J O U R N A L O F B I O L O G Y

T H E B R O N X H I G H S C H O O L O F S C I E N C E 2 0 1 9 - 2 0 2 0 Volume Cll Issue 1 Contributors Editor in Chief Copy Editors Sarah Aktari '21 Bianca Vama '20 Jane Chen '21 Jane Chen '21 Tonia Curdas '21 Tonia Curdas '21 JK Aroni Goongoon '21 Dorothea Dwomoh '22 Zhaleh Mahootian '20 Aliya Fisher '22 Managing Editor Aviva Schwarz '21 Abigail Glezer '21 Oviya Sivapalan '21 JK Aroni Goongoon '21 Akshay Raju '20 Jean Wong '23 Sonia Lin '21 Wei Ni Zhang '22 Subah Mehrin '22 Akshay Raju '20 Artistic Directors Aviva Schwarz '21 Faculty Consultant Sonia Lin '21 Luke Siegel '21 Tracy LaGrassa, PhD Jean Wong '23 Sophie Silbert '21 Oviya Sivapalan '21 Lily Womack '21 Cover Design Sonia Lin '21 Jean Wong '23 Wei Ni Zhang '22 Journal of Biology 2019 - 2020 The Bronx High School of Science

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Make a difference in your community, and help educate Bronx Science on the latest developments in Biology! CONTENTS

COVID-19 & NEWS ECOLOGY CORONAVIRUS: WHAT IS A VIRUS? DROSOPHILA: THEY’RE PRETTY FLY! 06 SUBAH MEHRIN '22 27 TONIA CURDAS '21 08 POTENTIAL TREATMENTS FOR COVID-19 MOVE ASIDE WATER STRIDER, THE DOROTHEA DWOMOH '22 29 GECKO HAS ARRIVED JANE CHEN '21 INSIGHT INTO THE SEASONALITY OF 09 INFECTIOUS DISEASES CHYTRIDIOMYCOSIS, THE AMPHIBIAN KILLER! ALIYA FISHER '22 30 SARAH AKTARI '21

THE HOPE FOR A UNIVERSAL FLU OOPS, THE FISH ARE DEAD: ALGAE TAKES 11 VACCINE 32 CENTER STAGE IN AQUATIC ENVIRONMENTS WEI NI ZHANG '22 AVIVA SCHWARZ '21 THE HIDDEN EFFECTS OF E-CIGARETTES 33 DR. LYNN MARGULIS: AN INDEPENDENT 13 OVIYA SIVAPALAN '21 SCIENTIST WHO SHOWED US THE POWER OF COOPERATION AKSHAY RAJU '20

NEUROSCIENCE SCIENTIST SPOTLIGHT

A FULL LIFE WITH HALF A BRAIN KARIN BLOCK, ON GEOCHEMISTRY AND 16 DOROTHEA DWOMOH '22 36 PETROLOGY JK ARONI GOONGOON ‘21 UNEXPECTED LINKS 17 JEAN WONG '23

THE DANGERS OF SLEEP DEPRIVATION APPLICATIONS OF 19 TONIA CURDAS '21 GENETICS

ALZHEIMER’S AND ITS CONNECTION TO LIKE HOMO NEANDERTHALENSIS, LIKE HOMO 21 DISORDERED SLEEPING 39 SAPIENS: A TALE OF HUMAN DOMESTICATION SOPHIE SILBERT '21 & LILY WOMACK '21 JANE CHEN '21

SELECTIVE SEROTONIN REUPTAKE 23 INHIBITORS DON'T WORK FOREVER LUKE SIEGEL '21

INDUCED PLURIPOTENT STEM CELLS 24 FROM BLOOD TO BRAIN AND BACK ABIGAIL GLEZER '21

JOB is a collaborative, innovation-based, free- spirited publication project for the masses. | http://www.journalofbio.com Drawing by: Sonia Lin '21 COVID-19 and News

JOB | 5 2 0 1 9 - 2 0 2 0 18

CORONAVIRUS: WHAT IS A VIRUS?

BY SUBAH MEHRIN '22

“We sometimes underestimate the influence of little The host’s enzymes also use the viral genome as a things” said author Charles Chesnutt (1). One example of template to synthesize viral mRNA (an instruction code this is a virus, so small, yet so significant. It has the for protein synthesis), which is then used to make power to take away our daily routines and interactions. proteins for the capsid. The host does all the work for One strong and recent case of this is the SARS-CoV-2 the virus, including replicating the virus’ genome and coronavirus. As the cause of COVID-19, it has caused making the proteins necessary to form the capsid to such havoc that people are desperately looking for ways create new copies of the virus (3). to avert the coronavirus. But is there really a way to prevent a viral infection? We first have to delve deep There are many consequences in the process of viral into what a virus actually is. replication that can harm the host. For animal hosts, viruses can induce certain molecules to be released that Beginning with the virus’ molecular structure, viruses can damage cells and surrounding tissue. As mentioned vary in their genetic information. A virus may have before, viruses have a host range that allows a virus to either double stranded or single stranded DNA or RNA as infect different types of cells, and some viruses are able its genetic material, and each virus varies from another to infect multiple cell types (3). Some cells that are genetically. Every virus has a protein shell engulfing the infected cannot be repaired, such as nerve cells. genome called the capsid. Capsids can also be surrounded by viral envelopes that assist the virus in Regardless of the cell’s ability to fight the virus, the entering the host cell. Viral envelopes are found in immune system is essential in countering viral coronaviruses and influenza viruses. There are also infections. The immune system can recognize when cells viruses that infect bacteria called bacteriophages. are infected with virus and will destroy them. Our bodies can also make antibodies against viruses which are then Viruses have found many ways to enter our body. Some captured by other immune cells. This is how vaccines may say that viruses “borrow life” from their hosts. This work. A vaccine is a weaker form of the virus that makes is because viruses are inactive when they are not inside our immune system aware of the virus, prompting us to a host, however, within a host they can replicate. This is make antibodies against it. This way, we can block out why viruses are considered obligate intracellular the actual, more potent, virus when it infects the body parasites. By definition, a parasite is an organism that (4). survives at the expense of another organism’s nutrients. A virus alone cannot cause harm since it cannot There is really no way to completely prevent getting a replicate alone; but within a host, a virus takes the virus, but there are ways to evade it. For example, necessary materials within the host that it needs to vaccines are used worldwide to prevent viruses from replicate. SARS-CoV-2 is a virus that belongs to the taking hold of our body. Like many organisms, viruses do Coronaviridae family of viruses, generally known for evolve, meaning that they can change over time. This is respiratory infections. Symptoms of this particular virus why we have to get the influenza shot every year, are fever, cough, hard time breathing and a general because the influenza virus changes every year. fatigue (2). However, other viruses change very slowly, therefore, vaccines for these viruses may need to be taken only Viruses are able to replicate within the host by taking once or twice in our lifetime. However, for SARS-CoV-2, over the host’s protein making mechanisms. Each virus there is no vaccine, so the only thing we can do is is only able to spread to specific hosts, meaning that strengthen our immune system and minimize exposure they have a host range. Upon entering the host, the to the virus (4). There are many clickbait methods that virus releases its genetic information, and the host suggest that their remedy will cure the virus, but instantly starts to replicate the viral genome.

JOB | 6 2 0 1 9 - 2 0 2 0 18 these are not effective as cures, and at best they may only slightly strengthen one’s immune system. Thus, instead of searching for 'coronavirus cures' it is wiser to "maintaining a search for methods to enhance your immune system as well as practice social distancing. healthy lifestyle Generally, maintaining a healthy lifestyle keeps your immune system strong, but at times like these, there is a need for more serious measures. Staying in isolation can keeps your bore someone out and make them worried; one way to cope with this is to work out at home. Setting personal goals and working out raises our mood through immune system endorphin release while also strengthening our immune system. Some molecules are necessary for our survival and can bolster our immune system. They include strong, but in vitamin C, vitamin A, vitamin D, zinc, prebiotics and general hydration, so it is a good idea to eat foods that are high in these nutrients. General hygiene such as times like these, washing our hands and wearing masks is also essential because it prevents contact with pathogens that can weaken our body. One type of health that is not stressed there is a need enough is mental health. Mental health is very important to be aware of because having too much stress can weaken the immune system. Some ways to for more serious boost our mental health include journaling, yoga, and talking to people. Another tip is to keep a humidifier at home, which helps to relax and aids with breathing. measures" Lastly, sleep is also important because while we are asleep, our body undergoes many functions to regenerate itself. Keeping these in mind while staying at home will strengthen us against the virus. -SUBAH MEHRIN '22 It is imperative that everyone make an effort to stop the spread as hospitals can get overwhelmed with patients leading to potential shortfalls in care for those who need it most. As the world fights COVID-19, it is necessary to know what a virus is and how it works to actually be safe from it. Areas around the world that are in isolation are starting to realize how much they took for granted, and many are grieving due to it. Thus, everyone must work together to stop the spread and reinforce our immune systems until a vaccine is found.

Sources 1.McElrath, J. R., Leitz, R. C., & Crisler, J. S. (1999). Charles W. Chesnutt: Essays and Speeches [Google Books] (1st ed.). Retrieved from https://books.google.com/books? id=ENLBdGYNB- 8C&printsec=frontcover#v=onepage&q&f=false 2.Fehr, A. R., & Perlman, S. (2015). Coronaviruses: An overview of their replication and pathogenesis. Methods in Molecular Biology, 1282, 1–23. https://doi.org/10.1007/978-1-4939- 2438-7_1

3.Reece, J. B., & Campbell, N. A. (2011). Campbell Biology: Bio 3 2 '

107. Boston: Pearson Learning Solutions. 4.The Immune System. Retrieved June 23, 2020, from g n

https://www.hopkinsmedicine.org/health/conditions-and- o W

diseases/the-immune-system n a e J

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g n i w a r D

JOB | 7 2 0 1 9 - 2 0 2 0 18 POTENTIAL TREATMENTS FOR COVID-19

BY DOROTHEA DWOMOH '22

Drawing by: Jean Wong '23

Worldwide, over 9.4 million people have COVID-19, and over According to a review in the American Chemical Society, 483,000 have lost their lives to this disease as of June 25th. there are other drugs that can have similar effects to With many aspects of life disrupted, people are anxious remdesivir (5). One of these drugs is called baricitinib, a about the future. Although it’s an unprecedented situation, drug that has been used for rheumatoid arthritis. Clinical there is hope in the treatments and vaccines that are being trials have shown that it may be able to relieve tested, which will come early-mid 2021 at the earliest. inflammation associated with the more severe symptoms of Scientists are hard at work investigating some of the COVID-19 (5). Lopinavir is another drug being tested treatments being used to curb and even stop the spread of because researchers predict that it interferes with the viral SARS-CoV-2, the virus that causes COVID-19. proteases needed for the production of infectious viruses (5). However, lopinavir does have some concerning side- Remdesivir looks like a promising drug. In a study published effects. In a study published by the New England Journal of by the New England Journal of Medicine, 95% of those who Medicine, lopinavir was associated with gastrointestinal took remdesivir recovered in eleven days as opposed to problems in the patient group that was treated with the those who didn’t take the drug, who took an average of drug (6). This is a dilemma: although scientists are testing a fifteen days to recover. The death rate was lower, since 7.1% vast number of drugs, the public distribution of these drugs died while taking remdesivir, as opposed to 11.9% who took cannot be allowed until they are thoroughly tested and the placebo (1). The drug is especially useful because it shown to be safe and effective. stops the virus from replicating. According to the study, remdesivir is a nucleotide analog that tricks the viral Vaccines work by preventing infection in the first place. One polymerase into inserting it into the replicating genome, vaccine candidate that is gaining popularity is a vaccine thus crashing the production of the virus (1). from the company Moderna. Instead of using a dead or weakened virus like traditional vaccines do, they use Hydroxychloroquine, famously touted by President Trump as messenger RNA (mRNA) to get your cells to synthesize viral a “game-changer,” ended up not being one. A paper in the proteins, signaling the immune system to produce Journal of the American Medical Association showed that antibodies which then could induce a quicker and stronger taking hydroxychloroquine is deadlier than not taking the immune response in the future if one gets the virus. drug. 19.9% of people died while taking hydroxychloroquine, which is greater than the 12.7% of In a crisis, it’s important to know that we can rely on the people who died without taking any drug. advancements of science to perform new clinical trials and Hydroxychloroquine gave people more abnormal heart investigate certain drugs that could make a pathway to a rhythms, showing that the drug might also be very cure for COVID-19. dangerous; 27.3% of patients who took hydroxychloroquine

