The Age of Optogenetics: Lighting Up Neurons to Explore Brain Function

Jabale Rahmat

Sophomore

School of Life Sciences

Independent University, Bangladesh

June 13th, 2018

“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.

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.

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.

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.

Light being shone onto the brain of a mouse. Britannica

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.

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. 

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.

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.

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].

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.

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. 

Further Reading:

[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.

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.

Examining a Lesser Known Side of Cystic Fibrosis

Nuzhat Faizah
Sophomore
School of Life Sciences
Independent University, Bangladesh

February 10th, 2018

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.

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.

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.

Impeded chloride ion transport leads to mucus buildup. University of Utah

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).

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.

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.

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.

Cancer: An Unwanted Guest

Jabale Rahmat

Freshman

School of Life Sciences

Independent University, Bangladesh

May 26th, 2017

Lamia, a middle-aged woman, is sitting in the waiting room of a clinic with a receipt in her hand. She is waiting for her number to be called to collect her mammography report. She is watching the preview window which shows the call number for the next patient. When her number comes, she stands up with fear on her face. She moves toward the reception desk and collects her report. She is scanning the report with frightened eyes and praying to God for a negative result for breast cancer.

If just the possibility of cancer can be so frightening, how much more suffering will come from a positive diagnosis?

“Cancer”, the word, carries a lot of weight. The disease, cancer, has an effect on both the person and his or her family. Cancer patients are not only devastated by physical pain, but their mental health also gets affected due to the economic burden that they have to bear. A cancer patient essentially becomes a prisoner from the moment they are diagnosed.

How does cancer develop? Cancer at its root is a genetic disease, caused by mutations after birth that cause abnormal cell division. Cell division is a process by which a single cell multiplies into two. From growth to the replacement of dead cells, cell division plays a vital role in all living organisms, including human beings. When we cut our hair, new hair grows through cell division. Millions of red blood cells die in our bodies every day and new blood cells are generated through cell division.

There are many factors that affect cell division. Cell division is not a random process. When a cell receives a certain signal, the cell divides. Cells in the heart hardly divide unless there is any abrupt change, for example cell death. To compensate for the loss of dead cells, a signal is sent from nearby cells, which in turn triggers a cell to divide and replace the lost cells. Therefore, cell division is a “programmed” process. Unlike healthy cells, cancer cells divide randomly and continuously – i.e. cell division in cancer cells is a broken program.

Experiments have shown that cultured human cells can only grow outside the body if special chemical growth factors (normally produced by human tissues) are added to the nutrient broth. But cancer cells are often able to grow on simple nutrient broth that completely lacks any added growth factors. This suggests that cancer cells manage without the growth factors that are necessary for normal cells to grow inside organs and tissues. Thus, the question arises – how do the cancer cells manage to divide without growth factors?

Probable genesis of cancer. Stanford

The program for cell division is contained within the genetic content of a cell. When a cell reproduces, the contents of that cell reproduce as well. During normal cell division, several genes are involved in making sure that the cell has enough resources to divide into two cells. Genes are made up of DNA. DNA molecules are very inert, that is, they are resistant to many chemical reactions, but they can still get damaged when they come into contact with certain chemicals. We call these chemicals carcinogens. Cigarette smoke is a potent carcinogen that can damage DNA molecules when inhaled. The DNA damage can result in mutations that trigger abnormal cell division by affecting genes that are involved in regulating cell division. This in turn can result in cancer.

The genes which cause cancer when damaged can be characterized as either proto-oncogenes (genes whose activity normally promotes cell division) or tumor suppressor genes (genes that normally prevent cancerous cell division in healthy bodies). I will discuss some examples of these genes below.

Under normal circumstances, proto-oncogenes induce cell division, and then stop. Mutations in proto-oncogenes can transform them into oncogenes that cause continuous cell growth. HER2 is a proto-oncogene that in its mutated, oncogene form gets overexpressed in many types of cancer cells, and makes them hypersensitive to very low levels of growth factors. Growth factors mediate their effect by binding to receptor proteins present on the surface of the cell. When they come into contact with the growth factors, these receptor proteins cause chemical changes inside the cell that trigger cell division. HER2 encodes one such receptor, and overexpression of the gene results in the presence of large amounts of receptors on cancer cell surfaces, which is what makes them hypersensitive to growth factors. This causes the cells to divide uncontrollably. Some mutations in HER2 can also induce cell division without the presence of the growth factors. In other cancers, researchers have seen that cancer cells can start to produce their own growth factors, leading to cancerous cell proliferation. Many oncogenes cause cancer in this manner by reducing the dependency of cancer cells on external growth factors.

