Plant Biologist

Biological, Human & Life Sciences Projects

A Comprehensive Review of Safety, Efficacy, and Dosage of Ramipril, Enalapril and Lisinopril.

Hypertension is a leading cause of death in the United States, and ACE inhibitors have proven to be potent for arterial relaxation. The results of double-blind studies with randomized controlled trials were analyzed for the ACE inhibitors lisinopril, ramipril, and enalapril. Our paper used electronic databases such as Wiley Online Library and NCBI to collect necessary medical research. In patients with mild to moderate (Stage 2) hypertension (SDBP = 90-115 mm Hg), there was a significant decrease in all four types of blood pressure at a dosage of 10 mg compared to placebo for enalapril (P < 0.01) and ramipril (P < 0.05). Lisinopril shows a strong linear dose-response relationship, but lacks a significant difference from placebo at 10 mg lisinopril, with the exception of SSBP (P
Daphne He,
Aarya Morgaonkar,
Ishanvi Kommula,
Naina Sabbineni,

Gupta

A Global Network Analysis of COVID-19 Vaccine Distribution to Predict Breakthrough Cases Among the Vaccinated Population

The ongoing COVID-19 pandemic, also known as the coronavirus pandemic, is a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Multiple vaccines have been developed, underwent clinical trials, and distributed along with many boosters and doses. While these vaccines are currently being distributed the virus still spreads as we have not reached herd immunity. As the virus spreads new variants like enter. This study aims to map the vaccination candidate connectome using network analysis with the Barabási-Albert model. This network science will provide scale-free networks that accurately model the powerful distribution of SARS-CoV-2 vaccines on a global scale. From there, the study will use R & Java Script as well as Gephi to visually model these networks. Along with modeling, we will use machine learning to predict the next pandemic among vaccinated candidates on a global scale.
Pragyaa Bodapati, Sathya Padmanabhan, Medha Bhattacharya, Aniket Dey, Ananya Pinnamaneni, Roshni Koduri

Jahanikia

A comprehensive review of dietary and nutritional-based therapeutic approaches for ALS

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease that causes patients to progressively lose their motor function. In this study, we review research conducted on transgenic mice that have a human SOD1 transgene with a G93A mutation. One key approach that is used to extend the lifespan of ALS patients lies in nutritional and dietary management approaches, given that ALS patients tend to experience rapid weight loss and metabolic instability as the disease progresses. Our review paper analyzes the effects of the ketogenic diet and the Deanna Protocol with regards to increases in mice longevity. Transgenic mice put on the Deanna Protocol had an increase in mean survival by 7.5% compared to the control group on the standard diet, whereas the mice fed the ketogenic diet had a mean survival increase of 20%. However, due to the nature of the differences between disease development and progression and the varying effects of the aforementioned diets in mice and humans, further research is still needed to conclude that the same diet-related benefits lie in human ALS patients as well.
Addison, Arlidge,
Garv, Mehdiratta,
Ashlee, Liu,
Cynthia, Zhi,
Dishita, Rajan,

Gupta

Aggregation of Computer-Based Cognitive-Training/Rehabilitation and Personalized Brain-Care Interventions into the CognoTrain App

Methods of CBCT/CBCR (Computer-based Cognitive Training/Rehabilitation or Brain-Care) have shown effectiveness as a means of positive intervention for groups of early-stage Alzheimer’s disease and Dementia patients, but their development and testing occurred independent of one another. CognoTrain will function as an aggregate of these therapies to provide a holistic means of rehabilitation. Implemented CBCT measures in the app such as an address reminder system have proven to minimize symptoms such as topographical disorientation. The combined power of these techniques would produce an unprecedented level of cognitive improvement, introducing the possibility of a better life for more than 50 million dementia patients worldwide.
Jonathan Ma, Krishnaveni Parvataneni, Harsha Samavedam, Shashank Sastry, Deniz Yilmaz

Jahanikia/Downing

Alzheimer's Disease

Summary: C. elegans rely on their olfactory neurons to learn about their surrounding environment. They will form associative memories with different types of odorants which will provide them information regarding food, survival, safety, etc. Based on the length of the exposure and starvation period, there is a temporal relationship between pairing time and memory formation. The presence of a stimuli may temporarily or permanently alter the behavior of C. elegans because the activation of calcium signaling induces neuronal plasticity. Using a transgenic C. elegan model, we will be assessing the effect of amyloid beta aggregation in muscle cells and neurons on its ability to form short term and long term associative memory. We will be testing this by conditioning it to associate hunger with butanol as a “learning task.” We will track how this learning association is retained and lost in different strains (CL2120 - Ab in muscle cells and CL2355 - Ab in neurons). We are also continuing our summer project where we looked CL2122 (WT for CL2355) and CL2355 - so we will rerun the STAM to see if we get the same results and then do the LTAM assay. The overall goal is to understand how amyloid beta affects learning and memory formation and the impacts of neurodegeneration overall.
Aden Sun, Arnav Rao, Jay Subbiah, Khushi Yadav, Sripradha Manikantan, Tanvi Sri, Sai Penugonda, Simran Tawari

Truong

Alzheimer's disease

Our research focuses on the effect of amyloid beta (Aβ) aggregation on associative memory formation and motility in C. elegans. Our experiment is to study the effects of Amyloid beta aggregation on STAM and LTAM in muscle cells and neurons on strains of Caenorhabditis. The first step of our experiment is to synchronize N2 WT C. elegans. This would ensure that our sample of worms would grow at relatively the same rate. After synchronization, we would assess their baseline chemotaxis levels by conducting a chemotaxis assay with butanol. When C. elegans are deprived of food, the presence of butanol will result in a positive association between food and butanol. In N2 WT C.elegans, short term associative memory (STAM) typically lasts for 2 hours while long term associative memory (LTAM) can last up to 24 hours. Using this assay, we will assess the effect of Aβ aggregation on the memory formation of short term and long term memory in the three transgenic AD C. elegans. We hypothesize that Aβ aggregation in the neurons will significantly reduce the duration of associative memory and negatively affect motility.
Sripradha Manikantan, Khushi Yadav, Frances Jing, Aden Sun, Simran Tawari
Arnav Rao, Jay Subbiah, Tanvi Sri Sai

Truong

Amyloid Beta Aggression on C. Elegans

The aggregation of the protein called amyloid-beta has been theorized to cause Alzheimer’s disease (AD), the most common type of neurodegenerative dementia. This aggregation forms plaques around neural cells which causes cell lysis. Our research project is directed towards understanding how amyloid-beta (Aβ) aggregation affects learning and memory formation.To study the effects of Aβ aggregation, we are using the model organism called Caenorhabditis elegans with overexpression of Aβ in neurons To understand the effects of amyloid-beta aggregation on C. Elegans, we test the C. Elegans’ short-term and long-term associative memories through STAM and LTAM assays. We hypothesize that Aβ aggregation in the neurons will significantly reduce the duration of associative memory and negatively affect motility. The results yielded by the STAM assay demonstrated that the Aβ aggregation affected the duration of short term associative memory in transgenic C. Elegens strain relative to the control. Given this behavior, we expect similar trends in their long term associative memory assay. By understanding the effect of Aβ aggregation on associative memory in transgenic C. elegan models of AD, we will be able to develop appropriate treatments to assess its effectiveness in treating neurodegeneration and memory-related disorders.
Tanvi Penugonda,
Riya Sanampudi,
Ashneet Dhami,
Jay Subbiah,
Aden Sun,
Daniel Nguyen,
Simran Tawari,
Thoya Raman

Truong

Barnacles

Oceans are a crucial part of the Earth’s anatomy; they give life to marine organisms, allows for transportation for ships, acts as a storage area for inorganic material, and prevents extreme heating of the Earth by absorbing excess CO2 from the Earth’s atmosphere. Specifically, our experiment is geared towards understanding the effects of how an increase in ocean acidification affects its ability to maintain a sustainable environment for marine creatures. In our experiment, we placed two types of barnacles(balanus aquila-acorn and tetraclita rubescens-volcano) into saltwater tanks of different pHs. The control tank was at 8.1 pH, and the other two were at levels of 7.8 pH and 7.5 pH. Barnacles were fed zooplankton per data collection, and their feeding activity was measured by counting the amount of cirri extensions at 10 minute intervals leading up to 30 minutes. We also tested predator avoidance response for barnacles by using a sponge to replicate its predator's effects, and our previous finding that a light brush to the barnacle’s surface by a sponge caused it to retract still holds true. Previous data presented itself as statistically significant, but current findings show possible changes, and further study is needed to rectify a proper conclusion
Anish Jupudy, Anushree Chanda, Brady Lucas, Meghana), Muzainah Uddin, Pamela Yung

Benson

Biomolecular Characterization of Vernonia amygdalina Using RNA Sequencing and Proteomics

Vernonia amygdalina (bitter leaf) is tropical West African shrub in the Asteraceae family. It is part of traditional diets in countries such as Nigeria and the Democratic Republic of the Congo, and consumed for its purported antimalarial, antidiarrheal, and anthelmintic effects in humans and animals alike. Validation of the medicinal use of a plant is possible through proteomic quantification and RNA sequencing. A handful of small molecules have been identified as molecules of interest in V. amygdalina, but research remains limited. Using next-generation RNA and protein sequencing, we intend to compile a comprehensive transcriptome and proteome of V. amygdalina in order to identify RNA sequences and potential bioactives. These will then be analyzed using LC-MS, GC-MS, post-translational modification (PTM) proteomics, and next-generation RNA sequencing. Next, we will evaluate this data to assess the medicinal efficacy of V. amygdalina.
Sunny Ding, Meghana Babu, Rachel Johnson, Isha Kale, Lakshmi Narasimhan, Desiree Poon, Arjun Saini, Aryana Satheesh, Paul Woo, Cynthia Xu

Amadi

CognoTrain

With over 50 million patients worldwide, Alzheimer’s is a pervasive neurodegenerative disease that lacks Computer-based Cognitive Training/Rehabilitation (CBCT/CBCR) testing at the consumer level. So far, applications of CBCT/CBCR have had promising results on studies of Alzheimer’s patients, resulting in mental state and quality of life improvements, a decrease in patients' Clinical Dementia Rating (CDR), and improved short term memory. The purpose of CognoTrain is to show the potential of a personalized implementation of CBCT/CBCR and provide rehabilitation to Alzheimer’s patients. CognoTrain addresses common manifestations of Alzheimer’s such as topographical disorientation, loss of self, and declined recognition ability through the various features of the application. Currently, we are working on collecting data from Alzheimer’s patients and tracking their progression by monitoring their activity on the app. To ensure scientific rigor and replicability, we will document sample size, details about each patient, and the patient’s progression over time.
Krishnaveni Parvataneni, Jonathan Ma, Deniz Yilmaz, Shashank Sastry,
Aaditya Karnataki

Jahanikia

Comparing AMF and Fertilizer in Roma Tomato Plants Growing Under High pH and Drought Conditions

California is the largest agricultural state in the United States, and its wildfires have adverse effects on the crops being grown. These wildfires deplete most soil moisture, and the ash produced from wildfires raises soil pH to threatening levels. This study compares the growth of Solanum lycopersicum (Roma tomatoes) with two different soil treatments: one with Arbuscular Mycorrhizal Fungi (AMF), a known biofertilizer, and one with store-bought fertilizer. Plants with both of these treatments were placed in a high pH environment and a drought condition. The purpose of this study is to aid the agriculture industry by demonstrating the most effective way to regrow plants following a wildfire, or to even help farmers grow plants that are able to withstand a soil pH increase or lack of water. The total sample size was 9 Roma tomato plants, and the plants were separated into three groups: a group with a drought condition (3 plants), a group with high pH (3 plants), and a control group (3 plants). After four weeks, data was collected on the plants’ color, height, and stomatal density. The Roma tomatoes with added fertilizer–in both the high pH and drought conditions–had a greater change in height, were greener, and had a higher stomatal density compared to the Roma tomatoes with AMF. In conclusion, the fertilized Roma tomato plants grew best in the high pH and low water conditions, whereas the Roma tomatoes with AMF did not grow as well in general.
Delisha Doppa,Akul Murthy, Alexander Turtle

Kaur

Comparing the Efficacy of Different Polyphenols in Alzheimer's Disease Using Caenorhabditis Elegans as Model Organisms

Alzheimer's Disease is caused by an aggregation of amyloid beta and tau proteins in the brain. Polyphenols, a broad class of naturally-existing compounds, have shown to inhibit the aggregation of those proteins. This project aims to focus on expressing different combinations of those proteins through a plasmid vector in bacteria and assaying those proteins for aggregation inhibition using polyphenols to determine which polyphenol is most effective in doing so. Molecular docking is also used after our assays to rank the polyphenols in terms of effectiveness and to eliminate less desired polyphenols or acquire new potentially better ones to use. Previous progress has been made through virtual screening to identify potential compounds that effectively inhibit protein aggregation, and those compounds will continue to be analyzed for bioactivity through more computational work and bioassays. However, we focused more on the biological aspect of it, such as conducting multiple assays such as Congo Red, Avoidance, and Chemotaxis, to receive tangible results.
Sumayyah Ismail, Bridget Liu, Bhoomi Jain, Grace Hahn, Jay Subbiah

Renganathan

Comparing the Efficacy of Different Polyphenols in the Inhibition of Aggregation of Amyloid Beta Proteins in Alzheimer's Disease Using Caenorhabditis Elegans as Model Organisms

