Stony Brook Young Investigators Review Fall 2019 Issue

10

Dr. Thomas Hemmick: His Life and Research

16

Newly Discovered Tyrannasaurs Diversify the Dynasty

24

Social Media May Shorten Our Attention Span

Fall 2019 Volume 13

STAFF 2019-2020 Editor-in-Chief: Stephanie Budhan ’21

Head of Cabinet: Jesse Pace ’20

Layout Chief: Lauren Yoon ’21

Managing Editors: Nomrota Majumder ’21 Shrey Thaker ’22

Cabinet: Rohan Dayal ’23 Jessica Hui ’22 Hannah Philipose ’23

Layout Editors: Priya Aggarwal ’21 Debolina Chanda ’22 Matthew Ng ’22

Webmaster Vinny Han ’20

Faculty Advisors: Dr. John Peter Gergen Dr. Nicole Leavey Dr. Laura Lindenfeld

Associate Editors: Elen Deng ’21 Nina Gu ’21 Nita Wong ’21 Gabrielle Zanko ’23 Copy Editors: Riya Gandhi ’22 Claire Garfield ’20 Kimberly Lu ’22 Caleb Sooknanan ’20 Rohan Shah ’21

Writers: Ayesha Azeem ’23 Joyce Chen ’23 Fatin Chowdhury ’20 Travis Cutter ’22 Kailyn Fan ’23 Simran Kaur ’20 Aditi Kaveti ’23 Natalie Lo ’21 Mariam Malik ’22 John McMenimon ’20 Aaradhana Natarajan ’20 Priyanshi Patel ’22 Jorge Pincay ’20 Adrienne Posescu ’20 Ellie Teng ’21

LETTER FROM THE EDITOR-IN-CHIEF Stony Brook Young Investigators Review (SBYIR) is proud to release its 13th biannual publication. As an undergraduate research journal, SBYIR strives to provide a forum for students interested in scientific writing, to make science accessible to the students and faculty here on campus and far beyond, and finally to highlight the incredible research being done on campus by both faculty and undergraduates.

New changes were brought to the journal this fall semester including the introduction of a journal theme. This edition’s journal theme is, “The Big and the Small: Science on both the Microscopic and Macroscopic Level.” In this issue, readers will find articles that discuss the different types of DNA repair mechanisms on the molecular scale as well as a review of recently discovered relatives of the Tyrannosaurus Rex. This issue also features an interview with reputable Stony Brook professor and researcher Dr. Thomas Hemmick of the Physics Department.

To celebrate the release of each issue, we host a colloquium during which an honorary speaker is invited to share their work. Speakers such as esteemed biologist Dr. Dany Adams who is the founding Editor- in- Chief of the new MaryAnn Liebert Inc. journal Bioelectricity and most recently Dr. Chris Rozell who is a professor of electrical and computer engineering at the Georgia Institute of Technology.

As always we would like to thank our staff of writers, editors, and cabinet members for their hardwork and commitment, without whom none of this would be possible. Additionally, we would like to thank our partners at the Alda Center for Communicating Science for their constant support, as well as our faculty advisors, Dr. Nicole Leavy and Dr. Peter Gergen for their guidance and support.

Welcome to SBYIR. We sincerely hope you enjoy.

STEPHANIE BUDHAN

TABLE OF CONTENTS Fall 2019 Volume 13

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SCIENCE REVIEWS Targeting DNA Repair to Combat Cancer

10

INTERVIEW Dr. Thomas Hemmick: His Life and Research

By John McMenimon ’20

By Natalie Lo ’21

14

Newly Discovered Tyrannasaurs Diversify the Dynasty

By Travis Cutter ’22

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STUDENT RESEARCH Modeling the chlorination of conjugated steroids

By Debra A. Keiser, Eugene Chung, and Eric V. Patterson

Evaluating Pose Reproduction Success Across Docking Platforms

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The Internal Ecosystem

By Aaradhana Natarajan ’20

By Scott Laverty, Stephen Telehany, John Bickel, and Robert C. Rizzo

The loss of Krüppel-like factor 15 in Foxd1D stromal cells exacerbates kidney fibrosis

By Jesse Pace et al.

Media Use 22 Social May Shorten Our Attention Span

By Kailyn Fan ’23

Yeast Xrn1p, a defense against TMV in Nicotiana benthamiana

By Anh Vo, Chris Helenek, John Peter Gergen and the 2019 Stony Brook University iGEM Team

Highlights

EARLY BREASTFEEDING IS BENEFICIAL TO NEWBORNS PRIYANSHI PATEL ’22 Sepsis is the common pathway that leads to neonatal death due to severe illnesses and various infections. Neonatal sepsis is the main cause of neonatal deaths in most developing countries and causes 13% of deaths during the neonatal period and 42% of deaths just after 7 days. The World Health Organization (WHO) recommends early initiation of breastfeeding within 1 hour of giving birth in or-

der to facilitate optimal breastfeeding throughout infancy. Studies in Egypt, India, Nepal, and Ethiopia have examined the correlation between the time at which newborn is first breastfed and neonatal survival. Breastfeeding in a timely matter builds newborns’ immune system against infectious pathogens. The mechanism underlying the success of early breastfeeding initiation has not yet been investigated.

To observe this further, research scientists from the University of Sydney collaborated with the Maternal and Child Health Division of Bangladesh to investigate the effect of breastfeeding initiation time on early newborn danger signs and severe illness.

A trial was conducted in 5 rural districts of Bangladesh with a focus on women between the ages 15 and 49. These women were followed through pregnancy and until 6 weeks after birth. Data was collected from a large community-based cohort to determine the effect of early initiation of breastfeeding on severe illnesses in the early period.

The results of the study showed that the earlier breastfeeding was initiated, the lower the risk of devel-

oping illnesses in the early stage of birth. It was established that starting breastfeeding after the first hour can increase the chances of having severe illnesses.

These findings mean that neonatal mortality is decreased if the newborn is breastfed within an hour of birth, and a reduction in the rate of severe illnesses, including suspected sepsis, also mediates this effect. This study highlighted that there needs to be some intervention to encourage women to support early initiation of breastfeeding, especially those who are at the greatest risk of delaying breastfeeding.

1. S. Raihana, et al., Early initiation of breastfeeding and severe illness in the early newborn period: An observational study in rural Bangladesh. PLOS Medicine, (2019). doi: 10.1371/journal.pmed.1002904

EATING JUNK FOOD CAN POSSIBLY LEAD TO BLINDNESS

A LONG-TERM SOLUTION FOR PEANUT ALLERGIES

ELLIE TENG ’21

ADITI KAVETI ’23

A case report presented a 14 year old male adolescent with “fussy” eating habits feeling fatigued. Scientists from Bristol Medical School and the Bristol Eye Hospital performed tests that showed anemia and low levels of vitamin B12 but the patient was otherwise well. At 15, he was suffering from hearing loss and not long after, deteriorating vision. He was referred to an otolaryngologist and opthamologist but they found no abnormalities. Two years later, his vision loss progressed yet doctors could not find a direct cause. The patient admitted to a diet limited to fatty, processed meats and ‘junk’ food, and was given supplements.

He was diagnosed with nutritional optic neuropathy, usually caused by malabsorption or poor diet, but had become blind by the time the diagnosis was made. Deficiencies in vitamin B1 (thiamine), vitamin B2 (riboflavin), vitamin B3 (niacin), vitamin B6 (pyridoxine), vitamin B9 (folate), vitamin B12 (cobalamin), and copper all contributed to the patient’s hearing and vision loss. Junk foods are low in

nutrition but energy-dense and affordable. High calorie diets are associated with high BMI, low socioeconomic status, and poor health.

Given the situation, “fussy eating” is considered an eating disorder. It falls under the category of avoidant-restrictive food intake disorder which, unlike anorexia nervosa, is not driven by weight or body image concerns. Nutritional optic neuropathy is reversible if caught early and treated. If allowed to progress, it results in permanent blindness.

This case expressed the importance of diet on physical health, and that the amount of calories consumed and BMI are not reliable indicators of nutrition level. This condition could become more prevalent in the future, either due to widespread consumption of ‘junk food’ or to the rising popularity of the vegan diet when not properly supplemented. This case study should also raise awareness of topics such as malnutrition and poverty in the population.

1. R. Harrison, et al., Blindness caused by a junk food diet. Annals of Internal Med, (2019). doi: 10.7326/L19-0361

Peanut allergies affect 6% to 8% of children around the world.

Living with severe allergies is extremely dangerous and requires close monitoring of the ingredients in packaged foods and at restaurants. Many packaged products warn that the food was manufactured in a facility that processes peanuts or tree nuts. These trace amounts seem inconsequential, but they can lead to severe allergic reactions. At restaurants, simply ordering the dish without the allergen is not enough. People with severe allergies can face consequences if the allergen is near the meal.

The purpose of immunotherapy is not to completely reverse an allergy, but instead to make sure that trace amounts that may be hidden in foods do not trigger severe reactions.

Existing immunotherapies rely on the process of desensitization of the immune system through small amounts of peanut protein.

However, ingesting these small amounts of peanut protein may have serious side effects. Patients can go into anaphylactic shock if

the amount of peanut protein is too much. A new approach to immunotherapy, called sublingual immunotherapy, uses peanut protein as well, but places it under the patients’ tongues where it is immediately absorbed.

At UNC School of Medicine, a small study of 18 patients demonstrated that sublingual immunotherapy is safe and effective over the course of one year. Researchers then followed 48 patients that absorbed 2 mg of peanut protein daily for five years. They found that 67 percent of the patients could tolerate 750 mg of peanut protein. This study was as effective as other immunotherapies, without the risk of serious side effects. Sublingual immunotherapy provides a long-term solution for children with severe allergic reactions to peanuts. It is a new and safe form of desensitization that protects people from hidden trace amounts of allergens in their foods.

1. E. Kim, et al., Long-term sublingual immunotherapy for peanut allergy in children: clinical and immunologic evidence of desensitization. Journal of Allergy and Clinical Immunology, (2019). doi: 10.1016/j.jaci.2019.07.30

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NOVEL DRUG FORMULA MIGHT REVERSE BIOLOGICAL AGE JOYCE CHEN ’23 Biological age is the measurement of the true ages of humans through the chemical changes in their DNA. Previous research and hypotheses inferred that reversing this can allow humans to acquire better immune systems and healthier bodies in general. To test if biological age reversal is actually possible, determined scientists from Intervene Immune and the University of California, Los Angeles, completed a one year clinical trial utilizing a drug cocktail to deter the effects of aging.

Dr. Gregory Fahy, an immunologist from Intervene Immune, led the trial, also known as TRIIM or Thymus Regeneration, Immunorestoration, and Insulin Mitigation.

Dr. Fahy and the other researchers aimed to prevent the thymus, a gland in the chest that fights against diseases and infections, from shrinking, as it naturally shrinks after puberty. Rejuvenating the thymus allows for the elderly and people with weaker immune systems to be able to fight off numerous diseases, such as pneumonia. For the trial, researchers obtained a sample of nine healthy men between the ages of 51 and 65. The subjects were given three types of drugs, including a recombinant human growth hormone (rhGH), dehydroepiandrosterone (DHEA) and metformin. Both DHEA and metformin are drugs used to fight or prevent diabetes.

To the surprise of the researchers, the studies revealed that the subjects regained two and a half years of biological age. With the use of blood samples and MRI technology, scientists discovered that seven of the participants restored thymus tissue and had an increased amount of blood-cells due to the use of the growth hormone, which stimulates the regeneration of thymic cells.

DHEA and metformin also seemingly intervened with the inflammation that leads to aging in the hypothalamus. In addition, six months after the study, six participants still showed signs of the treatment after providing final blood samples.

The study not only demonstrates that our biological clock can be slowed, but it also shows that it can also be reversed with beneficial side effects. However, the study had a rather small sample size and was poorly controlled. However, Dr. Fahy’s company, Intervene Immune, is planning on conducting a larger and more diverse study that will include different age groups, sexes, and ethnicities. Perhaps eternal life is not as impossible as people initially thought. With consistent research, it is becoming closer to reality.

1. G. Fahy, et al., Reversal of epigenetic aging and immunosenescent trends in humans.

Aging Cell, (2019). doi: 10.1111/acel.13028 2. Image retrieved from: pexels.com/photo/ light-sunset-people-water-34014/

Figure 1 The studies revealed that a human’s biological age can not only be slowed, but it can also be reversed, thereby improving many different areas of human health, such as the immune system.