experienced abnormal cardiac rhythms, while 14.0 % Sources experienced abnormal heart rhythms in the no-drug group. 1.Beigel JH, Tomashek KM, Dodd LE, et al (2020). Remdesivir for the Treatment of Those exposed to hydroxychloroquine also had higher rates Covid-19 — Preliminary Report. The New England Journal of Medicine. 2.Rosenberg ES, Dufort EM, Udo T, et al (2020). Association of Treatment With of cardiac arrest (2). Hydroxychloroquine or Azithromycin With In-Hospital Mortality in Patients With COVID-19 in New York State. Journal of the American Medical Association. In March, Elon Musk pointed to chloroquine as another 3.Vincent MJ, Bergeron E, Benjannet S, et al (2020). Chloroquine is a potent inhibitor of SARS coronavirus infection and spread. Journal of Virology, 2, 69. potential treatment. Chloroquine is an old anti-malarial 4.Wang M, Cao R, Zhang L, et al (2020). Remdesivir and chloroquine effectively inhibit drug that has been around since the 1940s. In a 2005 study, the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Research, 30, 269- the drug showed promising effects against SARS, a virus 271. 5.Liu C, Zhou Q, Li Z, et al (2020). Research and Development on Therapeutic Agents that shares many commonalities with COVID-19. and Vaccines for COVID-19 and Related Human Coronavirus Diseases. ACS Central Chloroquine was shown to raise the pH of the cellular Science, 6, 315-331. environment and interfere with the cell receptor ACE2, 6.Cao B, Wang Y, Wen D, et al (2020). A Trial of Lopinavir–Ritonavir in Adults Hospitalized with Severe Covid-19. The New England Journal of Medicine, 382, 1787- possibly making the SARS virus unable to bind to the cell 89. and continue to replicate (3). In a more recent study, chloroquine was 80% inhibitive when Vero E6 Cells, which are monkey cells, were infected with the coronavirus (4). JOB | 8 2 0 1 9 - 2 0 2 0 INSIGHT INTO THE SEASONALITY OF INFECTIOUS DISEASES

BY ALIYA FISHER '22

Amidst the COVID-19 outbreak, scientists are Immune System scrambling to find answers to their questions such as, There are several functions of our immune system that “When will there be a vaccine?” or, “How do we stop cause us to be more vulnerable to infection in the the spread of the coronavirus?” But one question that colder winter months. First, in colder months, humidity is on the mind of scientists and non-scientists alike is is lower, so the mucosal layer in our throats and lungs “When will this end?” Many hypotheses have been is thinned. This mucosal layer provides a barrier thrown around, some reasonable, but others with little between the external air and our respiratory cells, and scientific backing. The fact is, the scientific community when it is thin, pathogens can slip through more easily knows very little about the seasonality of disease, or in and enter our cells. Additionally, the mucosal layer other words, the behavior of disease across different allows the cilia of our respiratory cells to push out seasons. While there are many hypotheses, no one can pathogens and filter them through the mucus, so when predict with total accuracy how diseases will behave the layer is thin, the pathogens remain in our when the seasons change. This article will review some respiratory system longer (1). of these hypotheses in order to get a better idea of what might be controlling the seasonality of diseases. Another factor that is affected by the winter climate is The explanations will be broken down into three vitamin D levels. While vitamin D was previously different categories, and how these factors are altered thought to only be associated with bone growth and seasonally: human behavior, human immune system health, recent studies have revealed that vitamin D strength, and virus survivability. plays an important role in the immune system because it regulates the inflammatory response. This is because Human Behavior vitamin D inhibits the proliferation of inflammatory The way humans interact, or don’t interact, can provide cytokines in the immune system, and upregulates the some explanation for why the flu, for example, is more production of non-inflammatory cytokines. This allows common in the winter and not in the summer. During an active but less severe immune response to certain the winter months, people are more likely to be at pathogens (3). Since vitamin D is synthesized in the school or work, whereas in summer months children presence of sunlight, our vitamin D levels are lower in and adults are more likely to take vacations. When the winter months than in summer. This may help people are stuck together inside small, poorly explain why we are more vulnerable to infection in the ventilated rooms for long hours, such as when they are winter. at work or school, transmission risk is increased. This is because people are coming in close contact with one Lastly, studies have shown that our immune system is another and sharing the same air, which may contain overall more inflammatory in the winter, although the pathogens (1). cause of this is unclear. One study showed that proinflammatory gene modules are upregulated in the However, this is not to say that human contact winter (4). More research needs to be done to show increases when the weather is bad. One study showed why, but proinflammatory cytokines, which cause that the number of social contacts a person had on a tissue damage and illness symptoms are more active in daily basis was not affected by the daily weather (2). the winter and may explain why rates of sickness are With this in mind, we must question why flu season generally higher in the winter. doesn’t extend into the spring, since people are still in school and at work. Since we know that nicer weather doesn’t necessarily mean less human contact, there must be another reason why flu season is confined to the colder months. To explain that, we can look to our immune response, and how it fluctuates with the season.

JOB | 9 2 0 1 9 - 2 0 2 0 Virus Survivability While the factors discussed so far have provided possible reasons why infection rates are generally increased in the winter, it is still unclear why there are exceptions, such as enteroviruses like coxsackie virus, which peak in the summer. The reason why different "our immune diseases have different seasonality patterns is still unclear, but there is evidence pointing to humidity and temperature as the key modulator of which viruses are system is most active. Some viruses are enveloped in a lipid layer, or a fat-molecule layer, which provides two complementary potential explanations for virus seasonality. overall more

The first is that this lipid layer keeps the virus protected against dry conditions by retaining water inflammatory inside the envelope (5). This means that enveloped viruses can survive better when it’s dry, while non- enveloped viruses require more external moisture. This could provide an explanation for why enveloped in the winter" viruses can survive in the winter, when it is cold and dry, but non-enveloped viruses cannot.

The second explanation based on this lipid envelope is -ALIYA FISHER '22 that lipids are relatively unstable in warmer and wetter conditions. One study showed the lipids of the influenza viral envelope became increasingly disordered as the temperature and humidity were increased (6). This disorder indicates that the envelope is less stable and viral transmission is less efficient at higher temperatures and higher humidities. Sources 1.Fares, A. (2013). Factors influencing the seasonal Using this information, can we predict how COVID-19 patterns of infectious diseases. International will behave when the weather becomes warm? In Journal of Preventive Medicine, 4(2), 128-132 terms of human behavior, most places affected by 2.Willem, L., Kerckhove, K. V., Chao, D. L., Hens, N., & Beutels, P. (2012). A Nice Day for an Infection? COVID-19 have issued social distancing orders to Weather Conditions and Social Contact Patterns decrease the transmission of the virus, so human Relevant to Influenza Transmission. PLoS ONE, behavior is relatively controlled, and is most likely not 7(11). doi: 10.1371/journal.pone.0048695 a factor that will affect seasonality. Our immune 3.Aranow, C. (2011). Vitamin D and the Immune systems will likely be stronger as we enter the warmer System. Journal of Investigative Medicine, 59(6), months and become more effective at fighting off the 881–886. doi: 10.2310/jim.0b013e31821b8755 virus. As the humidity increases, the mucosal layer in 4.Dopico, X. C., Evangelou, M., Ferreira, R. C., Guo, our throats and lungs will thicken, and provide a more H., Pekalski, M. L., Smyth, D. J., … Todd, J. A. effective barrier between our respiratory system and (2015). Widespread seasonal gene expression the external environment, perhaps reducing the ability reveals annual differences in human immunity of this respiratory virus to infect us. Lastly, the and physiology. Nature Communications, 6(1). doi: coronavirus is an enveloped virus, which means that it 10.1038/ncomms8000 is likely to be less stable when the weather becomes 5.Firquet, S., Beaujard, S., Lobert, P.-E., Sané, F., warmer and more humid. Caloone, D., Izard, D., & Hober, D. (2015). Survival of Enveloped and Non-Enveloped That being said, warmer weather might not Viruses on Inanimate Surfaces. Microbes and significantly reduce the spread of virus, since even Environments, 30(2), 140–144. doi: warm places such as Florida and Texas have high and 10.1264/jsme2.me14145 increasing COVID-19 rates. Furthermore, the factors 6.Marr, L. C., Tang, J. W., Mullekom, J. V., & described in this article don’t provide the whole Lakdawala, S. S. (2019). Mechanistic insights into picture of how diseases behave year-round. It’s unclear the effect of humidity on airborne influenza virus survival, transmission and incidence. Journal of whether or not our immune system will develop a The Royal Society Interface, 16(150), 20180298. specific response to COVID-19, which is another factor doi: 10.1098/rsif.2018.0298 that will determine the fate of the pandemic. It also 7.Powell, A. (2020). Warm weather may have no depends on whether or not a vaccine is developed, and impact on COVID-19. Retrieved from until then, scientists say it is best to maintain social https://news.harvard.edu/gazette/story/2020/04/ distancing measures until we know more, and until we covid-19-may-not-go-away-in-warmer-weather- see clear trends that the virus is slowing down (7). as-do-colds/

JOB | 10 2 0 1 9 - 2 0 2 0 THE HOPE FOR A UNIVERSAL FLU VACCINE BY WEI NI ZHANG '22

Influenza, commonly called the flu, is an infection we are all familiar with. This could be from having contracted it ourselves to having to visit the doctor’s to get a yearly flu shot. The virus that is responsible for the flu are constantly evolving, so in order to keep up, scientists must modify and engineer new vaccines every year. Think of these viruses as shapeshifters that are constantly changing. Once they shape-shift, or mutate, a vaccine taken one year ago will have a reduced ability to protect a person against the following year’s flu strain. That’s why it’s crucial for vaccines to be up to date, and it’s also why scientists are change the world of public health. It would constantly developing new influenza vaccines. eliminate the threat of a possible flu pandemic and the need for annual flu vaccine adjustments. The variability and complexity of influenza comes There are currently many candidates for the from the fact that there are so many different universal flu vaccine under way. One of them is a strains of the flu virus that a new vaccine has to double-layered nanoparticle vaccine developed by be made each flu season to target that specific researchers from Georgia State University. In their strain. The process that goes into making a flu study, the researchers used two important vaccine is exceedingly time-consuming and influenza proteins, matrix protein 2 ectodomain expensive. Oftentimes, it involves having to (M2e) and neuraminidase (NA) to create a double- predict which strains of virus will be present in layered protein nanoparticle that could provide the upcoming year and then having to long-lasting immunization against six influenza manufacture the vaccine using eggs and cell strains in mice (4). The gene encoding the protein cultures (1). This cycle repeats for the next flu M2e, found in all influenza strains, undergoes season and so forth. Even then, the process isn’t mutations at a slower rate compared to other perfect as a vaccine’s effectiveness can vary, and genes in influenza strains. The protein NA has there is always the possibility that mutations or been commonly believed to be a weak antigen, new strains can appear mid-season. This never- but scientists have come to discover its prominent ending cycle of vaccine development can be significance in vaccine research. The gene arduous, and that’s where the "universal flu encoding for the protein mutates much more vaccine" comes in. slowly than other influenza proteins, making it a better target to study. In the study, researchers Many researchers have been on the search for a injected mice with the nanoparticle vaccine, universal flu vaccine that is able to protect consisting of M2e at its core and NA on the against multiple strains of the influenza virus over surface, and later exposed them to six different a long period of time. Influenza A viruses are the influenza strains. They found that the double- only known type of flu virus that can cause a layered protein nanoparticles induced higher pandemic. Within these viruses, there are two levels of cellular responses when compared to subtypes: group I and II (2). According to the single-layered M2e nanoparticles. These cellular National Institute of Allergy and Infectious responses include increased expression of CD8 T Diseases (NIAID), the following are requirements cells, which are necessary in adaptive immunity for a universal flu vaccine: 75% efficacy, and the killing of infected cells. The double- protection against group I and II influenza A layered nanoparticle vaccine was successful in viruses, and compatibility with all ages (3). The providing long-lasting protective immunity development of a universal flu vaccine would against the six tested influenza strains. The mice

JOB | 11 2 0 1 9 - 2 0 2 0 were unaffected by viral complications and mutations for up to four months, showing promise as a potential candidate for the universal flu vaccine (4).The results from this study demonstrate the significance and versatility of double-layered M2e-NA protein "The development of nanoparticles in vaccine research as they can be applied a universal flu to many different pathogens, not just influenza, and may serve as the stepping stone for future developments. vaccine would