Our project focuses on neurodegenerative disorders. Specifically, we looked at Alzheimer's Disease, which is caused by an aggregation of proteins in the brain. One of the proteins involved is called amyloid-beta (Aβ), which forms plaque deposits around brain cells. The other protein is called tau, which builds up and creates tangles within brain cells. Polyphenols, a broad class of naturally-existing compounds, have been shown to inhibit the aggregation of these proteins. Our research focus is on expressing different combinations of these proteins and assaying them for the aggregation inhibition. Using polyphenols that are prevalent in everyday foods — such as curcumin, caffeic acid, and epigallocatechin gallate (EGCG) — we aimed to determine which is the most effective in reducing protein aggregation around brain cells, and, as a result, which polyphenol best reduces the effects of Alzheimer's Disease. Additionally, we used transgenic strains of Caenorhabditis Elegans as model organisms to perform these tests. Molecular docking was also used after our assays to rank the polyphenols in terms of effectiveness and to eliminate less desired polyphenols or acquire new potentially better ones to use. Past studies have made progress through virtual screening to identify potential compounds that effectively inhibit protein aggregation and those compounds will continue to be analyzed for bioactivity through more computational work and bioassays. However, our work focuses primarily on the biological and in-vitro aspect of it. Overall, since the start of our project, our group has conducted multiple bioassays including Congo Red, Avoidance, and Dynamic Light Scattering in order to receive tangible results. Our most recent work includes the Lifespan Toxicity assay and the 5-HT Sensitivity assay in which we are able to rank (add the list of compounds here) based on their effectiveness in inhibiting Aβ42 and Aβ40 peptide aggregation during Alzheimer's. In the future, we aim to continue this trend and by running assays like Fluorescence Staining, Western Blotting, and Peroxide-Induced Mitochondrial Dysfunction to better understand the effectiveness of our polyphenol compounds.
Maahir Sachdev, Isabel Lai, Aliana Tang, Aadya Sreenivas,Uma Nathan, Rishi Singh,

Renganathan

Comparing the Efficacy of Different Polyphenols in the Inhibition of Aggregation of Amyloid Beta Proteins in Alzheimer's Disease Using Caenorhabditis Elegans as Model Organisms

Alzheimer's Disease is caused by an aggregation of amyloid beta and tau proteins in the brain. Polyphenols, a broad class of naturally-existing compounds, have shown to inhibit the aggregation of those proteins. This project aims to focus on expressing different combinations of those proteins through a plasmid vector in bacteria and assaying those proteins for aggregation inhibition using polyphenols to determine which polyphenol is most effective in doing so. Molecular docking is also used after our assays to rank the polyphenols in terms of effectiveness and to eliminate less desired polyphenols or acquire new potentially better ones to use. Previous progress has been made through virtual screening to identify potential compounds that effectively inhibit protein aggregation, and those compounds will continue to be analyzed for bioactivity through more computational work and bioassays. However, this project focuses more on the biological and in-vitro aspect of it, such as conducting multiple assays including Congo Red, Avoidance, and Dynamic Light Scattering in order to receive tangible results.
Sumayyah Ismail, Bridget Liu, Bhoomi Jain, Jay Subbiah, and Rishi Singh

Renganathan

Consensus Computational Drug Screening for DNMT Inhibitors using molecular docking and deep-learning approaches

Deep-learning and algorithmic methods, such as MolTrans and AutoDock Vina, have been developed to discover potential treatments to diseases. We aim to utilize these search algorithms and neural networks in our research. We are looking for novel drugs to treat colon cancer by utilizing such computational methods. To treat colon cancer, the drug, or ligand, needs to bind to DNA methyltransferase 1, or DNMT1. Due to hypermethylation in CRC cancer, tumor suppressor genes are inactivated. So far, our research has confirmed results of previous studies using AutoDock Vina and MolTrans. Knowing that the tools work correctly, we can now look for and identify more potential DNMT1 inhibitors and test them in the wet lab.
Aksithi Eswaran, Maya Poghosyan, Aparnaa Ananthakrishnan

Cunha

CovidFatigue: Characterization and Severity Assessment of COVID-19 After-Effects

In our study, we are surveying the long-term effects of COVID-19. These effects are referred to as brain-fog and are characterized by fatigue and difficulty concentrating. To study the physiological and cognitive symptoms of brain-fog, we are designing a survey on Gorilla that will ask people who have been infected with COVID-19 to answer a series of questions about their recovery from COVID-19 as well as to complete certain cognitive tasks. Data from this questionnaire will allow us to learn about the frequency of certain symptoms of brain-fog and will help us determine how long these symptoms typically last. Collecting this data also enables us to look for external factors that affect recovery, such as vaccination status and age. We have developed a scoring scale for this questionnaire and have tested it with a sample group.
Ishani Shah, Jasmine Sayed, Keerthana Noru, Cassandra Leo, Jiya Dalal, Rishika Mallu, Rohan Vijayvikram, Rohit Mathur, Shashank Sastry, Simran Tawari

Jahanikia

Detecting Steelhead Trout (Anadromous Oncorhynchus Mykiss) Presence in the Alameda Watershed after Habitat Modification Using Environmental DNA Sampling Technique

Dams, diversions, and other infrastructure Alameda Creek built initially for flood control, pose an undeniable threat to migrating fish species. One such species is the Steelhead trout, the anadromous (ocean-going) life-history form of O. mykiss (a salmonid native to the Pacific’s cold-water tributaries). With their ordinary route obstructed and breeding grounds demolished, the Steelhead trout's abundance in the Alameda Creek watershed decreased extensively to the point that all Distinct Population Segments of the Steelhead Trout were eventually listed as threatened under the Endangered Species Act. In response to these habitat modifications, the Alameda County Water District has installed and/or is in the process of installing fish ladders and fish screens. Baseline steelhead population data is essential to investigate the efficacy of these restoration measures. We used a relatively non-invasive approach, i.e the environmental DNA sampling method, which involved collecting and filtering water samples from 3 sites along the Alameda Creek, running Polymerase Chain Reaction on DNA extracted from the residue (using primers specific to steelhead), and analyzing the products via gel electrophoresis. This presentation will cover how our results will help enhance current conservation methods.
Chahak Gupta,
Anushree Marimuthu,
Sylvia Lyu,
Shelley Fernando,
Alexzendor Misra,
Emily Dai,

Suresh

Development of synthetic aptamers for use as low-cost PLD1 inhibitors.

PLD1 is a gene that codes for an enzyme that breaks down phosphatidylcholine into phosphatidic acid and choline. The phosphatidic acid then leaves the cell and attaches to an mTOR receptor in another cell, which launches the signal transduction pathway. As a result of signal transduction and a phosphorylation cascade, the cell starts performing mitosis. Due to excessive amounts of phosphatidic acid, the mTOR receptor constantly signals to the cell to start mitosis through DAG kinases. PLD1 amplifies the anti-apoptotic functions that cause inflammation and create a roadblock for chemotherapy. Our goal is to design synthetic aptamers using specialized DNA or RNA bases to act as competitive inhibitors for PLD1, allowing patients to continue chemotherapy.
Anushka Sinha, Dhruv Pathak, Chehakdeep Kaur, Shreeya Sawant, Elora Das, Pranav Gopal, Kush Bhalala, Gayathri Nair, Hima Shringeri

Amadi

Dissonance

Cognitive dissonance theory is a theory stating that when there exists a discrepancy between someone’s external actions (behaviour) and their internal values (attitude), this discrepancy will cause dissonance. To justify this dissonance, cognitive rationalization occurs. Cognitive dissonance has been studied and measured using neuroimaging modalities, namely EEG and fMRI. Our group is studying the effects of COVID-19 on cognitive dissonance in adolescents. We have developed a questionnaire to measure the dissonance teens hold between their attitudes about the pandemic and their behaviours during it. Constant streams of new, conflicting, and complicated information make young people increasingly likely to experiences dissonances between their actions and their beliefs, and we hope to investigate the level of this dissonance through our questionnaire.
Myra Malik, Aanika Bedi, Advika Govindarajan, Amulya Harish, Heejee Yoon, Janaki Rakesh, Krishi Jaladi, Lale Kurtulush, Maddy Zhang, Mano Tatapudi, Rohan Kondapalli, Rujuta Jambe, Tanisha Mehta, Vishruth Dinesh

Jahanikia

Does Social Media Engagement From Consumers Increase the Creativity of Social Media Influencers?

Creativity is defined as the application of originality to create unique works of art. While creativity isn’t dependent on skill, it is fueled by imagination and individuality. The age of social media has dramatically expanded the traditional definition of creativity as creative individuals can connect with millions of people. This makes it crucial for one to identify the difference between creative influencers and influencers. To measure how creative an individual is, some creativity assessments analyze the degree of achievement that someone has achieved in a certain skill. Other assessments ask individuals to think of ways to repurpose something in a certain amount of time. The Creative Achievement Questionnaire (CAQ) examines achievement in a variety of categories, including music, art, and dance, among many others. Another assessment, the Inventory of Creative Activities and Achievements (ICAA), evaluates the frequency of creative actions alongside the level of achievement obtained. One category that is not currently present in the CAQ or ICAA is creative influencers — people who utilize social media to promote their creative skill and influence others to help spread their expertise. Our aim is to develop a subset of questions that accurately identifies creative influencers and eventually include this portion in the CAQ or ICAA. In this research study, we are examining several types of creativity assessments, alongside the questions we believe are appropriate. This allows us to determine whether an individual is a creative influencer based on an analysis of their current social media and the types of platforms they run.
Rucha Kulkarni, Angeline Yeh, Meenakshi Yarlagadda, Rihalya Sivakumar,
Rasya Ramakrishnan, Daphne Chao

Jahanikia

Effects of Excess Arbuscular Mycorrhizae on Phosphorus Deprived Lactuca Sativa

The associations between roots and fungi are called mycorrhizae. There is a mutualistic relationship between them fosters better water and nutrient absorption by plants, and can enable plants to share resources. The main nutrients required by plants for optimal growth are nitrogen, phosphorus and potassium (NPK). We hypothesised that when there is deficiency of any of these nutrients, arbuscular mycorrhizae may compensate by sharing the limited amount of the nutrient between various plants. We are studying the growth pattern of Lactuca Sativa (Buttercrunch Lettuce) in low and optimal phosphorus soil environments. We are testing the effect of low, natural and elevated levels of mycorrhizae in each of these soil environments. The growth of plants will be monitored based on leaf size, plant height, root depth and more. If the plants growing in phosphorus deficient soil compare or grow better than plants in optimal phosphorus soil, this will support our claim that mycorrhizae can replace soil nutrients.
Shreyan Phadke, Siddh Saxena, Shrinad Bangalore

Kaur

Emerging Potential of Thymoquinone and Piperine Nanostructured Lipid Carriers for Cancer Treatment

Nanostructured lipid carriers (NLCs) are drug delivery systems that can improve oral administration of drugs that have poor aqueous solubility and poor metabolic stability, while also reducing toxicity and increasing the dosage of drugs delivered to the body. Thymoquinone (TQ), a flavonoid, is obtained from black cumin (Nigella sativa) and possesses anti-inflammatory and antioxidant qualities that prevent damage to cells and induce apoptosis in cancer cells. However, thymoquinone has poor aqueous solubility leading to limited bioavailability, the dose of drugs that reach the treatment site. To combat this, we chose piperine (PP), an alkaloid responsible for the pungency of black pepper (Piper nigrum), to increase the bioavailability and absorption of drugs such as curcumin, making it a likely component in increasing thymoquinone’s solubility and anticancer effects via NLCs. We report that the NLCs are viable delivery systems with a constant release rate and high entrapment efficiency of 99.64% and 99.74% average entrapment of TQ-loaded and TQ and PP-loaded NLCs. With the NLCs, we investigated TQ’s anticancer mechanism that targets copper located in cancer cells to induce oxidative damage. Post-gel electrophoresis assay, the DNA damage and elongation of HCT116 cells exposed to TQ and PP loaded NLCs averaged out to be greater than that of the cells exposed to unloaded NLCs and TQ loaded NLCs, respectively. Our findings indicate that the NLCs are optimal for drug delivery, and based on the cell morphology and quantitative results, piperine is a favorable candidate in enhancing thymoquinone’s anticancer abilities.
Archana Satish, Harshita Bathina, Shreya Gulati, Meghana Iyer

Renganathan

Hybridoma Cell Expansion for HER2 Breast Cancer-Specific Antibody Production

Breast cancer is an expansive disease that affects upwards of 2 million patients per year. HER2 Breast cancer cells have specific antigens bound on to them. ADCs, antibody-drug complexes, can attack these breast cancer cells by latching the antibody onto the antigen which causes it to release a toxic payload, thereby killing the cell. Our project is to culture Hybridoma cells, which are cells that secrete mouse cell-specific mouse IgG. After these cells secrete the antibodies, we detect the antibody presence and estimate antibody concentration by conducting ELISA assay. In the future, we hope to continue our project by purifying antibodies to get rid of extra proteins bound onto them. We hope to use methods such as HIC-HPLC, UV-Vis, ultrafiltration, and others to optimally purify these antibodies. After a load of purified antibodies are obtained, another group at ASDRP will conjugate chemical linkers and drugs to them to form the ADC.
Suraj Kumar,
Ashwin Vijayvikram

Yamamoto

Hypoglycemic activity of Trigonella foenum-graecum in the C. elegans model

Diabetes Mellitus is a high-risk chronic metabolic disease and is the seventh leading cause of death in the United States. There are several types of diabetes mellitus, including type 1 DM, type 2 DM, maturity-onset diabetes of the young, and gestational diabetes. Insulin is a key hormone that converts glucose to energy. Because of the lack of insulin production, cells are unable to use glucose in order to produce energy, resulting in hyperglycemia. Even though diabetes is one of the oldest diseases, no cure has been discovered; however, several drugs have been developed to manage it more effectively. Recently, natural products are becoming a major part of the pharmaceutical drug industry, and are widely used especially in the east. Trigonella foenum-graecum, or fenugreek, is one of these drugs. Fenugreek is a medicinal plant known to have antidiabetic properties which stem from its bioactive compounds like diosgenin, trigonelline, 4-hydroxyisoleucine, leucine, and L-lysine. Our research is focused on determining the most efficient method in which different phytoconstituents can be extracted, conduct total content assays and assess their anti-diabetic potential and chemical properties.
Aditi Adapala, Sahana Ravishankar, Shrimayi Chaganti, Shrinithi Sathiyaseelan, Amrita Guha, Aarya Morgaonkar, Tanvi Sri Sai Penugonda

Renganathan

Identification and Analysis of Plant Growth Promoting Bacteria in LEAF Community Garden Soil