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ULTRASOUND DELIVERY OF GENE THERAPY ACROSS THE BLOOD BRAIN BARRIER JORGE PINCAY ’20

Figure 1 The blood-brain-barrier is incredibly impermeable to pathogens and protects the brain from most infections.

Huntington’s disease (HD) is an autosomal dominant neurodegenerative disease that results in the degradation of nerve cells in the brain over time. This disease is the result of a DNA mutation -- a cytosine-adenine-guanine (CAG) trinucleotide repeat expansion-- that occurs in the gene that encodes for the huntingtin (Htt) protein. This repeat expansion causes a highly toxic form of the Htt protein to flood the brain, leading to brain atrophy and deterioration of a person’s mental and physical abilities. Currently there are no treatments to reverse or slow down the progression of this disease. However, gene therapies aimed to increase the expression of neurotrophic factors in the central nervous system (CNS) are currently undergoing testing in transgenic HD mouse models. These neurotrophic factors play an essential role in the health of the CNS by promoting growth, development, survival, and plasticity of neurons associated with motor function.

The current method for the delivery of this therapeutic is direct delivery. Neurotrophic factors encapsulated in a liposome complex are injected directly into the brain using a needle. However, the invasiveness of this procedure poses the risk of neurological damage, bleeding, and infection. A group of scientists from Chang Gung University and National Tsing Hua University recently developed a

new, less invasive form of delivery of a neurotrophic factor called gilial cell line-derived neurotrophic factor (GDNF) in order to avoid the risks associated with direct injection. This novel method involves the use of focused ultrasound (FUS) in the presence of microbubbles, small gas-filled bubbles that are injected intravenously, to open the blood-brain-barrier and effectively deliver GDNF. The results of this therapy, delivered by a combination of focused ultrasound and microbubbles have demonstrated the potential for this therapy to slow down or even reverse the effects of HD in transgenic mouse models. More specifically, the results of this therapy, delivered by ultrasound and microbubbles, have shown a decrease in the rates of apoptosis and oxidative stress along with increased protection of neurological cells.

The positive effects of this study have shown that there is a possibility of applying this form of therapy to human patients in the future. Furthermore, the results of this therapeutic administration have shown potential for revolutionary treatment of neurological disease.

1. C. Lin, et al., Focused ultrasound-induced blood brain-barrier opening enhanced vascular permeability for GDNF delivery in Huntington’s disease mouse model. Brain Stimulation 12, 1143-1150 (2019). doi:10.1016/j. brs.2019.04.011 2. Image retrieved from: commons.wikimedia. org/wiki/File:Blood_vessels_brain_english.jpg

ASSOCIATION BETWEEN COFFEE PRODUCTS AND BREAST CANCER RISK IN HONG KONG AYESHA AZEEM ’23 Coffee is one of the most popular drinks in the world, especially in Hong Kong. Researchers sought to investigate whether coffee contributed to breast cancer development in women. Though coffee was classified as a possible carcinogen in 1991 by the World Health Organization, evidence remains controversial. Additionally,

Figure 1 Coffee intake differs amongst the

different parts of the world, with the people of Western countries consuming more coffee products than those of Asia.

Western and Asian countries consume coffee different amounts of coffee. While studies conducted in the West involved drinking more than four cups of coffee every day, participants in Asian studies only drank one or more cups per day.

Chinese researchers Priscilla Ming Yi Lee and Wing Cheong Chan led a case-control study to examine the association between coffee and breast cancer risks in Hong Kong Chinese Women.

Participants selected to partake in the hospital-based study included 1,156 newly-diagnosed breast cancer patients and 1,013 controls. The breast cancer cases were predominantly older, overweight and had a family history of cancer compared to the controls.

About 20.7% and 17.7% of the cases and the controls were customary

ENVIRONMENT DEPENDENT DIETARY ADJUSTMENT BY INVASIVE AQUATIC SPECIES FATIN CHOWDHURY ’20 Recently, researchers at three Brazilian universities examined patterns of feeding behavior displayed by the Knodus moenkhausii fish invasive to Brazil. The researchers described a two-fold hypothesis.

Firstly, the species is expected to be non-specialist and opportunistic, feeding on whatever food source is most readily accessible. Secondly, resource abundance affects the nature of the trophic niche it resides in. Accordingly, flexibility in diet and occupied trophic niche were observed based on differing environmental conditions.

Specimen samples were collected from six streams located in the Paranaı´ba River’s sub-basin.

Three of the streams were positioned in locations that were predominantly used for pasture, while the other three streams were adjoined by river water influencing vegetation. The percentage cover of pasture and vegetation was determined via satellite imagery.

Stomach content data was collected in order to discern how selective the species behaved when feeding, while 2 to 5 grams of entire-specimen carbon and nitrogen based isotopic data, analyzed via mass spectrometry, were used to pinpoint relevant trophic levels. Food resource specimens were collected, including organic matter and benthic macroinvertebrates. Diet

coffee drinkers, respectively. Researchers experimented with both instant coffee and brewed coffee.

While there was no significant association demonstrated between habitual coffee drinking or the number of cups of coffee and breast cancer risk, there is a positive correlation between instant coffee consumption and the risk of breast cancer, especially among premenopausal women. This may be because instant coffees often contain less caffeine and more additives, including creamers, sugars, and hydrogenated and trans-saturated fats that may increase breast cancer risks.

Additionally, instant coffee consumers tend to have lower levels of high density lipoprotein (HDL) cholesterol. HDL is considered “good” cholesterol because it transports the toxic forms of cholesterol to the liver where it can be broken down and removed from the body. Thus, low levels of HDL may lead to buildup of toxic cholesterol in the bloodstream and development of breast cancer.

Interestingly, researchers discovered that the duration and

number of cups of brewed coffee drunk had a negative association with breast cancer risk among Hong Kong Chinese women. Specifically, women who drank more than one cup of brewed coffee per day for more than ten years had a 60% decreased risk of breast cancer. This may be because a high level of caffeine intake can lower estrogen levels.

Lee and Chan’s study revealed that in Hong Kong, breast cancer in women was inversely associated with brewed coffee consumption but positively correlated with instant coffee intake. Other types of coffee products should be further studied to completely assess the role of coffee products in breast cancer development. Furthermore, it should be noted that the results of this study may not apply to women living in Western countries, as coffee consumption is variable across the world.

patterns were detailed in part by utilizing a feeding index equation which incorporated frequency of a food’s appearance in samples, and other factors.

The researchers employed linear regression when analyzing stomach content data, while the isotopic data of fish from pasture and natural cover proximate areas of river were examined via generalized linear mixed models. Trophic position of the fish was found via a calculation based model, while t-test based statistical analysis was used to analyze whether there was a significant difference in trophic level according to river area. The data confirmed K. moenkhausii as an omnivorous species. Pasture adjacent stream data indicated that macroinvertebrates consumed by the fish were found in the stomach at levels proportional to their natural distribution. The researchers found that the fish’s diet was dominated by non-predator macroinver-

tebrates in streams near abundant natural cover. The researchers asserted that these findings indicate how a species, in response to changing aspects of a habitat, can be flexible in exploiting environmental resources and adjusting their trophic niche occupation.

1. P. Lee, et al., Associations between coffee products and breast cancer risk: a case-control study in Hong Kong Chinese women. Scientific Reports, (2019). doi: 10.1038/s41598-01949205-x 2. Image retrieved from: pexels.com/photo/ aroma-aromatic-art-artistic-434213/

Figure 1 Knodus moenkhausii is a fish

species that invades Brazil, including its Paranai´ba River. In the detailed research article, researchers explain how the fish’s diet and related environmental conditions were investigated.

1. D.R. de Carvalho, et al., Stable isotopes and stomach content analyses indicate omnivorous habits and opportunistic feeding behavior of an invasive fish. Aquatic Ecology 53, 365–381 (2019). doi: 10.1007/s10452-019-09695-3.

2. Image retrieved from: unsplash.com/photos/JZ4GNQzNxTU

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GLUTAMATE RECEPTOR GLR-3 ENCODES FOR EVOLUTIONARY COLD-SENSING RECEPTOR

CHANGES IN RETINAL CHROMATIN ALLOW ANIMALS TO BE NOCTURNAL

SIMRAN KAUR ’20

MARIAM MALIK ’22

Figure 1 Glutamate receptor GLR-3 is important in responding to cold temperatures.

The capacity to detect cold temperatures is essential for many living organisms because cold temperatures can cause detrimental effects like severe soft-tissue damage and hypothermia. Some organisms have evolved the presence of thermoreceptors, which are specific nerve endings that are sensitive to changes in temperature and exist in the skin, skeletal muscle, and the hypothalamus.

Thermoreceptors relay electrical signals to the central nervous system (CNS). Glutamate receptors can create disturbances in the CNS if defected, causing neurological conditions ranging from epilepsy to neurodegenerative diseases. The researchers in this study used this notion to determine the function of GLR-3, a glutamate receptor, in the sensation of cold temperatures in the model organism C. elegans. It was already known that cold receptors are abundant in the intestine of C. elegans, and physiologically respond to cold by releasing calcium intracellularly.

Researchers designed an activity-based and unbiased genetic screen with mutant C. elegans, and isolated a specific mutant allele of the GLR-3 gene that encodes for a glutamate receptor. Wild type and

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mutant species were used for the experiment, the latter is defective in the gene encoding for the GLR-3 gene. A real-time PCR thermocycler was used to rapidly cool and heat the organisms, in addition to amplifying cDNA. Standard calcium imaging was performed using fluorescent microscopy to detect intestinal calcium levels.

Results showed that while wild-type nematodes would release intestinal calcium in response to temperature changes, mutant C. elegans did not. Further experiments showed that cooling caused normal C. elegans to swim away to evade the cold, whereas the individuals lacking cold receptors did not. Mutated C. elegans displayed a significant deficiency in this evolutionary behavioral response. This experiment highlights the evolutionary role of GLR-3 in the detection and avoidance of cold temperatures in numerous organisms. Nevertheless, future studies are necessary to determine the role of transduction channels apart from GLR-3 in cooling-evoked calcium release.

1. J. Gong, et al., A cold-sensing receptor encoded by a glutamate receptor gene. CellPress 178, (2019). doi: 10.1016/j.cell.2019.07.034 2. Image retrieved from: pexels.com/photos/989946/pexels-photo-989946.jpeg

Night vision allows nocturnal animals to be active at nighttime and sleep when the sun is out, while diurnal animals are active during the day and sleep at night. However, when both diurnal and nocturnal animals are born, their ocular abilities are equal until a change in the cells of the eye occurs, allowing the animal to see in the dark. Through mathematics, Sungrim Seirin-Lee, Associate Professor, and Hiroshi Ochiai, lecturer at the University of Hiroshima in Japan, discovered that it is the chromatin’s structure in the cells of the eye that cause this change.

First, the team of researchers observed the differences in nocturnal and diurnal mice, finding that there was a drastic difference in nuclear architecture around the retina between the two types. In nocturnal animals, DNA is in the middle of the nucleus. Heterochromatin, a type of DNA, usually remains on the nuclear envelope or on the roof of the nucleus. Lee and Ochiai, however, found that the heterochromatin can move if the nucleus changes shape. To further understand how the chromatin can move, researchers used a form of modeling called phase-field modeling. Scientists took numerous factors into account to formulate an equation, such as defining the free energy functions for the nucleus, chromosome territories, heterochromatin and chromocenters (CCs), and each composite’s individual volume. Another

important aspect of the equation was to be able to manipulate the nuclear deformation, due to the fact that the nucleus deforming occurs independently of chromatin states.

The team calculated the degree of deformation by the total area deviated from the circle divided by the area of the nucleus times 100.

Furthermore, when observing heterochromatin in mice’s eyes, they discovered that conditional architecture caused deformation, which resulted in the inversion of the architecture of the nucleus. More specifically, two proteins are removed, allowing heterochromatin to move.

To put their model to test, Seirin-Lee and Ochiai used neural stem cells, the most similar option to retinal cells. They treated cells with lamin B receptor (LBR) and lamins A/C (LamA/C), the proteins that keep heterochromatin on the nuclear envelope or at the top of the nucleus. Deformation of the nucleus stopped and a rise in chromatin clusters was seen, while nuclear architecture did not complete inversion. Both Seirin-Lee and Ochiai hope to conduct further research on if this revelation applies to all nocturnal mammals, and if there is even the possibility that humans could possess these structures by nuclear deformation.

