Congratulations to our 2018 CJSJ Finalists!
Click here for our 2018 journal.
Caitlin brown- Fruit Fly Models of Noonan Syndrome to Screen for Therapeutic Drugs
Noonan Syndrome (NS), the common RASopathy, can be modeled in Drosophila melanogaster, the fruit fly. This genetic disease causes hematological abnormalities, developmental delays, and cardiac problems. Most patients die before reaching adulthood due to heart defects. There is no cure for this disease, but fruit fly genomes can be manipulated to model NS and help find therapeutic drugs that will cure NS in humans. Six NS mutations were inserted into fly genomes, which caused them to develop defective wings with ectopic veins. Four drugs were given to the flies to see which was most successful in rescuing the ectopic vein phenotype.
diane zhang- Copy Number Variations and Their Impact on Gene Expression in Liver Cancer
The aim of this study was to identify regulatory relationships between genomic variants and gene expression associated with liver hepatocellular carcinoma (HCC). Specifically, an integrative analysis combining gene expression and copy number variations (CNVs) in HCC tumor-normal matched samples was performed on RNA- seq and whole-genome sequencing data, respectively, identifying 11 CNV-driven genes. Through these analyses, it was possible to extract biomarkers associated to HCC.
matthew belzer- Improving the Yield of Perylene Monoanhydride Diester
Perylene monoanhydride diester is a compound used to produced organic semiconductors, which is used in electronics. Currently, the most common type of semiconductor are silicon semiconductors, but they are expensive to produce. Therefore, to lower the cost of electronics, this study produced perylene monoanhydride diester more efficiently using acid- catalyzed carbocation formation reaction.
Joon Young Park and Richard Kyung- A Study on the Development of Efficient Low-Pass Filters on Enhancing the Quality of Bioimages
Sound data used in modern bioimaging techniques such as MRIs require high clarity in addition to fast processing methods for raw data. However, many image processing techniques suffer from artifacts caused by inefficient filtering. In this study, computer simulations were developed to find filters with more efficient noise rejection and better image resolution. Fourier transformations were performed on MRI data from a human brain using simulations of various low-pass filters (LPFs) such as square, Gaussian, and round to determine which LPFs offer the clearest image with the most efficient audio. Based on advantages of different LPFs, a new filter with different capabilities and benefits was proposed.
Janathan zHao- Exploring the Role of Notch Cell Signaling in Harpegnathos saltatoR
Notch cell signaling is a well-known and an important cell-signaling pathway, responsible for processes including differentiation and cell fate specification as well as linked to multiple diseases. This study attempts to increase knowledge of eusocial insect colony structure and determine the effect of Notch signaling on reproductive behavior of Harpegnathos saltator workers by inhibiting the Notch pathway with DAPT. Results from this experiment indicate that inhibition of Notch is correlated with reproductive development in H. saltator. This correlation and the mechanisms behind it will facilitate the study of other eusocial insects. In addition, the association of the Notch pathway with diseases like cancer may yield important information regarding the role of Notch in animals. Future research should focus on exploring eusociality in H. saltator and expanding upon the understanding of Notch.
richard lee and annie miller- A Novel Approach to Harvesting Energy from Agriculture in Microbe-Polluted Water: The Implementation of Plant Microbial Fuel Cells in Hydroponic Chambers
As urban populations are reaching nearly 63% of the world population, renewable energy and space- efficient agricultural sustainability are essential for extended development [1]. In order to generate clean energy and to promote agricultural efficiency, a hydroponic system was constructed with an interior plant-microbial fuel cell: enabled via the decomposition of glucose by E. coli into free electrons, and then transported by hydroponic water effluent. This novel design was most efficient with 80 colony forming units (CFU) of E. coli and the addition of bio-catalyst Graphene oxide, generating a maximum of 1.9 W/m2 and promoting space-efficient, self-sufficient agricultural development.
julia v. parsley- Alpha Synuclein and Cellular Death in Lewy Body Dementia
Lewy Body Dementia (LBD) is a family of fatal, incurable neurodegenerative diseases characterized by aggregation of alpha synuclein (SNCA). A current model for neuron death in LBD relies on aggregation of SNCA leading to loss of SNCA mediated dopamine transporter protein (DAT) inhibition, and subsequent lethal dopamine influx [5]. The nature of the SNCA- DAT interaction and its role in neuron survival, however, has not been resolved [1, 6]. Therefore, this study aims to determine the effect of SNCA knockdown on neuron survival and intracellular dopamine in order to discern the nature of the SNCA-DAT interaction, and thereby the accuracy of this model. Neuroblastoma cells underwent SNCA knockdown, and viability, intracellular dopamine, and gene expression were assessed. It was found that SNCA knockdown had a transient yet significant cytotoxic effect coinciding with a short-term significant increase in intracellular dopamine. After cytotoxicity ceased, upregulation of protein phosphatase 2A (PP2A) proteins and protein kinase C iota (PRKCI) was observed. SNCA knockdown was also found to increase susceptibility of cells to DMSO-induced apoptosis, which may explain why Parkinson’s disease, a type of LBD, is associated with exposure to toxins [3]. These results suggest that SNCA does inhibit DAT, but that PP2A and PRKCI may regulate DAT when SNCA is absent, and that therefore lack of SNCA-DAT interaction may not be a major contributor to neurodegeneration in LBD.
