and bringing an end to antibiotic-resistant supervillain bacteria such as MRSA!</span><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiw3pH1Vi3FWqpenrTtWfNafthtcTtD-jDt_iQUhGsoqeSV7K8MrEACv4BSqfbR3Tc2Ag0W7Lz4WCfQZ-fIlVBHO3lcEqaYKW8k4M1rxeQwix3Re8JmlA-qEBLn7W5Ajp8PQIyysJeshZ0/s1600/Photo.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><span style="clear: left; float: left; font-family: inherit; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="933" data-original-width="525" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiw3pH1Vi3FWqpenrTtWfNafthtcTtD-jDt_iQUhGsoqeSV7K8MrEACv4BSqfbR3Tc2Ag0W7Lz4WCfQZ-fIlVBHO3lcEqaYKW8k4M1rxeQwix3Re8JmlA-qEBLn7W5Ajp8PQIyysJeshZ0/s320/Photo.jpg" width="179" /></span></a></div>
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<i><span style="font-family: inherit;">Ramisa is a freshly minted second-year Microbiology student. She writes:</span></i></div>
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<i><span style="font-family: inherit;">Biology has been the most intriguing subject to me for as
long as I can remember. After being introduced to Microbiology, I found my
passion in learning all about microscopic life that we interact with every day.
I hope to indulge my passion by getting into the field of research and contribute
to knowledge about microbes.</span></i><o:p></o:p></div>
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com5tag:blogger.com,1999:blog-7127526334419423499.post-9857902049518466732017-11-25T06:51:00.000-08:002018-03-07T23:25:17.608-08:00Lessons from Biochemistry: The Use of Enzymes in the Food Industry<div dir="ltr" style="text-align: left;" trbidi="on">
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<span style="line-height: 107%;"><span style="font-family: inherit;">Enzymes are among
the most abundant molecules found in all living creatures. They are proteins
that speed up specific chemical reactions which are ultimately the basis of
life. Without them, many reactions can still occur but they would be too slow
to support life. Each enzyme has a specific three-dimensional shape that allows
it to bind its substrate and facilitate its conversion into a product. Alongside
their importance in the chemistry of living organisms, enzymes have also been
applied in the food industry for decades, to improve quality and stability of products,
and to increase production efficiency.<o:p></o:p></span></span></div>
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<span style="line-height: 107%;"><span style="font-family: inherit;">Starting
from the breakdown of protein and starch to the processing of raw materials for
alcohol fermentation, enzymes in the food industry play a range of important
roles. Advances in biotechnology have allowed us to isolate, clone, produce,
and optimize the activity of many natural enzymes for our use. Let us look at
some examples from some of the most prominent arms of the food industry. <o:p></o:p></span></span></div>
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<span style="line-height: 107%;"><span style="font-family: inherit;">Enzymes like
chymosin, pepsin, lipase, and lactase, have been used to great effect in the
dairy industry. Cheese production utilizes an enzyme complex called rennet, which
is a mixture of chymosin, pepsin, and lipase extracted from animal and
microbial sources. The enzyme coagulates milk in the initial stages of cheese
production breaking . Lactase treatment improves the solubility and sweetness
of various dairy products by breaking lactose down into the smaller and sweeter
sugars glucose and galactose. In addition, many people who are unable to
consume dairy products due to lactose-intolerance can take supplemental lactase
to help break down the lactose, and thus safely consume dairy products. <o:p></o:p></span></span></div>
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<span style="line-height: 107%;"><span style="font-family: inherit;">Enzymes are
also used to augment baking. One of the major enzymes used in bread production
is amylase. It helps to maximize fermentation by efficiently breaking down starch
into smaller sugars for yeast to use. As a result, the end product has an even
crumb structure and a fine high loaf volume. Lipases are used to break down
many natural lipids found in flour in order to make the dough firmer.<o:p></o:p></span></span></div>
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<span style="line-height: 107%;"><span style="font-family: inherit;">The brewing
industry is not left behind in its use of enzymes. Multiple enzymes are used in
the industry for better production of low-carbohydrate beer (light beer), to shorten
the beer maturation time, and to produce beer from cheaper raw materials. Proteases
are used to break down many proteins and free up amino acids. This improves the
malt and yeast growth. Proteases also reduces the haziness formed in beer by breaking
down certain proteins.<o:p></o:p></span></span></div>
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<span style="line-height: 107%;"><span style="font-family: inherit;">Not many (if
any) branches of the food industry are left untouched by enzymes. Enzymes are
often used to pre-digest various components found in baby food to make absorption
of the nutrients simpler for the babies’ developing digestive systems. The