1. S.S. Lee, et al., Role of dynamic nuclear deformation on genomic architecture reorganization. PLOS Computational Biology 15, 9 (2019). doi: 10.1371/journal.pcbi.1007289 2. Image received from: peakpx.com/wallpaper/160/391/651/lemur-red-ruffed-portraithead-fur-wallpaper-preview.jpg

Figure 1 Researchers at the University of Hiroshima discovered that nocturnal animals, such as lynxes, bats, and owls, are able to see at night because of changes in their retinal DNA.

Targeting DNA Repair to Combat Cancer NATALIE LO ’21 Introduction While biopsy, immunotherapy, and cisplatin are words that may be unfamiliar to the public, they are part of the everyday vocabulary of cancer patients. One of the leading causes of death in the United States, cancer took the lives of 599,108 Americans in 2017 (1). “Almost no one thought I would survive the initial cancer for six months, but here I am 31 years later,” says Sharolyn, who was diagnosed with ovarian cancer in 1983 (2). With the help of gynecologic oncologists, surgery, and chemotherapy, she was able to extend life expectancy. Behind these physicians and treatments are decades of basic and translational science research that have paved the path for decreasing global cancer death rates.

A major characteristic of cancer is incorrect replication of deoxyribonucleic acid (DNA), which leads to mutations.

DNA is a material essential for all living things and carries genetic information that is passed down from one generation to the next. Every time a single cell divides, the cell’s nucleus makes copies of 6 billion base pairs of DNA (3). This process is tightly regulated by the replisome, a complex of different proteins that ensures that the billions of bases in every genome are accurately replicated. Nonetheless, during the process of replication, mistakes can be made and many DNA lesions, such as base deletions or base alteration, can accumulate.

In order to maintain the genome, the DNA damage response (DDR) detects DNA lesions to promote cell cycle arrest and DNA repair (4). Furthermore, if this DNA repair is not sufficient to prevent genomic instability, the DDR can also set off a chain of events that lead to apoptosis, programmed cell death, or senescence, which is a state of cell dormancy (4). One of the consequences of accumulated DNA damage is uncontrolled cell growth and genetic instability, which are hallmarks of cancer. This basic process of DNA replication and DNA damage repair has become a growing field of interest as researchers search for methods to prevent or cure this prevalent disease.

While DNA replication is a highly controlled process that has allowed for reproduction and the passing of genes to thousands of generations of organisms, there are both environmental and endogenous causes of replication stress that lead to DNA lesion formation. An example of an environmental source of damage is UV radiation, which causes adjacent thymine bases to link, forming a thymine dimer (5).

These linked bases increase the likelihood of DNA polymerase pairing an incorrect nucleotide to the DNA templates strand during replication, leading to mutations in the DNA sequence.

Endogenous sources of replication error include insufficient concentration of substrates necessary for replication in the cell nucleus, which causes replication to stall; such substrates include histones, which are the proteins that DNA winds around as it condenses into chromatin, and deoxyribonucleotide triphosphates (dNTPs), the bases that make up DNA (6).

Replication stress causes the replication fork to slow down, leading to an uncoupling of the helicase and DNA polymerase,

which in turn leads to the formation of single-stranded breaks (SSBs), the signal to activate the DDR (5).

Figure 1 Different types of DNA lesions lead to different DDR repair pathways.

Regulation of the Cell Cycle The cell cycle is composed of a series of processes during which a cell divides. It is split into two stages -- interphase (composed of G1, S, and G2) and the mitotic (M) phase. During interphase, the cell grows and produces more organelles. In the S phase, it duplicates its DNA in preparation for the mitotic phase, a phase in which it splits into two cells.

These processes are highly controlled by cell cycle checkpoints spread throughout interphase to ensure that each phase is carried to completion without issues. These checkpoints include the G1 checkpoint, the intra-S phase checkpoint, and the G2/M checkpoint. The G1 checkpoint ensures that the cell has grown to the proper size and that there is no damage to the DNA prior to replication (4). In the presence of DNA damage, the intra-S phase checkpoint stalls the replication fork progression to allow time for DNA repair; if DNA damage is present, Ataxia Telangiectasia and Rad3-related (ATR) kinase detects the damage and activates Checkpoint Kinase 1 (CHK1), which phosphorylates downstream proteins to be recruited to the stalled fork (4,7,6). Finally, the G2/M checkpoint ensures the proper replication of both sets of DNA prior to cell division (1). The DNA repair pathway through which the DNA Damage Response progresses depends on the phase of the cell cycle during which these DNA lesions occur (7,8).

DDR Promoted Repair Each DNA lesion initiates a specific pathway through which the DDR promotes repair. Some DNA repair processes, such as mismatch repair (MMR), are coupled with the replisome, allowing repair to take place concurrently with replication via the removal of incorrect nucleotide basespolymerases (6). Small changes to DNA that do not distort the helical structure may be caused by oxidation, deamination (or removal of the amino group), and methylation (or addition of a methyl group). Such non-bulky base damage is repaired by the base

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excision repair (BER) pathway (9,10). Firstly, DNA glycosylases recognize the damaged base and remove the base at the nucleotide, leaving an abasic site. Short patch or long patch BER subsequently fills in the abasic site with the proper base.

Bulkier base damage -- such thymine dimers caused by UV radiation -- is removed by nucleotide excision repair (6).

Some DNA lesions block the polymerase from progressing through the template DNA. Damage to the bases in the template, for example, causes DNA polymerase to stall.

Rather than slowing down replication to fix these lesions, another possible pathway skips these lesions with translesion synthesis (TLS) DNA polymerase. In the lagging template strand, DNA polymerase generally does not stall. Replication of the lagging strand is already discontinuous, creating gaps that must be ligated together. Primase is able to skip over the lesions and make a new primer to continue synthesis. After replication, the gaps are filled with translesion bypass polymerases. In contrast replication of the leading strand is continuous. Lesions, therefore, block the progression of DNA polymerase, which leads to an uncoupling. On the other hand, TLS polymerase is able to skip these lesions because it has a larger active site that can accommodate bulkier nucleotides (6). However, this repair pathway may lead to more mutations as TLS is more error prone than DNA polymerase and does not proofread while synthesizing.

Figure 2 Overview of the cell cycle and the its checkpoints.

The last type of repair is for double stranded breaks (DSBs). There are two pathways: homologous recombination (HR) or non-homologous end-joining (NHEJ). In homologous recombination, the replisome utilizes the homologous sister chromatid as a template for new DNA to repair the break.

First, the site of the DSB is resected to expose the 3’ end of the DNA molecule. Recombinases then bind to this site, allowing invasion into the other sister chromatid, creating a cross-like structure composed of the four nucleotide strands. This structure is called a Holliday junction (10). In NHEJ, rather than utilizing a sister chromatid, the two ends of the DSB are ligated together. A Ku protein dimer complex consisting of Ku70 and Ku80 slides onto the ends of the DSB and forms a protein complex with DNA-PKs, which eventually leads to ligation by XRCC4 and Ligase IV (11). Compared to HR, which has less mistakes because it uses the sister chromatid as a template, NHEJ is more error prone and could result in more mutations at the break site.

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Figure 3 A new generation of anticancer drugs targets inherit DDR deficiencies.

Targeting DDR in Cancer Therapies The study of how each of these DNA lesions is repaired plays an important role in understanding cancer, a disease that stems from insufficient activation of DNA repair pathways. A major hallmark of cancer is genomic instability driven by errors in replication, resulting in changes to the genome (12).

The DNA Damage Response helps maintain genomic integrity in spite of endogenous and exogenous replication stress; therefore, researchers have been studying its mechanisms to determine if drugs can be utilized to specifically target cancer cells through these different repair pathways.

One strategy is to force the cell into mitotic catastrophe and eventually cell death by using drugs to force the cancer cells to bypass the checkpoints to enter mitosis with DNA damage (13). Mitotic catastrophe is a bona fide mechanism activated in the cell cycle as an oncosuppressor by promoting cell death or senescence when the cell senses mitotic failure.

Although this process is still not clearly understood, it can potentially be exploited in cancer prevention and treatments.

This pathway can be induced by treatments that damage DNA or prevent mitosis from progressing, such as the use of agents that target the microtubules needed to separate chromosomes.

However, many of the current agents used contain side effects and are cancer cell-specific. For example, Taxol, which was approved for use in 1995, targets the formation of microtubules but also affects neuropathy (13,14). While these drugs are helpful in combating cancer, they are not specific and also attack healthy cells, leading to harmful side effects.

On the other hand, scientists have made advances that have exploited defects in DDR to specifically target cancer cells. In chemotherapy and radiotherapy, scientists have exploited defects in the DDR to artificially activate its repair pathways. For example, to target ovarian cancers, platinum salts such as carboplatin and cisplatin are used to cause inter-and intrastrand crosslinks that are normally repaired by homologous recombination and NER. These platinum salts are especially effective against ovarian tumors that have defects in HR (11).

An alternative to chemotherapy is a new generation of drugs that targets parts of the DDR. An example of this is the case of topoisomerase inhibitors such as camptothecin and irinotecan, which prevent the rejoining of the DNA backbone during DNA replications, leading to DNA breaks in the cancer cells (12). These drugs utilize a method called synthetic lethality, which takes advantage of the inherent DDR deficiency found within cancer cells, producing a new class of anticancer drugs. Since a cancer cell has mutations in one of the DDR pathways, it relies on other DDR pathways for survival; this

dependence can be exploited in cancer treatments with drugs that inhibit important substrates needed in these alternative pathways (12). Furthermore, because this form of treatment specifically targets a gene, it is lethal only to mutated cancer cells; therefore, it only targets cancer cells and spares the normal cells (12). The first clinically approved anticancer drug to utilize this approach is Olaparib, a PARP1 inhibitor (15). This drug is extremely toxic to BRCA1 or BRCA2 deficient cells, which are commonly found in breast and ovarian cancers and highly dependent on PARP1 (15,16,17).

Another class of drugs target the ataxia telangiectasia mutated (ATM) response, which is the signal for downstream checkpoint activators and utilized in homologous recombination. Researchers have shown that synthetic lethality can be used for ATM-deficient cells, which are sensitive to PARP inhibitors. The many parts of the DDR can be targeted in synthetic lethality based anticancer treatments; ATM inhibitors, specifically, are potential anticancer agent because they block HR repair and especially because they are able to bypass the blood-brain barrier (16,17,18). ATR inhibitors targets the ATR kinase which, when activated, helps protect stalled forks by phosphorylating CHK1. Despite the potential of this form of treatment, current research on ATM signaling and its role in DDR is not as robust as that on PARP and ATR. While PARP inhibitors have only been recently developed drugs for anticancer therapy, there is still much research to be done: patients with advanced cancers have already acquired resistance to this form of treatment (15). Researchers have discovered several possible causes, such as an inactivation of DNA repair proteins which restores homologous recombination and a loss of other proteins needed to protect the fork. Another form of resistance derives from a frameshift mutation which restores BRCA function, negating the effect of PARP inhibitors. (19) Potential ways to overcome this resistance includes combining PARP inhibitors with other DDR targeting agents. Lord and Ashworth(2012) suggest that areas of research still needed to further PARP inhibitors’ effectiveness include studying the mechanism of PARP inhibition to identify and develop drugs specific to patients, to combat drug resistance, and to optimize combination therapy, which utilizes different combinations of drugs in addition to PARP inhibitors (15).

Research everyday is gradually expanding to discover and improve on anticancer drugs that can be used to target the DNA Damage Response, and each day science is getting closer to saving the many patients who receive devastating cancer diagnoses.

Figure 4 Synthetic lethality leads to a rising new generation of anticancer drugs that targets inherit DDR deficiencies found in cancer cells.

Conclusion The American Cancer Society estimates that in 2019 alone, 22,530 women like Sharolyn will be diagnosed with ovarian cancer (21). One patient who was examined at Memorial Sloan Kettering Cancer Center had less than a 10 percent chance for two-year survival when she was diagnosed with ovarian cancer (22). Many survivors have fought their cancers with surgery, continuously improving anticancer drugs. One cancer survivor states that she is “thankful for the cancer research that developed the chemotherapy drugs that [her] body reacted so well to. To [her, survival] feels like a miracle, definitely worth all the pain, nausea, and hair loss” (22). The development of these drugs are possible because of research on DNA replication, cell cycle processes and cancer progression.