In today’s largely populated modern world, crop yield is becoming increasingly more important. To increase crop yield, new modern technologies for farming are continuously being innovated. The aim of this study is the identification of Plant Growth Promoting Bacteria (PGPBs) and their properties. In order to conduct the experiment, soil samples were collected from the community garden LEAF (Local Ecology and Agriculture Fremont). These samples were grown in agar solutions, and the two bacterial strains that grew from them were analyzed to determine the species of the bacteria. Using a DNA extraction kit, DNA was removed from the bacteria and then amplified versions were sent to RF Biotech for DNA sequencing. The DNA sequences were then used to determine that the two bacterial species in question are Bacillus cereus and Morganella morganii. Afterwards, multiple assays were used to measure the efficiency of each bacterial species to absorb various substances that would be helpful for plant growth. The aim of this research is to better understand which bacterial strains are more beneficial for plants, and which ones are more harmful. Through having greater zones of inhibition, the bacterial species M. morganii proved to be more efficient in the CAS and phosphate solubilization assays. On the other hand, the bacterial species B. cereus proved to be more efficient in the CMC and Amylase assays. These results will assist LEAF in enriching their soil in order to increase their crop yields by allowing them to increase the concentration of advantageous bacteria and decrease that of detrimental bacteria.
Pooja Ramadas,
Dhruv Pathak,

Kaur

Identification of Mycorrhizal Fungi in Urban Garden Soil

The vast majority of plant species benefit from mutualistic relationships with mycorrhizal fungi. Mycorrhizae protect the plant from root pathogens and significantly improve uptake of water and vital nutrients. Therefore, fungi play a huge role in the survival of plants in natural ecosystems as well as in man-made gardens. In this study, we investigated the species of mycorrhizal fungi in an urban garden. Specifically, we hoped to find Cenocuccum geophilum as it is a common mycorrhizal fungus found in Northern California.
Soumya Appalla,Matthew Pang, Kimberly Khow

Kaur

Identification of Plant Growth Promoting Bacteria in LEAF Soil

In today’s largely populated modern world, crop yield is becoming progressively more important. As a result, an aim of modern farming techniques has become to maximize crop yield through understanding the crop’s microbiome. The objective of the present study was to identify PGPBs (Plant Growth Promoting Bacteria), or bacteria that are optimal for plant growth, in the plant sol. To conduct this experiment, soil samples from the community garden LEAF (Local Ecology and Agriculture Fremont) Center were collected, and bacteria from these samples were grown and analyzed. The bacteria were first grown using agar solutions such as nutrient agar and LB (Luria Bertani) broth. These bacteria were then used in different assays that determined their properties and functions in the plant. Through aforementioned procedures, we have isolated two distinct species of bacteria, one white and one orange in appearance. Current assays on the bacterial colonies have identified zones of inhibition for bacterial characteristics such as phosphate solubilization. Subsequent assays will include cellulase production (CMC), siderophore solubilization (CAS), amylase production, and more. DNA extraction, polymerase chain reaction (PCR), and DNA sequencing will also be used to identify the particular species of bacteria in question. These results will assist LEAF in enriching their soil in order to increase their crop yields by allowing them to increase the concentration of beneficial bacteria and decrease the concentration of harmful bacteria.
Pooja Ramadas
Ashneet Dhami
Karan Saini
Dhruv Pathak
Maya Singla
Riya Sanampudi
Angeline Ho

Le

Identification of Plant Growth Promoting Bacteria in LEAF Soil

In today’s largely populated modern world, crop yield is becoming progressively more important. As a result, an aim of modern farming techniques has become to maximize crop yield through understanding the crop’s microbiome. The objective of the present study was to identify PGPBs (Plant Growth Promoting Bacteria), or bacteria that are optimal for plant growth, in the plant soil. To conduct this experiment, soil samples from the community garden LEAF (Local Ecology and Agriculture Fremont) Center were collected, and bacteria from these samples were grown and analyzed. The bacteria were first grown using agar solutions such as nutrient agar and LB (Luria Bertani) broth. These bacteria were then used in different assays that determined their properties and functions in the plant. Through aforementioned procedures, we have isolated two distinct species of bacteria, one white and one orange in appearance. Current assays on the bacterial colonies have identified zones of inhibition for bacterial characteristics such as phosphate solubilization. Subsequent assays will include cellulase production (CMC), siderophore solubilization (CAS), amylase production, and more. DNA extraction, polymerase chain reaction (PCR), and DNA sequencing will also be used to identify the particular species of bacteria in question. These results will assist LEAF in enriching their soil in order to increase their crop yields by allowing them to increase the concentration of beneficial bacteria and decrease the concentration of harmful bacteria.
Pooja Ramadas, Ashneet Dhami, Karan Saini, Dhruv Pathak, Maya Singla, Riya Sanampudi, Angeline Ho

Le

Impacts of Vegetation Recovery on Wildfire Affected Soil

Wildfires are the most common natural disaster in California, with 2020 being the worst fire season on record. Besides the cost of wildfires on humans, they also have a significant effect on the environment. Although wildfires can benefit ecosystem health, frequent and repeated burnings may inhibit complete vegetation recovery and sterilize the soil. While the separate effects of fires and ecological factors on soil and vegetation have been studied extensively, our project aims to confirm past findings for a California site and also relate wildfire-affected soil with post-fire vegetation recovery. Using GIS, we mapped vegetation cover and soil quality measurements, such as pH and above-ground litter volume, to determine the relationship between post-fire poor soil quality and vegetation recovery.
Kai Doemling, Jiaming Yuan, Alissa Doemling, Ashley Heck, Kari Lee

Suresh

In vitro characterization of human DNA Methyltransferase inhibitors on HCT-116 Colorectal cancer cells

In vitro characterization of human DNA Methyltransferase inhibitors on HCT-116 Colorectal cancer cells Colorectal cancer (CRC), the development of cancer in the colon or rectum, is a common cancer which leads to death (American Cancer Society, 2019). Epigenetic therapy is a novel cancer treatment method displaying promising clinical results (Nepali, Liou, 2021). Epigenetic modifiers activate genes regulating the cell cycle and apoptosis by demethylating certain regions of DNA to inhibit the expression of cancer (Nepali, Liou, 2021). This project focuses on the use of new analogs of the drug N-Phthaloyl L Tryptophan (RG108), a non-nucleoside DNA Methyltransferase 1 (DNMT1) inhibitor able to reverse the effects of DNA methylation while reactivating tumor suppressor genes (Hagemann et al., 2011). Certain tumor suppressor genes were chosen based on their antiproliferative traits. These genes work to slow down cell cycle progression and induce apoptosis. Our interest in RG108 and its analogs was initiated by studies on effective inhibition of proliferation by nucleoside and non-nucleoside inhibitors (Brueckner et al., 2005). RG108 is not an FDA-approved treatment for colorectal cancer, so this work hopes to derive any meaningful insights by using RG108 as a control along with similar analogs to RG108 to potentially find novel or better inhibitors for DNMT1 (Medina-Franco et. al, 2015). The cell line used was the epithelial human HCT116 cell line. Current experimentation focuses on validating RG108’s role on HCT116 cells to ensure accurate technique. Cell proliferation assays and gene expression analysis will be used to test the efficacy of RG108 (Riss et al, 2016). In the future, analysis of the reactivation of tumor-suppressor genes when treated with RG108 will be implemented with qPCR (Assis et. al, 2018). Immunoblotting will serve a similar purpose, determining levels of tumor suppressor proteins involved in cell cycle checkpoint regulation or levels of proteins involved in the intrinsic and extrinsic apoptotic pathways after RG108 treatment (Jan et. al, 2019). Cytotoxicity of RG108 will be analyzed with the study of migration and colony formation with the clonogenic and cell migration assay (Ou et. al, 2018). Further analysis of cell viability will be done using flow cytometry, examining cell cycle progression in the context of G2/M checkpoint status (Ou et. al, 2018). Fluorescent microscopy will be used to visualize caspase activation (Zheng et. al, 2021) After conducting the validation experiments mentioned above, future work aims to isolate connections between treatment with novel RG108 analogs and reactivation of tumor suppressor genes and determining whether the analogs capability for immunomodulation would have increased efficacy when compared with RG108 and other FDA-approved drugs. Key Words: Colon Cancer, Biology, Methylation, RNA, Cancer Cell Lines, Epigenetics, Biochemistry
Sanjana Vadapalli, Hena Patel,Alfiya Raja,Sreshta Yelisetti,Arya Kulkarni,Samantha Wu,Ojasvi Mudda, Aditya Seetharaman

Cunha

In vitro characterization of human epigenetic inhibitors (DNA Methyltransferase inhibitors and HDACs) on HCT-116 Colorectal cancer cells

Colorectal cancer (CRC), the development of cancer in the colon or rectum, is a common cancer which leads to death. Epigenetic therapy is a novel cancer treatment method displaying promising clinical results. Epigenetic modifiers activate genes regulating the cell cycle and apoptosis by demethylating certain regions of DNA to inhibit the expression of cancer. This project focuses on the discovery/characterization of potential DNMT inhibitors in the context of colorectal cancer, which are able to reverse the effects of DNA methylation while reactivating tumor suppressor genes. Certain tumor suppressor genes were chosen based on their antiproliferative traits. These genes work to slow down cell cycle progression and induce apoptosis. Our interest in epigenetic inhibitors were initiated by studies on effective inhibition of proliferation by nucleoside and non-nucleoside inhibitors. The cell line used was the epithelial human HCT116 cell line. Current experimentation focuses on validating decitabine and RG108’s (another DNMT inhibitor) role on HCT116 cells to ensure accurate technique. Cell proliferation assays and gene expression analysis will be used to test the efficacy of these drugs. In the future, analysis of the reactivation of tumor-suppressor genes when treated with these drugs will be implemented with qPCR. Immunoblotting will serve a similar purpose, determining levels of tumor suppressor proteins involved in cell cycle checkpoint regulation or levels of proteins involved in the intrinsic and extrinsic apoptotic pathways. Cytotoxicity of these drugs will be analyzed with the study of migration and colony formation with the clonogenic and cell migration assay. Further analysis of cell viability will be done using flow cytometry, examining cell cycle progression in the context of G2/M checkpoint status. Fluorescent microscopy will be used to visualize caspase activation. After conducting the validation experiments, future work aims to isolate connections between treatment with novel DNMT analogs and reactivation of tumor suppressor genes, along with expanding to HDAC (histone deacetylase) inhibitors for better efficacy.
Ojasvi Mudda, Aditya Seetharaman, Aayushi Ahlawat, Arya Kulkarni, Alfiya Raja, Aksithi Eswaran

Cunha

In-silico characterization of epigenetic inhibitors of DNA methyltransferase and histone deacetylases on the HCT116 colorectal cancer cell line

In cancerous states, DNA methyltransferase 1 (DNMT1), an enzyme that catalyzes the addition of methyl groups, adds excess methyl groups to the CpG islands in tumor suppressor genes, which results in the genes being silenced. DNMT1 inhibitors reverse this process and activate the genes again (Hu, Liu, Zeng, et al., 2021). Similarly, the upregulation of histone deacetylases (HDACs) increases the suppression of DNA transcription in certain areas, including tumor suppressor genes. HDAC inhibitors ensure that this does not happen (Ceccacci, Minucci, 2016). There are many obstacles to finding novel inhibitors in the modern era, such as narrowing down potential inhibitors from the large chemical space, with the largest one being cost challenges to testing a large number of compounds (Wouters, McKee, Luyten, 2020). Furthermore, after a compound likely to have high efficiency has been identified, the materials to synthesize the compound could be inaccessible or dangerous to handle. Even if these obstacles are overcome and the drug is created, it might not work as efficiently as predicted. Instead of finding drugs the conventional way, we are taking a more computational approach to finding novel treatments to colon cancer with the processes of dimensionality reduction (Rhys, 2020) and molecular docking (Meng, et al., 2011). With various clustering techniques, we used the knowledge of pre-existing inhibitors, such as RG108, to cluster compounds with similar chemical properties together from a ChemBL (Mendez, et al., 2018) dataset representing the chemical space. Then using Avogadro (Hanwell, et al., 2012), Orca (Neese, et al., 2011), and AutoDock Vina (Trott, Olson, 2010), we will batch dock those similar compounds with AutoDock Vina. With the binding affinities that AutoDock Vina outputs, we can narrow down the list of possible drugs that will be effective against colon cancer. Next, we will use DeepCDR, a silico tool, to determine different drugs’ efficiency on colon cancer cell lines based on the transcriptomic, genomic and epigenomic data of cell lines along with previous drug-cell line pair patterns (Liu et al, 2020). Many drugs, although useful in fighting many diseases, are harmful to the liver, one of the most vital organs in the human body. The MLDL Liver Tool plans to reduce this problem by predicting drug-induced liver injury (DILI) from compounds, with the use of Morgan molecular fingerprints converted from simplified molecular-input line-entry systems (SMILEs), by using convolutional neural networks (CNN) to process curated datasets and make predictions . Our research aims to discover new protein inhibitors by combining a variety of software tools. With this method, we can look through multiple compounds and spot structural and chemical connections between different drugs that are hard to see through manual and physical experiments.
Samarth Shah, Aksithi Eswaran, Aparnaa Ananthakrishnan, Ashley Lin, Nandini Anantha, Shikha Kathrani, Alice Guo, Alexis Nguyen, Eda Ugurlar, Ivan Zhang

Cunha

Investigating limits to divergent thinking through creativity assessments that indicate functional fixedness

Functional fixedness is a cognitive bias that limits one’s ability to think of novel and creative uses for an object. The phenomenon is known to limit divergent thinking, a key component in an individual’s level of creativity. Divergent thinkers are able to think of multiple unique solutions to one problem. The Alternate Uses Test is a test that asks the participant for as many unique uses for an object as they can think of, assessing functional fixedness and divergent thinking. The Remote Associates Test gives participants three random words and asks them to come up with a fourth related word. Our project aims to understand how functional fixedness affects human creativity through the development and administration of original creativity tests.
Hayden Fu, HeeJee Yoon, Jack Poon, Jasmine Traidman, Mina Fedor, Nicole Jin, Rishabh Bhargava, Pranjal Bhartia, Rucha Kulkarni

Jahanikia

Investigating the Ecological Impacts of Invasive Mud Snail Species, Ilyanassa obsoleta, on Native San Francisco Bay Mudflat Inhabitants