Even though our body is constantly exposed to carcinogens, for instance in the form of UV radiation in sunlight, this does not result in cancer in the vast majority of cases. This is because tumor suppressor genes like TP53 can respond to the DNA damage caused by carcinogens and prevent the development of cancer cells. For example, p53, the protein encoded by the TP53 gene, can respond to DNA damage by triggering apoptosis, a form of programmed cell death, and clear tissues of potentially cancerous cells.

But what happens where is a mutation in the TP53 gene itself? This can be caused by DNA damage caused by carcinogens like cigarette smoke. This will impair the gene’s ability to identify and respond to further DNA damage in the future. Thus, the unwanted guest, cancer, can enter. Normally, multiple mutations of the types we discussed need to occur before cancer arises.

Some people may have increased risk for certain forms of cancer due to the presence of some mutation that they inherited from their parents. But it is always true, regardless of whether a patient inherited genetic risk factors from their family, that all forms of cancer are genetic diseases caused by mutations in cellular DNA.

Despite this increased understanding, to this day there is no permanent cure for the disease. Millennia after its discovery and after a century of biomedical research, scientists have made incredible progress in treating cancer, but many forms and stages of cancer remain untreatable. There are also many moments when physicians think that they have cured a cancer patient fully, only to find that a few months later the same patient comes back with a powerful and resistant form of the disease. The disease can be cured but not its successors.

The war against cancer is an ongoing struggle that brings together patients, oncologists, and biomedical researchers. Chemotherapy results in the evolution of resistant cancers, forcing researchers and oncologists to come up with new technologies and strategies. This war is not new, but has been going on for thousands of years. Until scientists can develop reliable permanent cures, the war against cancer will never end, and people like Lamia will have to live with the fear and possible trauma of cancer.

Jabale is a Fresher 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.

The BRCA1 Gene: Understanding Why Some Women Opt for Mastectomy

Fabiha Atiq
Freshman
School of Life Sciences
Independent University, Bangladesh

March 23rd, 2017

Ever wonder why people say your nose looks like your mom’s nose or that your eyes remind them of your dad? The answer to your question is DNA. DNA (deoxyribonuleic acid) determines characteristics that are passed from parents to children, such as blood type, hair colour, eye colour, etc.

Genes are made of DNA and they contain information to build and manage cells (smallest unit of life) in the body. The BRCA1 gene is a human tumor-suppressor gene, found in all human beings. BRCA1 stands for BReast CAncer susceptibility gene1.

Tumor-suppressor genes are genes that normally prevent cancer by controlling cell division. When they do not work properly cells start dividing rapidly and uncontrollably, which can lead to cancer. Mutations are changes in the genetic sequences that can lead to changes in their function. BRCA1 is a tumor suppressor gene; when it undergoes certain mutations it leads to an elevated risk for breast cancer.

When women are diagnosed with breast cancer, doctors may suggest a lumpectomy or surgical removal of the affected part of the breast. In extreme cases, a mastectomy, which is the surgical removal of the complete breast/breasts, may also be recommended. The purpose of these procedures is to treat and preemptively reduce chances of recurrence of breast cancer by surgically removing cancerous tissues, along with adjacent healthy tissue in the surrounding area.

The mutated BRCA1 gene increases the likelihood of developing breast cancer by 55% or more. While regular monitoring after detection of the mutated BRCA1 could effectively deal with the risk if cancer does arise, there have been a few cases of women opting for preventative mastectomy to avoid developing breast cancer in the future. Often, women who opt for preventative mastectomies are the ones who have a history of breast cancer in their family and are carriers of this mutation.