While it is a conserved process that has empowered eukaryotic reproduction for many millennia, DNA replication can potentially result in many mistakes in the genome; the activation of these many DNA repair pathways, however, promotes the maintenance of genomic stability. Nonetheless, many parts of these repair pathways remain unknown; the numerous research groups and scientists that are elucidating the roles of various proteins and other molecules that play roles in the DDR are bringing us closer to understanding this complex process. Furthermore, such basic research brings scientists in translational research closer to developing more drugs and anticancer treatments, improving the odds against the disease that takes the lives of thousands every year.

References

1. M. Heron, Deaths: leading causes for 2017. National Vital Statistics Reports 68, (2019).

2. Sharolyn’s cancer survivor story. Centers for Disease Control and Prevention.

3. Human genome project FAQ. National Human Genome Research Institute.

4. M. O’Connor, Targeting the DNA damage response in cancer. Molecular Cell 60, 547-560 (2015). doi: 10.1016/j.molcel.2015.10.040.

5. J. Forment & M. O’Connor, Targeting the replication stress response in cancer.

Pharmacology & Therapeutics 188, 155-167 (2018).

6. D. Cortez, Replication-coupled DNA repair. Molecular Cell 74, 866-876 (2019).

7. K. Barnum and M. O’Connell, Cell cycle regulation by checkpoints. Methods in Molecular Biology 1170, (2017). doi:10.1007/978-1-4939-0888-2_2.

8. D. Iyer and N. Rhind, The intra-s checkpoint responses to DNA damage. Genes 8, 74 (2017). doi: 10.3390/genes8020074.

9. H. Krokan and M. Bjoras, Base excision repair. Cold Spring Harbor Perspectives in Biology 5, a012583 (2013). doi: 10.1101/cshperspect.a012583.

10. X. Li and W. Heyer. Homologous recombination in DNA repair and DNA damage tolerance. Cell Res 18, 99-113 (2008). doi: 10.1038/cr.2008.1.

11. M. Lieber, The mechanism of human nonhomologous DNA end joining. The Journal of Biological Chemistry 283, 1-5 (2008). doi: 10.1074/jbc.R700039200.

12. C. Lord and A. Ashworth, The DNA damage response and cancer therapy.

Nature 481, 287-294 (2012). doi: 10.1038/nature10760.

13. R. Visconti, R. Monica and D. Grieco, Cell cycle checkpoint in cancer: a therapeutically targetable double-edged sword. Journal of Experimental & Clinical Cancer Research 35, 153 (2016). doi: 10.1186/s13046-016-0433-9.

14. M. McGee, Targeting the mitotic catastrophe signaling pathway in cancer.

Mediators Inflamm. (2015). doi: 10.1155/2015/146282.

15. C. Lord and A. Ashworth, PARP inhibitors: Synthetic lethality in the clinic.

Science 355, 1152-1158 (2017). doi: 10.1126/science.aam7344.

16. S. Jackson and J. Bartek, The DNA-damage response in human biology and disease. Nature 461, 1071-1078 (2009). doi: 10.1038/nature08467.

17. M. Shaheen, et al., Synthetic lethality: Exploiting the addiction of cancer to DNA repair. Blood 117, 6074-6082 (2011).

18. M. Jin and D. Oh, ATM in DNA repair in cancer. Pharmacology & Therapeutics (2019). doi: j.pharmthera.2019.07.002.

19. A. Michom, C. Aversa and J. Lopez, Dancing with the DNA damage response: Next-generation anti-cancer therapeutic strategies. Therapeutics Advances in Medical Oncology 10, 1-10 (2018).

20. A. Motegi, et al., Aberrations in DNA repair pathways in cancer and therapeutic significances. Seminars in Cancer Biology 58, 29-46 (2019).

21. Key statistics for ovarian cancer. American Cancer Society, (2019).

22. Thankful for ovarian cancer research. National Ovarian Cancer Coalition.

Image retrieved from: 1. ars.els-cdn.com/content/image/1-s2.0-S109727651500831X-gr1_lrg.jpg 2. ars.els-cdn.com/content/image/1-s2.0-S109727651500831X-gr1_lrg.jpg 3. medium.com/@CRUKresearch/olaparib-realising-the-promise-of-synthetic-lethality-f5f61d84ad99 4. https://commons.wikimedia.org/wiki/File:Olaparib.svg

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Dr. Thomas Hemmick: His Life and Research JOHN MCMENIMON ’20 Many students remember Dr. Tom Hemmick as the introductory classical physics professor who makes funny noises when describing friction and potential energy—the professor who speaks in exaggerated tones and is prone to wild tangents.

Apart from his teaching, however, Professor Hemmick is an experimental nuclear physicist whose current research on ion backflow contributes to sPHENIX, an experiment headed by Brookhaven National Lab that is designed to study quark-gluon plasma and has the potential to revolutionize high-energy physics. Hemmick leads a team of post-doctoral, graduate, and undergraduate students that spearheads the construction of the experiment’s Time Projection Chamber (TPC). His previous research included the PHENIX experiment, the predecessor to sPHENIX. I worked under Hemmick for a year as a research assistant. During my tenure, I often found myself pondering how he got to his current standing. We sat down in his office over the course of two days and talked about his life and research.

Part One: Hemmick’s Path to Nuclear Physics Akin to the lair of a genius supervillain, Dr. Hemmick’s lab, a series of rooms tucked away in the corner of the physics building basement, is home to a very independent-minded research group. It is only in recent weeks that he has established a set schedule regarding when certain tasks around the lab are to be worked upon; in the past, the lab was a revolving door throughout the week, and student research assistants did whatever the circumstances of that particular day demanded.

The jobs, which range from building the tensioner systems that apply critical materials onto the TPC’s mandrels to designing and testing circuit boards to grunt work like painting beams or decluttering the wrenches and wires strewn about,

are worked upon by undergraduates, graduate students, and post-docs alike. Hemmick’s philosophy – that everybody can contribute something – is apparent.

Despite his success, Hemmick claims that his career path was all an accident. “When I was in high school, I was an old-fashioned phrase, ‘a ne’er do well,’ and I never studied for anything. But science and math were always easy, so I got very good grades in science and math; everything else was sort of lousy. I got a D in an English class because I wrote four words for the term paper: ‘not worth my time.’ One high school teacher apparently thought she could get to me by saying, ‘Well, you could earn an A in this class if you tried.’ So then I got an A there.”

His first experience studying didn’t occur until his last semester of high school when a girl invited him to her house to study for their AP Calculus exam. “I didn’t have real direction.

My father thought I should be an engineer, but I didn’t come from a well-to-do family, and my family couldn’t afford college. I had to have a scholarship somewhere, and I got a [full] scholarship to Towson University.” Hemmick had decided to pursue physics with the goal of attending graduate school afterwards. He graduated with a 3.97 GPA as one of the three valedictorians in his class.

During his undergraduate years, Dr. Hemmick worked in the optics lab of Jacob Huang, the professor who taught his freshman physics class and one of only two researchers in the physics department at Towson. “The way he did research was very interesting. He was into holography, so he would get grants to get all kinds of equipment. He would read literature, and every single new invention of a new kind of anything that anybody ever invented, we would make too. Even though none of these new ideas were entirely his, every kind of holography

“

...THROUGH A SCREW UP I GOT OVER MY FEAR OF MESSING WITH STUFF MYSELF. that has ever been done, as soon as it came out, we did it too.

That’s what happened in that lab for several years, and that’s also where – through a screw up – I got over my fear of messing with stuff myself.” There was a spatial filter in the lab that was designed to cut down on the interference produced by the lenses when a laser beam was directed through them, a piece of equipment into which he was told specifically not to bump.

Of course, Hemmick bumped into it one day and knocked it out of alignment. Rather than inform his professor of what he had done, he attempted to fix it before anybody else noticed.

He messed with it to no avail for hours before he realized that the issue would be simpler if the filter were on axes. It worked.

“I suddenly aligned it. Immediately there were two of them in the setup, and I took the other one apart and realigned that one. It was better than it was before, and that’s when I got over my fear of messing with stuff.” Nonetheless, he never told his professor about the incident out of embarrassment.

Dr. Hemmick’s first paper, a piece on holographic interferometry, was published during his time in that lab -- once again, as the result of a mere accident. Holographic interferometry is a means to understand how an object has moved using an interference pattern reconstructed from two holographic exposures taken before and after the movement; any material deformations appear as shifts in the white stripes of the interference pattern. The challenge that Huang’s lab hoped to overcome was posed by a metal piece that had been bent, cracked, and smoothed over so that the crack was only visible on its backside. They had failed to see the crack when the metal was bent again, so Hemmick was tasked with figuring out a novel approach. “I thought we should try to make the thing thermally expand,” he says. “We could hold something hot behind it and let it expand and then see if the expansion was different in different locations. Because there was a crack, the heat would go in funny manners from one place to another, and so the metal wouldn’t expand uniformly. I went down to the machinist and explained what I wanted – something that would grab one end of the bar and hold it steady so that I could take my two exposures. Now, through miscommunication or whatever, he somehow made it so that the apparatus didn’t just hold one end of the bar but both ends of the bar. Normally, the piece of metal would just expand if it were held at one end, but now it had to buckle. And when it buckled, the place where it buckled more was where there should be a crack. That was my first paper, and it was published in the American Journal of Physics.”

Due to his experiences in Huang’s lab, Hemmick decid-

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ed to pursue a PhD in optics. He had been accepted to Rochester’s graduate school, which offered PhD programs in both physics and optics. In order to increase its appeal, Rochester flew out prospective students on weekends to the campus to show them around the facilities. That Friday, Hemmick attended a beer weekly seminar for first-year physics graduate students featuring faculty talks, pizza, and beer- given by Doug Cline, who worked in the nuclear structures lab on campus.

What happened there had immense, unintended consequences. “After the Friday afternoon seminar, I walked up to [Cline] and said that I thought he gave a very interesting talk, and he shook my hand and took my name. That changed my career. I had acceptances to both the physics and optics departments at Rochester. Despite the fact that I was certain that I was going to study optics my whole life, back at Towson, Huang encouraged me to keep some flexibility. So I accepted physics. When I arrived there, I was a research assistant at [Cline’s] nuclear lab. I thought to myself, ‘Oh well, it would be impolite to tell him that I’m doing optics,’ so I’ll go over [to nuclear physics] for a little while, and then I’ll get back. Dabbling in it for a little while, I’m pushing forty years, and I haven’t gotten back to optics yet. That’s how I wound up in nuclear physics.”

Part Two: Hemmick’s Research in Nuclear Physics According to the Standard Model of particle physics, which explains three of the four fundamental forces, the electromagnetic, strong, and weak forces are mediated by the exchange of force carrier particles. Gluons are the strong force carriers and keep the atomic nucleus from blowing itself apart by overriding the repulsive positively charged protons. In addition to the force carriers, the Standard Model includes six types of quarks: top, bottom, up, down, strange, and charm.

Quarks are the building blocks of hadrons, which are divided into mesons and baryons, of which protons and neutrons are the most notable examples. Quarks have fractional electric charges and always come in multiples, never by themselves, and it is these unique combinations of the six quark types that make up the different hadrons and give them their total electric charge. If one were to melt an atomic nucleus, one would find quarks and gluons, which is exactly what sPHENIX intends to do through the intense heat and multitudinous particles produced by many Au-Au collisions and p-p collisions.

A way to interpret matter phase transitions is that the addition of heat leads to a new level of disassembly. Solids are tight and unmoving, liquids move within a set volume, and gases move in a variable volume. Plasma reduces an atom to

a nucleus and free electrons, yet the nucleons are still bound together, and even those can be broken apart if a temperature a million times greater than what produces plasma is applied.

Moreover, the protons and neutrons themselves can be further melted to produce quark-gluon plasma (QGP). QGP behaves more like a liquid than plasma because the quarks interact with one another and give the system a surface tension.

Hemmick implies that an analogy between the study of QGP can be drawn to the development of quantum mechanics.