industrial production of fruit juices utilizes an enzyme called pectinase to
break down pectin. Pectinase treatment improves texture and clarity by breaking
down components of pulp. The enzyme pectinase is extracted from the fungus <i>Asperigillus niger</i>., and is also used in
the processing of tea leaves to more effectively bring the flavor out.<o:p></o:p></span></span></div>
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<span style="line-height: 107%;"><span style="font-family: inherit;">Enzymes therefore exert an enormous although largely unseen influence on our daily lives
by being involved in the majority of the food production processes that we rely
on. Starting from the refreshing morning tea to the after-dinner gulp of
velvety wine, enzymes have helped introduce the human world to new dimensions
of taste, flavor, and efficiency.<o:p></o:p></span></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjCF1NOjGMbXmi3uG7Cf-X435rKsHbhg1VXxGSLpC0IiBgTg8XMRCA_jyaUn5ydK5PxEsmDtJwEBpPD5RA_aBAtFeFmQyRvFXU3n_zIimNJhDWrrqKt7TSyXAF2KOKfYRkzNZtLfSfIIoo/s1600/Photo.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><span style="clear: left; float: left; font-family: inherit; margin-bottom: 1em; margin-right: 1em;"><span style="font-family: inherit;"><img border="0" data-original-height="720" data-original-width="720" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjCF1NOjGMbXmi3uG7Cf-X435rKsHbhg1VXxGSLpC0IiBgTg8XMRCA_jyaUn5ydK5PxEsmDtJwEBpPD5RA_aBAtFeFmQyRvFXU3n_zIimNJhDWrrqKt7TSyXAF2KOKfYRkzNZtLfSfIIoo/s200/Photo.jpg" width="200" /></span></span></a></div>
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<i><span style="font-family: inherit;"><br /></span></i>
<i><span style="font-family: inherit;"><br /></span></i>
<i><span style="font-family: inherit;">For Yusra,
biology has always been a magnet of interest. She has always wanted to know the
why's and how's of the living world. Being a future microbiologist, she looks
forward to doing research on microbial interactions with human lives.</span></i></div>
</div>
Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-56079242038157082022017-11-08T22:19:00.003-08:002018-02-09T13:22:57.543-08:00CRISPR/Cas9: An Introduction and a Brief Glimpse of Recent Literature<div dir="ltr" style="text-align: left;" trbidi="on">
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<i>Ridwan Hossain</i></div>
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<i>Sophomore</i></div>
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<i>School of Life Sciences</i></div>
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<i>Independent University, Bangladesh</i></div>
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<i>November 9th, 2017</i></div>
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CRISPR/Cas9 is a new revolutionary gene editing tool that is
causing quite a stir in the world of science. It is opening up possibilities to
cure cancer, HIV and other major diseases which are incurable by other methods
till now. To learn how CRISPR works, we need to understand what genomes, genes,
and gene editing are. Every living organism ranging from the most sophisticated
ones like humans to the simplest but deadliest of organism like viruses
contains specific instructional codes called genes. The complete set of genes
carried by an organism is its genome. With the exception of some viruses, genomes
are made up of DNA. These instructional
codes decide the characteristics of the organisms; genes code for their
physical structures, and determine the biochemical processes that they utilize
to make use of nutrients and produce energy. Your eye color, how a virus will
infect an organism, how a plant will carry out photosynthesis, the fur color of
a dog, these are all decided by each of their respective genetic codes.
Changing these genetic codes will alter different characteristics of an organism.
We have discovered and developed multiple methods to modify genetic codes and
this is what gene editing refers to. CRISPR/Cas9 is a promising new tool that
can carry out very specific gene editing in less time than the other methods we
have traditionally used. Now, what exactly is CRISPR/Cas9?<o:p></o:p></div>
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Viruses are a type of microorganism that survive by feeding
on other organisms. Certain viruses, known as bacteriophages, only infect
another type of microorganism known as bacteria. Bacteriophages bind to the surface
of bacteria and inject their genetic information inside the bacteria. The
bacteriophage takes over the building machinery of the bacterium, and uses it
to make hundreds of copies of itself (that is, its offspring). Bacteria have
evolved several mechanisms to defend themselves from bacteriophages. The
CRISPR/Cas system, found in many bacteria, allows them to recognize and cut
foreign pieces of genetic material (such as viral DNA), and if they survive,
store this information into their own genome using the CRISPR system. Now that
it has information about this particular phage, if it is attacked again, it
will use this stored information to specifically recognize and rapidly destroy
the phage. We have adapted a particular bacteria’s CRISPR/Cas system (namely the
CRISPR/Cas9 system of <i>Streptococcus pyogenes</i>)