Another possible universal flu vaccine that shows promise ultimately change is FLU-v, a synthetic vaccine that uses peptide antigens to target specific areas of the flu virus. The vaccine, the world of public developed by the pharmaceutical company SEEK, activates immune cells that send signals through health" interferon gamma (IFNγ) and other protein messengers to neighboring immune cells. These signals then set off a chain of reactions in the immune system, such the activation of cytotoxic T cells, that would stop and kill the infection (5). Because FLU-v is synthetically manufactured, it takes away the usual hassle that comes with vaccine development, which consists of using eggs and cell cultures. The vaccine has already successfully "It would eliminate passed the first two phases of clinical testing and is now moving on to Phase III, the final stage. A major concern the threat of a surrounding this vaccine is whether or not it’s safe for human use and whether it’s actually effective in possible flu preventing the flu. Encouragingly, in a study published by Annals of Internal Medicine, researchers tested the pandemic and the effectiveness of a single dose of FLU-v against a placebo in a randomized clinical trial of 175 participants. They need for annual flu found that those who were exposed to FLU-v showed vaccine adjustment" greater cellular and immune responses than those who were exposed to the placebo (6). While this doesn’t demonstrate FLU-v’s ability to defend against actual flu virus strains, it does suggest that FLU-v has potential -WEI NI ZHANG '22 effectiveness. Questions about the long-term safety of Sources FLU-v and its effectiveness in actual flu prevention will 1.Krisch, J. A. (2020). Scientists may be 'on the cusp' of a universal hopefully be answered in the Phase III clinical trials, the flu vaccine. Retrieved from final and most extensive round of clinical trials. https://www.livescience.com/universal-flu-vaccine-closer.html 2.Types of Influenza Viruses. (2019). Retrieved June 28, 2020, from https://www.cdc.gov/flu/about/viruses/types.htm Despite the substantial progress that has been made in 3.Universal Influenza Vaccine Research. (n.d.). Retrieved from https://www.niaid.nih.gov/diseases-conditions/universal- regards to a universal flu vaccine, it is important to keep influenza-vaccine-research in mind that these vaccines are still far from making their 4.Wang, Y., Deng, L., Gonzalez, G. X., Luthra, L., Dong, C., Ma, Y., … Wang, B. Z. (2019). Double‐Layered M2e‐NA Protein way to the market. This is in part because a universal Nanoparticle Immunization Induces Broad Cross‐Protection vaccine for a virus that is constantly changing and against Different Influenza Viruses in Mice. Advanced Healthcare evolving is extremely challenging and difficult to perfect. Materials, 9(2), 1901176. doi: 10.1002/adhm.201901176 5.Pleguezuelos, O., Robinson, S., Fernández, A., Stoloff, G. A., It might take years or even decades before a true Mann, A., Gilbert, A., … Caparrós-Wanderley, W. (2015). A universal flu vaccine is developed and implemented Synthetic Influenza Virus Vaccine Induces a Cellular Immune Response That Correlates with Reduction in Symptomatology worldwide. Vaccines are crucial to our world, and they are and Virus Shedding in a Randomized Phase Ib Live-Virus important now more than ever in our fight against COVID- Challenge in Humans. Clinical and Vaccine Immunology, 22(7), 828–835. doi:10.1128/cvi.00098-15 19. The advancements we make toward a universal flu 6.Pleguezuelos, O., Dille, J., Groen, S. D., Oftung, F., Niesters, H. G., vaccine could serve as a helpful guide for scientists in the Islam, M. A., … Hak, E. (2020). Immunogenicity, Safety, and race for a COVID-19 vaccine. Efficacy of a Standalone Universal Influenza Vaccine, FLU-v, in Healthy Adults. Annals of Internal Medicine, 172(7), 453. doi: 10.7326/m19-0735

JOB | 12 2 0 1 9 - 2 0 2 0 Drawing by: Sonia Lin '21

The Hidden Effects Of E-Cigarettes BY OVIYA SIVAPALAN '21 5.4 million. That's the number of American teens who use e-cigarettes according to a 2019 census, and that smokers, non-smokers, and vapers, they saw that number keeps rising as the misconception that e-cigs vaping promotes cellular production of proteases are safer than conventional cigarettes persists (1). such as neutrophil elastase and matrix However, recent research suggests that e-cigarettes metalloproteinases 2 and 9, all of which are elicit similar if not the same inflammatory responses associated with several respiratory diseases and tissue damage as cigarettes, suggesting that (2).When an excess of these enzymes are there are many hidden effects that vaping might have produced, they can damage the air sacs in the on young teens. lungs (known as alveoli) that are important for gas exchange and the movement of oxygen in the Scientists at the University of North Carolina (UNC) bloodstream. This damage results in serious have tested whether vaping exhibits similar effects respiratory issues such as chronic obstructive to those of smoking. By examining the bronchi of pulmonary disease (COPD) and emphysema (2).

JOB | 13 2 0 1 9 - 2 0 2 0 "E-cigarettes have a lot of these same carcinogens, including compounds such as propylene glycol and glycerin, which are toxic to humans"

-OVIYA SIVAPALAN '21

More specifically, the UNC The misconception of vaping being Sources 1.Youth and Tobacco Use. (2019). researchers saw a connection safer than cigarette smoking stems https://www.cdc.gov/tobacco/data_statistic between nicotine from e-cigarettes from the idea that only burning s/fact_sheets/youth_data/tobacco_use/inde x.htm and an increase in protease levels. tobacco releases carcinogenic 2.University of North Carolina Health Care. After exposing immune cells to the particles that are toxic to the body. (2019). E-cigs can trigger same lung various components of e-cigarettes, Although smoking does release changes seen in smokers, emphysema. ScienceDaily. it was seen that the presence of carcinogens, many people fail to www.sciencedaily.com/releases/2019/08/1 nicotine led to increased levels of realize that e-cigarettes have a lot 90822101425.htm 3.Ghosh, A., Coakley, R. D., Ghio, A. J., calcium ions, the messengers that of these same carcinogens, Muhlebach, M. S., Esther, C. R., Jr, Alexis, N. help induce protease secretion (3). including compounds such as E., & Tarran, R. (2019). Chronic E-Cigarette Use Increases Neutrophil Elastase and As a result, higher nicotine levels propylene glycol and glycerin which Matrix Metalloprotease Levels in the Lung. resulted in an overproduction of may be harmful to humans when American Journal of Respiratory and Critical these proteases. inhaled (5). Care Medicine, 200(11), 1392–1401. https://doi.org/10.1164/rccm.201903- 0615OC This study isn’t the only reporting Despite the vast amount of research 4.American Chemical Society. (2018). E- cigarettes can damage DNA. ScienceDaily. the harmful health effects of e-cigs. currently being done on e- www.sciencedaily.com/releases/2018/08/1 Another group of researchers saw cigarettes, much is still unknown 80820085208.htm 5.National Academies of Sciences, that the sputum (the mixture of about their long-term effects on Engineering, and Medicine; Health and saliva and mucus) from vapers and public health, especially Medicine Division; Board on Population smokers contained proteases that considering that e-cigs haven’t Health and Public Health Practice; Committee on the Review of the Health contribute to respiratory illnesses. been around for a long time. Effects of Electronic Nicotine Delivery Additionally, researchers at the However, these studies step up our Systems; Eaton DL, Kwan LY, Stratton K, editors. Public Health Consequences of E- University of Minnesota analyzed knowledge of e-cigarettes and help Cigarettes. Washington (DC): National the saliva samples of e-cigarette to point out the potential harmful Academies Press (US); 2018 Jan 23. 5, Toxicology of E-Cigarette Constituents. users and found that multiple and perhaps hidden effects of e- Available from: compounds responsible for DNA cigs on the respiratory system. https://www.ncbi.nlm.nih.gov/books/NBK50 damage were elevated after vaping, 7184/ which suggests possible genetic modifications associated with vaping (4).

JOB | 14 2 0 1 9 - 2 0 2 0 NEUROSCIENCE A FULL LIFE WITH HALF A BRAIN BY DOROTHEA DWOMOH '22

Drawing by: Usually, our brain is separated into a left Jean Wong '23 and right hemisphere. The left hemisphere is responsible for logic and reasoning, while the right side is In another study, scientists at the responsible for creative tasks (1). Most California Institute of Technology people have two hemispheres, but a few analyzed the brains of six adults having individuals only have one. You might undergone a hemispherectomy. Those think that living with one hemisphere with half a brain still had similar rates of simply isn’t enough to be able to function. functional connectivity compared to those However, that isn’t true. Some people with a full brain (2). When it came to in- with half a brain can still perform many of between network connectivity, which are the same tasks that their whole-brain connections within one hemisphere, those counterparts can. In fact, some have with hemispherectomy actually had stronger connections between the stronger neural connections (2). This different parts of their hemisphere in demonstrates how the brain can adapt comparison to those who have a full brain well to significant changes, such as when (2). major parts of a system are removed. Scientists also found increased blood flow Most people with one hemisphere of the in the remaining hemispheres, which was brain have it due to a hemispherectomy. A because of the increased brain activity. hemispherectomy is when one Those who had hemispherectomy in the hemisphere is removed after severe brain study showed an increase in connectivity injury or for the purpose of reducing of the motor and visual networks seizures (3). A good percentage of those especially (2). with hemispherectomy can still live normal lives. Researchers at the Despite the radical procedure, most with Department of Epileptology at the hemispherectomy aren’t limited in their University of Bonn Medical Centre found ability to think and perform daily actions. that 74% of a 61 patient cohort that had a Instead, because they have lost half a hemispherectomy performed six years brain, the one brain hemisphere they have prior were completely cured of seizures, left works harder at providing the skills in turn allowing them to focus on daily and tools they need to still function. activities and education. The intelligence levels were maintained for 79% of Sources 1.Corballis M. C. (2014). Left brain, right brain: facts and fantasies. PLoS Biology, 12(1), patients post surgery and 86% of patients e1001767. https://doi.org/10.1371/journal.pbio.1001767 2.Kliemann, D., Adolphs, R., Tyszka, J. M., Fischl, B., Yeo, B., Nair, R., Dubois, J., & Paul, L. K. did not need permanent assistance (4). (2019). Intrinsic Functional Connectivity of the Brain in Adults with a Single Cerebral Hemisphere. Cell Reports, 29(8), 2398–2407. https://doi.org/10.1016/j.celrep.2019.10.067 Additionally, out of 30 patients operated 3.Lew S. M. (2014). Hemispherectomy in the treatment of seizures: a review. Translational Pediatrics, 3(3), 208–217. https://doi.org/10.3978/j.issn.2224-4336.2014.04.01 on between the ages of 6-19, 40% 4.Althausen, A., Gleissner, U., Hoppe, C., Sassen, R., Buddewig, S., von Lehe, M., … Helmstaedter, C. (2012). Long-term outcome of hemispheric surgery at different ages in 61 reported improved school performance epilepsy patients. Journal of Neurology, Neurosurgery & Psychiatry, 84(5), 529–536. (4). doi:10.1136/jnnp-2012-303811