Quantum mechanics was developed when statistical mechanics was applied to the electromagnetic force. Statistical mechanics has the ability to ignore the noise produced by the random and arbitrary behaviors of individual particles because it looks at how the entire system behaves on average. Similarly, the study of QGP is the application of statistical mechanics to the strong force. “The idea is [to] measure first, figure out what QGP is like, and then see what wild ideas you need to put into theory which are only at the fundamental level. Nobody has to say, ‘Well, you didn’t really understand a pion to begin with very well, so learning more about the pion hasn’t taught you anything.’ But freeing yourself from the quantized bound states of particles you can’t understand and instead going down to the basest level of the statistical mechanics may be revealing.”

Since nobody expected quantum mechanics to emerge, there is an anxious anticipation and eagerness as to what these present studies will reveal. Rather than impose conjectures on nature and then see what is out there, Hemmick’s philosophy is to “let nature do the teaching by using the fact that statistical mechanics integrates over all the irrelevancies, and all you have to do is have a fundamental mechanism of what to put in your partition function.” Hemmick claims that although this approach “pushes the details away,” it is in fact the neglection of such details that is revealing. It is this that sPHENIX hopes to accomplish, and it is to this effort that Hemmick contributes to through his construction of the sPHENIX TPC. The TPC is a tracker that uses the property that charged particles move in helical spirals when placed in a magnetic field. Thus, by measuring the radius of curvature of the spiral, the momentum of the particle is determined which is easier said than done. “You need to detect a collection of positions all in a row. You need to figure out which set of positions go with one another because there will be thousands of charged particles each collision…because it could be, given a momentum, a pion at a higher velocity or a proton at a lower velocity that give you the same momentum, and you don’t know what the particle is just from the curvature alone.” In addition to the large number of particles, each of their tracks will decay by ionizing other particles or interacting with nuclei or bremsstrahlung radiation away. To minimize these occurrences, the TPC is filled with a molecular gas. The gas helps detect the charged particles because the particles will ionize a small portion of the gas and produce fifty electrons per centimeter.

That is not a lot at all. “For that reason, you have to find a mechanism by which you amplify those fifty before you send them into a wire and detect them to make them a completely measurable signal that is large compared to the noise and then everything else will happen.”

Here is how the TPC works. As electrons in an electric field collide with gas molecules, the rate of bumps acts as a

backwards velocity-dependent force that equates with the average forward electric force to give drift velocity. That only works if the electrons do not have enough energy to ionize the gas molecules. If they do, however, then the collisions will produce an ever-increasing number of electrons in an avalanche.

More electrons will exit than enter, which produces a measurable signal detected on a grid of wires. Now, the drift velocity is slow relative to the speed of the electronics employed, so the time difference between when the original particle came in from somewhere else to when the electron reached the end of the drift chamber can be measured, and that gives the time dimension. All of this ionization also produces positive ions, which leave image charges on the wires; using a grid system of pixels and electrodes known as PAD chambers, the charge location can be specified. Since the positive ions can interfere with subsequent trajectories, a gating grid is operated to control the ion flow by cutting off the positive ions. The PADs give the x and y spatial dimensions. Stagger the PAD chambers, and you have a three-dimensional TPC. sPHENIX will collect its data in the coming years. After that, the future is uncertain, and that is a consequence of the nature of high energy physics. In the past, smaller experiments were conducted at low energies, and there was no shortage of possible tests. If one could think of it, one could test it. But since more complicated experiments at higher energies require larger facilities, the economics of the science have become pressing. “As energies go up and experiments become more complicated, it is beholden on the experiment to measure with some sort of completeness. You really want to measure everything. So sPHENIX is basically targeting the things that have not been possible yet. And so it is entirely targeted at the things that are rare because all the things that are not rare [have] been measured for nearly twenty years now...only rare stuff is left.” The hope is that the Electron Ion Collider (EIC) will be built at RHIC and become the new hub of high energy physics. Hemmick contemplated the future of the field. “There will be one more round of heavy ion experiments at CERN at a minimum that will finish up around the time the EIC might turn on, and there will probably be somebody who proposes what to do subsequently even though it’s not really clear what to do subsequently.”

It is once again time for nature to do the teaching. Major experiments like sPHENIX have millions of triggers that account for all that occurs inside the detectors. Within the mountains of collected data, there could lie new physics and new theories to be tested. “It’s sort of the benefit of the experiments that you’ve made so far…by recording everything, most of what you could ask has already been recorded. There are plenty of times when a theorist comes up with a brand new concept, and the data’s already [been] recorded -- you just need to analyze it with respect to that concept.”

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Newly Discovered Tyrannosaurs Diversify the Dynasty BY: TRAVIS CUTTER ’22

Figure 1 An artist’s rendering of how Suskityrannus hazelae may have looked. Image credit: Andrey Atuchin.

Introduction

In the modern day, an animal referred to as the “tyrant lizard king,” is almost guaranteed to conjure an image of a creature unimaginable in its size and power. In this regard, Tyrannosaurus rex certainly lives up to its name being one of the largest terrestrial carnivores in the planet’s history. As such, it has become one of the most iconic dinosaurs in the popular conscious. And yet, many relatives of T. rex defy the expectations regarding what it means to be a tyrannosaur. These animals, many only recently discovered,would not be considered monstrous in the same way as their larger descendants, but they are no less awe-inspiring as a predator to be reckoned with.

Moros intrepidus Adhering to a basic principle of ecology, predators are never as great in number as their prey and this is especially true of the tyrannosaurs. Because of this, there is a large gap in the evolutionary record of North American tyrannosaurs.

Looking at the various genera chronologically, after Stokeosaurus, which lived during the Late Jurassic about 150 million years ago, there is not another known member of the clade until the Late Cretaceous animal Lythronax, which lived about 80 million years ago. That is a 70 million year void in the lineage of one of the most well-known apex predators (Tyrannosaurus lived about 66 million years ago, just before the extinction event that killed the dinosaurs occurred). However, this changed with the discovery of Moros intrepidus, which lived about 95 million years ago, making it the oldest North American Cretaceous tyrannosauroid. Moros precedes various apex predators, such as Tyrannosaurus, Albertosaurus, and Gorgosaurus, by 20 to 30 million years. Furthermore, it is significantly smaller than those animals, and is much more in agreement with what the popular conscious would erroneously consider a raptor. Indeed, the animal is considered an “intermediate tyrannosauroid,” most closely related to other small tyrannosaurs living in modern-day Asia from the mid-Cretaceous, which was still prior to the age of the true tyrannosaurids.

Despite the fact that the only bones discovered from this animal are from the legs and teeth, there are many indications that this animal is a tyrannosaur. Notably, the teeth possessed ridges and serrations characteristic of other tyrannosaurids.

These characteristics in Moros are especially close in character to older members of the genus Tarbosaurus, the Asian equivalent of Tyrannosaurus. Furthermore, the structure of the leg bones are reminiscent of those of Alioramus, another relative of T. rex. As such, it is assumed that the animal still had the distinctive shape of the tyrannosaurs - a spine that is parallel to the ground, tiny forelimbs, a proportionally large head - but in a much smaller package. Since Moros is a critical part of the tyrannosaur lineage, prey learned to fear this species even though it was a mere stepping stone to the peak of tyrannosaur evolution (1).

Suskityrannus hazelae Just as Tyrannosaurus rex conjures the appearance of the massive carnivorous beast at the end of the food chain, a genus meaning “coyote king,” the name Suskityrannus denotes this is, similar to Moros, a smaller, yet still deadly tyran-

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nosaur. In contrast to Moros, the skull of Suskityrannus has been partially recovered as well as vertebrae and leg bones.

The animal, being a tyrannosauroid rather than a true tyrannosaurid, has qualities that align with the latter group and qualities that are contrary to them. For example, the skull’s snout is a broad U-shape, akin to Late Cretaceous tyrannosaurs, but the animals lower dentaries do not converge into a “chin,” characteristic of tyrannosaurids. The animal’s skull likely had the other characteristics of tyrannosaurs, such as the antorbital fenestra, which are the holes present in front of the eye sockets.

Suskityrannus is not as old as Moros, living approximately 90 million years ago, but it still fills in a part of the original 70 million year gap that existed in North American tyrannosaur history. Despite the fact that it existed more recently, Suskityrannus is not as closely related to the true tyrannosaurids as Moros is. Instead, it is more firmly related to the “mid-grade” tyrannosauroids. However, the animal is still considerably useful in filling in the evolutionary record, as there are not as many fossils from this time period, thanks in large part to the increased sea levels of the time. This decreased the possibility of successful preservation significantly enough that any animal, even one that is more distant, like Suskityrannus, is essential in understanding the tyrannosaur family tree (2).

Phuwiangvenator yaemniyomi and Vayuraptor nongbualampheunsis Even more distantly related to the tyrannosaurids, the megaraptorans are a large group of theropod dinosaurs that do not contain tyrannosauridae, but could potentially be the closest family to it. Megaraptora is hypothesized to be placed in one of three areas of the dinosaur phylogenetic tree. It is either immediately adjacent to tyrannosauridae within Coelurosauria, a more basal section of Coelurosauria, or an even more basal group within tetanurae. Regardless, the description of these two new animals does contribute to the evolutionary history of the tyrannosaurs.

In the case of Phuwiangvenator, the animal’s dorsal vertebrae are an hourglass shape most similar to Tyrannosaurus rex. The animal’s tibia curves similarly to Tyrannosaurus and Lythronax, another tyrannosaurid. Vayuraptor, in contrast, as a basal coelurosaur, is not quite as similar in its skeletal structure to Tyrannosaurus as Phuwiangvenator. The researchers are sure to note at the end of their report that the placement of these animals, specifically Vayuraptor, is incredibly tentative, awaiting the further discovery of more materials. Regardless, these two animals serve as sort of evolutionary cousins of the tyrannosaurs, and are thus no less important to understanding the group’s lineage. The various clades are rearranged so frequently, and in such confusing, overlapping manners, that learning about any animal that could conceivably be related to a well-known family, like the tyrannosaurids, can solidify the placement of groups further along the tree. Having concrete placement for these broader groups allows for animals discovered later on to be added to the tree with more confidence than before. Essentially, new discoveries, and new classifications, contribute to a cycle of new knowledge that can only help define the evolutionary timeline, not just for tyrannosaurs, or even just for dinosaurs, but for all animals (3).

Figure 2 A cladogram of Archosauria, specifically demonstrating the relationship between Tetanurae, Coelurosauria, and Tyrannosauroidea.

Conclusion It’s unlikely that, in the popular consciousness at least, the image evoked when one says “tyrannosaur,” will ever change from the antagonistic, iconic mascot character of the Jurassic Park films. The large, lumbering apex predator with the terrifying, awe-inspiring name will always be the most iconic theropod dinosaur, possibly the most iconic dinosaur.

That said, to disregard the distant relatives of Tyrannosaurus, despite their perhaps less impressive stature and presence, would be folly. While the closest relatives to these animals still alive today are various species of birds, which don’t bear much resemblance to the described animals, it is no less important to discover how the creatures that have died out came into being. The further back in time you view the evolutionary tree, the more you can see the connections between all creatures.

These animals are an essential piece of the evolutionary puzzle, and should be celebrated as such.

References 1. L. Zanno, et al., Diminutive fleet-footed tyrannosauroid narrows the 70-million-year gap in the North American fossil record. Communications Biology 2, (2019). doi: 10.1038/s42003-019-0308-7 2. S. Nesbitt, et al., A mid-Cretaceous tyrannosauroid and the origin of North American end-Cretaceous dinosaur assemblages. Nature Ecology & Evolution 3, (2019). doi: 10.1038/s41559-019-0888-0 3. A. Samathi, P. Chanthasit, and P. Sander, Two new basal coelurosaurian theropod dinosaurs from the Lower Cretaceous Sao Khua Formation of Thailand. Acta Paleontologica Polonica 64, (2019). doi: 10.4202/app.0050.2018 Images retrieved from: 1. http://cdn.sci-news.com/images/enlarge6/image_7161_1e-Suskityrannus-hazelae.jpg 2. https://upload.wikimedia.org/wikipedia/commons/f/f3/Phylogenetic_tree_ of_Theropods_respiratory_system_01.jpg

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T he I ntestinal E cosystem AARADHANA NATARJAN ’20

Figure 1 Multiple forms of bacteria, such as those that digest lactose, inhabit our intestinal ecosystem.

Introduction In the murky depths of our alimentary canals, there flourishes an entire microscopic world. Populated by beneficial bacteria that can affect everything from immunity to mental health, this unseen ecosystem’s importance in biological functioning, which is belied by its size.