to target genes for editing. So how does this system really work?<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIgpO_JNa0nebc6J1iAiGmcGIsihUsy9lDPwdyjW70nevYhgHYsfVy6rWzu8LwlHon5opwS6u8poKFxuJAyHkkbQU2dN3NtctmpTIFk0hx7K6Jf2lFCLtVhh8Egj0gjqUC_0qYGSjcFg8/s1600/maxresdefault.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="900" data-original-width="1600" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIgpO_JNa0nebc6J1iAiGmcGIsihUsy9lDPwdyjW70nevYhgHYsfVy6rWzu8LwlHon5opwS6u8poKFxuJAyHkkbQU2dN3NtctmpTIFk0hx7K6Jf2lFCLtVhh8Egj0gjqUC_0qYGSjcFg8/s400/maxresdefault.jpg" width="400" /></a></div>
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<span style="font-size: x-small;">An animated Cas9 targeting a gene. <span style="text-align: left;"><i>McGovern Institute for Brain Research at MIT</i></span></span></div>
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<o:p></o:p></div>
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We do not need the initial step of recognizing DNA as
foreign for our gene-editing system. The CRISPR/Cas9 system works based on
stored sequences in the CRISPR genetic region, an enzyme called Cas9 for
cutting DNA, and a guiding RNA. The guiding RNA is transcribed from the stored
sequence in the CRISPR region. We have the technology to target any part of the
genome (in any organism) by making the appropriate guiding RNA. The guiding RNA
carries the Cas9 enzyme to the gene we want to cut. Cutting a gene can lead to
its deactivation, and also allow us to introduce mutations of our choice by
providing an appropriate repair template for the cell’s repair machinery. Let us look at a couple of recent studies and potential applications of the system.<o:p></o:p></div>
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An increasingly large number of studies are using
CRISPR/Cas9 to edit genes for a variety of purposes. <a href="https://www.nature.com/articles/nbt.3055" target="_blank"><span style="color: orange;">One recent study used thesystem to target the nervous system in adult living mice</span></a>. The target gene in
this study was an X-chromosome gene known as MECP2. The normal functioning of
nerve cells depends on the protein encoded by MECP2. A mutated version of this
gene causes a syndrome called Rett syndrome. Rett syndrome is a disease that
causes problems in development of a victim’s brain and causes major
disabilities and symptoms similar to autism spectrum disorders. In this study,
they were able to use CRISPR/Cas9 to specifically target this gene and thereby
reduce the production of its products, which resulted in Rett syndrome. This
seems counter-intuitive and scary, but what they did is basically show that it
is possible to target and alter a gene in an adult living organism. The next
step would be to figure out how to fix a defective gene through CRISPR-mediated
targeting.<o:p></o:p></div>
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But deactivating genes can be quite beneficial on its own,
as demonstrated by <a href="https://retrovirology.biomedcentral.com/articles/10.1186/s12977-015-0150-z" target="_blank"><span style="color: orange;">a study where they targeted HIV genes with CRISPR/Cas9</span></a>. HIV,
which is the virus that ultimately causes AIDS, still eludes a complete cure.
According to WHO there were 36.7 million people living with HIV by the end of
2015. HIV is particularly hard to find a cure for because it reproduces really
fast and its genome goes through rapid changes. So if we come up with a way to
destroy HIV virus they just change into something different and our cure does
not work anymore. Additionally, the virus incorporates itself into the host
genome, and can stay dormant, making viral clearance impossible. Maybe CRISPR
can change that. Current methods target different steps of the HIV lifecycle
simultaneously as multiple resistance mutations are less likely to occur.
CRISPR could do even better. A study was recently conducted to see how CRISPR
could stop HIV. A CRISPR/Cas9 system with ten different types of guiding RNAs,
each with its specific genome sequence, was used to target different areas of
the HIV genome infecting cells in laboratory cell culture. Results showed that
this process was highly effective in the inhibition of HIV-1 (a certain lineage
of HIV) genome. CRISPR was working by inserting inactivating mutations into
different parts of the HIV genome. An important advantage to this is that HIV viruses
that had been directly incorporated into the host genome were directly
deactivated, unlike what current drugs do (which only work on actively
replicating viruses). This effectively means viral clearance, and if developed
further, could completely cure AIDS.<o:p></o:p></div>
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CRISPR/Cas9 holds the cure for genetic and viral diseases and so much
more. The technology is, in fact, still being developed for even greater
efficiency. CRISPR could be used to get rid of disorders that children are
born with such as Down Syndrome. More excitingly, and perhaps scarily, we can
decide the characteristics of our offspring and even modify and change ourselves
with complete freedom. It is hard to say what will be possible with it in the
near future but it will eventually change the way we live and see our world.
