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Colloquia Week

Every week, senior researchers in each department at ASDRP give public seminars presenting the current state of the field and disseminating how their research at ASDRP fits into the broader context of the frontiers of modern science and engineering. Colloquia are public events, and anyone can join. Click on the "Join the Colloquia" link to add the event to your calendar.

Summer 2021 Colloquia Schedule - updated 7/13/2021

Week of Aug 14 - 21: 

  • Tuesday, Aug 17 @ 8:00pm        BIOL- see Friday

  • Wednesday, Aug 18 @ 8:00pm  CSEN - Shivi N. (see description below)

  • Friday, Aug 20 @ 8:00pm            CHEM/BIO -  Jane W. (see description below)

Combined Biological, Human, and Life Sciences and Chemistry, Biochemistry and Physics
Friday @ 8:00-9:00 PM PDT

Friday, August 20, 2021

Synthesis of NRTI Analogs Using Click Chemistry and Structure-Activity Relationships

HIV, a retrovirus that attacks the body’s immune system, binds to surface receptors on CD4 cells, injects viral RNA, and converts itself into DNA through the reverse transcriptase enzyme. Ultimately embedding itself into the host DNA, it can then replicate, assemble, and bud out of the cell. Nucleoside reverse transcriptase inhibitors, a class of antiretroviral drugs, bind directly to the RT active site by mimicking DNA nucleotide bases to halt the replication process. Zidovudine (AZT) is a particular NRTI of interest due to its azide chain, which can undergo a Copper-catalyzed cycloaddition reaction that enables clicking different alkynes onto the resulting triazole ring. In this manner, we can create and test a vast library of Zidovudine analogs on the HIV-RT enzyme for enhanced potency and other medicinal properties. This presentation will cover the synthetic objectives of the CuAAC mechanism and biological testing methods on target proteins.

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Researcher: Jane W., Amador Valley High School

Advisor: Njoo, Organic & Medicinal Chemistry, Chemical Biology, Catalysis

Keywords: Organic synthesis | antiretrovirals | click chemistry | HIV | AZT



Department of Computer Science and Engineering
Wednesdays @ 8:00-9:00 PM PDT

Wednesday, August 18, 2021

Detecting Intracranial Hemorrhages In Computerized (Axial) Tomography Images Using Image Classification Technologies Such As TensorFlow And OpenCV

 

Machine learning models and deep learning techniques have been proven to be quite helpful to clinical professionals accurately diagnose many medical conditions. Inspired by the recent use of machine learning models, we develop a deep learning model that detects intracranial hemorrhages in CT brain scans. The model classifies the scans into two classes, hemorrhagic and normal. We evaluate this model using multiple public datasets. Our model 1) increases the speed of diagnosis, removing the significant dependency on highly trained professionals 2) reduces the cost for diagnosis, 3) increases accessibility in rural areas, where highly trained specialists may not be found, and 4) reduces the strain on overworked radiologists that have to go through thousands of CT scans a day.

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Researcher: Shivi N., Mission San Jose High School; Vajraang P., Dougherty Valley High School; Aarav B., Mission San Jose High School; Aditya V.,  Prospect High School

Advisor: Subramaniam, Data Science and Computer-Guided Statistical Modeling

Keywords: Intracranial Hemorrhage | Machine Learning | Computerized Tomography Scans (CT) | Neural Networks | TensorFlow



Department of Computer Science and Engineering
Wednesdays @ 8:00-9:00 PM PDT

Wednesday, August 11, 2021

Comprehensive review of the brain network vs. the brain connectome

 

The Human Connectome Project, commonly abbreviated as HCP, is a large-scale initiative involving teams of researchers at universities around the world. Through the use of various different types of MRI scanners, the brain connectome can be mapped, and the role of neural pathways in the development of things ranging from personality to mental disorders can be determined and analyzed. Structural and functional connectivity and their key differences can also be examined. This review will include a comparison between the connectome and the brain network, and as well as the specifics of what each teaches about the human brain. There will also be a brief discussion of the origins of the human connectome and the first species for which it was mapped.