JOB 16 2 0 1 9 - 2 0 2 0 Drawing by: Jean Wong '23 UNEXPECTED LINKS

BY JEAN WONG '23

You think you know what an epileptic Neurogenesis also takes place in the seizure is. But do you really? An epileptic human amygdala, which plays a key seizure is defined as an electrical role in emotion (5). Researchers have disturbance in the brain. When most found that learning and exercise people think about a seizure, they think increase neurogenesis, and in the same of a tonic clonic seizure, where the vein, depression and aging decrease it affected person goes unconscious, their (6,7,8,9). This may seem that muscles go stiff, and they may fall neurogenesis has positive implications; backwards. However, there are also many however, it may not always be a good other types of seizures, such as atonic thing. Laboratory animals showed seizures, where the person’s muscles mixed results on whether neurogenesis relax or flop in an instant. Even lesser improved their functionality or not (10). known, some seizures occur while the Mice without neurogenesis performed person remains awake, conscious, and better in certain memory tests, such as even remembers what happened during in a repetitive maze. However, the seizure (1)! neurogenesis did not appear to improve spatial learning (11). In other words, Another neuroscience topic with room neurogenesis has a limited effect on for further exploration is neurogenesis. only some behaviors. Neurogenesis is the growth of new neurons inside of the brain. This process How are these two topics connected? occurs during the development of a fetus in the womb, but surprisingly, it occurs In a recent study at the University of in adult brains as well (2). In recent Texas Southwestern Medical Center, studies, adult neurogenesis was found to Dallas, neurogenesis was suppressed in occur in rodents, non-human primates, the brains of epileptic mice. The results and in humans, specifically in the showed that if neurogenesis was hippocampus, which regulates learning stopped for over four weeks, the and memory (3). Neurogenesis was found occurrence of spontaneous recurrent to occur in the hippocampus even up till seizures was reduced by 65% (12). a person is approaching their 90's (4). However, this may not affect long-term seizure reduction, JOB 17 2 0 1 9 - 2 0 2 0 18 as this result only continued for 10 days "in some cases, (12). This may imply a correlation between increased neurogenesis and the neurogenesis is occurrence of epileptic seizures. This is a beneficial, and in huge development in the field of epileptic seizures, as the cause of other cases, epilepsy is sometimes murky. It may also harmful" offer an additional solution for the short- term halt of seizures. Furthermore, exercise induced neurogenesis may be a potential link between seizure reduction and the prevention of the onset of epilepsy. After 1 month of voluntary "correlation exercise, seizure manifestation in mice was recorded as decreasing from over between... 70% to 40% (13). A study conducted by neurogenesis and neuroscientists in Sweden studied a group of participants from Vasaloppet, a the occurrence of Swedish cross-country ski race, were epileptic seizures" investigated for a period of 20 years for the development of epilepsy. When compared to a control group, a 40-50% decrease in focal and unspecialized epilepsy was recorded (13). These results -JEAN WONG '23 Sources suggest that increased neurogenesis 1.Seizures. (2019, June 18). Retrieved from https://www.mayoclinic.org/diseases- conditions/seizure/symptoms-causes/syc-20365711 actually decreases the rate of epilepsy 2.What is neurogenesis? (2017, May 18). Retrieved from https://qbi.uq.edu.au/brain- basics/brain-physiology/what-neurogenesis 3.Adult neurogenesis. (2018, March 14). Retrieved from https://qbi.uq.edu.au/brain- development. Comparing these two basics/brain-physiology/adult-neurogenesis 4.Moreno-Jiménez, E. P., Flor-García, M., Terreros-Roncal, J., Rábano, A., Cafini, F., Pallas- studies, it can be hypothesized that Bazarra, N., . . . Llorens-Martín, M. (2019). Adult hippocampal neurogenesis is abundant in neurologically healthy subjects and drops sharply in patients with Alzheimer’s disease. Nature Medicine, 25(4), 554-560. doi:10.1038/s41591-019-0375-9 neurogenesis may only be detrimental 5.Jhaveri, D. J., Tedoldi, A., Hunt, S., Sullivan, R., Watts, N. R., Power, J. M., Bartlett, P. F., & Sah, P. (2018). Evidence for newly generated interneurons in the basolateral after the development of epilepsy. amygdala of adult mice. Molecular Psychiatry, 23(3), 521–532. https://doi.org/10.1038/mp.2017.134 6.Blackmore, D. G., Vukovic, J., Waters, M. J., & Bartlett, P. F. (2012). GH mediates Peculiar indeed that in some cases exercise-dependent activation of SVZ neural precursor cells in aged mice. PloS one, 7(11), e49912. https://doi.org/10.1371/journal.pone.0049912 neurogenesis is beneficial, and in other 7.Kuhn, H. G., Dickinson-Anson, H., & Gage, F. H. (1996). Neurogenesis in the dentate gyrus of the adult rat: age-related decrease of neuronal progenitor proliferation. The Journal of Neuroscience: The Official Journal of the Society for Neuroscience, 16(6), 2027– cases it is harmful, like how neurogenesis 2033. https://doi.org/10.1523/JNEUROSCI.16-06-02027.1996 8.Lloyd, A. J., Ferrier, I. N., Barber, R., Gholkar, A., Young, A. H., & O'Brien, J. T. (2004). negatively influences memory. Even so, Hippocampal volume change in depression: late- and early-onset illness compared. The British Journal of Psychiatry: The Journal of Mental Science, 184, 488–495. https://doi.org/10.1192/bjp.184.6.488 further experimentation will still be 9.Leuner, B., Mendolia-Loffredo, S., Kozorovitskiy, Y., Samburg, D., Gould, E., & Shors, T. J. (2004). Learning enhances the survival of new neurons beyond the time when the needed to help us fully understand the hippocampus is required for memory. The Journal of Neuroscience: The Official Journal of the Society for Neuroscience, 24(34), 7477–7481. relationship between neurogenesis and https://doi.org/10.1523/JNEUROSCI.0204-04.2004 10.Scharfman, H. E., & Hen, R. (2007). NEUROSCIENCE: Is More Neurogenesis Always Better? Science, 315(5810), 336–338. doi: 10.1126/science.1138711 epilepsy prevention. 11.Snyder, J. S., Hong, N. S., McDonald, R. J., & Wojtowicz, J. M. (2005). A role for adult neurogenesis in spatial long-term memory. Neuroscience, 130(4), 843–852. https://doi.org/10.1016/j.neuroscience.2004.10.009 12.Varma, P., Brulet, R., Zhang, L., & Hsieh, J. (2019). Targeting Seizure-Induced Neurogenesis in a Clinically Relevant Time Period Leads to Transient But Not Persistent Seizure Reduction. The Journal of Neuroscience: The Official Journal of the Society for Neuroscience, 39(35), 7019–7028. https://doi.org/10.1523/JNEUROSCI.0920- 19.2019 13.Ahl, M., Avdic, U., Strandberg, M. C., Chugh, D., Andersson, E., Hållmarker, U., … Ekdahl, C. T. (2019). Physical Activity Reduces Epilepsy Incidence: a Retrospective Cohort Study in Swedish Cross-Country Skiers and an Experimental Study in Seizure-Prone Synapsin II Knockout Mice. Sports Medicine - Open, 5(1). doi: 10.1186/s40798-019-0226-8

JOB 18 2 0 1 9 - 2 0 2 0 THE DANGERS OF SLEEP DEPRIVATION

BY TONIA CURDAS '21

High school can be a stressful time with Missing nights of sleep can affect the all the homework, projects and tests back immune system. Decreased sleep leads to to back. Most students deal with their an increase in neutrophil count, a type of workloads by staying up all night to white blood cell (2). The increase is a complete their assignments. As you walk natural response to injury, infection, and through the hallways of any high school, stress revealing that the body considers you’ll hear comments related to the hours sleep deprivation to be a stressor (3). A of sleep students get each night. Those reduction in sleep also leads to an numbers are usually way below the increase in IL-6 secretion, which is an recommended amount of around 8-10 important signaling molecule within the hours per day. Anyone who has pulled an immune system (4). The increase of IL-6 all-nighter can usually feel the effects of can lead to chronic inflammation through sleep deprivation throughout the school the promotion of T cell differentiation and day, but what are the actual detriments the inhibition of regulatory T cells, a of not getting enough sleep? combination that often leads to autoimmune or inflammatory responses Particularly, how does it affect your (5). brain? First of all, there needs to be a clear definition of what sleep deprivation A lack of sleep can also negatively impact actually is. Dr. Clifford Saper, an MD PhD our brain's productivity and efficiency. from Harvard Medical School, defines it Without enough sleep, neurons as gradually losing sleep, specifically communicate more slowly and signals rapid eye movement (REM) sleep, over drag out for longer, making time. REM sleep is the sleep phase during communication inefficient. Comprehension which the body relaxes and the brain is also decreased because it becomes more increases activity. We spend about 20% of difficult for neurons to translate visual our time in REM sleep, but if it is input into coherent thoughts (6). The disrupted there are negative influence of sleep deprivation on the brain consequences (1). is similar to intoxication and includes

JOB 19 2 0 1 9 - 2 0 2 0 cognitive lapses leading to slow reaction times (7). However, researchers at Pennsylvania State University’s Department of Psychiatry have shown that alertness increases immediately after a nap or a period of rest (2).

Sleepless nights have detrimental effects on our mental health. For example, researchers Ben Simon and Matthew Walker proposed that one sleepless night can lead to “a 30% rise in anxiety levels” (8). Also, studies showed that sleep deprivation led to more activity in regions of the brain responsible for generating emotions. Although it is sometimes difficult, catching up on sleep is important to combat the effects of sleep deprivation. In a study, when zebrafish were kept awake for long periods of time and were finally allowed to have “recovery sleep," they produced a molecule known as galanin. Galanin is a neuropeptide that plays a role in anxiety, Sources 1.DiSalvo, D. (2018) Understanding The Link Between Sleep And Anxiety, depression, appetite, and other And Other Findings From The Neuroscience Of Sleep. Forbes; https://www.forbes.com/sites/daviddisalvo/2018/11/12/understanding- mechanisms in the central nervous the-link-between-sleep-and-anxiety-and-other-findings-from-the- neuroscience-of-sleep/#30f7d4a236ae system. This molecule was even produced 2.Faraut B, Boudjeltia KZ, Dyzma M, Rousseau A, David E, Stenuit P, Franck T, Antwerpen TV, Vanhaeverbeek M, Kerkhofs M. (2019) Benefits of at a higher rate during recovery sleep Napping and an extended duration of recovery sleep on alertness and immune cells after acute sleep restriction. Elsevier: Brain Behavior and compared to regular sleep (9). Immunity. 25(1): 16-24. https://doi.org/10.1016/j.bbi.2010.08.001 3.Huizen, J., (2018) What are neutrophils and what do they do? Medical News Today. https://www.medicalnewstoday.com/articles/323982.php#causes This recovery night allows for your body 4.Pejovic, S., Basta, M., Vgontzas, A. N., Kritikou, I., Shaffer, M. L., Tsaoussoglou, M., … Chrousos, G. P. (2013). Effects of recovery sleep after to regain control of emotions, which can one work week of mild sleep restriction on interleukin-6 and cortisol secretion and daytime sleepiness and performance. American Journal of help with anxiety that is worsened by Physiology-Endocrinology and Metabolism, 305(7), E890–E896. doi:10.1152/ajpendo.00301.2013 sleep deprivation. Forbes states that 5.Tanaka, T., Narazaki, M., & Kishimoto, T. (2014). IL-6 in Inflammation, Immunity, and Disease. Cold Spring Harbor Perspectives in Biology, 6(10), anxiety levels can become normal after a016295–a016295. doi:10.1101/cshperspect.a016295 6.Mathewson S. (2017) Here's What Happens in the Brain When You Don't one night of recovery sleep (1). If Get Enough Sleep. LiveScience. https://www.livescience.com/60875- sleep-deprivation-sluggish-brain-cells.html consistently getting adequate hours of 7.Nir, Y., Andrillon, T., Marmelshtein, A. et al. Selective neuronal lapses precede human cognitive lapses following sleep deprivation. Nat Med 23, rest is a challenge, it's a good idea to try 1474–1480 (2017). https://doi.org/10.1038/nm.4433 8.Ben Simon, E., & Walker, M. P. (2018). Sleep loss causes social and get at least one recovery night of withdrawal and loneliness. Nature Communications, 9(1), 3146. https://doi.org/10.1038/s41467-018-05377-0 sleep. 9.University College London. (2019) Brain activity intensity drives need for sleep. Science Daily. https://www.sciencedaily.com/releases/2019/09/190916110556.htm

JOB 20 2 0 1 9 - 2 0 2 0 ALZHEIMER’S AND ITS CONNECTION TO DISORDERED SLEEPING

BY SOPHIE SILBERT '21 &

LILY WOMACK '21 Drawing by: Sonia Lin '21

More than 45 million people worldwide groups: healthy mice, mice genetically are affected by Alzheimer’s disease (AD), engineered to have amyloid-beta (Abeta) the most common form of dementia. protein deposits (also known as senile Sleep-wake disturbances are commonly plaques), and mice genetically engineered observed among people diagnosed with to have neurofibrillary tangles (NFT) (2). Alzheimer’s disease, including a modest NFT are aggregates of abnormally decline in total sleep time, an increase in phosphorylated tau, a protein found nocturnal awakenings, a greater tendency inside nerve cells that normally maintains for daytime sleep, and sundowning - a the shape of neurons (3). Senile plaques symptom of Alzheimer’s disease also and NFT are two major biological traits of known as "late-day confusion" (1). Recent Alzheimer’s disease in humans. discoveries connecting biological changes caused by Alzheimer’s disease have given The results showed that in the healthy further insights into why these symptoms mice, injections of glucose into the blood occur. led to a spike in nerve cell activity, a moment of heightened metabolism, and a The results of a study conducted in 2015 longer time spent awake. Similarly, a by researchers at the Hope Center for decrease in blood sugar levels, caused by Neurological Disorders in the Knight insulin injections, also led to increased Alzheimer’s Disease Research Center nerve cell activity and a spike in show that Alzheimer's disease affects wakefulness. However, in comparison levels of brain activity, which in turn with the results of these healthy mice, affect sleep-wake centers. The study used the transgenic Alzheimer’s Disease mice mice to simultaneously measure the experienced significantly decreased effects of the amount of blood sugar on responses to changes in blood sugar the rate of nerve cell activity and the levels. Mice with senile plaques amount of time that the mice spent responded to high blood sugar levels with sleeping. The experiment had three test a limited rise in brain metabolism, but

JOB 21 2 0 1 9 - 2 0 2 0 with significantly lower levels of activity They found that the Locus coeruleus and than normal mice. Conversely, mice with the Tuberomammillary nucleus had lost tau proteins experienced no changes in over 70% of these nerve cells, and the brain metabolism in response to changes destruction of these nerve cells by the in blood sugar level alterations (2,4). formation of NFT may be a factor in the common drowsiness of patients with These results suggest that the presence Alzheimer’s. On May 12th in the of senile plaques and neurofibrillary Alzheimer’s & Dementia journal, Dr. Lea tangles may affect metabolic processes Grinberg suggested that “disordered and the sleep-wake circuit, which could sleeping isn’t just an early indicator of contribute to disordered sleeping. Alzheimer’s” (5). Instead, sleep trouble is However, the results of this study may “part of the disease,” as demonstrated by not be completely predictive of human both of these studies.