Are we ready to accept all the changes though?<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhRarBaJu_4F7f2nRsDyZzjpZD2Ue_xCKNUQyjD1w7y4L_W4yeh4Zct_iLuFH8KAAYgIwrreLWDige9UZVllX47SVBAKlu-ybkbfyWrP5mS5ePszL2H9MUyzCMfC58pat6dsgzl8rF6VGA/s1600/Blog+picture%252C+Ridwan.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="640" data-original-width="960" height="133" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhRarBaJu_4F7f2nRsDyZzjpZD2Ue_xCKNUQyjD1w7y4L_W4yeh4Zct_iLuFH8KAAYgIwrreLWDige9UZVllX47SVBAKlu-ybkbfyWrP5mS5ePszL2H9MUyzCMfC58pat6dsgzl8rF6VGA/s200/Blog+picture%252C+Ridwan.jpg" width="200" /></a></div>
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<i>Ridwan is a sophomore at IUB whose dream is to be a renowned mad scientist. He will be a Nobel laureate.</i></div>
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-74016372827934997852017-11-03T06:41:00.002-07:002019-04-30T00:16:30.717-07:00Meet Magneto Anew: Evolving Enhanced Magnetism in Bacteria<div dir="ltr" style="text-align: left;" trbidi="on">
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<span style="font-family: inherit;"><i>Maliha Tanjum Chowdhury</i></span><br />
<i><span style="font-family: inherit;">Sophomore</span></i><br />
<i><span style="font-family: inherit;">School of Life Sciences</span></i><br />
<i><span style="font-family: inherit;">Independent University, Bangladesh</span></i><br />
<i><span style="font-family: inherit;"><br /></span></i>
<i><span style="font-family: inherit;">November 3, 2017</span></i><br />
<i><span style="font-family: inherit;"><br /></span></i>
<span style="font-family: inherit;">Magneto. A
mutant arisen during the tyranny of Nazi rule – an abominable villain who
possesses the power to wield and crumple all that is metal-made, vowing to
crush anything and anyone obstructing </span><span style="font-family: inherit;">his path. There stands not a single X-Men
fan who hasn’t been mesmerized and equally appalled by the terror this mutant
is capable of. This article, too, discusses mutants with a special affinity for
metals (more specifically, iron). However, they are thankfully much more benign
than our infamous bad-boy Magneto. I’m talking about bacterial mutants that have
enhanced magnetism in their iron-binding protein. My fellow geeks, this may not
be as groundbreaking as a human being who is able to spontaneously generate
magnetic fields, but the fact that a natural protein present in bacteria has
been selectively evolved to bring about considerable magnetic properties is in
itself pretty incredible. As we will later discuss, these magnetic bacteria
could have important applications in research and medicine. Now sit back, read
on and let your minds be blown.</span><br />
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<span style="font-family: inherit; line-height: 115%;">The paper I am
about to break down is heftily titled, “<a href="https://www.nature.com/articles/srep38019" target="_blank"><span style="color: orange;">Engineering Genetically-encoded Mineralization and Magnetism via Directed Evolution</span></a>.” The subject of
experimentation was the natural iron-sequestering protein ferritin in the
bacteria <i>E. coli</i> (versions of the
protein are found widely in all domains of life, including humans). This
protein mainly serves as a homeostatic regulator of cellular free-iron levels,
storing iron to be released in times of need (incorporating free iron into a
cellular protein is an example of biomineralization). Ferritin stores iron in a
hydrated, amorphous form of iron oxide, which is a biocompatible substance
(harmonious with living tissue), and is known to be magnetic when crystalline. The
mineralized iron stored in ferritin displays poor crystallinity, and thus has a
very low magnetic moment, which confers it with the ability to release iron
with sufficient ease in times of deficiency. Though the factors affecting
crystallinity and hence magnetic properties of the iron oxide core within
ferritin remain largely unclear, this protein was deemed a model starting point
for this study which sought to find ways of increasing the innate magnetism of
the core by changing the structure of the protein. As an aside, magnetic bacteria do exist in nature (magnetotactic bacteria), but here they were building magnetic versions of a normally non- or poorly magnetic protein.<o:p></o:p></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYcWI1vOJk0rrVBDZO7QnPkUiZQSqgNHlCN74IFF8AhTMWWqv3HKS8P6HNDu4n70j7aNcKEwNeb7I3lLvlAh35c5gewgw7UiReDf9tZn7rft37cR_-W_IIaveIOEyFdQn2JII4JI0TJfI/s1600/magnetic.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: inherit;"><img border="0" data-original-height="189" data-original-width="441" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYcWI1vOJk0rrVBDZO7QnPkUiZQSqgNHlCN74IFF8AhTMWWqv3HKS8P6HNDu4n70j7aNcKEwNeb7I3lLvlAh35c5gewgw7UiReDf9tZn7rft37cR_-W_IIaveIOEyFdQn2JII4JI0TJfI/s1600/magnetic.JPG" /></span></a></div>
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<span style="line-height: 115%;"><span style="font-family: inherit; font-size: x-small;"><i>The mutant ferritin-containing bacteria (H34+T64I) demonstrably concentrate around magnets</i></span></span></div>
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<span style="font-family: inherit; line-height: 115%;">The
scientists first needed a system to assess iron uptake by ferritin. The problem
was that cells have other means of dealing with any iron that is provided to
them, such as other iron-storage proteins and metal cation exporters. To solely
observe iron-sequestration by ferritin, the scientists created special “knock-out”
strains of the bacteria that had all genes that interact with iron deleted.
They could then add mutant ferritin genes to these bacteria via plasmids, and
measure iron uptake or select mutants with greater ability to bind iron.