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Researcher: Shreya D., American High School

Advisor: Jahanikia, Neuroimaging & Bioinformatics

Keywords: Neuroscience | HCP | connectome | brain network | MRI



Department of Computer Science and Engineering
Wednesdays @ 8:00-9:00 PM PST

Wednesday, August 4, 2021

Statistical report of the studies related to the COVID-19 pandemic and sleep disorders on different populations

 

The COVID-19 pandemic has drastically altered typical living habits, including vital circadian cues, and is linked to new pressures, new responsibilities, and new concerns about one's health and financial security, all of which are likely to disrupt sleep. Our research group aims to study the effects of the COVID-19 vaccine on sleep during the pandemic by assessing vaccinated and unvaccinated participants. To characterize the populations/participants (females, healthcare workers, children, etc.), we gathered data from numerous papers on the correlation between the COVID-19 pandemic and the quality of sleep. In each paper, the impact level of the pandemic on sleep disorders was quantified through assessments (The PSQI, SCC and K10 to name a few). With this information, we will provide a statistical report analyzing different populations’ sleep quality relative to the COVID-19 pandemic and discuss how our understanding of each population will direct our research.

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Researcher: HeeJee Y., Amador Valley High School & Tejas G., Dougherty Valley High School

Advisor: Jahanikia, Neuroimaging & Bioinformatics

Keywords: statistical analysis | COVID-19 | pandemic | sleep disorders

Department of Chemistry, Biochemistry, and Physics
Fridays @ 8:00-9:00 PM PST

Friday, August 5, 2021

Synthesis and Structure-Activity Relationship of 2-Substituted Benzimidazole KRAS Inhibitors

The KRAS gene, first identified as an oncogene in Kirsten Rat Sarcoma virus, provides instruction towards the production of the K-Ras protein. The KRAS protein is responsible for relaying the signals instruct the cell to grow and divide or to mature and take on specialized functions from outside of the cell to the cell’s nucleus. When mutated, KRAS can fail to deactivate, leading to uncontrolled cell growth and signaling, causing cancerous growths. Mutations of KRAS proteins occur in approximately 25 percent of all human cancers, including more than 90 percent of pancreatic cancers and approximately 25 percent of lung cancers. Despite its prevalence as an oncogene, KRAS’s lack of clear binding sites has made KRAS one of the most challenging and elusive targets as a cancer therapeutic. However, benzimidazole derivatives have been demonstrated to play a role in suppressing KRAS-related cancer cells, and the Clark groups plan to synthesize a variety of benzimidazole derivatives, and plan on testing the compounds effectiveness through a wide array of bio-assays. These include the use of HCT116 cells to test for anti-proliferative activity, the use of MTT Assays to trach morphological change, and potentially even SDS-PAGE and Western Blots in order to track the ligand's mechanisms.

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Researcher: Zaid V., Mission San Jose High School 

Advisor: Clark, Organic & Medicinal Chemistry

Keywords: Organic synthesis | Medicinal Chemistry | Benzimidazoles | KRAS Oncogene



Department of Computer Science and Engineering
Wednesdays @ 8:00-9:00 PM PST

Wednesday, July 28, 2021

Understanding the cortical plasticity, gamma-band activity, and motor processing of musical multi-instrumentalists

 

It is widely understood that the neurological networks of musicians who have extensively practiced their craft are developed differently than those who are not musically trained. Numerous structural, cortical, and emotional changes in the brains of those that play music are commonly observed. However, an area that has not yet been extensively explored is the difference between the brains of people who play one instrument and people who are proficient in multiple. Our aim is to understand how playing two or more instruments affects neuroplasticity and brain function. This presentation will cover why we believe that the brains of multi-instrumentalists are more sensitive to a larger range of timbres, reflected by an increase in cortical plasticity, gamma-band activity, and motor processing.

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Researcher: Aditya A., Mira Loma High School

Advisor: Jahanikia, Neuroimaging & Bioinformatics

Keywords: Musicians | Instruments | Multi-instrumentalists | Timbre | Gamma-band activity | Neuroplasticity | Neuroscience

Department of Biological, Human and Life Sciences
Tuesdays @ 8:00-9:00 PM PST

Tuesday, July 20, 2021

Investing the Effectiveness of Clozapine on the Schizophrenic C. elegan Model

Affecting twenty million people worldwide, schizophrenia is a neurological disorder in which disturbances to the brain’s ability to process information causes patients to be unable to accurately perceive reality. Currently, only palliative treatments are known, and past studies suggest that psychosocial therapies and medication may be effective treatments. This study assesses the efficacy of the antipsychotic, clozapine, on relieving depressive symptoms and lack of motivation in the transgenic schizophrenic e1370 strain of C. elegans.