The genes of these symbiotic microbes contribute to the hologenome, where they are used for the production of proteins and metabolites that have important biological functions within the human body (1). For example, there are bacteria that produce the essential vitamin K compound, which is not found in any natural food source. This piece focuses particularly on the bacteria that inhabit the lower parts of the alimentary canal, namely, the intestines or “gut”. We will cover the physical and health implications of gut dysbiosis, or problems related to gut microbiome makeup, as well as exploring the interplay among the microbiome, diet and culture.

Of the various species living in the gut, one group of butyrate-producing bacteria is of particular interest to scientists.

The butyrate they produce is essential for biological functioning, as it is a key modulator of histone deacetylase inhibitors, which regulate DNA transcription and protein synthesis in the body (2). It also acts as a source of energy and facilitates the energy-production activities of mitochondria and cells in the colon (2,3).On a broader level, butyrate also protects against colon cancer, inhibits pathogen growth, reduces oxidative stress and stimulates gut absorption for better physiological functioning (2). A related product, acetate, also has similar effects.

But not all microbes are beneficial. One of the most infamous is the all-too-common species known as Heliobacter pylori. Best known from Barry Marshall’s iconic experiment, in which the scientist consumed a living sample of the microorganism, H. pylori is commonly associated with ulcerative colitis and gut disease (4, 5). Recent research has found that

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the greater the Helicobacter abundance in an individual’s gut, the lower the diversity of their gut microbes (5). These infectious organisms are also known to create local micro-environments to aid their colonization, namely through affecting the local immune response and types of microbes that can survive in that region (6). This implies that the presence of certain microbes can affect the overall makeup of the gut microbiome, as well as have immunomodulatory effects.

Health Implications The health implications of the microbiome are still being explored. Recent research has attempted to link gut dysbiosis with heart disease, irritable bowel syndrome, colorectal cancers, and immune problems. Breastfed children show different gut microbiome compositions from their their formula-fed peers. Breastmilk has also been linked to increased levels of Bifidobacteria and the immunoglobin A antibody, which is important in the functioning of mucosal membranes in the stomach and gut (2). Bifidobacteria, in particular, have been linked to carbohydrate catabolism, production of B vitamins and immune activity. Butyrate-producing bacteria have similarly been linked to carbohydrate catabolism and are essential to the production of ATP from food (2).

The effects of early-life gut microbiome composition carry on after the introduction of solid foods. Studies have shown that diets high in animal products, fat and protein is correlated with lower gut diversity and lower levels of acetate and butyrate production by the gut microbiome (7). Going on a low-carbohydrate diet also has a different effect on the ratios of microorganisms than does going on a low-fat diet. Individuals not only experienced greater weight loss from these dietary changes, but also showed greater changes in their microbiome composition after a year (8). Diet, and therefore microbiome diversity, also vary with age. Lifetime microbiome diversity essentially follows a normal distribution, with relatively low di-

versity both in early infancy and old age, and maximal diversity in youth and middle age (1). Of course, changes in living situation and diet during youth and middle age contribute an effect, but the net diversity remains higher during this time in a person’s life when other factors are controlled. This research has great scientific potential, namely in the development of “personalized diets” that can either lead to a healthier microbiome or be tailored to suit the microbiome an individual already has.

In terms of the former, much of the existing research seems to agree on two things. One, consuming fermented foods such as yogurt can increase the population of beneficial microbes in the gut, leading to better health outcomes. Second, eating diets rich in fiber, specifically plant fiber, can improve gut health and increase microbiome diversity (9).

Along with longitudinal analyses of human microbiomes, researchers have discovered some startling results in mouse model transplant studies. A study by Smith et al. (10) dmonstrates that when gut microbes from humans suffering from Kwashiorkor disease, or protein-related malnutrition, were transplanted into mice with germ-free intestines, the mice began to exhibit symptoms of the disease such as weight loss, vision problems, and issues with weight gain. This indicates that gut microbiota and their products have a role in the development of disease conditions related to diet.

Another similar study transplanted gut microbes from obese/non-obese twin pairs into germ-free mice and observed that the mice phenotypes changed to mimic that of the human individual whose microbes had colonized the rodents’ guts (11). Specifically, the mice given microbes from the obese twin showed extreme weight gain, while the mice given microbes from the non-obese twin showed no significant weight gain while both groups were on the same diet (8). This suggests that gut microbiota and their products may play a significant role in metabolism and fat deposition.

Dietary Effects There are also instances where the consumption of microbes leads to the colonization of the gut, as in the case of fermented foods. The microbes responsible for the fermentation process can continue to assist human metabolism even after being consumed, surviving the gauntlet of stomach acid and immunoglobulins to maintain activity in the gut (12). Contrary to popular misconception, the stomach is not remotely sterile, harboring diverse populations of microbes that influence metabolism (5).

These beneficial microbes can also assist in the digestion of foods a person may not have the enzymes for otherwise. For example, lactose intolerance occurs when individuals lack a functional lactase enzyme. Yogurt, however, is often well-tolerated by people missing this enzyme, since the lactobacilli that ferment milk into yogurt can assist in digestion in vivo (13).

Interestingly, short-term dietary changes produced similarly short-lived microbiome variation, with the microbiota populations restored to their initial levels after such transient changes (14, 15). Such changes can include going on antibiotic regimens, fad diets, or experimenting with cuisine while on vacation.

The levels of fats, proteins, carbohydrates and fiber in an individual’s diet appear to play the most significant role.

Research has shown that diets high in fiber and carbohydrate content correlate with increased levels of Prevotella species, while diets high in protein and fat tend to correlate with increased levels of Bacteroides species (15). Of the broader Bacteroidetes phyla, Prevotella exists in balance with Bacteroides.

In guts with greater Prevotella presence, Bacteroides levels were lowered, and vice versa. Researchers have also demonstrated that the addition of Prevotella to mice microbiota improved their glucose metabolism, and that increases in human gut Prevotella levels that resulted from increased barley consumption also appeared to aid in glucose metabolism (16).

Similarly, study by Ley et al (17) also shows that the ratio of Bacteroidetes to Firmicutes increases in individuals who go on fat or carbohydrate restriction diets for a year. Firmicutes and Bacteroidetes are the two most abundant phyla in gut microbiomes across ethnicities, and the ratio between the two is known to have a strong correlation with the proportion of plant-based foods present in an individual’s diet (18). Because of these two factors, this ratio is often used in research methods as a means of examining individuals’ plant consumption versus animal product or processed food consumption.

Not all diets are created the same, either. High-fat diets can get their name from being rich in fibrous plant fats, like those found in avocados and seeds, or from animal-based fats like lard or butter, which have limited fiber and mineral content. Similarly, carbohydrates can be obtained from grains or simple sugars, both of which have very different interactions with the gut microbiota (3).

Diet and Culture - Africa Diet has a significant effect on the composition of the microbiome and is in turn affected by the cultural and geography a person inhabits. Since different diets are linked to different microbiome makeups, it follows that people from different parts of the world will have different gut systems.

Fecal microbiomes especially seem to show strong concordance with culture. Samples from European adults is more similar to those from the USA than those of South America or Malawi (3). This is reflective of the plant-rich diet characteristic of individuals from tropical and rural settings, and the animal-protein-rich diet found in American and most European settings.

This is substantiated by research comparing the microbiota found in Tanzanian Hadza foragers and Italian urbanites. There appears to be a relative reduction in microbial diversity in western populations, with the Hadza also showing seasonal variations in microbiome composition related to the availability of plant species (19). However, though Actinobacteria (including Bifidobacteria) are almost entirely absent in the Hadza samples, they are a considerable component of the Italian gut microbiota. These results produce an interesting parallel between European vegans and the Hadza. Both groups have very low representation of Actinobacteria and Bifidobacteria in their microbiomes, suggesting that there is likely a relationship between levels of these bacteria, and the consumption of dairy and livestock animal products (19, 20, 21).

The researchers also found an interesting gendered split in Hadza microbiota. Women, who are primarily plant and tuber foragers, had greater abundance of Treponema bacteria, which is tied to traditionalist, non-urbanized lifeways (22). On

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the other hand, the men who act primarily as game hunters and honey foragers had greater abundances of Eubacterium and Blautia (19). The researchers speculate that this can be tied back to differences in snacking habits. While their major communal meals are shared, during their food gathering, women tend to snack more on the foods they procure, while men tend to snack more on the foods they procure. Since the gathering is divided, so is the snacking and the gut microbiomes.

Expanding on these differences within an ethnic demographic, research has shown that when foods of animal origin, or those rich in fats and simple sugars are introduced into a traditional, grain-and-legume based African diet, individuals demonstrate changes in gut microbiota profiles (22). When controlling for geography and ethnicity, children living in urban Burkina Faso had microbiomes in which unique bacteria associated with the fermentation of fibers and polysaccharides from vegetables had been outcompeted by bacteria better suited to the metabolism of animal proteins, fats and sugars (23).

The researchers attributed these changes to the fact that children living in more developed parts of Burkina Faso had more access to bread, dairy, juices, baked sweets and processed snacks. This observation is compared to children in more rural areas, who subsist largely on a vegetarian diet supplemented with very occasional meat consumption. Urbanization and migration of rural laborers to urban environments in Burkina Faso is also associated with reduced fiber intake and increased daily caloric intake, often due to increased fat, animal protein and simple sugar intake. Interestingly, the rural population showed a higher ratio of Bacteroidetes to Firmicutes, which decreased in fecal samples from children living in more urban settings (24). The children in Burkina Faso’s capital and Europe also exhibited an absence of Treponema, while the children in the most rural parts of Burkina Faso exclusively had an abundance of this microbial group. Connecting back to the research with the Hadza population, it appears that the presence of certain microorganisms is as good an indicator of urbanization and organized agriculture as it is of dietary intake.

Diet and Culture – Asia Asia is the world’s largest continent, and home to a wide variety of cultures, ethnicities and geographical distributions.

This means that consolidating research spanning its entirety is a vast task deserving of its own review. The following section will focus on a few interesting examples of microbiological diversity across nationalities and ethnicities.

For example, there is a bacteria with a beta-porphyrase gene that is found almost exclusively in people of Japanese extraction (25). This compound is linked to the catabolization of seaweed glycans, which is a dietary staple in the region. This suggests that historical diets may have influenced gut microbiomes in the current population, and that geographic location affects metabolism of different foodstuffs.

A Canadian study also highlights disparities in the microbiomes of mothers and infants of South Asian versus European extraction. The South Asians had higher levels of Actinobacteria, such as Bifidobacterium, compared to their white peers. Researchers attributed this to the observation that the South Asian infants tended to be breastfed for longer (26).

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Figure 2 Some bacteria can only be isolated from certain populations.

A Chinese sample bore out the correlation between Prevotella and plant-based diets high in carbohydrates and fiber (18). Individuals from rural and agrarian backgrounds had higher numbers of these microorganisms than those in more urban settings who consumed more meat and animal products.

Conclusion The idea that we are what we eat has never been more substantiated. This burgeoning area of study holds great promise in explaining physiological phenomena at both the micro and macro levels. But one must be cautious. Changes in diet may not lead to changes in microbiome composition, rather changes in microbiome composition might be promoting dietary changes. Independent changes in microbiome makeup triggered by environmental or other factors could lead to the production of bacterial metabolites that influence the brain to desire different types of foods. The development of mental illness could also be a causal agent in microbiome population shifts. Rather than the gut bacteria affecting mental health, cognitive well-being could also be affecting microbiome composition. Contemporary researchers believe that the connection between the gut and the brain is bidirectional, though the specifics have yet to be determined.

However, these gaps in scientific knowledge that there is considerable scope for new research. For example, there is evidence indicating that the endocannabinoids produced within the body affect gut permeability. Endocannabinoids are a class of substances that modulate cognitive and motor functioning in the human body. If endocannabinoids are such strong mediators of gut permeability, so-called “leaky gut” syndrome can then be connected back to the production of endocannabinoid molecules by microbiota and human cells (27). As the permeability increases, microbes and their metabolites can pass from the intestinal submucosa to the systemic blood circulation, leading to adverse health outcomes. Since consuming marijuana is known to upset the delicate balance of endocannabinoids in the body, it could also have drastic effects on the microbiome and gut health. As marijuana is legalized across the country and vaping becomes more common, this area of study becomes increasingly medically relevant.