Ilyanassa obsoleta, native to the Atlantic coast, is a foreign yet abundant mollusk in the San Francisco Bay mudflats. It is a well-established invasive species noted for displacing the native mud snail, Cerithidea californica (Race, 1982). The objective of this study was to analyze the impact of I. obsoleta’s presence on the biodiversity, species abundance, and size distribution of native mudflat species. Using random sampling and biodiversity hotspot methods, our team collected samples from four different locations: Berkeley Marina (North and South), Point Emery, and Crab Cove. We processed samples based on specimen wet weights and sizes and compared data from sites with a presence to sites with an absence of I. obsoleta. We plan to extend our project by acquiring more field data, especially in sites observed to have an abundance of I. obsoleta, and diversifying our means of processing and analysis.
Rachel Jiang, Aryel Zhang, Anusha Sainarayanan, Nitya Sharma, Pranav Prakash

Benson

Investigating the Effect of Alpha-Synuclein Aggergation in Parkinson's Disease Model using a transgenic C. elegans model

Parkinson’s disease (PD) is a progressive neurodegenerative disorder that mainly affects individuals over 65 years old, making up ~2% of the US population. PD, like other neurodegenerative diseases such as dementia with Lewy bodies (DLB) and multiple system atrophy (MSA), has been linked to the aggregation of misfolded alpha-synuclein (a-syn) proteins in the brain. The misfolding of a-syn is caused by a mutation in the SNCA gene which leads to insoluble aggregates of proteins present in dopaminergic neurons, causing progressive neuronal cell death. Our project is studying the effects of a-syn aggregation in movement and learning in transgenic C. elegan models to understand the underlying effects of alpha-synuclein. We are investigating the potential therapeutic effects of curcumin, a polyphenol with antioxidant and neuroprotective properties, to reduce the aggregation of a-syn and possibly recover movement deficits induced by a-syn aggregation in transgenic C. elegans. Overall, we hope our research will further the development of curcumin as a therapeutic treatment for Parkinson’s disease.
Arushi Singhal, Aryan Makhija, Allen Ni, Anirudh Ramadurai, Katherine Xie, Sunanditha Vempati, Amulya Harish, Bhumika Iroji, bhumikairoji56@gmail.com, Akshita Ponnuru, ponnuru@gmail.com

Truong

Investigating the Effect of Amyloid Beta Aggregation on Associative Memory In Transgenic Alzheimer's Disease Models

The aggregation of the protein called amyloid-beta has been theorized to cause Alzheimer’s disease (AD), the most common type of neurodegenerative dementia. This aggregation forms plaques around neural cells which causes cell lysis. Our research project is directed towards understanding how amyloid-beta (Aβ) aggregation affects learning and memory formation.To study the effects of Aβ aggregation, we are using the model organism called Caenorhabditis elegans with over-expression of Aβ in neurons To understand the effects of amyloid-beta aggregation on C. elegans, we test the C. elegans’ short-term and long-term associative memories through STAM and LTAM assays. We hypothesize that Aβ aggregation in the neurons will significantly reduce the duration of associative memory and negatively affect motility. The results yielded by the STAM assay demonstrated that the Aβ aggregation affected the duration of short term associative memory in transgenic C. elegans strain relative to the control. Given this behavior, we expect similar trends in their long term associative memory assay. By understanding the effect of Aβ aggregation on associative memory in transgenic C. elegans models of AD, we will be able to develop appropriate treatments to assess its effectiveness in treating neurodegeneration and memory-related disorders.
Jay Subbiah,
Aden Sun,
Simran Tawari,
Sripradha Manikantan,
Ashneet Dhami,
Thoya Raman,
Riya Sanampudi,
Daniel Nguyen,
Tanvi Sri Sai Penugonda

Truong

Investigating the Effect of Amyloid Beta Aggregation on Associative Memory In Transgenic Alzheimer's Disease Models

The aggregation of the protein called amyloid-beta has been theorized to cause Alzheimer’s disease (AD), the most common type of neurodegenerative dementia. This aggregation forms plaques around neural cells which causes cell lysis. Our research project is directed towards understanding how amyloid-beta (Aβ) aggregation affects learning and memory formation.To study the effects of Aβ aggregation, we are using the model organism called Caenorhabditis elegans with overexpression of Aβ in neurons To understand the effects of amyloid-beta aggregation on C. Elegans, we test the C. Elegans’ short-term and long-term associative memories through STAM and LTAM assays. We hypothesize that Aβ aggregation in the neurons will significantly reduce the duration of associative memory and negatively affect motility. The results yielded by the STAM assay demonstrated that the Aβ aggregation affected the duration of short term associative memory in transgenic C. Elegens strain relative to the control. Given this behavior, we expect similar trends in their long term associative memory assay. By understanding the effect of Aβ aggregation on associative memory in transgenic C. elegan models of AD, we will be able to develop appropriate treatments to assess its effectiveness in treating neurodegeneration and memory-related disorders.
Aden Sun,
Ashneet Dhami,
Jay Subbiah,
Riya Sanampudi,
Simran Tawari,
Sripradha Manikantan,
Tanvi Penugonda,
Thoya Raman,

Truong

Investigating the Effect of Curcumin on Alpha-synuclein Aggregation in Parkinson’s Disease Using a C. Elegan Animal Model

Parkinson's disease (PD) is a progressive neurodegenerative disorder that mainly affects individuals over 65 years old, making up ~2% of the US population. PD, like other neurodegenerative diseases such as dementia with Lewy bodies (DLB) and multiple system atrophy (MSA), has been linked to the aggregation of misfolded alpha-synuclein (a-syn) proteins in the brain. The misfolding of a-syn is caused by a mutation in the SNCA gene which leads to insoluble aggregates of proteins present in dopaminergic neurons, causing progressive neuronal cell death. Our project is studying the effects of a-syn aggregation in movement and learning in transgenic C. elegan models to understand the underlying effects of alpha-synuclein. We are investigating the potential therapeutic effects of curcumin, a polyphenol with antioxidant and neuroprotective properties, to reduce the aggregation of a-syn and possibly recover movement deficits induced by a-syn aggregation in transgenic C. elegans. Overall, we hope our research will further the development of curcumin as a therapeutic treatment for Parkinson's disease.
Arushi Singhal, Aryan Makhija, Allen Ni, Anirudh Ramadurai, Katherine Xie, Sunanditha Vempati, Amulya Harish, Bhumika Iroji, Akshita Ponnuru

Truong

Investigating the Influence of Clozapine on Schizophrenic Transgenic C. Elegans Models

Schizophrenia is a chronic mental illness characterized by a distorted perception of reality, affecting 20 million people worldwide (World Health Organization, 2019). Current treatments are only palliative treatments, using typical and atypical antipsychotic drugs and psychosocial therapies to mediate symptoms such as social isolation, aggression, and apathy (Bustillo et al., 2001). Clozapine is an atypical antipsychotic drug that acts on both dopaminergic and serotonin receptors, mediating symptoms of depression, hallucinations, etc. In this study, we assessed the efficacy of clozapine on treating depression and avolition displayed by transgenic C. elegan models of schizophrenia. The transgenic C. elegan model has a genetic mutation in the daf-2 gene, resulting in avolition and altered social feeding behavior, which are representative of antisocial behaviors and schizophrenic symptoms in humans. The overall goal of this research is to understand the effects of clozapine as a treatment for depressive symptoms in schizophrenic patients. Following the administration of clozapine over 72 hours, we observed an improvement in the behavior of the E1370 schizophrenic worms’ depressive symptoms in which they were more likely to move faster and gravitate toward their desired food source, similar to the untreated wild type worms. Surprisingly, wild type worms treated with clozapine began to display a lack of motivation and slow movements, suggesting that clozapine may pose negative effects to healthy non-schizophrenic C. elegans. This research provides an in-vivo aspect to clozapine’s effect on an animal model and can be used to assist the development of therapeutic drugs that will treat and alleviate depressive symptoms found not only in schizophrenia, but in various psychiatric diseases.
Arushi Maheshwar,
Cameron Tran,
Gia Oscherwitz,
Isha Kale,
Khushi Kethana,
Mohika Pandey,
Raynard Khow,
Sinchana Hallyal,
Sylvia Ni,
Yuanjun Cai,

Truong/ Downing/ Njoo

Investigating the Influence of Clozapine on Schizophrenic transgenic C. Elegans Models

As of October 2019, schizophrenia, a chronic mental illness characterized by a distorted perception of reality, affects 20 million people worldwide (World Health Organization, 2019). Although it is currently incurable, current treatments are palliative, using typical and atypical antipsychotic drugs and psychosocial therapies to mediate the symptoms such as social isolation, aggression, and apathy (Bustillo et al., 2001). Clozapine is an atypical antipsychotic drug that has been prescribed to many patients. It acts on both dopaminergic and serotonin receptors, mediating symptoms of depression, hallucinations, and etc. In this study, we will be assessing the efficacy of clozapine on treating depression and avolition displayed by transgenic C. elegan models of schizophrenia. The E1370 strain has a genetic mutation in the daf-2 gene that displays avolition and altered social feeding mechanisms, which are representative of antisocial behaviors in humans and indicative of schizophrenic symptoms. The overall goal of this research is to understand the effects of clozapine as a treatment for depressive symptoms in schizophrenic patients. Following the administration of clozapine over 72 hours, we observed an improvement in the behavior of the E1370 schizophrenic worms’ depressive symptoms in which they were more likely to move faster and gravitate towards their desired food source, similar to the untreated wild type worms. Surprisingly, wild type worms treated with clozapine began to display a lack of motivation and slow movements, suggesting that clozapine may pose negative effects to healthy non-schizophrenic C. elegans. This research provides an in-vitro aspect to clozapine’s effect on an animal model and can be used to assist the development of therapeutic drugs that will treat and alleviate depressive symptoms found not only in schizophrenia, but in various neurodegenerative diseases.
Isha Kale,
Gia Oscherwitz,
Cameron Tran,
Khushi Kethana,
Yuanjun Cai,
Mohika Pandey,
Nithya Ganti,
Sadhana Chari,
Stacey Le,

Truong

Investigating the Influence of Clozapine on Schizophrenic transgenic C. Elegans Models

As of October 2019, schizophrenia, a chronic mental illness characterized by a distorted perception of reality, affects 20 million people worldwide (World Health Organization, 2019). Although it is currently incurable, current treatments are palliative, using typical and atypical antipsychotic drugs and psychosocial therapies to mediate the symptoms such as social isolation, aggression, and apathy (Bustillo et al., 2001). Clozapine is an atypical antipsychotic drug that has been prescribed to many patients. It acts on both dopaminergic and serotonin receptors, mediating symptoms of depression, hallucinations, and etc. In this study, we will be assessing the efficacy of clozapine on treating depression and avolition displayed by transgenic C. elegan models of schizophrenia. The E1370 strain has a genetic mutation in the daf-2 gene that displays avolition and altered social feeding mechanisms, which are representative of antisocial behaviors in humans and indicative of schizophrenic symptoms. The overall goal of this research is to understand the effects of clozapine as a treatment for depressive symptoms in schizophrenic patients. Following the administration of clozapine over 72 hours, we observed an improvement in the behavior of the E1370 schizophrenic worms’ depressive symptoms in which they were more likely to move faster and gravitate towards their desired food source, similar to the untreated wild type worms. Surprisingly, wild type worms treated with clozapine began to display a lack of motivation and slow movements, suggesting that clozapine may pose negative effects to healthy non-schizophrenic C. elegans. This research provides an in-vitro aspect to clozapine’s effect on an animal model and can be used to assist the development of therapeutic drugs that will treat and alleviate depressive symptoms found not only in schizophrenia, but in various neurodegenerative diseases.
Khushi Kethana,
Stacey Le,
Cameron Tran,
Nithya Ganti,
Mohika Pandey,
Isha Kale,
Sadhana Chari,
Gia Oscherwitz,
Kira Cai

Truong

Investigating the ecological impacts of invasive mud snail species Ilyanassa obsoleta on native San Francisco Bay mudflat inhabitants

Ilyanassa obsoleta, native to the Atlantic coast, is a foreign yet abundant mollusk in the San Francisco Bay mudflats. Its presence in the Pacific coast was first recorded in 1907. The mud snail has since been recognized as an invasive species in the San Francisco bay, known to disrupt the native ecosystem through resource domination, larvae predation, and mass reproduction. In this study, we attempt to analyze the impact of I. obsoleta’s presence on the biodiversity, species abundance, and size distribution of native species. Our team collected and processed samples from the Berkeley Marina and Point Emery mudflats and used biostatistical methods to draw relations based on the samples’ weights and sizes. We plan to extend our project by acquiring more field data, especially in sites observed to have an abundance of I. obsoleta, and diversifying our means of processing and analysis.
Aryel Zhang,
Rachel Jiang,
Jennie Wang,
Alonzo Bradford,
Pranav Prakash,

Benson

Investigating the effect of Curcumin on a-synuclein aggregation in Parkinson's Disease using a C. Elegan animal model

Parkinson’s disease (PD) is a progressive neurodegenerative disorder that mainly affects individuals over 65 years old, making up ~2% of the US population. PD, like other neurodegenerative diseases such as dementia with Lewy bodies (DLB) and multiple system atrophy (MSA), has been linked to the aggregation of misfolded alpha-synuclein (a-syn) proteins in the brain. The misfolding of a-syn is caused by a mutation in the SNCA gene which leads to insoluble aggregates of proteins present in dopaminergic neurons, causing progressive neuronal cell death. Our project is studying the effects of a-syn aggregation in movement and learning in transgenic C. elegan models to understand the underlying effects of alpha-synuclein. We are investigating the potential therapeutic effects of curcumin, a polyphenol with antioxidant and neuroprotective properties, to reduce the aggregation of a-syn and possibly recover movement deficits induced by a-syn aggregation in transgenic C. elegans. Overall, we hope our research will further the development of curcumin as a therapeutic treatment for Parkinson’s disease.
Arushi Singhal, Aryan Makhija, Allen Ni, Anirudh Ramadurai, Katherine Xie, Sunanditha Vempati, Amulya Harish, Bhumika Iroji, Akshita Ponnuru

Truong

Investigating the effect of alpha-synuclein aggregation in Parkinson’s disease using a transgenic C. Elegan model

Parkinson’s disease (PD) is a progressive neurodegenerative disorder that affects individuals over 65 years old, making up ~2% of the US population. PD, has been linked to the aggregation of misfolded alpha-synuclein (a-syn) proteins in the brain, like other neurodegenerative diseases such as dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). The misfolding of a-syn is caused by a mutation in the SNCA gene which leads to insoluble aggregates of proteins present in dopaminergic neurons, causing progressive neuronal cell death. Our project is studying the effects of a-syn aggregation in transgenic C. elegan models with overexpressed a-syn in its muscle walls to understand the underlying effects of alpha-synuclein in movement and learning. We are investigating the potential therapeutic effects of curcumin, a polyphenol with antioxidant and neuroprotective properties, to reduce the aggregation of a-syn and possibly recover movement deficits induced by a-syn aggregation in transgenic C. elegans. Overall, we hope our research will further the development of curcumin as a therapeutic treatment for Parkinson's disease.
Bhumika Iroji,
Arushi Singhal,
Amulya Harish,
Anirudh Ramadurai,
Aryan Makhija,
Sunanditha Vempati,
Karan Saini,
Sophie Menon,
Neha Nabar

Truong

Investigating the effect of alpha-synuclein aggregation in Parkinson’s disease using a transgenic C. Elegan model.