Plasmids are circular pieces of DNA that replicate inside bacterial cells
independently of the bacterial chromosome, and express their own genes. <o:p></o:p></span></div>
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<span style="font-family: inherit; line-height: 115%;"><br /></span></div>
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<span style="font-family: inherit;"><span style="line-height: 115%;">So how did
they produce the different mutant versions of the ferritin gene? This brings us
to one of the coolest parts of the study; they did it via error-prone PCR. They
used a faulty PCR process, taking advantage of an error-prone DNA polymerase,
which introduced random changes into the ferritin gene that was being copied.
This allowed them to produce hundreds of randomly mutated versions of the
ferritin gene. Each mutant ferritin gene was inserted into a plasmid as stated
above. </span>The most
magnetic of these mutants were then isolated from the total mutant population
by magnetic column retention characterization: the cells suspended in buffers
were passed through a magnetic column of high magnetic field gradient placed
between two permanent magnets; the most magnetic cells remained bound to the
walls of the column while the cells that failed to bind were flushed out by
washing with more buffer solution. </span></div>
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<span style="font-family: inherit;">The isolated magnetic cells were grown and
then passed through the magnetic column again to select for the more magnetic
cells. This was repeated ten times as part of the process of directed
evolution: providing selection pressure on the cells to facilitate evolution of
the greater expression of a certain trait, in this case, magnetism. After thus
evolving highly magnetic cells (presumably containing mutations in the ferritin
gene that enhanced magnetism), the mutant cells were plated, and several of
them were sequenced thoroughly – this can be defined as the process of mutant
screening in the concept of forward genetics. They were thus able to figure out
the exact mutations required in ferritin to increase the magnetism of the
assembled iron oxide core. To add to this understanding, they then applied the
principles of reverse genetics, in that they introduced each of the mutant
genes into the initial wild-type ferritin gene on a plasmid in order to verify
whether the change in iron-sequestration was solely due to these mutations.</span></div>
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<span style="font-family: inherit;"><br /></span></div>
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<span style="font-family: inherit; line-height: 115%;">In total, 38
mutants were tested, and the results revealed that the majority of these
significantly increased the magnetism of the cells compared to wild-type
ferritin. Also, the most magnetic mutant is seen to display double point
mutations which change the amino acid configuration of the protein constituting
the B-type channel, through which iron molecules enter the ferritin molecule. The
mutated B-type channel appears to be changed in shape to facilitate increased
iron influx into the ferritin core region. Via SDS-PAGE gel, it was observed
that the mutant ferritin genes had lower protein expression compared to the
wild-type ferritin gene, confirming thus that the increased iron-sequestration
was due to increased magnetism and not due to more protein being present to
work. Interestingly, the mutants were also
observed to exhibit the startling ability to sequester other metal, namely zinc,
cobalt, and nickel.<o:p></o:p></span></div>
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<span style="font-family: inherit; line-height: 115%;"><br /></span></div>
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<span style="font-family: inherit; line-height: 115%;">To say that
that this experiment was beyond thorough in verifying the genotype-phenotype
link would be an understatement. Aside from checking magnetic retention, the
researchers adopted a handful of other methods to make confirmatory
observations. For instance, MRI and fancy techniques such as SQUID
Magnetometry (basically a very sensitive device for detecting and measuring
magnetic fields) were used, again, to check degree of magnetism, all of which
showed favorable results. The mutant cells were also placed in welled-plates
directly above cylindrical magnets and were observed to take the
cross-sectional shape of the magnets below them in alignment to the magnetic
field. Overjoyed, the scientists remembered to take snaps of this plate – a
lovely picture in the memory (and as evidence) of an undoubted success.<o:p></o:p></span></div>
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<span style="font-family: inherit; line-height: 115%;">The discoveries
from this elaborate study spell out the opposite of Magneto’s aspirations – the
benefiting of mankind using mutants as pawns. Indeed, the evolved magnetic
protein, with a little help from biosynthetics, could be applied to countless
bio-applications. A simple example could be the utilization of genetically
modified cells which attract and store toxic or valuable metals for
bioremediation (neutralization of harmful waste from contaminated sites using
microorganisms) or mining. The magnetic ferritin gene could also be used as a
genetically-encoded reporter gene – i.e. as a genetic tag which can be made to
be expressed with the gene being studied. The greater the expression of the
gene, the higher the amount of magnetism of the cell due to the co-expression
of the mutant ferritin. In addition, ferritin mutants could function as
non-invasive reporters of biological signals from engineered cells, for
instance, immune cells targeted towards a cancerous tumor (you could trace them
by their magnetic fields). <o:p></o:p></span></div>
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<span style="font-family: inherit; line-height: 115%;"><br /></span></div>
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<span style="font-family: inherit; line-height: 115%;">Given that
the natural size of the ferritin cage – a miniscule 8 nm in core diameter- is
too small to create sufficient magnetic moment to acquire optimum sensitivity
and reliability, all of this is considerably ambitious. However, like with DUF892,