There is also a working hypothesis that the consumption of termites by rural populations in Burkina Faso might contribute to the presence of plant-polysaccharide-digesting mi-

crobiota in their gut. It is hypothesized that the consumption of these insects might lead to enzymatic transfer, a hypothesis that requires more research. This can also be expanded to include other diets, and theories that consuming certain foodstuffs leads to cross-species transfer of microbes and enzymes.

Lastly, there is the scope for research beyond the biology. Diet is heavily influenced by sociocultural factors, so investigating the effects of urbanization, globalization and migration on microbiome composition would go a long way in providing context for the patterns observed in the literature. It could also increase the scientific community’s understanding of the role larger global interactions have on such a fundamentally microscopic level.

References 1. G. Sharon, et al., Specialized metabolites from the microbiome in health and disease. Cell Metabolism 20, 719-730 (2014).

2. A. Rivière, et al., Bifidobacteria and butyrate-producing colon bacteria: importance and strategies for their stimulation in the human gut. Frontiers in Microbiology 7, 979 (2016).

3. K.P. Scott, et al., The influence of diet on the gut microbiota. Pharmacological Research 69, 52-60 (2013).

4. B.J. Marshallet, et al., Urea protects Helicobacter (Campylobacter) pylori from the bactericidal effect of acid. Gastroenterology 99, 697-702 (1990).

5. A. Das, et al., Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks. Scientific Reports 7, 15438 (2017).

6. A. Sheh & J.G. Fox, The role of the gastrointestinal microbiome in Helicobacter pylori pathogenesis. Gut Microbes 4, 505-531 (2013).

7. R. Levy & E. Borenstein, Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules. Gut Microbes 5, 265-270 (2014).

8. Z. Xu & R. Knight, Dietary effects on human gut microbiome diversity. British Journal of Nutrition 113, S1-S5 (2015).

9. P.D. Cani & W.M. de Vos, Next-generation beneficial microbes: the case of Akkermansia muciniphila. Frontiers in Microbiology 8, 1765 (2017).

10. M.I. Smith, et al., Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 339, 548-554 (2013) 11. V.K. Ridaura, et al., Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341, 1241214 (2013).

12. M. Derrien & J.E. van Hylckama Vlieg, Fate, activity, and impact of ingested bacteria within the human gut microbiota. Trends in Microbiology 23, 354-366 (2015).

13. D. A. Savaiano, Lactose digestion from yogurt: mechanism and relevance. The American Journal of Clinical Nutrition 99, 1251S-1255S (2014).

14. C. Jernberg, et al., Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology 156, 3216-3223 (2010).

15. G.D. Wu, et al., Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105-108 (2011).

16. R.E. Ley, Gut microbiota in 2015: Prevotella in the gut: choose carefully.

Nature reviews Gastroenterology & Hepatology 13, 69 (2016).

17. R.E. Ley, Turnbaugh, P. J., Klein, S., & Gordon, J. I., Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022 (2006).

18. J. Zhang, et al., A phylo-functional core of gut microbiota in healthy young Chinese cohorts across lifestyles, geography and ethnicities. The ISME Journal 9, 1979 (2015).

19. S. L. Schnorr, et al., Gut microbiome of the Hadza hunter-gatherers. Nature Communications 5, 3654 (2014).

20. J. Zimmer, et al., A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. European Journal of Clinical Nutrition 66, 53 (2012).

21. M. Ventura, et al., Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiology and Molecular Biology Reviews 71, 495-548 (2007).

22. A.J. Obregon-Tito, et al., Subsistence strategies in traditional societies distinguish gut microbiomes. Nature Communications, 6, 6505 (2015).

23. C. De Filippo, et al., Diet, environments, and gut microbiota. A preliminary investigation in children living in rural and urban Burkina Faso and Italy. Frontiers in Microbiology 8, 1979 (2017).

24. C. De Filippo, et al., Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences 107, 14691-14696 (2010).

25. J.H. Hehemann, et al., Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464, 908 (2010).

26. J.C. Stearns, et al., Ethnic and diet-related differences in the healthy infant microbiome. Genome Medicine 9, 32 (2017).

27. P. D. Cani, et al., Endocannabinoids—at the crossroads between the gut microbiota and host metabolism. Nature Reviews Endocrinology 12, 133 (2016).

Images retrieved from: 1. https://www.flickr.com/photos/ibm_research_zurich/36256920123 2. https://commons.wikimedia.org/wiki/File:Wild_garden_of_the_gut_bacteria_6.jpg 3. https://unsplash.com/photos/4_hFxTsmaO4

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S ocial M edia U se M ay S horten O ur A ttention S pan KAILYN FAN ’23

Figure 1 Globally, over 3 billion people actively use social media.

Introduction In the era of digital media, people rely on smartphones and other handheld devices more than ever. Social media plays a major factor in this dependency, capturing the attention of over 3 billion users today. As apps like Instagram, Facebook, Snapchat, and Twitter become increasingly prevalent in our lives, the attention span of the average human mind has diminished greatly. Despite what it may advertise, social media actually eliminates face-to-face interactions with additional detriments ranging from poor multitasking habits to an increased risk of attention-deficit/hyperactivity disorder (ADHD). The seemingly harmless tiny squares on our phone screens may cause larger-than-life issues in the long run, if people continue to scroll a considerable percentage of their day away, unaware that businesses purposefully design these apps to exploit their attention.

Background Much of the recent research conducted on attention span has taken the technological revolution of the twenty-first century into consideration. With the advent of devices like smartphones and smartwatches and the social media access they entail, interactions with these devices on a consistent basis can consequently diminish attentional capacity and produce “scatter-brained” tendencies (1). In other words, the brain’s ability to process huge influxes of information and break down what is important versus what is not deteriorates.

Social media apps take advantage of designs and features to entice their users with instant gratification. A clear example of this is the notifications social media generates once the smartphone downloads the app. Studies have even discovered that “within-phone” interruptions fostered by notifications can delay the completion of a single task by up to 400% (1). Other studies have shown that the mere sound or vibrating sensation of the smartphone is enough to prompt thoughts and behaviors unrelated to the primary task (1). Overall, these factors, which social media networks encourage, can reduce attention span substantially.

Often, attention span is generated visually, when stimuli capture the human eye and elicit certain behaviors in response. Alternatively, individuals can jumpstart their attention span by purposely selecting a stimulus to organize their own behavior. In a study conducted on Drosophila (fruit flies), researchers specifically analyzed the insects’ selective visual attention (SVA). SVA represents the duration throughout which an organism’s focus of attention (FoA) is fixed on a particular location before shifting to another (2). The results of this study suggest that similarities exist between the attention span of Drosophila and that of humans. For one, the flies in this experiment were drawn to a region of their controlled environment for a longer period of time when they experienced fewer distractors (2). Although this particular study used flies as its model organism, it provides a convincing model for the quantity of distractors that may affect human attention span.

Secondly, because the observed Drosophila underwent entrapment at a torque meter, a presumably stressful situation for them, researchers speculate that the flies could have achieved a longer attention span had they been exposed to more relaxed conditions (2). Although future research on this topic would be necessary, this plausible behavior from Drosophila can be linked to a human’s natural tendency to scatter their attention when faced with distractions or placed under pressure.

Figure 2 Social media notifications such as the badge app icons effectively distract smartphone users from the primary task at hand.

Social media encourages multitasking habits It’s no surprise that the easy accessibility of mobile phones from the pocket of our jeans has posed great day-today distractions, but easy social media access through these devices has also triggered multitasking tendencies. Multitasking, a form of divided attention, is the process of doing more than one thing at one time which, according to Michael Posner, may play a role in lowering attention span (3).

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Recent research has shown that frequent multitasking by using social media and performing another activity may have negative consequences on a person’s social and psychological well-being. In a 2015 study conducted by Shan Xu, Zheng (Joyce) Chen, and Prabu David, 375 undergraduate and graduate students from 59 universities in Beijing, China, completed an online survey about their daily media consumption.

Questions inquired how long each individual typically spent watching video content, texting, talking to someone through phone call or video chat, and performing five other communication activities. The college students selected a one to seven hour range to measure their approximate engagement with each of the eight activities. Among these forms of activities, the participants were then asked to estimate the percentage of occasions in which they would also be simultaneously performing another communication activity. The sum of an individual’s percentages equals the extent of their multitasking.

The remainder of the survey asked students to rate their levels of social success, normalcy, and self-control on a 5-point scale of agreement (1 = strongly disagree, 5 = strongly agree). In this survey, an individual’s friendships constituted social success, normalcy involved a feeling of belonging, and self-control had to do with concentration, sleep, studying, and other healthy habits (4).

Despite inconclusive results overall, the multitasking tendencies in most contexts exceeded 100%, and this indicates that many participants added one or more communication activities to the primary task at hand and accessed technology, especially handheld devices, which can contribute to multitasking tendencies. Researchers created regression models displaying the statistics of success, normalcy, and self-control, all defined as indicators of well-being. Normalcy was the only factor that displayed a negative correlation with multitasking.

Social success displayed a positive correlation and self-control displayed ambiguous correlations, depending on whether communication activities were cognitive related (reading, studying, doing homework) or entertainment-driven (gaming, music, video) (4).

These inconclusive results may be due to limitations such as the study’s small sample size and observational data, meaning that the results of this study cannot be applied to the global population of college students nor be used to establish causation. However, given the thoroughness of the survey questions, it is likely that with an increased number of participants, more conclusive results would be obtained. The design of this study in particular already strengthens the plausibility of a causal relation between technology-based activities and multitasking tendencies.

Multitasking worsens attention span Since multitasking divides the individual’s attention from the primary task at hand with another stimuli, the positive correlation between social media and multitasking directly affects attention span. In a 2009 study performed by Eyal Ophir, Clifford Nass, and Anthony Wagner, participants completed a questionnaire about their media use, then completed activities that tested their filtering and task-switching abilities. The questionnaire addressed the participants’ use of Youtube and other media forms and allowed researchers to create a Media Multitasking Index (MMI) to categorize par-

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ticipants into Heavy Media Multitaskers (HMMs) and Light Media Multitaskers (LMMs). After scaling the participant’s multitasking tendencies with the MMI, the researchers had them engage in tests of their ability to filter irrelevant information and switch between tasks quickly. The results found that HMMs have greater difficulty filtering out irrelevant stimuli in their environment and were less likely than LMMs to suppress their tendency to switch tasks (5). This furthermore indicates the dangerous connection between multitasking and good attention habits.

Possible causes of multitasking While previous research has confirmed multitasking as a global phenomenon, less research has explored the motives behind this harmful practice. A 2014 Korean study conducted

by Yoori Hwang, HyuongJee Kim, and Se-Hoon Jeong recruited 462 adults for a survey. Researchers first recorded each participants multitasking tendencies by rating the frequency of multitasking from 1 (never) to 5 (very often). They then referred them to a list of motives and asked them, “To what extent do you engage in multitasking habits due to each of the following reasons?” (6).

The results narrowed down five categories of potential multitasking motives: information, social, habit, efficiency, and enjoyment. The information category encompassed seeking additional information (general), resolving curiosity, checking facts, and gaining information about products or services. The social category included a desire to express their opinion, feel part of a community, maintain a relationship, and learn about others’ ideas. This particular set of social motives has a strong link to social media or Internet-related multitasking, as these technological advancements facilitate virtual connections. The habit category involved the desire to maintain a routine. Efficiency mainly involved saving time.

The enjoyment category, however, suggested that some people multitask because it is boring to use one medium, providing evidence for a disturbing new reality in which one task isn’t enough to occupy an individual’s attention, further truncating their overall attention span (6).

Social media links to ADHD So far, multitasking habits have proved to be a hindrance to focused attention, but how does this change in attention span affect mental well-being? In a cumulative survey conducted from 2014 to 2016, Ra et al. discovered a statistically significant association between high-frequency media use and ADHD symptoms (7).

Attention-deficit/hyperactivity disorder, or ADHD, is a psychiatric condition in which the individual experiences many symptoms related to inattention including: trouble organizing and completing tasks, impulsivity, difficulty concentrating, and rarely remaining still. As of 2014, ADHD affects 7% of adolescents, but other studies have shown a steady increase in that percentage in recent years (7).