Parkinson’s disease (PD) is a progressive neurodegenerative disorder that mainly affects individuals over 65 years old, making up ~2% of the US population. PD, like other neurodegenerative diseases such as dementia with Lewy bodies (DLB) and multiple system atrophy (MSA), has been linked to the aggregation of misfolded alpha-synuclein (a-syn) proteins in the brain. The misfolding of a-syn is caused by a mutation in the SNCA gene which leads to insoluble aggregates of proteins present in dopaminergic neurons, causing progressive neuronal cell death. Our project is studying the effects of a-syn aggregation in movement and learning in transgenic C. elegan models to understand the underlying effects of alpha-synuclein. We are investigating the potential therapeutic effects of curcumin, a polyphenol with antioxidant and neuroprotective properties, to reduce the aggregation of a-syn and possibly recover movement deficits induced by a-syn aggregation in transgenic C. elegans. Overall, we hope our research will further the development of curcumin as a therapeutic treatment for Parkinson's disease.
Arushi Singhal, Aryan Makhija, Allen Ni, Anirudh Ramadurai, Katherine Xie, Sunanditha Vempati, , Amulya Harish, Bhumika Iroji, Akshita Ponnuru,

Truong

Investigating the efficiency of the saltwater mussel Mytilus californianus’s ability to filter microplastics from aquatic ecosystems

With the rapid proliferation of microplastics within marine environments, multiple studies have scrutinized the potential role of mussels in filtering these contaminants. However, there lacks a clear quantification of the types and amount of microplastics mussels take in and retain within a natural habitat, specifically for the Mytilus Californianus mussel. Thus, our research seeks to determine how effectively mussels filter microplastics over a period of multiple months, as well as any effects microplastics have on the health of mussels. Microplastics made by sanding plastics will be dyed red and distributed among 3 tanks between control, low, and high tanks at respectively 0 grams, 0.02 grams, and 0.04 grams. Mussel tissues from each tank were digested using potassium hydroxide solutions. These digestions were then filtered using a vacuum filtration machine and a sonication bath. In the future, we hope to quantify and classify our data through using a blue light microscopy and Fournier transform infrared spectroscopy. If results indicate that mussels can effectively capture microplastics, mussels could potentially be implemented as microplastic filters in various seabeds.
William Sun, AJ Sidhu, Angel Shi, Mansha Gupta, Aarsh Mittal, Aryaman Gupta,

Adams

Investigating the efficiency of the saltwater mussel Mytilus californianus’s ability to filter microplastics from aquatic ecosystems

The increase of microplastic pollution, otherwise known as plastics smaller than five millimeters, actively contributes to the threats faced by life in marine ecosystems. Microplastic pollution has the ability to adversely affect aquatic and human life by manipulating organisms’ functions. However, novel research has demonstrated that as filter feeders who have been shown to intake and retain microplastics, mussels may have the ability to minimize such pollution. Therefore, we explored the potential that mussels may have in filtering and retaining microplastics and worked towards developing a method to extract, purify, clean, and quantify microplastics from mussels, as there currently is not a standardized method to do so. Given the rising trends of microplastic pollution, different-sized mussels collected from a local tidepool were exposed to varying levels of microplastics over a period of time. After exposure, the retained microplastics from the mussels were isolated and quantified using a mussel digestion process and vacuum filtration. In the future, we plan to analyze this digestion using a dissecting microscope, ultraviolet light, centrifuge technology, and FTIR spectroscopy. All microplastics used in the experiment were created using a power sander, including 1 PETE, 2 HDPE, 3 PVC, 4 LDPE, and 5 PP plastics. Elementary data suggests that mussels may be able to efficiently filter microplastics, illuminating the role mussels play in microplastic pollution. While we are still pursuing results, these findings may prove to be insightful for addressing an environmental issue presently affecting aquatic ecosystems and we hope to be able to implement our findings in a real water system.
Advay Chatterji, Ankita Gadepalli, Olivia Ho, Mallika Saoji, Connie Yang

Benson

Investigating the efficiency of the saltwater mussel Mytilus californianus’s ability to filter microplastics from aquatic ecosystems

With a rise in plastic pollution, life in marine ecosystems is facing increasingly drastic threats. Within plastic pollution, microplastics, or plastics smaller than five millimeters, are actively contributing to this rise. These microplastics may adversely affect aquatic life by manipulating organisms’ functions. However, novel research has demonstrated that as filter feeders, mussels may have the ability to minimize such pollution. Therefore, we explored the potential that mussels may have in filtering and retaining microplastics. Given the rising trends of microplastic pollution, different-sized mussels from a local tidepool were exposed to varying levels of microplastics over a period of time. After exposure, the retained microplastics from the mussels were isolated, quantified, and analyzed using a mussel digestion process, dissecting microscope, ultraviolet light, centrifuge technology, and FTIR spectroscopy. Elementary data suggests that mussels may be able to efficiently filter microplastics, illuminating the role mussels play in microplastic pollution. While we are still pursuing results, these findings may prove to be insightful for addressing an environmental issue presently affecting aquatic ecosystems.
Andrew Benson, Serena Ramanathan, Manu Thakur, Bhoomi Jain, Aanika Bedi, Dylan Wang, Sai Tanvi Kodangal

Benson

Modeling Alzheimer’s Disease in Genetically Modified Caenorhabditis Elegans Strains

Alzheimer's disease (AD) is a neurodegenerative condition that affects over 50 million worldwide. Its main symptoms include loss of mobility and memory. While current treatments seek to relieve the symptoms, there is no known cause yet to stop the disease's progression. There is indication that multiple factors work to cause the disease, since some types (Early-Onset AD) are more impacted by genetics, while others (Late-Onset AD) worsen with age and other unknown factors. Amyloid beta aggregation has been observed to cause toxicity in neurons and is highly common in AD patients, and thus its role in the propagation of AD has been studied extensively. Here, the observations of amyloid beta aggregation's effects on the muscle cells and neurons of C. Elegans will be discussed, taking in data from both our lab work and past studies. We predict that amyloid beta aggregation will cause a loss of short term associative memory (STAM) and long term associative memory (LTAM), as well as decreased mobility. We will be also testing the effects of curcumin on Alzheimer’s Disease on C. Elegans.

Khushi Yadav,
Frances Jing,
Tanvi Sri Sai Penugonda,
Arnav Rao,
Sripradha Manikantan,
Aden Sun,
Jay Subbiah

Truong

Monastrol : Anti-Cancer Drug - Effect on Colon Cancer Cells

Cancer, one of the leading causes of death in the world, is characterized by the uncontrollable growth of defective cells in the body, creating lumps of cells known as tumors. Cells undergo uncontrollable growth when checkpoints in the cell cycle are overridden, allowing faulty cells to continue to grow without being killed. In recent studies, scientists have found that the compound monastrol is effective in arresting cells in the cell cycle and experiencing apoptosis or programmed cell death. Monastrol is of particular interest because it affects a kinesin called Eg5, a popular target for cancer therapies since it plays a crucial role in the formation of bipolar spindles during mitosis, which is responsible for dividing the cells. A kinesin is a class of protein that is involved in various cellular functions. Most importantly, their involvement in mitosis is what makes them important in cancer. By inhibiting the basal and microtubule stimulate ATPase activity of the Eg5 motor domain, the monastrol alters the ability of the Eg5 to generate force, thereby preventing it from maintaining the bipolar spindles and leading to cell death. In our study, we plan on performing MTT and spindle formation assays to better understand how effective monastrol is at treating cancer cells.
Sanika Sharma, Yashvi Monani, Siddharth Sivalanka, Anoushka Kolluru, Mayukhi Katragadda, Shreyan Phadke

Renganathan

Mud snails

Ilyanassa obsoleta, native to the Atlantic coast, is a foreign yet abundant mollusk in the San Francisco Bay mudflats. It is a well-established invasive species noted for displacing the native mud snail, Cerithidea californica (Race, 1982). The objective of this study is to analyze the impact of I. obsoleta’s presence on the biodiversity, species abundance, and size distribution of native mudflat species. Using random sampling and biodiversity hotspot methods, our team collected samples from four different locations: Berkeley Marina (North and South), Point Emery, and Crab Cove. We processed samples based on specimen wet weights and sizes and compared data from sites with a presence to sites with an absence of I. obsoleta. With biostatistical analysis, we found an overall decrease in biodiversity and size distribution in sites abundant in I. obsoleta, however, conducting an unpaired t-Test (p=0.05) concludes that there is no statistically significant difference. We used Whittaker plots among others to access species abundance and found an overall higher species abundance and species richness in sites absent in I. obsoleta. We plan to extend our project by acquiring more field data, especially in sites observed to have an abundance of I. obsoleta, and diversifying our means of processing and analysis.
Rachel Jiang, Nitya Sharma,Pranav Prakash,Miles Blackhart, Christina Fiedler

Benson

Obesity, type-2 diabetes, and other cardiovascular related diseases

The fat mass and obesity-related (FTO) gene, located on human chromosome 16, has been proven to increase the risk of obesity, type-2 diabetes, and other cardiovascular related diseases. The gene contains the code for the FTO protein. The FTO protein is a DNA/RNA demethylase, and is part of the AlkB family. The RNA demethylation caused by FTO is what links the FTO protein with cardiovascular diseases. The way the FTO protein interacts with molecules and compounds can provide a basis for design of FTO inhibitors.
Rohinee, Shivani

Brah

Overview of Cognitive Dissonance Theory With Associated Neuroimaging Modalities

Cognitive dissonance theory is a theory stating that when there exists a discrepancy between someone’s external actions (behaviour) and their internal values (attitude), in most people this discrepancy will cause dissonance, and, to justify this dissonance, cognitive rationalization. Cognitive dissonance has been studied and measured using neuroimaging modalities, namely EEG and fMRI. Certain event-related potentials, measured by EEG, and areas of the brain, detected by fMRI, are involved primarily in cognitive dissonance and cognitive rationalization. This information can be utilized to analyse cognitive dissonance and its applications in aspects of everyday life by contrasting a positive behavior with a negative/biased attitude, as opposed to the typical model of a negative behavior and a positive/morally 'just' attitude, as well as to develop a psychological assessment to measure someone’s individual level or experience of cognitive dissonance.
Aanika Bedi, Amulya Harish, Heejee Yoon, Lale Kurtulush, Mano Tatapudi, Myra Malik, Rohan Kondapalli, Rujuta Jambe, Tanisha Mehta, Tanvi Vidyala, Tanya Naveen

Jahanikia

Polyphenols

Polyphenols can relieve oxidative stress in plant cells through anti-inflammatory properties and are therefore an area of interest in neurodegenerative disease research. Glycine max, or soybean, was selected for polyphenol research due to the presence of polyphenol oxidase genes. Four test groups of Glycine Max plants were cultivated; one group was drought stressed and treated with auxins, one group was drought stressed but not treated with auxins, one group was only treated with auxins, and one group was left completely untreated as a control group. Although drought stress has been shown to increase polyphenol production, auxins’ effects on polyphenol production were the main focus of this project due to the lack of prior research on them. Leaves from each plant were collected and tested for active polyphenol oxidase genes via 2-step Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) to determine levels of polyphenol production. Activated auxins or increased polyphenol production in Glycine Max would indicate potential for further research.
Ana Hoffman, Anna Subbanna,
Erin Yang,
Radha Srinivasan,
Shelley Fernando,

Suresh

Role of Piperine as a Bioenhancer in Thymoquinone Encapsulated Nanolipid Carriers (NLC)

Thymoquinone (TQ), a phytochemical compound obtained from black cumin (Nigella Sativa), has been known to possess anti-oxidative, hepatoprotective, neuroprotective, anti-diabetic, anti-inflammatory, anti-mutagenic, and anti-carcinogenic qualities. Its anti-inflammatory and antioxidant properties prevent damage to cells and induce apoptosis in cancer cells. Unfortunately, TQ’s poor aqueous solubility leads to limited oral bioavailability. Piperine (PP), from the plant Piper Nigrum, combined with TQ, enhances TQ’s anticancer effects as well as its bioavailability by increasing thymoquinone’s solubility. Furthermore, TQ has lipophilic tendencies, the inability to dissolve in polar solvents such as water, which is where nanolipid carriers prove to be beneficial in the delivery of TQ and PP. NLCs are delivery systems that improve water solubility, increase dosage amount, reduce toxicity during administration, and provide long-term storage. To calculate the effectiveness of thymoquinone and piperine loaded NLCs, the release rate and entrapment efficiency of the drugs were measured using the nanodrop spectrophotometer. With such measurements we can determine the the concentration of drugs we are working with and the amount retained by the NLCs. One example of TQ’s many anticancer mechanisms that we looked into into is its ability to target copper located in most cancer cells to induce oxidative damage; this damage can be quantified with a gel electrophoresis/comet assay. With such assays and further testing, we hope to prove piperine’s importance as a bioenhancer in TQ-loaded NLCs.
Archana Satish,
Harshita Bathina
Sameeksha Ramesh
Shreya Gulati
Julianna Chang
Aarti Anand

Renganathan

Sentimental analysis using natural language processing

Sentimental analysis using natural language processing
Shreya Udupa

Jahanikia

Separation Analysis of Novel Antibody Drug Conjugates Using High Performance Liquid Chromatography