which is a similar protein to ferritin that they discovered during this study,
there lies promise in other similar proteins in discovering a solution to overcome
this shortcoming. One slight limitation of the original paper is that they do
not explain why we cannot just use the magnetic properties of magnetotactic
bacteria (which use the earth’s magnetic field to direct themselves) for our
purposes, despite mentioning that they assemble more crystalline and magnetic
iron oxide. One possible reason for that is that the magnetic properties of
magnetotactic bacteria are conferred by membrane-bound organelles called
magnetosomes, which contain several transmembrane proteins. Ferritin is
therefore a much simpler system to work with, or insert into different
bacteria. Besides, they were also looking at what properties of an individual iron-binding protein can be modified to enhance its magnetism.<o:p></o:p></span></div>
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<span style="font-family: inherit; line-height: 115%;"><br /></span></div>
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<span style="font-family: inherit; line-height: 115%;">There’s a
saying that power is neither good nor evil- only the nature of its wielder
decides that. While Magneto remains a fictitious threat to our comic-book
heroes as well as mankind itself, the tiny mutants possessing his powers
in the real world give hope for amazing applications in biology. So let’s end
this piece wishing prosperity to the more innocent, bacterial versions of the
antihero – may they flourish in future research and take us further.<o:p></o:p></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeZtu7jedoR3X2dDbJ5z1Pkkoycb99ztRIG4P0tLVRSt5_8MyTSbnp2qQPrVhVwB_mx8w7wL6VkCOqynWvnDiMpphgpPnq1XW-lkXDbrIAGwCR9GNNIOcBLwx8zp3yNfV2NSdmylZsjtc/s1600/Picture.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><span style="clear: left; float: left; font-family: inherit; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="960" data-original-width="720" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeZtu7jedoR3X2dDbJ5z1Pkkoycb99ztRIG4P0tLVRSt5_8MyTSbnp2qQPrVhVwB_mx8w7wL6VkCOqynWvnDiMpphgpPnq1XW-lkXDbrIAGwCR9GNNIOcBLwx8zp3yNfV2NSdmylZsjtc/s200/Picture.jpg" width="150" /></span></a><br />
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<span style="font-family: inherit; line-height: 115%;"><i style="background-color: #cccccc;">Maliha is a weirdo who somehow believes she's from a different planet. But she likes Earth just fine, and is fascinated by the science and beauty of life and has made it her purpose to explore it. Besides this, her most burning desires include becoming a synthetic biologist/ genetic engineer and running away with a heavy metal band.</i></span></div>
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-59121984800441368052017-10-13T01:46:00.000-07:002017-12-21T10:38:02.886-08:00"Breathe In, Breathe Out..." Acknowledging and Facing Anxiety<div dir="ltr" style="text-align: left;" trbidi="on">
<i>Fabiha Atiq</i><br />
<i>Sophomore</i><br />
<i>School of Life Sciences</i><br />
<i>Independent University, Bangladesh</i><br />
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<i>October 13th, 2017</i><br />
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A dear friend once described the following incident to me:<br />
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It was a Saturday night, which turned into a Sunday morning as she studied for a quiz. Her alarm went off, and she realized she hadn’t slept at all. “It’s okay. It’s fine. I’ll just go to class with a mug of coffee,” she said to herself. But then all of a sudden, without warning, this intense and hitherto unfamiliar feeling came crashing down on her. She felt weak, and even thought that she might die (her words not mine). Her head had started hurting, and she felt as if an earthquake was taking place inside her skull. She tried to get up from her bed but fell back, collapsing into what felt like an abyss.<br />
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Over the next few weeks, she skipped classes, quizzes, meals, and going out, paralyzed by the fear of another attack. All the blood tests in the next two weeks couldn’t help her or her family figure out what was wrong with her. Everything showed normal in the test results. Until, that is, one doctor recommended a psychologist.<br />
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The psychologist, after a lot of assessment and tests, diagnosed her with an anxiety disorder. What she had experienced was a panic attack. Note that panic disorder (which results in panic attacks) is a type of anxiety disorder, and anxiety attacks (characterized by a momentary fear and shortness of breath) tend to be milder and more short-lived than panic attacks.<br />
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<span style="font-size: x-small;">Art by<i> Gemma Correll</i></span></div>
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Now, in our culture, a psychologist is usually referred to as a “pagol-er-daktar” (translated – a doctor for crazy people). But in actuality, a psychologist is a mental health professional who analyzes behavior and mental processes, and recommends strategies for overcoming behavioral impediments to proper functioning. Psychiatrists are similar to psychologists, with one of the main distinctions being that psychiatrists can prescribe drugs.<br />
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Let us refresh our memory a little by recalling what mental health is, maybe? Mental health refers to one’s emotional, psychological and social well-being, and affects how one thinks, feels and hence, acts. Mental health disorders may or may not have clear biochemical bases.<br />
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The dictionary defines anxiety as a feeling of worry, nervousness or unease, typically about an imminent event. Science adds that it may not necessarily be about an imminent event or an identifiable trigger. Regardless of how it occurs, anxiety can rob a person of their appetite, their social skills, and their ability to function properly or study. There are different levels of anxiety, like any other illness out there; from mild cases to very severe ones.<br />