A famous case of preventative mastectomy that circulated on the internet was that of celebrity Angelina Jolie. She had both of her breasts surgically removed because she carried the mutated BRCA1 gene and was at high risk of getting cancer. Her mother, grandmother and aunt had all died from cancer. By opting for a preventative mastectomy, she showed women all over the world that this procedure can be a normal part of women's health, instead of a source of shame or embarrassment.

To put the public health burden of breast cancer into perspective, 508,000 women died from breast cancer in 2011 alone worldwide.  Once they turn 40, all women should get themselves checked for breast cancer, or at least start thinking about it, according to recommendations from the American Cancer Society.

“Knowing it exists isn’t enough. Get informed. Pass it on.”– Breast Cancer Awareness Slogan.

Fabiha is in her first year of IUB, and aspires to be a forensic scientist. She is a bookworm, a shutterbug, and loves to write.

Introducing GMOs

Ridwan Hossain
Freshman
School of Life Sciences
Independent University, Bangladesh

March 23rd, 2017

We are living in a time where technological advancement is at its peak. Everyday some new kind of technology is found and implemented into our society. Genetically modified organism or GMOs constitute one such technology that is in the process of being accepted into our lives. To understand what GMOs are, we need an idea of what a gene is. My skin color, your ability to digest dairy products, whether a plant can grow in salt water or not: these are all specific characteristics that can be inherited. Such characteristics are determined by genes which are present in the cells of all living organisms. Scientists can now identify genes in the cells of organisms and modify them. This lets us determine what characteristics we want certain organisms such as crops to have and these products of genetic manipulation are called genetically modified organisms. 

A useful application of genetic modification has been the creation of pest-resistant plants. Farmers use pesticides (chemicals that kill insects) to protect their crops from harm. Pesticides are known to be poisonous which harm the environment and any living thing that consumes food that it had been used on, including humans. Scientists can use genetic modification to create plants that produce certain biopesticides. Biopesticides are naturally occurring materials inside certain organisms which act as pesticides. For example, a bacteria named Bacillus thuringiensis (Bt) produces a protein which acts as a pesticide to certain insects. Scientists have incorporated the gene that produces this protein into plants such as corn and cotton, thereby enabling the plants to produce the protein on their own. Farmers can now grow these genetically modified plants without worrying about using artificial pesticides. The United States Environmental Protection Agency (EPA) has tested the safety of these GMOs, and determined that when these crops are consumed, the added protein acts as a normal dietary protein and is digested, posing no health problems to the consumers. Genetic modification can also be used to produce plants that are resistant to environmental stressors such as drought and high salinity, and these varieties – many of them still under development – are likely to be increasingly useful as many regions begin to experience less rainfall and rising salinity as a result of climate change.

In 2003 the total amount of GMO crops farmed worldwide was 168 million acres. In 2015 that number rose to 444 million acres. United States alone had 176 million acres of genetically modified crops growing in 2015. Even though we get so much out of GMO crops, it garners a lot of backlash from the general population. The idea of GMOs and the road leading to its state right now might be old, but the exposure of its products to the general population is relatively new and unknown. Most people who are against GMOs believe that they are harmful to ingest, and that they harm the environment. Such ideas mainly stem from a lack of knowledge about science and a certain amount of distrust toward scientists. An in-depth analysis of 1,783 scientific articles about the safety of GM crops published between 2002 and 2012 has been carried out and the results show no harmful effects of any kind occurring due to GM crops. There is a rigorous process that checks every GMO before making them available to the general population. U.S Department of Agriculture (USDA) tests the GMOs to see if they are safe to farm, the U.S Food and Drug Administration (FDA) tests food obtained from GMOs to see if they are safe to consume, and the EPA tests to see if the pest-resistant GMO crops harm the environment or not. 

Selecting for beneficial traits is nothing new as we have been manipulating animals' and crops' genes for centuries. We domesticated dogs, cows, sheep and other animals. We choose crops that have the highest yield and grow them in large amounts, thus selecting for certain characteristics. A good example of this is the crop maize whose ancestor is actually a grass plant known as teosinte. At the end of the day, GMOs are beneficial. The only thing we can do is to teach people more about the science behind GMOs, and that it does us no harm.

Ridwan is a freshman at IUB whose dream is to be a renowned mad scientist. He will be a Nobel laureate.