Antibody-drug Conjugates (ADCs) are biopharmaceutical drugs that combine monoclonal antibodies specific to surface antigens present on particular cancer tumor cells with highly potent anti-cancer agents linked via a chemical linker. The goal of this project is to determine the drug-to-antibody ratio (DAR) in a given ADC (Antibody Drug Conjugate) with IgG fragments as the antibody in developing a future cancer therapeutic. Analysis of the DAR is crucial, as low DAR could reduce the antitumor efficacy, while high DAR may affect antibody structure, stability, antigen-binding, etc, therefore causing loss of activity. Using RP-HPLC (Reverse Phase High Performance Liquid Chromatography) with C18 column, we developed a method to successfully separate Bovine IgG (immunoglobulin G) as the antibody, and are currently separating the drug, SN-38 (7-ethyl-10-hydroxycamptothecin). In our work, we will go over the steps of method validation, our HPLC conditions, and future directions when testing more novel ADCs.
Sumayyah Ismaill, Ella Jeon, Hannah Murry
4. Syona Bhide

Yamamoto

Sleep quality during the COVID-19 pandemic: Analyzing improvement of sleep behavior in adults prior to and after vaccination against SARS-CoV-2

COVID-19-related disturbances, such as the shelter-in-place order in 2020, have been linked with sleep disruption amongst the general population. Due to an increase of screen time and consumption of addictive substances correlated with the pandemic, sleep issues such as difficulty falling and/or staying asleep and imbalances in circadian rhythm have become increasingly common in adults. Such disturbances weaken the immune system, leading to an increased susceptibility to the COVID-19 virus, creating a further cycle of stress and loss of regular sleeping patterns. The purpose of the study is to examine the relationship between sleep quality and COVID-19 vaccination status by computing a sleep quality index score (SQI) for participants before and after vaccination. The study has had approximately 159 interested participants and 72 SQI scores from eligible participants, which includes 36% male and 64% female with an average age of 35.5 years. The average sleep quality index of the participants before vaccination date is 30.5 in comparison to their sleep quality after, which is 28.8. The mean average change in SQI was -1.7, indicating a slight improvement in sleep. The null hypothesis stated there was no significant difference between sleep quality index scores before and after vaccination. The T-test analysis from the ongoing study shows a significant effect of the vaccine, indicating that the null hypothesis can be rejected. The results of this study will introduce the possible psychological benefits, specifically related to sleep, of the COVID-19 vaccine to reduce biological and mental harm caused by the ongoing pandemic. Further, the study will focus on causal modeling and the various factors of sleep index based on mental, environmental, and biological factors.
Ananya Ravi, Anika Mantripragada, Avi Uppalapati, Destiny Pinto, Devan Melwani, HeeJee Yoon, Shreya Abhijit

Jahanikia

Steps Towards Developing NLP-based Software Associated with Open-Source Raspberry Pi Hardware

We extract key components/key words from phrases to reconstruct the shortened version of a conversation We aim to use NLP-based code in open-source software with hardware to analyze topics that two people have discussed during a given conversation. Keywords: NLP, Raspberry Pi, Data Science
Neo Sud, Parth Sharma, Shreya Udupa

Jahanikia

Steps towards developing a comprehensive resource to understand the Phases, Applications, and Exploring Real-Time Data from the Human Connectome Project (HCP)

The Human Connectome Project is a large-scale initiative involving teams of researchers at institutions around the world. The main goal of the project is to create a completed map of the human brain through the use of various MRI scanners and digital software. The map will serve as a baseline for future studies of brain connectivity during physical development, aging, and neurodevelopment, as well as aiding in the study and classification of neuropsychiatric and neurological disorders. The end goal of connectomics is to understand how brain areas are connected and contribute to human behavior, and how complicated systems are altered or exhibit different functions in individuals with neurological and psychiatric diseases. Once completed, the human connectome will provide valuable insights into what makes humans human, and what accounts for diversity in the behavior of healthy adults. This review includes an overview of the history of the HCP, a comparison between the brain network and the connectome, a discussion of how the human connectome can allow for the creation of neural biomarkers, a discussion of imaging techniques used in the project, a look into the C. elegans connectome, which is the first and only organism with a completed brain map, and a discussion of future research in this field. Our project aims at creating a comprehensive book/textbook to disseminate the knowledge of the Human Connectome Project, which includes studying all aspects of the project from its phases, to its costs, to its modalities, to its assessments, fMRI techniques, applications and implementations to psycho degenerative diseases.
Gia Oscherwitz, Hansika Daggolu, Neha Nabar, Sashvath Koyi, Sriya Gonuguntla, Anastasia Bubelich, Abhinav Satish,

Jahanikia

Study of Rhizobium Bacteria in Local Soil From Leaf C.R. Stone Garden

The purpose of this study is to identify the presence of mutualistic bacteria strains in Leaf Garden Fremont soil and investigate symbiotic relationships of the bacteria with the foliage in the garden. Rhizobium is a nitrogen fixing bacteria that forms mutualistic relationships with plants, usually legumes, and converts nitrogen in the air into something the plant can intake for nutrients (Miransari, 2016). For this study, our researchers from the Kaur Group at ASDRP collected soil samples from Leaf C.R. Stone Garden, an urban community garden in Fremont and went through multiple procedures and observations to determine if there was rhizobium in the soil. Three samples were taken from 3 areas at the garden with 50 grams of soil in each sample. Additionally, identification was conducted to classify the foliage in the area the soil samples were collected from in order to determine the plants that rhizobium is able to form mutualistic relationships with.
Riya Puvvada,
Anirra Kutty,
ha Bharadwaj,
Tanisha Deep,
Aparna Sureshbabu,

Kaur

Studying the Hypoglycemic activity of Trigonella Foenum-Graecum

Type 2 diabetes is an illness causing a lack of insulin/insulin resistance which affects the way the body processes sugar. This causes high bloodsugar levels and other associated health concerns. Trigonella foenum-graecum or fenugreek is a plant in which its phytoconstituents -- such as amino acids, phenolics, flavonoids, saponins, and alkaloids -- have been researched and shown to exhibit hypoglycemic, antioxidant and therapeutic effects. This study aims to find which of the aforementioned compounds has the greatest anti-diabetic effect through conducting a series of in-vivo assays, such as nile red staining and pharyngeal pumping assay, on the microscopic C. Elegans model; as well as studying the results of colorimetric assays measuring the antioxidant activity of each phytoconstituent. Antioxidant Assays including MTT and ABTS have also been researched and pursued by our group to measure the anti-diabetic potential that our extracts may have. Recently, we have been redoing our extracts and refining our processes as well.
Amrita Guha, Shrimayi Chaganti, Aditi Adapala, Anagha Rajesh, Shrinithi Sathiyaseelan, Riya Patel

Renganathan

Studying the Impact of the COVID-19 Pandemic on the Behavioral Plasticity of Adolescents

Cognitive dissonance theory states that when one’s attitude conflicts with their behavior, a discomfort arises in the brain; this discomfort is known as cognitive dissonance. The goal of our study is to collect information on the dissonance that high school students have experienced over the course of the COVID-19 pandemic and to truly understand the correlation between the effect of the pandemic and dissonant feelings teenagers have recently experienced. We hypothesized that new and constantly changing legislation concerning vaccines, masks, public safety, and school regulations have led to students experiencing cognitive dissonance. As of now, we have about 50 participants and about 120 consenting parents. Overall, participants have experienced mild dissonance; lowest dissonance was found in the vaccines group (statements regarding COVID-19 vaccines) and highest dissonance was found in the government/authority group (statements regarding government/authority). Here, we will discuss our findings in the preliminary data collection that we have conducted, and the primary data analysis that we have completed.
Amulya Harish, HeeJee Yoon, Janaki Rakesh,Krishi Jaladi, Lale Kurtulush, Maddy Zhang, Mano Tatpudi, Myra Malik, Rohan Kondapalli, Tanisha Mehta,Vishruth Dinesh,

Jahanikia

Studying the biological mechanisms of andrographolide and a related analog through quantitative gene expression screens

Andrographolide 1, a labdane diterpenoid lactone natural product isolated from the plant Andrographis paniculata, has been widely reported for its diverse biological properties, including its anticancer, anti-inflammatory, anti-bacterial, antiviral, anti-malarial, anti-diabetic, and antifeedant properties. This natural product derives its biological properties from its ability to act as a Michael acceptor and alkylate proteins by covalently inhibiting cysteine residues. In particular, 1 has shown strong activity as a covalent inhibitor of NF-kB, a transcription factor that lies at the crossroads of many biological pathways and mediates inflammatory, mechanotransductive, and cellular immune responses. Andrographolide has also been involved in clinical studies, including a clinical trial in Chile, where it diminished brain atrophy and was demonstrated to be well-tolerated in patients diagnosed with multiple sclerosis. We investigate the biological activities of both 1 and 2 through quantitative gene expression screens of 27 target genes involved in the NF-κB protein complex, the mitogen-activated protein kinase (MAPK) pathway, and in the general homeostasis of cells [Figure X]. We hypothesized that expression levels of all genes would be altered in cancer cell lines, particularly HCT 116 and Jurkat cell lines, treated with both 1 and 2 compared to cells left untreated. Similar gene expression trends between cells treated with 1 and 2 may suggest that both compounds follow a similar mechanism of action and that improvements in the biological activity of 2 are likely due to increased cell permeability. We performed reverse-transcription quantitative polymerase chain reaction (RT-qPCR).
Sophia Fung; Anushkaa Singhal, KaraTran, Saira Hamid

Tallapaka

Studying the effects of Paclitaxel on Cephalotaxine and Sulforaphane for improving bioavailability.

Cancer is identified by the abnormal accumulation of rapidly dividing cells, serving as the collective term for a multitude of similar conditions categorized through cell growth and proliferation. The disease continues to lead death tolls worldwide and extends to communities across the board regarding socioeconomic status. As a result, anticancer therapies with sufficient bioavailability and high efficacy are in demand. Our research focuses on two potential natural anticancer compounds, Sulforaphane and Cephalotaxine, to improve the bioavailability of the FDA-approved drug Paclitaxel. Sulforaphane (SFN) is a sulfur-rich isothiocyanate found in cruciferous vegetables. Multiple in-vitro and in-vivo studies have shown Sulforaphane’s chemopreventive activity against several types of cancer through the suppression of cellular proliferation, metastasis, angiogenesis, and other hallmarks of cancer. Cephalotaxine (CET) is a secondary metabolite of Cephalotaxus Harringtonia, a coniferous plant belonging to the family Taxaceae. CET has shown some anticancer activity, although it has not been widely studied. Through in-silico and in-vitro research, we have investigated both natural compounds and their relation to cancer.
Prachi Heda, Riya Parekh, Aditi Shankar, Dishita Rajan, Shrimayi Chaganti, Sahana Ravishankar

Renganathan

Synergistic Studies of Sulforaphane and Cephalotaxine and their effect on C.elegans

We focus on using a combination of two compounds linked to anticancer activity and apoptosis induction, Sulforaphane (SFN) and Cephalotaxine (CET), to achieve anticancer treatments, such as chemotherapy for Cancer, the abnormal cell growth of mutated cells with the capability spreading throughout the body. SFN is an organosulfur compound with a unique structure as it is classified in the isothiocyanate group. It can be obtained from cruciferous vegetables such as broccoli. The project aims to maximize sulforaphane activity by pairing it with another potent anticancer drug, Cephalotaxine. CET is a benzazepine alkaloid isolated from a coniferous plant of the Taxaceae family, Cephalotaxus Harringtonia. This project analyzes the anticancer effect of SFN and CET in combination treatments using assays on Caenorhabditis elegans (C. elegans) strains TJ 375 and JK1466 and molecular biology techniques on cell cultures such as cell lining, media/stock addition and incubation. The project consists of mtt assays and investigation of the drugs and protocols for the various techniques that will be used to determine the overall viability of the worms such as absorbance levels calculations and cell culturing as a whole.
Sirivennela Gade, Samir Kurudi, Anvi Madhavan, Siri Manthapuri, Avaneesh Wazarkar, Armaan Sharma, Shriya Sudini

Renganathan

Synthesizing Iron Oxide and Zinc Oxide Nanoparticles to Test Their Effects on C. Elegans Modified to Resemble Having Neurodegenerative Diseases

The blood-brain barrier (BBB) is a physiological defense to prevent harmful chemicals and pathogens from reaching the central nervous system. Pharmacological drugs, mainly because of their size, do not reach the brain due to the semi-permeable BBB. Nanoparticles, which are 1-100 nm in size and are selectable based on their targeting factors, can cross the BBB and are used to enhance drug delivery within the central nervous system (CNS). We have synthesized zinc and iron metal nanoparticles to deliver therapeutics to the CNS, specifically targeting neurodegenerative diseases. We used a green synthesis method with plant based extracts like cilantro and bay leaf to synthesize iron oxide and zinc oxide nanoparticles, respectively. Characterization of the nanoparticles were performed by using Ultraviolet-visible Spectroscopy (UV-Vis), Fourier Transform Infrared Spectroscopy (FTIR), and X-ray diffraction (XRD) techniques. We are further developing a protocol to add curcumin to the synthesized nanoparticles to enhance the anti-inflammatory effect. To test out the toxicity and effectiveness of the nanoparticles, we are using Caenorhabditis elegans, a transparent nematode that has 60-80% genetic homology to humans. Additionally, it has a simple, transparent CNS which can be visualized under a microscope. C. elegans can be genetically modified to produce strains to test different experimental conditions. The WLZ3 strain is a good model to study Parkinson’s disease, while the wild type is used as the control to test the toxicity and effectiveness of synthesized iron oxide nanoparticles. Similarly, the EAK103 strain, a model with Huntington’s disease will be used to test zinc oxide nanoparticles. By using the lifespan assay, we are testing for an appropriate dosage that C. elegans could withstand without the nanoparticles being toxic based on how many of the nematodes were able to survive. We hope to figure out the appropriate dosage after multiple assay runs. In the future, we will be conducting assays specifically to see the effects of the nanoparticles on the neurodegenerative diseases themselves with locomotion and neurodegeneration assay.
Kalpita Balu, Morgan Chan, Reeva Randeri, Abhiraj Bhaskar, Dhruv Sastry, Pranav Surapaneni, Shiven Patel, Sidharth Krishnan

Renganathan

Targeting Ephrin B2 and B3 Glycoproteins to Initiate Immune Response Against the Nipah Virus (NiV)