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A person with anxiety overthinks often and to an extent that they feel nauseous and faint. Breathing becomes difficult, and the person loses strength in their limbs, feels terribly weak, which can lead to to them thinking that they will collapse any second, which some actually do.<br />
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Several factors may contribute to triggering anxiety. Environmental factors, medical factors, genetics, brain chemistry, substance abuse, or a combination of these. Biologically speaking, anxiety appears to be tied to our fight-or-flight response, which involves the secretion of adrenaline and the priming of the body to respond to danger. But the problem is never the fight-or-flight system itself. The problem is the fight-or-flight response getting activated from a falsely heightened perception of danger, or when there is no danger at all.<br />
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Having said that, social factors also have a huge role to play here. Society tends to stress people out. Society often expects something from a person which they feel obliged to do even when they don’t want to (for instance, choose a subject they don’t want to study), which then stresses them out when they don’t like doing it, and thus cannot perform to live up to expectations. This can lead to anxiety. But there are can be a variety of reasons.<br />
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It is very easy to confuse anxiety with other similar mental illnesses, for example, depression. One might actually have questions as to how one differentiates between depression and anxiety. Depression is characterized by frustration, sadness and irritability amongst others whereas anxiety is associated with trembling, increased breathing rate and incredible sweating. They do, however, have some traits in common: restlessness, having trouble thinking/concentrating, having trouble with making decisions, excessive worrying, agitation and more. Many people with depression do suffer from anxiety. Truth be told, there is no differentiating between them on your own, and it is best to leave it to one’s psychiatrist or psychologist, who will prescribe the appropriate drug, therapy, or course of action.<br />
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I have close friends, and immediate family who suffer from anxiety. I myself suffer from anxiety. Anxiety which is so bad I shamelessly admit that I have to take medication (prescribed of course) to function properly on a regular basis.<br />
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To most people, anxiety is basically nothing. They will tell you to not worry about it. But it can quickly turn into a severe illness. It is better to pay attention, and address the symptoms early on, before it becomes severe and leads to loss of functioning, self-harm etc.<br />
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In our culture, people may be afraid to seek help because of social stigma.<br />
“Are they going to call me crazy?”<br />
“What will society say?”<br />
“Will people look at me differently?” and on and on it goes.<br />
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It doesn’t matter. Seek help, for it can get bad. Talk to your friends, talk to your family, and if you don’t feel comfortable enough, then don’t. For there is a place called the internet. There are so many people out there, going through what you are going through, and they will come through and help you, if you only reach out and ask.<br />
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Take a long, slow breath in through your nose, first filling your lower lungs, then your upper lungs. Hold your breath to the count of "three." Then release.<br />
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It isn’t a myth. It works.<br />
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Go online, make a blog, drink, eat, breathe, live.<br />
Take one step at a time. But live.<br />
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<i>Fabiha is in her second year at IUB. She is a bookworm, a shutterbug, and loves to write.</i></div>
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0tag:blogger.com,1999:blog-7127526334419423499.post-60760703777858998562017-10-05T13:06:00.003-07:002019-09-13T10:40:22.810-07:00Nipah Virus in Bangladesh: Communicating Science to Save Lives<div dir="ltr" style="text-align: left;" trbidi="on">
<span style="font-family: inherit;"><i>Anika Tabassum Hiya</i></span><br />
<span style="font-family: inherit;"><i>Senior</i></span><br />
<span style="font-family: inherit;"><i>School of Life Sciences</i></span><br />
<span style="font-family: inherit;"><i>Independent University, Bangladesh</i></span><br />
<span style="font-family: inherit;"><i><br /></i></span>
<span style="font-family: inherit;"><i>October 6th, 2017</i></span><br />
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<span style="font-family: inherit;">The flying fox, the creature that spread its wings and brought misfortune over Bangladesh. These fruit bats, more specifically identified as Indian flying foxes, are quite common in Bangladesh, and can have wingspans of up to six feet. Alongside being famous as one of the largest bats in the world, this species of fruit bat is also well-known for spreading a deadly virus called Nipah virus – one of the viruses that inspired the movie Contagion. Symptoms can include normal fever, vomiting, dizziness, brain inflammation, hallucinations, seizures, and coma, and mortality rates often exceed fifty percent. An unfortunate aspect of the disease is that there is yet to be a proper vaccine or cure.</span><br />
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<span style="font-family: inherit;">But how did a virus in bats which have little to no contact with people end up in people?</span><br />