Alzheimer's as these sample mice don’t Sources capture all aspects of the etiology of 1.Khachiyants, N., Trinkle, D., Son, S. J., & Kim, K. Y. Alzheimer’s disease, and while these (2011). Sundown syndrome in persons with dementia: an update. Psychiatry Investigation, 8(4), mice were engineered to produce high 275–287. https://doi.org/10.4306/pi.2011.8.4.275 levels of Abeta quickly, this is not the 2.Macauley, S. L., Stanley, M., Caesar, E. E., Yamada, case for people who develop Alzheimer’s S. A., Raichle, M. E., Perez, R., Mahan, T. E., Sutphen, C. L., & Holtzman, D. M. (2015). disease. Hyperglycemia modulates extracellular amyloid-β concentrations and neuronal activity in vivo. The In a separate study conducted by Lea Journal of Clinical Investigation, 125(6), 2463–2467. https://doi.org/10.1172/JCI79742 Grinberg, a neuropathologist at the 3.Kocahan, S., & Doğan, Z. (2017). Mechanisms of University of California, and her Alzheimer's Disease Pathogenesis and Prevention: colleagues, the results showed that The Brain, Neural Pathology, N-methyl-D- aspartate Receptors, Tau Protein and Other Risk Alzheimer’s disease destroys structures in Factors. Clinical Psychopharmacology and the brain that keep people awake. The Neuroscience: The Official Scientific Journal of the researchers looked for evidence of Korean College of Neuropsychopharmacology, 15(1), 1–8. https://doi.org/10.9758/cpn.2017.15.1.1 abnormal levels of tau inside nerve cells 4.Carroll, C. M., & Macauley, S. L. (2019). The of Alzheimer’s disease patients' post- Interaction Between Sleep and Metabolism in mortem brains. They found three small Alzheimer's Disease: Cause or Consequence of Disease? Frontiers in Aging Neuroscience, 11, 258. regions of the brainstem and the https://doi.org/10.3389/fnagi.2019.00258 hypothalamus - the Locus coeruleus, the 5.Oh, J., Eser, R. A., Ehrenberg, A. J., Morales, D., Lateral hypothalamic area, and the Petersen, C., Kudlacek, J., … Grinberg, L. T. (2019). Profound degeneration of wake-promoting Tuberomammillary nucleus - to be neurons in Alzheimer’s disease. Alzheimer’s & packed with tau (5). These are areas in Dementia, 15(10), 1253–1263. the brain that contain nerve cells that https://doi.org/10.1016/j.jalz.2019.06.3916 control sleep-wake cycles and keep people awake and attentive.

JOB 22 2 0 1 9 - 2 0 2 0 SELECTIVE SEROTONIN REUPTAKE INHIBITORS DON'T WORK FOREVER BY LUKE SIEGEL '21

Previously, selective serotonin reuptake these symptoms is known as discontinuation inhibitors (SSRIs) were seen as the primary syndrome, and is described as having treatment for major depressive disorder, withdrawal-like effects (3). attention deficit hyperactivity disorder, and anxiety. After the massive boom of Prozac Recently, alternative treatments for anxiety and other heavily marketed SSRIs, many felt and depression have been developed. as if the efficacy of SSRIs should be Psychedelics are now being used in clinical reevaluated and compared with their settings to rewire the brain and correct the potential harms. underlying issues that had caused the problems. Studies have predominantly In short, SSRIs work by preventing the focused on ketamine and psilocybin, reuptake of serotonin from the synaptic cleft although the strict and highly regulated (the chasm between two neurons). When laws around these drugs have made testing serotonin is released by a neuron, the extremely difficult. Although psilocybin is following neuron in a pathway binds much of still in its experimental phase, ketamine the serotonin, however, some remains. The clinics have opened up throughout the US. leftover serotonin is then reabsorbed back So far, ketamine administration has shown into the original neuron that released it. This to induce rapid antidepressant effects in process of reuptake allows the serotonin to patients with major depressive disorder, but be used at a later time. SSRIs prevent further testing still has to be done to reabsorption from occurring, meaning the determine its viability as a therapeutic (4). receiving neuron would utilize all of the serotonin released (1). In addition, traditional cognitive-behavioral therapy has seen a resurgence over the past Effects associated with serotonin include few years. With an increase in access to general happiness and anxiety relief, technology and communication through although serotonin also plays a major role in social media, stigma toward this therapy has sleep, body temperature, and motor function decreased and with it, the younger regulation. While SSRIs may provide a generations attend therapy in higher sufficient mood-boost to help cope with numbers. To some, talking through their depression or sufficient sedation to reduce problems is more effective than introducing anxiety, SSRIs do not address these problems drugs, be it pharmaceutical SSRIs or at their root and instead work as a sort of psychedelics. band-aid by masking the problem with Sources temporary relief (2). 1. Harmer, C. J., Duman, R. S., & Cowen, P. J. (2017). How do antidepressants work? New perspectives for refining future treatment approaches. The Lancet Psychiatry, 4(5), 409–418. Additionally, a resistance to SSRIs develops with doi:10.1016/s2215-0366(17)30015-9 prolonged use. When you take these medications, 2. Jakobsen, J. C. C. et al. (2017). Selective serotonin reuptake inhibitors versus placebo in patients with major depressive the user’s body gets acclimated to the increase in disorder. A systematic review with meta-analysis and Trial serotonin levels. When a patient ceases use of Sequential Analysis. BMC Psychiatry, 17(1). doi: 10.1186/s12888-016-1173-2 their medication, the body detects the harsh 3. Black, K., Shea, C., Dursun, S., & Kutcher, S. (2000). Selective decrease in serotonin levels. This often causes serotonin reuptake inhibitor discontinuation syndrome: proposed diagnostic criteria. Journal of Psychiatry & heightened symptoms of depression or anxiety Neuroscience : JPN, 25(3), 255–261. when compared to the same symptoms before 4. Bratsos, S., & Saleh, S. N. (2019). Clinical Efficacy of Ketamine for Treatment-resistant Depression. Cureus. SSRI administration began. The worsening of doi:10.7759/cureus.5189 JOB 23 2 0 1 9 - 2 0 2 0 INDUCED PLURIPOTENT STEM CELLS FROM BLOOD TO BRAIN AND BACK BY ABIGAIL GLEZER '21

Induced pluripotent stem cells are paving ectoderm and the mesoderm. This means the way for a future where science fiction that they have the ability to differentiate becomes reality. In simple terms, stem into any type of cell the body needs to cells are classified as a cell that has the heal itself, which is why they’re called ability to differentiate into a cell pluripotent. The transcription factors that belonging to any body tissue with the dictate differentiation are proteins that activation and inhibition of specific genes. bind to DNA and turn a gene on or off by One type of stem cell, embryonic stem making it more or less difficult for RNA cells, is sourced from a blastocyst three to polymerase to bind to the gene and five days after the fertilization of an egg transcribe it. The biological process behind by a sperm (1). Another major class of these stem cells is the very reason they’re stem cell is tissue-specific stem cells, considered such a sensational which are only able to differentiate into breakthrough, as they overcome issues cell types specific to their tissue location. faced by the previously established stem For example, bone marrow stem cells can cell types in the clinical setting. differentiate into red or white blood cells, but not heart or muscle cells (1). The most The major holdback on exploring the recent discovery, known as induced potential applications of stem cells is the pluripotent stem cells, are the most invasive sourcing methods necessary to clinically promising stem cells and are obtain them. Human embryonic stem cells already being considered a major are viable for differentiation, but the breakthrough (1). ethical dilemma of diminishing a potential “life” for scientific pursuits has been a But what are induced pluripotent stem controversial topic since the initial cells? Shinya Yamanaka of Kyoto discovery of stem cells. The cells are University made a crucial discovery in sourced from a blastocyst three to five 2006 in which he took already days after the fertilization of an egg by a differentiated specialized body cells and sperm, destroying the cell clump in the converted them back to their initial process (3). Certain groups of people view pluripotent state through the over- this as an unethical termination of expression of four gene transcription potential life to further scientific research. factors (Oct4, Sox2, Klf4, and cMyc) (2). In Pluripotent stem cells overcome this clearer terms, induced pluripotent stem ethical issue as they have the ability to cells (iPSCs) can become cells from all come from skin cells, blood cells, and three basic body layers: the endoderm, the other easily accessible cell types. The lack

JOB 24 2 0 1 9 - 2 0 2 0 of ethical dilemma means that the use of if someone has a failing liver, their skin these cells in modeling of disease, drug cells can first be sourced and reverted back development, and regenerative medicine to their pluripotent stage, and then be can be explored with fewer restrictions. differentiated into a liver cell, which will continue to reproduce until an entire liver Previously, animal models have been the has been grown. primary tool for both drug testing and for studying the progression of different Since this liver originated from a patient's diseases. The issue with this is that drugs body cell, it is genetically matched and gets that were shown to work in animal models rid of the threat of graft versus host disease oftentimes failed to be effective in humans. or GvHD. GvHD is a common cause of organ This is due to the fact that the failure where a donated organ is rejected development of disease in animal models by the immune system of transplant often does not correlate fully to the patients due to it being perceived as development of the disease in humans (4). foreign. The genetic compatibility of iPSCs Induced pluripotent stem cells have rapidly also presents them as a viable candidate in become a popular replacement as they cell replacement therapy (4). Patients with come directly from a human patient, Type 1 diabetes have pancreases with allowing for more accurate data and limited or no ability to produce insulin due monitoring of a disease. iPSC lines that to the lack of insulin producing beta cells. come from the body of a sick person are Using iPSCs, it would be possible to genetically specific to that person, meaning produce and transplant new insulin they can be monitored for future mutations secreting beta cells into the pancreas and the potential effect of medications on where they will continue to reproduce and a patient by patient basis. For example, a secrete insulin, ultimately reversing the cultured line of cells from a patient with diabetes. Amyotrophic lateral sclerosis - a degenerative disease where motor neurons Sources 1.Yamanaka S. (2012). Induced pluripotent stem cells: past, present, and future. die at increasing rates over time - showed Cell Stem Cell, 10(6), 678–684. https://doi.org/10.1016/j.stem.2012.05.005 2.Takahashi, K., & Yamanaka, S. (2006). Induction of Pluripotent Stem Cells that the cells were able to be differentiated from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors. Cell, 126(4), 663–676. doi:10.1016/j.cell.2006.07.024 into neurons (5). This means that cell 3.Yu, J., & Thomson, J. A. (2013). Embryonic Stem Cells. Handbook of Stem Cells, 275-286. doi:10.1016/b978-0-12-385942-6.00022-6 replacement therapy could be a possible 4.Tanabe, K., & Takahashi, K. (2011). The Past, Present and Future of Induced Pluripotent Stem Cells. Embryonic Stem Cells - Differentiation and Pluripotent cure for neurodegenerative diseases such Alternatives. doi: 10.5772/24198 5.Richard, J., & Maragakis, N. J. (2015). Induced pluripotent stem cells from ALS patients for disease modeling. Brain Research, 1607, 15-25. as ALS, Parkinson's, Alzheimer’s, and doi:10.1016/j.brainres.2014.09.017 others.