Given the context of the SARS-CoV-2 pandemic, understanding other major viruses, especially the Nipah Virus (NiV), is imperative to producing crucial prophylactic vaccines and other therapeutic treatments. While past research efforts on NiV have included monoclonal antibodies and the potential use of Remdesivir, there are currently no licensed treatments. This is a major concern since NiV poses a similar threat that Covid-19 did with regard to its rapid community transmission. Principally, our research aims to shed greater awareness and a potential solution for NiV through the synthesis of a recombinant vaccine; however, different varieties such as an oral form are still under consideration. Using in vitro and in silico models, PCR, bacterial transformation, directed evolution, NGS sequencing, mass spectrometry, and binding kinetics, we intend to construct a vaccine that effectively utilizes the fusion proteins of NiV to initiate a productive immune response against the virus. Additional work will be designed for Phase II, where collaboration for the development of lipid nanoparticles (LNPs) will be required to validate the viability of the vaccine through additional experiments (external partners). Ultimately, our efforts to target Ephrin B2 and B3 in the synthesis of an NiV vaccine holds great potential since it has been well substantiated that both of these glycoproteins are special entry receptors that allow the Nipah virus to infect mammalian cells. Furthermore, a nuanced understanding of these receptors are essential for the scientific community’s future steps to eradicate NiV from hard-hit countries, including India and Bangladesh.
Amiya Sheshadri, Sanika Sharma, Ajeeth Iyer, Caleb Yu, Dara Lin, Azhahini Krishnamoorthy

Amadi

Testing bioenhancers efficiency on p-gp inhibition to increase drug bioavailability

Bioenhancers are substances that increase drugs’ effectiveness by increasing their bioefficacy and bioavailability. Bioavailability is the rate at which a drug enters the cell and becomes available at the intended site of action. Therefore, bioenhancers can make drugs react with our bodies more efficiently when taken together. Our team plans on testing a wide variety of bioenhancers in our comparative study, namely Verapamil, Naringin, Curcumin, Genistein, and Quercetin, to investigate their ability to inhibit the p-glycoprotein. P-glycoprotein functions as an efflux protein by pumping drug substrates back into the lumen, decreasing the body’s absorption of the drug. By simultaneously administering p-gp inhibitors, also known as bioenhancers, with the drug, the bioavailability of the drug itself can thus be increased; more of the drug would be absorbed by the body. By boosting the bioavailability of drugs using bioenhancers, consumers can take a lower dose of the drug while still meeting the necessary concentration threshold. This has a variety of effects, such as higher affordability, as well as the possibility of reduced side effects to the drug. This would have great impacts on the medical field. We are conducting a comparative study between several bioenhancers to test their efficacy in helping enhance drug bioavailability. We are testing on HCT-116 cell lines as p-gp is overexpressed on the surface of cancer cells so it is easier for us to identify when it has been inhibited. Currently, we are working on ATPase assays using Verapamil as a standard. We are planning to do an MTT assay to check the metabolic activity in our HCT-116 cells. Add Keywords P-glycoprotein, p-gp, bioenhancer, bioavailability, HCT-116, bioefficacy, inhibition, MTT assay, ATPase assay
Smriti Kallahalla, Caleb Joo, Durga Dham, Sophia Wang), Sravya Mikkilineni , Gautham Ramshankar

Renganathan

Testing relative abundance and diversity of Rhizobium in urban gardens

Rhizobium bacteria, while characteristically living in the root nodules of mutualistic legumes, exist independently in soil as motile bacteroides. They are of great ecological and agricultural importance, for their ability of nitrogen fixation. In this study, we investigate the diversity and abundance of Rhizobium in differently developed soil types. Samples were collected in triplicate from the LEAF Urban garden in Fremont from three sublocations. qPCR with genus-specific nifH primers quantified the relative abundance of Rhizobium populations. Preliminary data suggests significant differences between groups. DNA extracted from group 1 (undeveloped with nearby vegetation) had an average Ct value of 15.22, group 2 (cultivated for 7 years) had an average Ct value of 30.60, and group 3 (undeveloped) did not reach the threshold position. Downstream RFLP analysis of amplified DNA can determine Rhizobium species diversity. In this presentation we will present the results of our research.
Sylvia Lyu, Antone Jung, Navya Gupta

Kaur

The Effect of COVID-19’s Impact on Human Activity on non-Protected and Protected Rocky Intertidal Tide Pools in San Mateo County

After watching the profound impacts the COVID-19 pandemic had on human activity – a reduction in large indoor events and an uptick in outdoor activities – our group sought to investigate the impact of the change in human activity on the Northern California rocky intertidal ecosystem. Our research centered around the question: How has the impact that COVID-19 has had on the amount of human interaction with rocky intertidal zones affected their ecosystem health, as well as species biodiversity and abundance, when compared between protected and non-protected marine areas? During the COVID-19 pandemic, people began to look to outdoor recreational activities to stay within COVID-19 restrictions. One of these activities was visiting non-protected tide pools such as Maverick’s Beach, which stayed open throughout the pandemic. Park rangers noted seeing a dramatic uptick in the number of visitors to the tide pools and the amount of species being taken. On the other hand, protected locations such as Fitzgerald Marine Reserve, shut down for a six month period during the peak of the pandemic. During this time, the tide pools were completely undisturbed as no one could enter the reserve or remove any species. Due to humans being able to take species from non-protected sites including but not limited to: moon snails, shore crabs, rock crabs, limpets, turban snails, sea urchins, mussels, oysters, hermit crabs, and even octopuses, the ecosystems of the non-protected tidepools have been severely affected. For example, because of predator species (ex: sea urchins are a predator to algaes and plants, and they are now being taken) being removed by humans, many species of seagrass and other organisms have grown dramatically due to the uncompetitive environment. In addition, overfishing is largely unregulated and reduces the population count of organisms belonging to a particular species. To support our hypothesis and the reality of the issue, we first went to Maverick’s Beach, a non-protected area. There, we took quadrat data using random sampling and transect lines. After collecting data from Maverick’s Beach through multiple trips, we obtained permits from the Fitzgerald Marine Reserve and began data collection for a protected area.
Amber Lu, Arohi Chirputkar, Ian Chen, Rowan Campbell, Zoe Chu

Benson

The Effect of Human Disturbances on Non-Protected and Protected Intertidal Zones

The issue that led to this research project was the human taking of species in non-protected areas that has severely affected the food chains in tide pool ecosystems, and in turn, the diversity of such tide pools. The question we had was to what extent human impact has had on these non-guarded sites, and how they compared to sites that were protected. Due to humans being able to take species from non-protected sites including but not limited to: Moon Snails, Shore Crabs, Rock Crabs, Limpets, Turban Snails, Sea Urchins, Mussels, Oysters, Hermit Crabs, and even Octopuses, the ecosystems of the non-protected tide pools have been severely affected and skewed. For example, because of predators being taken to the point of them being entirely absent from these inter-tidal locations, many species of seagrass and other organisms have in return grown drastically, due to the uncompetitive space. This cause and effect is observed throughout these locations, with either predator or prey being taken, which hurts or helps another species. While something like sea urchins being taken is not necessarily a bad thing, due to their impact on kelp forests, it is however likely affecting the abundance and diversity of other species in these areas, and the same goes with the other species being fished. To prove our theory and the reality of the issue, we went to a non-protected site known as Maverick’s Tide Pool. Once there, we took data by using quadrats, with random placement by the means of transect lines. Once we had an accurate amount of data to represent the tide pool as a whole, we analyzed photos of the quadrats, determined the variety of species, abundance of species, as well as the size (and health) of organisms, all with the help of ImageJ. While we have been facing complications to be able to take data at a protected site, we were able to compare our results with previous data from Fitzgerald, a protected site. In the protected areas, the likely observation of diversity and abundance of species will be normal, due to there being a much smaller impact from outside forces. This means that without the considerations of diseases or invasive species, the tide pools are thriving in the way they should; the food web is normal, with no species outnumbering another. While in the non-protected tide pools, seagrass has more or less overrun the whole area due to the absence of key predators, this is not the case with protected tide pools; everything is thriving at a normal pace, and the diversity is kept in check, due to nothing being taken. This is until further data has been obtained. The significance of this is the fact that many such tide pools across North America will continue to be stripped of their important species, which will only lead to the ecosystem being hurt.
Arohi Chirputkar,
Emma Tran,
Isaac Lee,
Ian Chen,
Rose Liu,
Rowan Campbell

Benson

The Effects of Ocean Acidification on Barnacle Feeding and Predator Avoidance Behaviors

Oceans are a crucial part of the Earth’s anatomy; it gives life to marine organisms, allows for transportation for ships, acts as a storage area for inorganic material, and prevents extreme heating of the Earth by absorbing excess CO2 from the Earth’s atmosphere. Specifically, our experiment is geared towards understanding the effects of how an increase in ocean acidification affects its ability to maintain a sustainable environment for marine creatures. In our experiment, we placed two types of barnacles(balanus aquila-acorn and tetraclita rubescens-volcano) into saltwater tanks of different pHs. The control tank was at 8.1 pH, and the other two were at levels of 7.8 pH(middle pH) and 7.5 pH(low pH). Barnacles were fed zooplankton per data collection, and their feeding activity was measured by counting the amount of cirri extensions at 10 minute intervals leading up to 30 minutes. We also tested predator avoidance response for barnacles by using a sponge to replicate its predator's effects, and our previous finding that a light brush to the barnacle’s surface by a sponge caused it to retract still holds true. Previous data presented itself as statistically significant, but current findings show possible changes, and further study is needed to make a more definitive statement.
Devam Parekh, Harshini Vakkalagadda, Aruja Gupta, Smriti Jha, Delisha Doppa, Anish Jupudy

Benson

The Effects of Ocean Acidification on Barnacle Feeding and Predator Avoidance Behaviors

As more carbon dioxide is pumped into the atmosphere, the acidity of the ocean will be drastically altered, affecting marine life. The purpose of this study is to determine how decreasing pH levels affect barnacle feeding habits, as well as predator detection and avoidance behaviors. This experiment was carried out on both Balanus aquila and Tetraclita rubescens (also known as acorn barnacles and volcano barnacles) by placing a few of each type into saltwater tanks with differing pHs. The control tank, at a pH of 8.1, mirrored the current ocean’s pH level, while the other two tanks, at a pH of 7.8 and 7.5, were meant to replicate the projected acidity of the ocean in the future. Barnacles were fed zooplankton every three days, and the amount they ate was measured by how often they extended their cirri in one minute, immediately after being fed, then after 10, 20, and 30 minutes. We also tested for predator avoidance behaviors by touching the barnacles with a sponge to mimic the feeling of a major predator, sea stars. We noticed that whenever the sponge touches the barnacles, the barnacles close up as a means of protection. Further study is needed to quantify how predator avoidance behaviors change with decreased pH levels. From preliminary analysis and observations, we believe that the barnacles in decreased pH levels are feeding more than those in the control tank. As the acidity of the ocean increases, our preliminary data indicates that barnacles’ feeding rates may increase. We believe this is a result of their metabolic needs increasing; however, this is something that requires further study.
Nadia Bianco,
Harshini Vakkalagadda,
Anjali Kalidindi,
Catherine Zhang,
Kamya Kainth,

Benson

The Effects of RG108, a human DNA methylation enzyme inhibitor, and its related analogs on HCT116 Colorectal Cancer Cells

Colorectal cancer (CRC) is a type of cancer that starts in the colon or the rectum. CRC is the third most common cancer, and it is also the second most common cancer leading to death amongst men and women (American Cancer Society, 2019). The cell line used in the following experimentation was the epithelial human colorectal carcinoma 116 (HCT-116) cell line derived from an adult male (Imanis Life Sciences, n.d.). The project is focused on the use of analogs from the drug RG108 to test their efficacy against DNA methylation. RG108 is a DNA methyltransferase inhibitor (DNMT inhibitor), which reverses the effects of DNA methylation by reactivating the tumor suppressor genes. (Brueckner et al., 2005) RG108 was specifically chosen because of its different structure and mechanism action, classifying it as a non-nucleoside inhibitor, contrasting to other frequently used DNMT inhibitors which are nucleoside analog inhibitors. (Kundakovic, 2014) RG108 is not an FDA-approved treatment for colorectal cancer, so this research takes a step forward in that process. To conduct our research, MTT assays, qPCR, and gene expression analysis will be utilized.
Alfiya Raja, Sreshta Yelisetti, Hena Patel, Ojasvi Mudda, Anika Aeka, Samantha Wu

Cunha

The Impact of Human Activity on Protected vs Unprotected Rocky Intertidal Tide Pools in San Mateo County

Our group sought to investigate the impact of human activity on the Northern California rocky intertidal ecosystem. Our research centered around the question: How has human interaction with rocky intertidal zones affected their ecosystem health, as well as species biodiversity and abundance, when compared between protected and non-protected marine areas? Due to humans being able to take species from non-protected sites including but not limited to: moon snails, shore crabs, rock crabs, limpets, turban snails, sea urchins, mussels, oysters, hermit crabs, and even octopuses, the ecosystems of the non-protected tidepools have likely been severely affected. For example, because of predatory species being removed by humans, a possible effect is that many species of seagrass and other organisms in turn grew dramatically due to the uncompetitive environment. In addition, overfishing is largely unregulated and reduces the population count of organisms in the intertidal community. To support our hypothesis and the reality of the issue, we first went to Maverick’s Beach, a non-protected area. There, we took quadrat data using random sampling and transect lines. After collecting data from Maverick’s Beach through multiple trips, we obtained permits from the Fitzgerald Marine Reserve and began data collection for a protected area.
Sally Han, Zoe Chu, Jishnu Saani, Brandon Tsai, Sanjay Ram

Adams

The in-silico and in-vitro characterization of epigenetic drugs (BET Protein Inhibitors and related analogs) on a colorectal cancer cell line