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Researcher: Mohika P., Irvington High School

Advisor: Truong, Schizophrenia

Keywords: C. Elegans | Schizophrenia | Antipsychotic | Clozapine | Neuroscience

Department of Chemistry, Biochemistry, and Physics
Fridays @ 8:00-9:00 PM PST

Friday, July 23, 2021

Utilizing Quantitative NMR to Monitor Reaction Kinetics Towards the Development and Evaluation of Anticancer and Antiviral Products.

Benchtop nuclear magnetic resonance spectroscopy offers specific insight into structural elucidation key to molecular characterization, and serves as a rapid & efficient alternative to traditional NMRs. By taking scans over a set period of time, benchtop NMR alongside quantitative NMR calculations can be used to monitor reaction kinetics over time, offering key insight as to the development and evaluation of anticancer and antiviral products. Here, multi nucleus NMR is used to track the in situ creation of singlet oxygen by berberine analogs towards developing solutions for cancer related to photodynamic therapy via proton NMR, as well as the use of fluorine NMR to track the formation of carmofur analogs for antiviral purposes.

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Researcher: Sarah S., Los Altos High School 

Advisor: Njoo, Organic & Medicinal Chemistry, Chemical Biology, Catalysis

Keywords: Organic Synthesis | Natural Products | Nuclear Magnetic Resonance | Berberine | Carmofur

Department of Computer Science and Engineering

Wednesdays @ 8:00-9:00 PM PST

Wednesday, July 14, 2021

The Exploration of Habitable Exoplanets using Data Mining Algorithms and Data Manipulation 

 

The NASA Exoplanet Archive is a dataset that is an extraction from the total sets of data from the Keck, Kepler, TESS, and Gaia observations, where observations show that the observed stellar objects have been determined to possess one or more planets. It is continually updated as more and more exoplanets, or planets outside our solar system, are discovered and documented. Our first objective was to see how many of these entries were duplicates, which would bring the total number of entries we would work with from 29,283 to 4,259. In previous research, this dataset was filtered by determining which of these exoplanets are inside their Circumstellar Habitable Zone (CHZ), commonly defined as the range of distance from a host star such that a planet may contain liquid water, a key requirement for life as we know it. However, this calculation was done only for exoplanets with M-type host stars. Over the course of our research, we were able to expand this calculation of the CHZ to exoplanets with host stars of all spectral types. We performed more in-depth investigation of planets with G, K, and M types stars by comparing them to planets in the Planetary Habitable Laboratory (PHL) exoplanet dataset to see how many similarities there are. The PHL catalog used its own set of criteria to define those planets in it as habitable. 

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Researcher: Hrithik P., Amador Valley High School

Advisor: Downing, Exoplanet Researcher and Computer Science

Keywords: HabitableZone | Kth Nearest Neighbor | PlanetRadius | Luminosity | Albedo

Department of Chemistry, Biochemistry, and Physics
Fridays @ 8:00-9:00 PM PST

Friday, July 16, 2021

The use of Pytochemicals in improving drug Bioavailabilitys

Bioavailability is the measure of what fraction of a drug from the initial dose enters the systemic circulation. Many orally administered pharmaceuticals have low bioavailability due to their affinity for efflux proteins such as p-glycoprotein (pgp) and the cyctochrome p450 3a4 (cyp3a4) proteins, this means that a larger dose of the drug has to be administered in order for it to be effective, and this can makes drugs costly. Bioenhancers are phytochemicals that improve the bioavailability of drugs through various mechanisms of actions including inhibition of efflux proteins such as pgp and cytochrome P450 3a4. Here, we are covering the past and recent research in herbal bioenhancers, and covering how they are used in our study.