Induced pluripotent stem cells are paving the way for a future where science fiction becomes a reality as we now have the potential to grow organs out of skin cells that are genetically identical to the person who’s receiving them (5). Current iPSC research centers around identifying specific regulating processes for each cell type to learn how to differentiate a stem cell into a specifically desired cell type. For example, JOB 25 2 0 1 9 - 2 0 2 0 Ecology and Evolution Drawing by: Sonia Lin '21 18

Drosophila: They’re Pretty Fly!

help understand more complex many genes that are similar to BY TONIA CURDAS '21 organisms such as humans.There are humans, so we are able to study many reasons why Drosophila has them and gather information that Have you ever left fruit out in the been an important model organism. could be helpful in understanding open and come back to a swarm of Most of the fruit fly's characteristics, human gene functions, mutations, fruit flies surrounding the discarded such as their simple genome and and disease. The relatively simple food? You must have thought they short generation time and life span, genome also allows for easier were pretty annoying. However, make it easier to study than other experimentation because the these tiny creatures are a valuable organisms while still maintaining process of inducing mutations is organism for many scientists. enough similarity to humans for the dependable and well established, Drosophila melanogaster, commonly research to be relevant. especially since most of the known as the fruit fly, has been Drosophila DNA was sequenced by used by scientists for decades as a The fruit fly was an important 2000 (4). This development played model organism for the many organism studied to gain early an important role in the Human developmental and cellular knowledge in the field of genetics Genome Project because the processes that it has in common mostly because of its special large sequencing of fruit fly DNA helped with humans and other animals (1). chromosomes in the salivary gland to improve DNA experimentation A model organism is studied so that that could be easily seen even (1,2,5). information gained in a “simpler” before the development of powerful model can be applied microscopes (2,3). The fruit fly has Drosophila melanogaster has a life

JOB 27 2 0 1 9 - 2 0 2 0 18 cycle that can be completed in about 12 days at room temperature, and the females release a

large number of offspring, up to 1,500 eggs in 1 2 ' their lifetime (2).Their short generation time n i

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mutations that affect offspring or multiple o S

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generations in a short amount of time, even y b

permitting studies of evolutionary change in g n animals (2,6). Researchers can easily collect and i w a

analyze large quantities of Drosophila embryos, r and unlike mammalian embryos, they can study D a large sample of offspring.

Drosophila melanogaster has been used in award-winning research in the 20th century and continues to be used today. By utilizing this incredible model organism, Thomas Hunt Morgan won the Nobel Prize for uncovering the location of genes on the chromosomes of the cell, how traits, genes, and chromosomes relate to one another, and the concept of crossing over, wherein segments of homologous chromosomes can trade places with one another during meiosis and generate genetic diversity "large (7,8). chromosomes in Fruit flies can even be used to model human behaviors. Interestingly, they have been used to the Drosophila understand alcoholism (8). In the wild, fruit flies ferment fruits in a process that releases a large salivary gland amount of alcohol, and they are immune to the process’s toxic and intoxicating effects. In the could be easily lab, however, scientists have been able to develop flies that are sensitive to alcohol and seen even before monitor how genetic and environmental factors affect their responses to the drug (9). the development With all the important scientific advancements of powerful that fruit flies have played a major role in, you could consider them to be pretty fly! microscopes" Sources 1.Adams, M. D., Celniker, S. E., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F., George, R. A., Lewis, S. E., Richards, S., Ashburner, M., Henderson, S. N., Sutton, G. G., Wortman, J. R., Yandell, M. D., Zhang, Q., Chen, L. X., … Venter, J. C. (2000). The genome sequence of Drosophila melanogaster. Science, 287(5461), 2185–2195. https://doi.org/10.1126/science.287.5461.2185 2.Drosophila as a model organism: An Introduction. modENCODE. http://modencode.sciencemag.org/drosophila/introduction 3.Dutchen S. (2018) Why the Fly? Harvard Medical School. https://hms.harvard.edu/news/why-fly 4.Celniker SE, Rubin GM. (2003) The Drosophila melanogaster Genome. Annual Review of Genomics and Human -TONIA CURDAS'21 Genetics. 4:89–117. https://doi.org/10.1146/annurev.genom.4.070802.110323 5.Simmons H. (2019) Drosophila as a Model Organism. News Medical: Life Sciences. https://www.news- medical.net/life-sciences/Drosophila-as-a-Model-Organism.aspx 6.Linford NJ, Bilgir C, Ro J, & Pletcher SD. (2013). Measurement of lifespan in Drosophila melanogaster. Journal of visualized experiments : JoVE, (71), 50068. https://doi.org/10.3791/50068 7.Thomas H. Morgan - Facts. NobelPrize.org. 8.Key CS. Alcoholism - Don’t Drink and Fly! modENCODE. http://modencode.sciencemag.org/drosophila/alcoholism/ 9.Devineni, A. V., & Heberlein, U. (2009). Preferential ethanol consumption in Drosophila models features of addiction. Current Biology : CB, 19(24), 2126–2132. https://doi.org/10.1016/j.cub.2009.10.070

JOB 28 2 0 1 9 - 2 0 2 0 Move Aside Water Strider, The Gecko Has Arrived

BY JANE CHEN '21 Drawing by: Sonia Lin '21

The gecko is known to be one of the most agile of The scientists also found that geckos possess a trotting creatures, and can be seen climbing up walls, sprinting gait using all four legs similar to that performed on land over rocky terrain, and swinging under leaves. Scientists when running. The movement of the forelimb of the gecko at the University of California - Berkeley have just one is synchronized with the contralateral hind limb, which more addition to these gravity-defying stunts. They then alternates with the movement of the ipsilateral, or discovered that geckos are also able to perform incredible same sided, limbs. This is a movement in the water locomotive behavior on the surface of water (1). In other running process that is unique to geckos and has not been words, they are able to “run,” and by extension, “walk” on reported for other reptiles (4). On the surface of the water, water. A video recorded at a wildlife reserve in Singapore the gecko alternates between energetic slapping and depicted a gecko moving across a body of water in a stroking motions that propel its body forward. During the rapid, quadrupedal motion that seemed almost identical slapping phase, the gecko’s limb is inserted vertically into to that of running. The scientists decided to delve into the water and then moves backward, and in the stroking the biomechanics of this gecko feat. Upon executing an phase, the gecko’s limbs continue to move in a backward experimental investigation on this locomotion of geckos, manner (1). In addition to the mechanism itself, the they have found the reasons as to how and why geckos physical features of the gecko, such as its tail and its skin, have this remarkable ability. aid in the water running process. The gecko tail promotes balance and stability as the limb motion occurs and First, to establish where the gecko and its locomotive contributes to forward velocity of the animal. The ability stand among other groups of animals who are able superhydrophobic nature of the gecko skin also bolsters to perform similar tasks, it is noteworthy that the gecko the reduction of drag, further increasing the speed at combines aspects of mechanisms that large and small which the gecko travels. sized animals use to get across bodies of water. Larger animals such as grebes slap the water’s surface at a rapid So the next time you spot a gecko in the rocky landscape rate and then stroke the water with their limbs in order to of Southern California darting into a body of water and stay in motion (2). For smaller organisms such as water appearing to be effortlessly “running,” you’ll know a little bugs, surface tension allows them to glide smoothly more about how these phenomenal creatures are able to across the water without difficulty (3). The gecko employs do what they do. the techniques and principles that organisms of all sizes use to propel themselves across the water’s surface, Sources which is logical because geckos are considered medium- 1.Clifton, G.T., Hedrick, T.L., Biewener, A.A. (2015) Western and Clark's grebes use novel strategies for running on water. Journal of Experimental Biology, 218: sized organisms in this context. 1235-1243. https://doi.org/10.1242/jeb.118745 2.Bush, J.W.M., & Hu, D.L. (2006). Walking on water: biolocomotion at the interface. Annual Review of Fluid Mechanics, 38: 339-369. The evolutionary advantage to this “water running” is that https://doi.org/10.1146/annurev.fluid.38.050304.092157 3.Nirody, J. A., Jinn, J., Libby, T., Lee, T. J., Jusufi, A., Hu, D. L., & Full, R. J. (2018). it allows organisms to be on the water’s surface with Geckos Race Across the Water's Surface Using Multiple Mechanisms. Current drastically lower levels of drag, which, in turn, increases biology: CB, 28(24), 4046–4051.e2. https://doi.org/10.1016/j.cub.2018.10.064 4.Ringma, J.L. & Salisbury, S.W. (2014). Aquatic locomotor kinematics of the the rate at which an organism can travel in order to eastern water dragon (Intellagama lesueurii). Journal of Herpetology, 48(2): 240- escape a predator or to attack prey (1). 248. https://doi.org/10.1670/12-041

JOB 29 2 0 1 9 - 2 0 2 0 Drawing by: Sonia Lin '21

Chytridiomycosis, the Amphibian Killer!

Biodiversity is a measure of genetic The aquatic pathogenic fungus, BY SARAH AKTARI '21 diversity among and within species in a Batrachochytrium dendrobatidis is particular habitat or ecosystem. Greater suspected to be behind the diminishing biodiversity generally boosts ecosystem populations. When we first hear the words “extinct productivity. Loss of biodiversity has species,” many of our minds may go been most acute in tropical biomes, Batrachochytrium dendrobatidis results straight to dinosaurs and woolly where up to 12 percent of all species in chytridiomycosis, an infectious mammoths from thousands of years are classified as endangered. The disease that often ends up killing ago. However, species extinction is an interactions between various species, amphibians. Chytridiomycosis, or issue that continues to affect our which are vital to generating diversity in chytrid, usually infects amphibian ecosystems today. Extinction is a life on Earth, are obstructed due to a species that reside primarily within natural phenomenon in which species chain effect with extinction. In addition, permanent water, such as streams and die out. Though extinction occurs the overall abundance of both plant and ponds. After infection, this disease naturally, humans have sped up the animal life across the globe has develops in the keratinized epidermal process by destroying habitats, decreased by roughly 20 percent in just cells of living amphibian skin (8). introducing invasive species, the past century. Chytrid is known to infect over 700 overfishing, polluting the environment, species of amphibians, being associated and overhunting. In addition, recent The spread of infectious disease is with the decline of 93 species and the accelerations of climate change and another cause of biodiversity losses. In decline of 200 species globally (6). global warming has also driven wildlife 1988, the World Congress of Chytrid does not affect all species decline, as many local climate patterns Herpetology emphasized the concern equally: it can be fatal to some while have been shifting (2). Based on for diminishing amphibian populations nearly harmless to others. The extent of extinction records, the average rate of Over the past few decades, 43 percent mortality is dependent on the vertebrate extinctions alone has been of amphibian species have declined amphibian species, the genetic and 100 times greater in the past century globally, while 32.5 percent are at risk phenotypic variation of the pathogen than before. This recent mass extinction for extinction, and 34 species have been (4), and the environment (7). After should have taken 800 and 10,000 confirmed as extinct (5). Rapidly studying amphibian decline due to years to accomplish, but with human declining amphibian populations are chytridiomycosis at various sites across interference, it occurred within the centralized in upland Neotropical or Central America, researchers have timespan of just a century (3). Paleotropical riparian habitats, which further concluded chytridiomycosis is are located in South America, Africa, likely responsible for the mass mortality A major issue that often comes along Asia, and Oceania events. These events can give rise to with species extinction is the loss of global amphibian extinctions (5). biodiversity.