Members of the bromodomain and extra-terminal domain (BET) family can lead to the overexpression of oncogenes (Shorstova et al., 2021). BET inhibitors (BETi), moderately reduce colorectal cancer cell (CRC) proliferation and MYC expression when used in monotherapy ​​(Ma et al., 2016).This study aims to determine potential BETi in colorectal cancer (in silico) and to identify the effects of these drugs on CRC (in vitro). JQ1, an extra terminal BET protein inhibitor that suppresses tumor progression, will be the control (Wen et al., 2020). PubChem datasets will be converted into a numerical format, chemical fingerprints, and used with unsupervised learning algorithms (Sydow et al., 2019) to assess the molecules’ similarity to each other and JQ1. After clustering, relevant clustered drugs will be molecular docked with Autodock Vina (Trott et al., 2010) and Rxdock (Ruiz-Carmona et al., 2014). The drugs found to have the greatest binding affinity to BRD4 will then be computationally tested on colon cancer cells using DeepCDR (Liu et al, 2020). These drugs will then be synthesized and tested on colorectal cancer cells to measure their effects with procedures including MTT (Freimoser et al, 1999) and qPCR (Mullis, 1985) to measure cell viability and gene expression levels.
Grace Zang, Aditi Deshpande, Sowkya Namburu, Prabhav Pragash, Sanjana Selvara, Sofia Penttila, Sreenidhi Challagundla, Madison Dee

Cunha

The in-silico and in-vitro characterization of epigenetic drugs (BET Protein Inhibitors and related analogs) on a colorectal cell line (HCT116)

Members of the bromodomain and extra-terminal domain (BET) family can lead to the overexpression of oncogenes (Shorstova et al., 2021). These include BRD2, BRD3, BRD4, and BRDT, with BRD4 being the most prominent protein (Shorstova et al., 2021). BET inhibitors (BETi), moderately reduce colorectal cancer cell (CRC) proliferation and MYC expression when used in monotherapy (Ma et al., 2016). This study aims to determine potential BETi in colorectal cancer (in silico) and to identify the effects of these drugs on CRC (in vitro). While prior studies have studied BETi in other cancer types, few studies focus on colorectal cancer, the third-most common cause of cancer deaths in the United States (The American Cancer Society medical and editorial content team, 2022). Therefore, using BETi as a therapeutic option for colorectal cancer could reduce mortality rates. JQ1, an extra terminal BET protein inhibitor that suppresses tumor progression, will be the control for the research to test computational programs and experimental molecules (Wen et al., 2020). The molecules found on PubChem will be converted into a numerical format, chemical fingerprints, and used with unsupervised learning algorithms (Sydow et al., 2019) to assess the molecules’ similarity to each other and JQ1. Once the molecules have been clustered, a few will be chosen and run through the respective programs, Autodock Vina (Trott et al., 2010) and Rxdock (Ruiz-Carmona et al., 2014). The drugs found to have the greatest binding affinity to BRD4 will then be computationally tested on colon cancer cells using DeepCDR (Liu et al, 2020). These drugs will then be synthesized and tested on colorectal cancer cells in different concentrations to measure their effects through procedures including MTT (Freimoser et al, 1999) and qPCR (Mullis, 1985) to measure cell viability and gene expression levels.
Maddie Ando, Grace Zang, Prabhav Pragash, Joanna He, Aditi Deshpande, Sanjana Selvaraj, Sowkya Namburu, Clinton Cunha

Cunha

The process of collecting data for a novel psychological assessment Measuring the Creativity of Social Media Influencers (MCSMI)

Creativity is defined as the application of originality to create unique works of art. While creativity isn’t dependent on skill, it is fueled by imagination and individuality. The age of social media has dramatically expanded the traditional definition of creativity as creative individuals can connect with millions of people. This makes it crucial for one to identify the difference between creative influencers and influencers. To measure how creative an individual is, some creativity assessments analyze the degree of achievement that someone has achieved in a certain skill. Other assessments ask individuals to think of ways to repurpose something in a certain amount of time. The Creative Achievement Questionnaire (CAQ) examines achievement in a variety of categories, including music, art, and dance, among many others. Another assessment, the Inventory of Creative Activities and Achievements (ICAA), evaluates the frequency of creative actions alongside the level of achievement obtained. One category that is not currently present in the CAQ or ICAA is creative influencers — people who utilize social media to promote their creative skill and influence others to help spread their expertise. Our aim is to develop a subset of questions that accurately identifies creative influencers and eventually include this portion in the CAQ or ICAA. In this research study, we are examining several types of creativity assessments, alongside the questions we believe are appropriate. This allows us to determine whether an individual is a creative influencer based on an analysis of their current social media and the types of platforms they run.
Alissa doemling,
Angeline Yeh,
Daphne Chao,
Meenakshi Yarlagadda,
Rasya Ramakrishnan,
Rihalya Sivakumar,
Rucha Kulkarni

Jahanikia

Tide Pools

After watching the profound impacts the COVID-19 pandemic had on human activity – a reduction in large indoor events and an uptick in outdoor activities – our group sought to investigate the impact of the change in human activity on the Northern California rocky intertidal ecosystem. Our research centered around the question: How has the impact that COVID-19 has had on the amount of human interaction with rocky intertidal zones affected their ecosystem health, as well as species biodiversity and abundance, when compared between protected and non-protected marine areas? During the COVID-19 pandemic, people began to look to outdoor recreational activities to stay within COVID-19 restrictions. One of these activities was visiting non-protected tide pools such as Maverick’s Beach, which stayed open throughout the pandemic. Park rangers noted seeing a dramatic uptick in the number of visitors to the tide pools and the amount of species being taken. On the other hand, protected locations such as Fitzgerald Marine Reserve, shut down for a six month period during the peak of the pandemic. During this time, the tide pools were completely undisturbed as no one could enter the reserve or remove any species. Due to humans being able to take species from non-protected sites including but not limited to: moon snails, shore crabs, rock crabs, limpets, turban snails, sea urchins, mussels, oysters, hermit crabs, and even octopuses, the ecosystems of the non-protected tidepools have been severely affected. For example, because of predator species (ex: sea urchins are a predator to algaes and plants, and they are now being taken) being removed by humans, many species of seagrass and other organisms have grown dramatically due to the uncompetitive environment. In addition, overfishing is largely unregulated and reduces the population count of organisms belonging to a particular species. To support our hypothesis and the reality of the issue, we first went to Maverick’s Beach, a non-protected area. There, we took quadrat data using random sampling and transect lines. After collecting data from Maverick’s Beach through multiple trips, we obtained permits from the Fitzgerald Marine Reserve and began data collection for a protected area.
Zoe Chu, Amber Lu, Arohi Chirputkar, Sally Han, Rowan Campbell

Benson

Tracking the correlation between COVID-19 vaccination status and sleep quality

COVID-related disturbances such as shelter in place, have been linked with sleep disturbances amongst the general population. The goal of this study is to examine the relationship between sleep quality and COVID-19 vaccination status by computing a sleep quality index score (SQI) for participants before and after vaccination. Outreach methods include distributing flyers, contacting college professors, and as of May 2022, this research has had over 120 interested participants and 62 SQI scores from eligible participants. Additionally, methods of statistical analysis (T-test, chi square test, etc.) were researched to start preliminary data analysis. The results of this study will assist in understanding the various ways in which the COVID-19 pandemic has altered our daily lifestyles.
Abinaya Senthil, Ananya Ravi, Anika Mantripragada, Avi Uppalapati, Claire Wu, Destiny Pinto, Devan Melwan, HeeJee Yoon, Prisha Purohit , Shreya Abhijit

Jahanikia

Understanding the Correlation Between COVID-19 Vaccines and Sleep Quality on Vaccinated versus Unvaccinated participants

The COVID-19 pandemic has significantly impacted people’s lives, including their sleep. The goal of this study is to track the correlation between sleep quality and COVID-19 vaccination status by assessing the sleep quality of both vaccinated and unvaccinated participants. In order to achieve this goal, an eligibility questionnaire, a demographic questionnaire, as well as a HIPAA-compliant digital questionnaire measuring sleep quality were constructed. As this study involves informed consent, the IRB has approved the study in relation to HIPAA compliance/IRB approval standards, which included the long and short consent forms for both adult and minor participants, as well as eligibility, demographic, and COVID-19 and sleep questionnaires. Dummy data is currently being collected in order to test Jotform, as real data collection is the next step for this study.
Aaminah Mohammad, Abinaya Senthil, Ananya Ravi, Anika Mantripragada, Avi Uppalapati, Claire Wu, Destiny Pinto, Devan Melwani, Erin Yang, HeeJee Yoon, Matthew Kang

Jahanikia

Understanding the Nature of Brain Imaging Data and Converting for Further Analysis of Musical Genre Perception

FMRI is a non-invasive neuroimaging technique that uses BOLD signals to construct high-resolution images of brain activity in response to stimuli. By using various neuroimaging tools and techniques, we will preprocess and analyze a fMRI dataset obtained from the University of Magdeburg Psycho- informatics Lab which contains scans of participants guessing the genre of music featured in clips from a movie both with and without audio. In order to preprocess the data, we first need to convert the raw data into the Brain Imaging Data Structure (BIDS), a standard way of organizing neuroimaging data. In our research, we aim to identify networks of the brain associated with guessing a music genre without audio and understand and explain the role of the auditory network in genre association.
Aditya Anantaraman, Anisha Grover, Brandon Brewer, Dhruv Bhargava, Julia Wind, Sruthi Sudarsan, Leo Sun

Jahanikia

Using Multidimensionality and Engagement through the Dopaminergic System to Increase Working Memory

N-back tasks are a form of cognitive training requiring patients to remember and recall information previously shown to them. In previous studies, cognitive patients completed N-back tasks while undergoing fMRI, and areas associated with working memory, such as the prefrontal cortex, fronto parietal network, and salience network, activated during this task. Working memory involves the use of attention to manipulate and store short term memory. There has been a scientifically proven correlation between N-back training and increase of working memory. Furthermore, the dopaminergic system, located in the midbrain, consist of the Mesolimbic, Mesocortical, Nigrostriatal, and Tuberoinfundibular pathways. Within this system contains dopamine, a neurotransmitter and hormone produced during blissful and pleasantful experiences. There is a scientific correlation between increase of dopamine and increase of productivity during cognitive tasks. Nevertheless, cognitive research patients often complain that cognitive tasks are boring and mundane. In this study, we aim to measure the effect of multidimensionality and gamification on cognitive research tasks.
Aidan Gor, Akshat Wajge, Ying Tzu Chen

Jahanikia

Using dimensionality reduction and molecular docking to find novel DNA methyltransferase 1 inhibitors for colon cancer

In cancerous states, DNA methyltransferase 1 (DNMT1) can silence tumor suppressor genes (Hu, Liu, Zeng, et al., 2021). DNMT1 inhibitors reverse this process and activate the genes again (Hu, Liu, Zeng, et al., 2021). We are taking a computational approach to finding novel treatments to colon cancer with the processes with unsupervised learning (Rhys, 2020) and molecular docking (Meng, et al., 2011). With unsupervised learning (McInnes, et al., 2018; Corsello, et al., 2020), we will use the knowledge of pre-existing inhibitors to cluster compounds together from a ChemBL (Mendez, et al., 2018) dataset representing the chemical space. Then using Avogadro (Hanwell, et al., 2012), Orca (Neese, et al., 2011), and AutoDock Vina (Trott, Olson, 2010), we will batch dock those similar compounds with AutoDock Vina. With the binding affinities that AutoDock Vina outputs, we can narrow down the list of possible drugs that will be effective against colon cancer. Finally, we will use DeepCDR to, in silico, to determine different drugs’ efficiency on colon cancer cell lines based on the transcriptomic, genomic and epigenomic data of cell lines along with previous drug-cell line pair patterns (Liu et al, 2020). We hope to find novel compounds using recognized software tools. With this method, we can look through multiple compounds and spot connections that are hard to see through the human eye and physical experiments.
Aksithi Eswaran, Shikha Kathrani

Cunha

fMRIusic

FMRI is a non-invasive neuroimaging technique that uses BOLD signals to construct high-resolution images of brain activity in response to stimuli. By using various neuroimaging tools and techniques, we will preprocess and analyze a fMRI dataset obtained from the University of Magdeburg Psychoinformatics Lab which contains scans of participants guess the genre of music from a movie both with and without audio. However, this term we shifted our focus to creating a blog listing the many different neuroimaging tools that can be used to easily analyze certain MRI data like FSL and fMRIprep. With these tools, we aim to identify the networks of the brain associated with guessing a music genre correctly without audio. However, before we can use the tools to preprocess the data, we first need to convert the raw data into the Brain Imaging Data Structure (BIDS), a standard way of organizing neuroimaging data. In our research we aim to publish a blog on the most accessible, yet powerful neuroimaging tools as well as using those tools to identify networks of the brain associated with guessing a music genre without audio and understand and explain the role of the auditory network in genre association.
Julia Wind, Aryan Kondapalli, Ayaan Khan, Brandon Brewer, Elizabeth Gayhart, Mounami Kayitha, Sachi Patel, Sasha Bahdanava, Sruthi Sudarsan

Jahanikia

fMRIusic: Understanding the Nature of Brain Imaging Data and Converting for Further Analysis of Musical Genre Perception

Functional Magnetic Resonance Imaging, known as fMRI, is a non-invasive neuroimaging technique. It utilizes BOLD signals to construct high resolution images of brain activity from subjects instructed to perform tasks or respond to stimuli within an MRI machine. To do any time of neuroimaging analysis, we have to first investigate MRI raw data. By using neuroimaging tools and techniques, such as AFNI and Freesurfer, we will preprocess and analyze a fMRI dataset obtained from the Psychoinformatics Lab at the University of Magdeburg in Germany. The dataset comes from fMRI scans of 20 participants who were shown clips of the movie “Forrest Gump” with different genres of music featured in the movie, such as Country, Symphonic, and 50s Rock’n’Roll. The participants were asked to guess the genre of a piece of music with and without audio. The purpose of our project for this term was to understand the nature of the raw data. In order to preprocess this data, we first need to convert the raw data into the Brain Imaging Data Structure (BIDS), a standard way of organizing neuroimaging data. Due to the uniform file format that BIDS provides, many tools and resources for neuroimaging adopted the BIDS format as their input. With these tools, the aim of our research is to identify the networks of the brain associated with guessing a music genre correctly without audio. In previous studies, researchers have gathered a large amount of data regarding the auditory network and its relation to music. We aim to understand and explain the role of the auditory network in genre association.
Aditya Anantaraman, Anisha Grover, Brandon Brewer, Dhruv Bhargava, Julia Wind, Sruthi Sudarsan

Jahanikia