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<span style="font-family: inherit;">There is more than one route that the virus took. In Malaysia, it came into humans from bats indirectly through pigs in farms. In Bangladesh, transmission was tied to a food preference that bats and humans share: the date palm sap. In many villages, it is one of the most popular drinks to have on a winter morning, or even consume in its fermented form as booze. The famous winter pitha-uthshob (pitha is a kind of sweet; uthshob means festival) includes sweet cakes made from the date palm sap. The sap is harvested by cutting a tap into the tree and collecting the sap into a pot. The pot is often left out overnight to collect the sap dripping from the tap, and during this time, the bats can take a few sips from the pot and even urinate in it. This is how the viruses came to be in humans in Bangladesh. Once in humans, person-to-person was possible through bodily secretions or saliva.<br /> </span><br />
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<span style="font-family: inherit; font-size: x-small;">How date palm sap is collected. <i>Wikimedia Commons</i></span></div>
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<span style="font-family: inherit;">Since the 2001 Nipah virus outbreak in Meherpur (a village in Bangladesh), there have been similar small but deadly outbreaks of the virus every few years in various rural regions of Bangladesh. The 2010 outbreak in Faridpur provides a particularly interesting case study in outbreak control [1]. Outbreak control simply refers to limiting the spread of a pathogen through a population by employing a variety of possible strategies such as quarantining and vaccination (if vaccines are available; in this case, it was not). It was the second outbreak of Nipah virus in Faridpur after the big 2004 outbreak, in which 27 out of 36 infected individuals had died.</span><br />
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<span style="font-family: inherit;">Early communication efforts during the 2010 outbreak had only focused on instructing people to follow guidelines such as stopping date palm sap consumption, via loudspeakers and household visits. The villagers were not listening, and the outbreak persisted To solve this problem, a team composed of three anthropologists and one sociologist was recruited to help. </span><br />
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<span style="font-family: inherit;">Before they could recommend strategies for better communication, they needed to understand the basis of the villagers’ mistrust. To that end, they established a rapport with them through frequent interactions, visits, and conversations. Through actually listening to the villagers, a multitude of issues came to light.</span><br />
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<span style="font-family: inherit;">After the 2004 outbreak, locals had remained uncertain as to the cause of death in these individuals, suggesting a lack of effective communication from healthcare professionals at the time. In addition, due to the high mortality rate, locals had developed suspicions over the healthcare providers’ ability to actually help. This mistrust carried over to the 2010 outbreak. The lack of trust in modern medicine reinforced the superstitious leanings of many of the villagers. They came to believe that the deaths were due to a curse that they called asmani bala, a curse sent from the heavens. Instead of going to doctors they resorted to religious healers, who prescribed superstitious treatments such as pani pora (drinking water that has been turned sacred by a priest blowing into it after recitating from the Quran). The early announcements to stop date palm sap consumption had not made it clear that the bats were responsible for transmission via sap. Date palm sap is very dear to these villagers, and they were understandably reluctant to listen to these outsiders who did not even provide a proper justification for their instructions.</span><br />
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<span style="font-family: inherit;">Having garnered an improved understanding of the problems, the investigators approached the matter in a more interactive and culturally sensitive manner, trying to take into account the villagers’ social beliefs, norms, and local practices. Instead of simply instructing people to do or not do things, they communicated risks and strategies as part of a conversation with the community, and described the causative mechanism of the illnesses and deaths. They offered solutions such as boiling the sap, and wearing gloves and masks while bathing the dead to prevent coming into contact with bodify fluids containing the virus. Such solutions allowed them to continue following their traditions, but with minimized risk. The villagers responded positively to this interactive approach; not only did they start following the recommended guidelines for preventing bat-to-person and person-to-person transmission, they also began participating in meetings and efforts to control the outbreak. Without this strategy, the outbreak would have been much harder to control.</span><br />
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<span style="font-family: inherit;">Effective communication with local communities is essential during disease outbreaks. Fighting a disease becomes much more difficult if victims do not understand how it is caused or how they might prevent it. Epidemics can therefore be dealt with much more efficiently if a holistic approach is taken as in the 2010 Nipah virus outbreak, in which investigators did not spare causative details while communicating with the affected community. The solutions themselves should ideally be sensitive to local culture while effectively dealing with the threat.</span><br />
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<span style="font-family: inherit;"><b>Bibliography:</b></span><br />
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<span style="font-family: inherit;">[1] S. Parveen et al., “It’s not only what you say, it’s also how you say it: communicating nipah virus prevention messages during an outbreak in Bangladesh,” BMC Public Health, vol. 16, pp. 726–726, Aug. 2016.<br /><br /> </span><span style="font-family: inherit;"><br /></span><br />
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<i><span style="font-family: inherit;">Anika is a Biochemistry student who loves experimenting with food, and is passionate about science and literature.</span></i><br />
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Ornob Alamhttp://www.blogger.com/profile/02979297697484789720noreply@blogger.com0