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Researcher: Anvita D.,Mission San Jose  High School

Keywords: Medicinal chemistry | Biopotentiatiors | Bioenhancers | Pgp | Cytochrome p45 | Metabolismy

Department of Chemistry, Biochemistry, and Physics
Fridays @ 8:00-9:00 PM PST

Friday, July 9, 2021

Synthesis and Structure-Activity Relationship of 2-Substituted Benzimidazole KRAS Inhibitors

Benzimidazole derivatives are a subset of organic compounds that show promise in the fields of medicinal chemistry and Pharmacology. Benzimidazoles are heterocyclic, aromatic, organic compounds that consist of a fused benzene ring and an imidazole ring. These two fused rings provide an electron-rich system capable of interacting noncovalently with many biological targets, which makes the use of benzimidazole derivatives such a promising solution to inhibiting elusive biological targets. Our research aims to synthesize eight different benzimidazole derivatives with the hope that they could act as inhibitors to the G12D mutant KRAS gene, an oncogene that was thought to be undruggable until recently.

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Researcher: Rosie Chen, Wilcox High School

Keywords: Benzimidazoles | Anti-cancer | KRAS gene |oncogenes |medicinal chemistry

Department of Biological, Human and Life Sciences
Tuesdays @ 8:00-9:00 PM PST

Tuesday, June 29, 2021

Impacts of Auxin and Cytokinin Addition Alongside Abiotic Stress on the Polyphenolic Content of Mentha piperita and Salvia rosmarinus and their Implications Towards Ameliorating Alzheimer’s Disease

Research on the use of plant-derived polyphenols to treat neurodegenerative diseases has become increasingly popular in recent years. One of the richest sources of polyphenols, Mentha x. piperita, has been found by multiple studies to have the highest quantities of the flavanone eriocitrin and the phenolic acid rosmarinic acid, of which the latter has also been researched to have potential in treating Alzheimers’ disease. We also conducted research on Salvia rosmarinus, also known as rosemary, because it, too, is known to have a high polyphenolic content. Our aim was to find which auxins would increase polyphenol production in peppermint and rosemary plants by use of oxidative stress and the addition of various plant hormones. We did our research using 12 of each type of plant which were divided into 6 droughted and 6 non-droughted, with 1 control for each sub-group. All plants including controls were sprayed with the cytokinin 6-benzylaminopurine (BAP), and the remaining 5 plants in each group were sprayed with a different auxin each, these being indole-3-butyric acid, o-chlorophenyl acetic acid, sodium naphthyl acetic acid, p-chlorophenyl acetic acid, and phenylacetic acid. We measured the phenolic contents of the plants 2 weeks after inoculation with hormones using the FOX assay. Both the non-droughted peppermint and rosemary plants sprayed with PAA had noticeably higher concentrations of polyphenols, indicating a potential for further study.

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Researcher: Nisha Andure, Mountain House High School

Keywords: Polyphenols | Mentha piperita | Auxins | FOX Assay | cytokinins.

Department of Chemistry, Biochemistry, and Physics

Fridays @ 8:00-9:00 PM PST

Friday, July 2, 2021

Leveraging GC-MS and NMR spectroscopy to gain insight into the reaction mechanics of the nitro-aldol reaction and synthesis of thymoquinone & other therapeutics

Quantitative NMR- and GC-MS- enabled kinetics can provide a multitude of information regarding the structure and reactivity of a compound. The metal-catalyzed synthesis of the cytotoxic, anticancer and antiinflammatory terpene thymoquinone, for instance, was able to be assessed for completion through these GC-MS methods. Although thymoquinone has highly beneficial biological properties, its chemical instability has rendered this terpene unable to be effectively administered as a drug parenterallically, leading to subsequent analysis on its photodimerization using proton NMR and in silico methods as well. Furthermore, studies involving 19F NMR monitoring, including the synthesis of anticancer dihydropyrimidine and anti-COVID-19 analogs, along with the investigation of C-C bond formation events on fluorinated molecules, allow for expedient reaction monitoring and data regarding the mechanism of action of the synthesis of essential medicinal compounds.

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Researcher: Neha Mandava, Santa Clara High School

Keywords: Thymoquinone | NMR spectroscopy | photodimerization | GC-MS | anti-cancer | nitro-aldol | fluorine