JOB 30 2 0 1 9 - 2 0 2 0 18

Drawing by: Sonia Lin '21

Sources Clearly, chytrid has drastically affected after chytrid, likely because of the 1.Zipkin, E. F., Direnzo, G. V., Ray, J. M., Rossman, S., & Lips, various amphibian populations across snake species’s heavy dependence on K. R. (2020). Tropical snake diversity collapses after widespread amphibian loss. Science, 367(6479), 814–816. the world, but what ends up happening the frogs (1). Substantial declines in doi: 10.1126/science.aay5733 2.Sartore, J., Hedges, B., & Toft, R. (2019). What is to the animals who prey on these frog snake populations include Rhadinaea extinction? The answer is complicated. Retrieved from https://www.nationalgeographic.com/animals/reference/e populations? Recent studies have decorata, Sibon argus, and Clelia clelia. xtinction-wild-endangered-species/ 3.Ceballos, G., Ehrlich, P. R., Barnosky, A. D., García, A., shown that a major decline in The species Sibon argus has specifically Pringle, R. M., & Palmer, T. M. (2015). Accelerated modern human–induced species losses: Entering the sixth mass amphibian prey species due to chytrid been reported to feed on amphibian extinction. Science Advances, 1(5). doi: 10.1126/sciadv.1400253 causes the population of their eggs at higher levels than other 4.Rosenblum, E. B. et al. (2013). Complex history of the predators, such as tropical snakes that documented Sibon species. Sibon argus amphibian-killing chytrid fungus revealed with genome resequencing data. Proceedings of the National Academy of feed on amphibians and their eggs, to was the most prominent species before Sciences of the United States of America, 110(23), 9385– 9390. doi : 10.1073/pnas.1300130110 plummet as well. Researcher Karen 2004 yet also experienced one of the 5.Lips, K. R., Brem, F., Brenes, R., Reeve, J. D., Alford, R. A., Voyles, J., Collins, J. P. (2006). From The Cover: Emerging Lips and her colleagues studied most severe declines in population as a infectious disease and the loss of biodiversity in a Neotropical amphibian community. Proceedings of the tropical snake populations in El Copé, result of frog depletion. National Academy of Sciences, 103(9), 3165–3170. doi: 10.1073/pnas.0506889103 a tropical region of central Panama, in 6.Stuart, S. N., Chanson, J. S., Cox, N. A., Young, B. E., 1997 before chytridiomycosis began Though chytrid does not directly infect Rodrigues, A. S. L., Fischman, D. L., & Waller, R. W. (2004). Status and Trends of Amphibian Declines and Extinctions affecting frog species in that region. snakes, it still may result in declines in Worldwide. Science, 306(5702), 1783–1786. doi:10.1126/science.1103538 After the illness hit El Copé in 2004, snake populations due to their 7.Lips KR, Reeve J, Witters L. (2003). Ecological factors predicting amphibian population declines in Central depleting the frog population by 75 dependence on the amphibians America. Conserv. Biol. 17, 1078–1088. doi: https://doi. org/10.1046/j.1523-1739.2003.01623.x percent, the team began documenting infected by the disease. Snakes are the 8.Longcore, J. E., Pessier, A. P., & Nichols, D. K. (1999). Batrachochytrium dendrobatidis gen. et sp. nov., a chytrid snake populations over the next direct predators of amphibians and pathogenic to amphibians. Mycologia, 91(2) 219– decade. chytrid may affect the populations of 227.doi:10.1080/00275514.1999.12061011 predators higher up in the food web as The overall number of species of well such as mammals and other snakes diminished from 30 to 21 over reptiles. The loss of amphibian the decade, and the team reported a biodiversity disrupts the food web decrease in snake biodiversity and structure and may lead to the decline average body size or even extinction of other species.

JOB | 31 2 0 1 9 - 2 0 2 0 Photo by: Subah Mehrin '21

Oops, the Fish are Dead: Algae Takes Center Stage in Aquatic Environments

BY AVIVA SCHWARZ '21 is a clear indicator of their harmful water plagued by the effects of capacities, and a reminder that humans eutrophication. Such conditions are a The ponds in Central Park weren’t need to understand these blooms in threat to the fishing industry of the always covered in green and yellow order to avoid danger. coastline populations nearby (5). muck. In Central Park, the algal blooms, Human waste products and runoff a term for a large collection of algae But the poisons that algal blooms correlate positively with the rise of growing in the same place, consist produce are not the only harms algal blooms, and it is only getting mainly of single-celled cyanobacteria. associated with them. Algae blooms can worse for marine life in the Arabian Cyanobacteria, often called “blue-green create oxygen deficiencies, or hypoxia, Sea. algae,” thrive in warm, nutrient-rich in bodies of water. This feels waters and can produce dangerous counterintuitive, because people know From the Arabian Sea to the Gulf of toxins as well as creating low oxygen that algae produces oxygen as a Mexico, runoff from human products "dead zones" in bodies of water (1,2). byproduct of photosynthesis. However, such as sewage or fertilizer into the in bodies of water with conditions that ocean cause the conditions to induce Despite existing for at least 3.5 billion allow algae to thrive due to an excess eutrophication and hypoxia. Fish years (with the fossils to prove it) algae of nutrients in the water, algae populations and other marine life and cyanobacteria populations have populations increase. This means that around the world are dying out due to a had recent spikes, posing a massive the total biomass of the algae in the lack of oxygen. Human populations threat to other aquatic life. In order to environment increases, and every time who rely on the fish as a source of understand the impact of the algal some of the algae cells die, nutrition or income face these issues, as blooms in NYC parks, city park officials decomposers feed on the dead biomass well as the spiking algae causing issues regularly sample the water (3). (1,4). This results in an increase of the by feeding specific algae-consuming According to a 2019 NY Times piece, decomposer population, leading to species which allows unprecedented officials discovered that many of the their consumption of oxygen at a and unbalanced population growth of algal blooms in NYC ponds produce greater rate than the algae can replace. those species. We need to understand neurotoxins that are dangerous to The fish, and other aquatic creatures our impact on the aquatic environment animals, including being fatal to dogs that need oxygen to survive, start to die and implement changes to avoid that might consume them (3). New out because, well, they can’t breathe. destroying it. warning signs around the ponds with This process is called eutrophication, Sources 1.US Department of Commerce, & National Oceanic and Atmospheric harmful algal blooms tell people to when a body of water with excessive Administration. (2004). Eutrophication. Retrieved from https://oceanservice.noaa.gov/facts/eutrophication.html avoid all contact with the water, and nutrients becomes oxygen-deficient 2.Engelhaupt, E. (2019). 'Slime' shows how algae have shaped our world. Retrieved from https://www.sciencenews.org/article/slime-book- shows-how-algae-shaped-climate-evolution especially to keep young children and and kills the organisms inhabiting it 3.Goldbaum, C. (2019). Algae That Can Kill Dogs Is Discovered in 3 N.Y.C. Parks. Retrieved March 2, 2020, from dogs away (3). (1,4). The Arabian Sea’s "dead zone," or https://www.nytimes.com/2019/08/25/nyregion/toxic-algae-nyc- parks.html oxygen minimum zone, is the size of 4.Schopf J.W. (2012). The Fossil Record of Cyanobacteria. In: Whitton B. (eds) Ecology of Cyanobacteria II. Springer, Dordrecht The deadly product of the algal blooms Texas and an example of a body of 5.Shift in Arabian Sea Plankton May Threaten Fisheries. (2014). Retrieved from https://www.earth.columbia.edu/articles/view/3189

JOB | 32 2 0 1 9 - 2 0 2 0 Dr. Lynn Margulis: An Independent Scientist Who Showed Us the Power of Cooperation Image source in works cited

BY AKSHAY RAJU '20 prehistoric bacteria to now create the The 1970’s brought forth new tools to eukaryotic cells that comprise every analyze genomes, and soon researchers “Your research is crap, do not bother to plant, animal, fungi, and protist known. found out that evolutionarily apply again," read a grant application. She proposed that these bacteria were chloroplasts have more similar genetic This was in response to Dr. Lynn in symbiosis, or a cooperative information to cyanobacteria - a Margulis’ groundbreaking paper, “On relationship, with early eukaryotes. This photosynthetic bacterium - than The Origin of Mitosing Cells” shortly relationship after many generations got eukaryotic DNA. They later confirmed after it was published in 1967. Margulis so intimate that these bacteria were this in mitochondria as well, with its was an adjunct assistant professor at endocytosed, or swallowed up, into the close ancestor being a bacterium that Boston University at the time but her eukaryotic cell. This arrangement causes typhus - Rickettsia prowazekii. work was barely taken seriously and allowed for efficient symbiosis, and This was later compounded by other received ridicule from the scientific eventually they became the integral evidence, such as the double membrane community. It was labeled as radical, organelles that they are today. The of the mitochondria that would suggest and a stark contrast to the traditional mitochondrion, for example, performs it was endocytosed, or swallowed up by “survival of the fittest” Darwinian cellular respiration which is a process the cell into a membrane. Furthermore, Theory that had dominated the field for that converts chemical energy from this evolutionary phenomenon was so long (1). Being a woman in a male compounds such as glucose into ATP - further explored as researchers at dominated field didn’t help either. the energy “currency” of the cell. Rockefeller University showed that Now, however, Margulis is viewed as Chloroplasts also play an integral role even centrioles might have similar one of the most important evolutionary in plant cells, as they carry out origins (4). biologists for her proposal of the serial photosynthesis (3). endosymbiotic theory that postulated Not only did that theory change the how eukaryotic cells came to be. Despite harsh criticism from the field, way that we see eukaryotes and their Margulis reasoned that genetic origins, but it also shifted the entire Margulis was born in Chicago in 1938 evidence would determine if this field of evolutionary biology in a new to Jewish parents. She was a gifted hypothesis had weight. The DNA of the direction. Before Margulis, many student and eventually got her PhD in mitochondria is separate from the DNA scientists such as Ernst Mayr and genetics from the University of of the eukaryotic cell found in the Richard Dawkins - who were later her California Berkeley. Margulis’ nucleus. She proposed that if the DNA harshest critics - had centered breakthrough came at her time at of these organelles was not similar to Darwinism as the end all be all of Boston University, where she the host cell DNA but rather bacteria, evolution. Evolution was driven by postulated the endosymbiotic theory her hypothesis would be confirmed. competition, where only the fittest (2). This theory suggested that survived and reproduced. However, organelles such as mitochondria and their mindset had pitfalls in that it chloroplasts actually originated from didn’t account much for how speciation JOB | 33 2 0 1 9 - 2 0 2 0 occurred. Margulis’ theory was founded different kind of scientist, one who does Margulis was a unique scientist, and on cooperation, not competition as not come along very often. Her great deserves to be recognized as not only another driving factor in evolution (5). gift was making connections, someone that proposed a theory that In her mind, “Natural selection connections that others just couldn't revolutionized how we see cells, but eliminates and maybe maintains, but it make" (2). She was always creating new also someone that dared to be different. doesn't create” (6). Speciation in her thoughts and ideas about how the She was different from many in her mind was not driven by selection but world worked, even if that meant field for a multitude of reasons, but that rather by pressure to cooperate with contradicting her colleagues. She was shaped her views as a scientist and other organisms or members in the truly a scientist in that she was always made her the trailblazer that she was. population. She continued to extend pushing boundaries by proposing bold this parallel pressure to cooperate as a ideas and then was not afraid to be means of survival and change from the wrong. The fact that she was a woman origin of eukaryotes to other also may have contributed to her evolutionary events, eventually also nonconformity as a scientist. She was proposing the controversial Gaia born only 18 years after women had hypothesis along with James Lovelock. gotten the right to vote in the United States, and lived much of her life during The Gaia hypothesis, however, remains a time when women were not seen as one of her most controversial theories scientists. By being an outsider, both in to date. She saw the world and all of its a societal and scientific perspective, elements, both biotic and abiotic, as all Margulis was not constrained by the in symbiosis with each other. It was collective mindset and rather forged almost an extension of her previous her own path. work of promoting symbiosis as an integral part of biology, as something She was also fiercely independent in much more than the obvious her work and oftentimes fought with Sources interspecies relationships that existed many people in her field. Margulis 1.Gray, M. W. (2017). Lynn Margulis and the in nature. She worked on this never had many to lean on throughout endosymbiont hypothesis: 50 years later. Molecular Biology of the Cell, 28(10), 1285–1287. hypothesis in her later years, working her career compared to others. Margulis doi:10.1091/mbc.e16-07-0509 closely with Lovelock to expand the had a poor upbringing and was never 2.NASA Science. (n.d.). Lynn Margulis (1938-2011) | Evolutionary Biologist –. NASA. Retrieved April 1, theory and even having a Gaia “nurtured” in the sciences, rather having 2020, from conference. Furthermore, she published to take her education into her own https://solarsystem.nasa.gov/people/1660/lynn- margulis-1938-2011/ books such as Symbiotic Planet and hands and be curious by herself. 3.Indiana University. (n.d.). Endosymbiotic Theory. What is Life, the latter being co-written Education for women was still Retrieved April 1, 2020, from https://www.biology.iupui.edu/biocourses/N100/2k2en by her son Dorian Sagan (7). somewhat taboo, which only furthered dosymb.html her self-reliance. Throughout her career 4.University of California Berkeley. (n.d.). Endosymbiosis: Lynn Margulis. Retrieved April 1, 2020, from The early ridicule for her ideas was she continued to be in her own bubble https://evolution.berkeley.edu/evolibrary/article/histor probably a reason that she strayed so of sorts as she sometimes fought tooth y_24 5.Horgan, J. (2011). R.I.P. Lynn Margulis, Biological far from her peers. Margulis preferred and nail to support her theories. Rebel. Scientific American. Retrieved April 1, 2020, from to do things herself as for a long time Independence even was something https://blogs.scientificamerican.com/cross-check/r-i-p- lynn-margulis-biological-rebel/ she was never accepted into the Margulis prioritized in her personal life 6.Teresi, Dick (2011). "Lynn Margulis says she's not scientific mainstream and distrusted as well. She was married to controversial, she's right". Discover Magazine. Discover Interview. No. April 2011. the “groupthink” that had emerged in astrophysicist and Cosmos curator Carl 7.Weber, B. (2011). Lynn Margulis, Trailblazing Theorist evolutionary biology. It has led her to Sagan for seven years until she decided on Evolution, Dies at 73. The New York Times. Retrieved April 1, 2020, from take many controversial stances aside that her career took precedence over https://www.nytimes.com/2011/11/25/science/lynn- from Gaia, such as her stances on the her marriage. Margulis mentioned in an margulis-trailblazing-theorist-on-evolution-dies-at- 73.html cause of AIDS (8). Margulis was, in that interview that she, "...quit my job as a 8.Knoll, A. H. (2012). Lynn Margulis, 1938-2011. sense, unconventional in her work. She wife twice… it’s not humanly possible Proceedings of the National Academy of Sciences, 109(4), 1022–1022. doi:10.1073/pnas.112047210 was always a radical in her field, from to be a good wife, a good mother, and a 9.Weil, Martin (26 November 2011). "Lynn Margulis, being a woman to the way that she first-class scientist. No one can do it — leading evolutionary biologist, dies at 73". The thought about the world. something has to go" (9). She chose to Washington Post. be free of the constraints of being a Image Credits 1.SINC. (2009). Lynn Margulis while attending the Steve Goodwin, the dean of Natural mother and a wife to focus on her work symposium "150 años de Darwin" ("150 years of Sciences at the UMass Amherst said even though it was not necessarily Darwin") [Digital]. https://commons.wikimedia.org/wiki/File:Lynn_Marguli about Margulis that, "She was a common at the time. s_SINC.jpg JOB | 34 2 0 1 9 - 2 0 2 0 Scientist Spotlight Karin Block, on Geochemistry and Petrology Interviewed by JK ARONI GOONGOON ‘21