The survey, set in Los Angeles, involved ninth graders from 10 randomly selected local public high schools. The participants were given follow-up surveys every 6 months for 2 years, where they answered questions from the Current Symptoms Self-Report Form, an official indicator of ADHD symptoms taken from the Diagnostic and Statistical Manual

of Mental Disorders - 4th Edition, or DSM-IV. From a scale of 0 to 2 (0 = sometimes, 1 = often, and 2 = very often), the high school students rated the frequency of each listed symptom. Participants who exhibited 6 or more of these symptoms were classified as at risk of ADHD. In addition, in the baseline 12-month and 24-month surveys, participants were asked for their frequency of engagement in media activities. Media usage many times a day was considered high-frequency, while media use 0-2 times a week or 1-2 times a day was considered of a lower frequency (7).

In the end, a total of 2,587 students were part of the data collection. Out of these students, 2,090 reported engaging in at least one media activity at a high-frequency. Results indicated a significant correlation between digital media use and exhibition of ADHD symptoms. For example, 9.5% of participants who reported 7 high-frequency activities showed signs of ADHD, but this percentage increased to 10.5% among participants who reported 14 high-frequency activities. Notably, checking social media websites was the most common activity among the sample, again suggesting there is an existing and possible causal relationship between social media and ADHD, which demonstrates the severe drawbacks of the former variable on attention span (7).

Conclusion Before we can conclude that increased social media use lowers attention span, future research would need to confirm a causal relationship between the two variables. Since establishing causation necessitates an experimental study, perhaps future studies can test whether the use of social media for various time intervals causes a delay to complete an activity that requires sharp concentration. The delay, likely miniscule, could prove statistically significant and indicate a short-term lack of focus. Although to confirm a causal link between social media use and ADHD would likely lead to ethical issues, further longitudinal studies can observe the development of the disorder in adolescents, depending on how frequently they utilize social media.

Additionally, studies like the survey on Chinese undergraduates still provide valuable data, despite their obvious limitations. To design a perfectly conclusive experiment with a large sample size, absence of bias, and a control of all natural variations would be exceedingly difficult. But newfound data such as that in Shan Xu’s study, combined in a meta-analysis, can help us identify trends not yet seen, including the possibility of reciprocal causation.

From a societal perspective, social media use has affected, to some extent, the human’s average attention span. A study conducted by Microsoft claims that the average human attention span today is lower than that of a goldfish (eight seconds). As compelling as this may seem, research articles that could elaborate on this potential concern have yet to be be published, suggesting a greater need for peer-reviewed analyses in order to fairly and abundantly inform the public of both sides of this health-related controversy. We can raise awareness about the dangers of social media to our ability to pay attention and our ability to be present in our lives.

Other studies have narrowed their focus on how we can shape, and even increase our attention span. This research is oriented towards people diagnosed with ADHD or

Figure 3 This infographic displays the trend of reduced human attention span since the early 2000s and how it compares to the attention span of a goldfish.

schizophrenia. A great discrepancy exists between the methods used to address attentional issues caused by each mental disorder, clearly contingent on the severity of each illness. A study conducted by Pritpal Sidhu tested the efficacy of mindfulness meditation on children ages seven to twelve years who displayed ADHD-related behavior. Sidhu discovered mindfulness meditation to be a highly effective intervention for ADHD and an alternative to prescribed medication (8). Another study delved into neurocognitive rehabilitation methods for schizophrenics, who also have serious issues with attention span.

Because scientists have yet to develop psychiatric medication that cures schizophrenia, Steven Silverstein et al. looked into a more behavioral approach to treating the illness partly by lengthening attention span. They found that a training technique known as shaping was effective in treating schizophrenia patients (9). However, shaping is a form of operant conditioning, a procedure best utilized for only the severely mentally ill. So while one hopes that the attention span of the average person never dwindles to such a low extreme, practicing mindful habits such as meditation may offer a simple yet effective way to increase attention span.

References 1. H. Wilmer, L. Sherman, and J. Chein, Smartphones and cognition: a review of research exploring the links between mobile technology habits and cognitive functioning. Frontiers in Psychology 8, (2017). doi: 10.3389/fpsyg.2017.00605 2. S. Koenig, R. Wolf, and M. Heisenberg, Vision in flies: measuring the attention span. PLoS ONE 11, (2016). doi: 10.1371/journal.pone.0148208.

3. Q. Chen, Z. Yan, Does multitasking with mobile phones affect learning?

A review. Computers in Human Behavior 54, 34-42 (2016). doi: 10.1016/j. chb.2015.07.047.

4. S. Xu, Z. Wang, and P. David, Media multitasking and well-being of university students. Computers in Human Behavior 55A, 242-250 (2016). doi: 10.1016/j. chb.2015.08.040.

5. E. Ophir, C. Nass, and A. Wagner, Cognitive control in media multitaskers.

PNAS (2009). doi: 10.1073/pnas.09036201006.

6. Y. Hwang, H. Kim, and S. Jeong, Why do media users multitask?: motives for general, medium-specific, and content-specific types of multitasking. Computers in Human Behavior 36, 542-548 (2014). doi: 10.1016/j.chb.2014.04.040.

7. C. K. Ra, et al., Association of digital media use with subsequent symptoms of attention-deficit/hyperactivity disorder among adolescents. JAMA 320, 255-263 (2018). doi: 10.1001/jama.2018.8931.

8. P. Sidhu, et al., The efficacy of mindfulness meditation in increasing the attention span in children with ADHD. ProQuest Dissertations & Theses Global (2013). doi: 10.1037/e613382013-001 9. S. Silverstein, A. Menditto, and P. Stuve, Shaping attention span: an operant conditioning procedure to improve neurocognition and functioning in schizophrenia. Schizophrenia Bulletin: The Journal of Psychoses and Related Disorders 27, 247-257 (2001). doi: 10.1093/oxfordjournals.schbul.a006871 Images retrieved from: 1. https://unsplash.com/photos/xv7-GlvBLFw 2. blog.hootsuite.com/social-media-advertising-stats/ 3. nature.com/articles/d41586-018-06213-7 4. venturebeat.com/2016/12/04/our-8-second-attention-span-and-the-future-ofnews-media/

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Undergraduate Yeast Xrn1p, a defense against TMV in Nicotiana benthamiana Anh Vo, Chris Helenek, Parisa Boukani, Nabil Chowdhury, Chyna Hardy, Anya Justin, Ayesha Kamran, Kiara Kolacyzk, Jesse Liu, Alex Maus, Jihu Mun, Vincent Peetz, Taylor Pressley, Agam Singh, John Peter Gergen ABSTRACT Pesticides are traditionally used to protect plants from viruses spread by insect vectors. The increased need for the usage of pesticides has led to detrimental environmental effects. Tobacco Mosaic Virus (TMV), a ssRNA(+) virus, uses insect vectors to infect and spread to a wide range of hosts in the Solanaceae family. A replicase and the 3’ end of the TMV genome which has a tRNA-like structure protects vRNA from RNA silencing mechanism of plants. TMV infected plants show symptoms of mosaic mottling, necrosis, and stunted growth. Current solutions to TMV infection include the use of pesticides.

Alternative solutions such as genetic engineering of plants are still being explored. The protein Xrn1p, a 5’ → 3’ exoribonuclease is integral to cellular mRNA and tRNA maintenance in yeast and other eukaryotes. Since Xrn1 is not found in Nicotiana benthamiana and plant expression of yeast Xrn1 has not been studied, we performed a transient expression assay expressing yeast Xrn1p in N. benthamiana. To express Xrn1p in N. benthamiana, a plant vector was synthesized to contain Xrn1p tagged with RFP. The N. benthamiana plants were infected by sap inoculation with GFP tagged TMV and after, agro-infiltrated with Xrn1p plant vectors tagged with RFP. Infection by GFP tagged TMV showed infection at the site of inoculation through fluorescence after two to three days. Mosaic mottling symptoms showed after five to seven days. Agro-infiltrated plant leaves did not show red fluorescence however, TMV fluorescence was notably decreased around sites of agro-filtration. Additionally, evidence of necrosis at the sites of agro-infiltrated infected plants was observed. However, after many trials and plants with some analysis results on the effectiveness of Xrn1 against TMV was inconclusive.

Evaluating Pose Reproduction Success Across Docking Platforms Scott Laverty, Stephen Telehany, John Bickel, Robert C. Rizzo ABSTRACT The field of molecular modeling, and in particular computational docking, is an important approach to help identify new drug leads to a biological target provided an atomic structure is known or can be inferred. Different programs attempt to predict how multiple ligands varying in conformation will bind to a target, based on their energetic and geometric compatibility. In this work, we aim to compare the accuracy of two widely used programs DOCK 6.10 and AutoDock 4.2.6 and examine their strengths and weakness over a large docking dataset derived from publicly available protein-ligand complexes in the protein data bank. More specifically, we examine pose reproduction accuracy, sampling failures, and scoring failures using experimentally known binding geometries (poses) taken from each crystallized protein-ligand complex. The primary experiment involves separating each complex into a protein “receptor” and “ligand” file and generating hundreds of potential solutions with each program. For a success, each top-scoring ligand pose is expected to fit into the binding site located within each protein receptor in the same manner as the original x-ray structure (RMSD < 2 angstroms). If not, the test is considered a failure because it did not match the experimentally known observable. Progress to date will be reported.

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Research The loss of Krüppel-like factor 15 in Foxd1+ stromal cells exacerbates kidney fibrosis Xiangchen Gu, Sandeep K. Mallipattu, Yiqing Guo, Monica P. Revelo, Jesse Pace, Timothy Miller, Xiang Gao, Mukesh K. Jain, Agnieszka B. Bialkowska, Vincent W. Yang, John C. He and Changlin Mei ABSTRACT Large epidemiological studies clearly demonstrate that multiple episodes of acute kidney injury contribute to the development and progression of kidney fibrosis. Although our understanding of kidney fibrosis has improved in the past two decades, we have limited therapeutic strategies to halt its progression.

Myofibroblast differentiation and proliferation remain critical to the progression of kidney fibrosis. Although canonical Wnt signaling can trigger the Wnt/b-catenin signaling activation of myofibroblasts in the kidney, mediators of Wnt inhibition in the resident progenitor cells are unclear. Recent studies demonstrate that the loss of a Krüppel-like factor 15 (KLF15), a kidney-enriched zinc-finger transcription factor, exacerbates kidney fibrosis in murine models. Here, we tested whether Klf15 mRNA and protein expression are reduced in late stages of fibrosis in mice that underwent unilateral ureteric obstruction, a model of progressive renal fibrosis. Knockdown of Klf15 in Foxd1- expressing cells (Foxd1-Cre Klf15fl/fl) increased extracellular matrix deposition and myofibroblast proliferation as compared to wildtype (Foxd1-Cre Klf15+/+) mice after three and seven days of ureteral obstruction. This was validated in mice receiving angiotensin II treatment for six weeks. In both these murine models, the increase in renal fibrosis was found in Foxd1-Cre Klf15fl/fl mice and accompanied by the activation of Wnt/b-catenin signaling. Furthermore, knockdown of Klf15 in cultured mouse embryonic fibroblasts activated canonical Wnt/b-catenin signaling, increased profibrotic transcripts, and increased proliferation after treatment with a Wnt1 ligand. Conversely, the overexpression of KLF15 inhibited phospho-b-catenin (Ser552) expression in Wnt1-treated cells. Thus, KLF15 has a critical role in attenuating kidney fibrosis by inhibiting the canonical Wnt/b-catenin pathway.

Modeling the chlorination of conjugated steroids Debra A. Keiser, Eugene Chung, Eric V. Patterson ABSTRACT

Multiple studies have proven that hypochlorous acid, which is commonly used to remove contaminants from wastewater, does not effectively eliminate steroids that are present in wastewater. Instead, reactions that occur between the steroids and added chlorine yield various chlorinated organic products.

It has been determined that many of these products are more bioactive than their parent compounds and pose noteworthy risks to one’s health. To demonstrate the reactivity of different types of steroids, addition and elimination reaction pathways of chlorinated enones, dienones, and trienones with water were modeled using quantum mechanical calculations. Specifically, the MN15 density functional and the Jul-cc-pDVZ basis set were employed along with the SMD aqueous continuum solvation model. Kinetic and thermodynamic properties of the mechanisms were assessed by collecting relative free energy values for each mechanism and plotting them to describe the corresponding reaction coordinate. While both types of reactions were successfully modeled, there is observable competition between the addition and elimination pathways. All calculations were performed using Gaussian 16.

Image retrieved from: https://commons.wikimedia.org/wiki/File:Cancer_cells_(1).jpg

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