Dr. Karin A. Block is an Associate Professor and the Undergraduate Research Coordinator at The City College of New York. Her work has covered a plethora of topics within earth and atmospheric sciences including petrology, mineralogy, high- and low-temperature geochemistry, geobiology, and geoinformatics! This interview provided us great insight into her Image source: Karin Block experiences as a scientist in her field.

Q: Why did you pursue the sciences of geochemistry and petrology? A: "Initially, when I went back to school to try to go to graduate school to get my Ph.D., I didn’t know that I was going to study geochemistry and petrology. I actually wanted to pursue atmospheric science and I became interested in atmospheric chemistry. So for a while, I was doing some research on cloud droplet crystals and snow crystals and looking at the morphology of those crystals. I wanted to see if I could correlate the contamination in the location I was sampling the crystals from to what was going on in the air. I did that for a while and intended to complete my Master’s on it. Then somehow, I was drawn to the geochemistry field. I was taking a geochemistry class and specifically studying mineralogy. I instantly fell in love with crystals in rocks. Crystals in rocks have a tremendous story to tell by virtue of just how they are arranged within a rock. We can actually tell physical conditions, like the temperature and pressure at which a rock forms, by looking at which minerals are in a rock and how they are arranged, along with their shapes and boundaries to each other. The whole thing fascinated me. These crystals under the microscope were just so beautiful to look at. That’s why I decided to do my Ph.D. on petrology and completely moved away from my initial atmospheric science endeavors."

Q: What do you think is really unique about geochemistry and petrology? A: "A very difficult question to answer, as within every subdiscipline of science there are so many things that are interesting and you can study. In petrology, you’re trying to learn about the process. So you’re using the chemical data that you extract from minerals in order to tell the physical story, which makes it special as it gives you a window into the rock’s ancient past , even in rocks that solidified 200 million years ago. The way I see it, petrology encompasses science in its purest form."

Q: How is this information useful? A: "With pure science, unlike engineering and other applied sciences, you can’t predict how someone would use the information they find. So petrology is a pure science in that it helps us understand what happened. In sciences like physics, initial discoveries in quantum mechanics in the 20th century helped facilitate the understanding needed to create communication technologies of today. Going back to geochemistry and petrology, geochemistry has a lot of applied uses, but petrology sometimes can be viewed as esoteric. A lot of modern petrologists are trying to investigate how ancient magma traps ancient atmospheric gases. From that material, which we call inclusions, we can find evidence of what climate might have been like millions of years ago. Petrology can thus be used in climate change applications, by refining earthquake models, and providing a context for the processes that shape our solid Earth."

JOB | 36 2 0 1 9 - 2 0 2 0 Q: A lot of your work evidently touched greatly upon the physical sciences. However, did any biological components come into play at any point? A: "Biology plays a factor all the time! Even though geosciences are often considered physical sciences, living things have had the capability of changing the earth tremendously for a very long time. A few billion years ago, we had an atmosphere with no free oxygen at all! There were no animals! The plants, specifically microbial plants, were responsible for changing the atmosphere permanently. Most introductory physical geology courses might not touch upon these topics initially. But as we look into the climate sciences and carbon cycle, the biological components start to come in. When we look at limestone, we see the accumulation of the carbonate exoskeletons of many millions of microscopic animals. Living things produce minerals! So an understanding of biology is also essential in my field."

Q: Did you find anything interesting while working on researching microbes? A: "Recently, my lab grew a flu strain which is usually used for developing vaccines to look into a particular kind of flu that birds carry and which causes many farm-raised birds to be infected; we wanted to find the environmental reason behind the spread. Migratory birds carry the bird flu! For example, if you see a goose in Van Cortlandt lake, it’s probably spreading the flu, but it might never show signs of sickness. However, poultry farms sometimes see flu infections at times when there is no migration. We hypothesized that when migratory birds shed the virus in ponds and lakes, it aggregates with clay minerals in the sediment. We learned that the virus-clay aggregates remained infectious. In our previous experiments using a different kind of enveloped virus, the virus particles fell apart due to electrostatic interaction with the clay particles. But with the influenza, the spikes on the outside of the virus particles made the envelope pliable or squishy. When influenza interacted with clay, the virus didn’t become inactive. We went on further to examine what would happen if the spikes were removed and found that the virus fell apart in that scenario. Therefore, if a bird ingests soil or dirt which contains flu particles, it could get sick. After looking at many electron microscope images and measuring approximately 1500 virus particles for statistical analysis, we published that work (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112063/)."

Q: Are you involved with research right now? A: "Yes! Two of my Master’s students are working on how clay-bacteria relationships stabilize carbon in soil: one is looking at actual soil and the other at synthetic solid by combining clay minerals with iron oxides synthesized in the lab. We’re measuring how long organic matter produced by microbes (which are composed of carbon as well) stay on the surface of the clay. This work is important because soil is the second biggest reservoir of carbon and soil is becoming vulnerable with the effects of climate change. As the planet continues to warm, the way microbes interact with the soil will be affected. Another one of my Master’s students is using X-ray fluorescence to study the incorporation of metals in corals and sediments in Guánica Bay, Puerto Rico, to determine the impact of contamination on fisheries. Her project is sponsored by NOAA."

Q: Did you ever get to work with databases? A: "Yes! For my post-doctoral fellowship, I worked at the Lamont Doherty Earth Observatory of Columbia University to develop several geochemical databases including PetDB (Petrologic Database of the Ocean Floor) and help start from scratch a database of mantle xenolith chemistry that would be incorporated into EarthChem. I still collaborate with those folks. In fact, we just got funded to develop machine learning procedures and artificial intelligence to facilitate access to the data." Q: Currently, what would you say are the most relevant or pressing questions that geochemists, like yourself, are trying to investigate? A: "There are a lot of questions within each subdiscipline of geoscience. But a big one right now centers on determining what are the chemical and physical factors that keep carbon stable in soil. There are many questions that are of interest to geochemists. But if I have to mention one, examining past climate data can help us have an understanding about current climate change and its impact on our future."

Q: Any advice for someone who would be interested in geochemistry? A: "Always keep an open mind and take advantage of opportunities, even if those opportunities don’t seem like exactly what you want. Consider each one, as you never know what you might end up liking. If I hadn’t been offered a summer job by a geochemist to look at minerals under a microscope, I would’ve never fallen in love with geochemistry. If I hadn’t been open to the idea of geoinformatics, I would’ve never gotten the chance to work with databases. So make sure to connect and network while having an open mind to new experiences within the broad spectrum of options within any field of science!"

JOB | 37 2 0 1 9 - 2 0 2 0 Applications of Genetics Drawing by: Sonia Lin '21

Like Homo neanderthalensis, Like Homo sapiens: A Tale of Human Self-Domestication

function, correlating to more modern, the BAZ1B gene is involved in making BY JANE CHEN '21 ‘childlike’ facial structures in humans (2). the difference between a more amicable At the crux of evolution remains the Most of us humans have changes in and a hostile human being is a further question of how species have changed regulation of this gene, but if we look at suggestion that our appearances and our throughout time. If we compare the DNA datasets of our Neanderthal behaviors are closely linked. ourselves to how our human predecessors, these changes are less predecessors looked in the past, we will prevalent (1). These findings imply that The novel concept of human “self- notice that we have developed smaller humans have "domesticated" themselves domestication” is one of many recent faces and subtler brow ridges. Do the through natural selection in favor of more developments in the field of evolutionary same for our dogs, and we see that they friendly physical attributes. biology, where the genetic mechanisms have shorter snouts and ears that are that drive behavior in humans and more floppy. But why does this shift to These researchers were led to this animals are still largely unknown. more juvenile and friendly physical candidate for human self-domestication, Researchers now, more than ever before, features occur, and what does this reveal by studying the DNA of patients afflicted have a greater understanding as to why about animal behavior? Researcher with developmental disorders. They humans have evolved to possess more Matteo Zanella and his team at Milan compared patients with Williams-Beuren amicable attributes. However, we have University explore possible genetic syndrome (WBS), a condition that results only scratched the surface in the quest to explanations. in a reduced dosage of the BAZ1B gene, understand exactly why we humans are to patients with Williams-Beuren the way we are. As the human embryo develops, a set of duplication syndrome (WBDS), a condition migratory cells known as neural crest that associated with a higher dosage of Sources cells –– similar to stem cells –– move BAZ1B. The results communicated that 1.Saey, T.H. (2019). A gene tied to facial development hints humans domesticated themselves. Science News. and eventually give rise to the various patients with WBS tend to be friendly and Retrieved from https://www.sciencenews.org/article/gene-facial- components of our body, from our talkative people with round faces and development-hints-humans-domesticated-themselves neurons to our facial structures. A gene and shorter noses (2). This theme is in 2.Zanella, M., Vitriolo, A., Andirko A., Martins, P.T., Sturm, S. et al. (2019). Dosage analysis of the 7q11.23 Williams known as BAZ1B affects the speed with direct contrast to patients with WBDS, region identifies BAZ1B as a major human gene which these neural crest cells move (1). who are characterized by broader patterning the modern human face and underlying self- domestication. Science Advances, 5(12): 1-15. In lab grown cells, Dr. Zanella found that foreheads and flatter rear heads, and are 3.Mervis, C.B, Morris, C.A., Klein-Tasman, B.P., Velleman, S.L., Osborne, L.R. (2015). 7q11.23 Duplication Syndrome. when BAZ1B protein less friendly and more aggressive (3). The GeneReviews. Retrieved from levels decreased, the neural crest cells idea that https://www.ncbi.nlm.nih.gov/books/NBK327268/pdf/Boo kshelf_NBK327268.pdf were less efficient in their

JOB | 39 2 0 1 9 - 2 0 2 0 Acknowledgments

The Journal of Biology would like to give the most grateful thanks to Dr. LaGrassa for advising the Journal of Biology and being so supportive through every step of our club's growth! From helping us print posters, to staying after school to advise us on how edit our work, we could not have had such a successful year without her generous aid!

We would also like to thank Dr. Davis for her support and assistance with the publication of the 2020 Journal of Biology.

Additionally, we give thanks to Mr. Thorp and the S.O. for enabling the advertisement of our club through 100+ posters! We are proud to say that our weekly club attendance grew by an average of 150%!

Finally, we would like to thank Dr. Gensert for always being available to supervise our club if Dr. LaGrassa was unavailable.