neelay trivedi- NodulePredict: Predicting Lung Cancer Onset with Segmentation & ClassificatioN
In this study, NodulePredict, an automated system for lung cancer diagnosis, was developed to segment lung nodule regions from CT scans and predicts whether they are cancerous. U- Net segmentation was used to isolate nodule regions from CT scans, in a series of six models. Using the best-performing feature set, an XGBoost classification pipeline was then developed to predict whether isolated nodules were cancerous, using individual nodule predictions to arrive at an overall scan-wise cancer probability.
Sahith Vadada, Rushikesh Patel, and Vedant Singh- Evaluating the Effects of Graphene-Loaded Poly(4-vinylpyridine) Electrospun Fibrous Scaffolds on the Biomineralization and Differentiation of Dental Pulp Stem Cells in vitrO
Stem cell based tissue engineering offers a therapeutic alternative that promotes the regeneration—rather than the replacement—of dental tissue. Dental pulp stem cells (DPSCs) possess tremendous in vitro regenerative potential on graphene-polymer scaffolds. Whereas current studies focus on 2-dimensional substrates, our study presents graphene-loaded poly(4-vinylpyridine) as a cost- effective, electrospun, and 3-dimensional (3D) fibrous scaffold that mimics the natural extracellular matrix and supports DPSC biomineralization and differentiation. Confocal microscopy, energy dispersive X-ray spectroscopy, scanning electron microscopy, and real- time polymerase chain reaction indicate poly(4-vinylpyridine) as a viable 3D scaffold that promotes the osteogenic differentiation of DPSCs by templating mineralized collagen-rich structures.
Manasi Soman, Sandip Kaledhonkar, Ziao Fu, and Joachim Frank- Comparison of Microfluidic PDMS and Silicon Device in Time-Resolved Cryo-electron MicroscopY
Time-resolved cryo-electron microscopy has revolutionized biology by imaging biomolecules such proteins and deadly viruses. A microfluidic device is used to mix two reacting biomolecules, before they are imaged. This study examines the differences between two microfluidic devices: polydimethylsiloxane (PDMS) and silicon. The PDMS microfluidic device could potentially replace silicon devices in labs to study biomolecules. PDMS device is less expensive and easier to manufacture. The data showed that the PDMS device produced consistent and repeatable results. The study concluded that the time frames of the PDMS device must be increased to match the performance efficiency of the silicon device.
SAI mamidala- Electrochemical Formate Oxidation on a Pd3Ni/C Nanoparticle Catalyst
This study examines the kinetics and mechanistic progression of the electrochemical oxidation of formate. Due to its high energy density, formate shows promise as both an electrochemical fuel for portable applications and a means of storing energy from renewable sources. We show that an electrocatalyst composed of carbon supported palladium-nickel alloy nanoparticles is both active and CO poisoning tolerant. Potentially due to a potential shift in rate determining step, Pd3Ni/C exhibits high peak current densities with more reversible behavior than other catalysts including Pt and Pd.
vignesh pernati- Evaluation of Transcytosis Mechanism in Lysosomal Storage Disorders
The study’s goal was to indicate the inhibition of therapeutic substances through the blood brain barrier and examine the three components of transcytosis including binding, endocytic uptake and release of agents across the cell. Additionally, to investigate the effect of lysosomal storage in brain endothelial cells upon endocytosis and transcytosis of antibodies and nanocarriers actively targeted to the clathrin pathway. Our findings identified that the transferrin receptor nanocarrier indicates more internalization of therapeutics in the cell, demonstrating its potential to deliver.
soo hyun kim- Investigating the Mechanism of C9orf72 Mutations in Amyotrophic Lateral Sclerosis
The GGGGCC hexanucleotide repeat expansion of the C9orf72 gene is the most common genetic cause for amyotrophic lateral sclerosis (ALS). This study examined the cloning of various 149 repeat expansions of C9orf72 and studied their stability in yeast. Conclusively, results demonstrated significant, undesirable shrinkage in cloned repeat expansions and low stability of the repeat expansions in yeast, thus furthering our understanding of yeast models in ALS research.
Supraja Kanipakam, Viswanath Ragupathy Ph.D, Indira Hewlett Ph.D, and Andrew Huang- NextGeneration Sequencing to Characterize Near Full Length Human Immunodeficiency Virus (HIV-1) Subtypes Evolving Within Infected Host
Human Immunodeficiency Virus (HIV) is a retrovirus that globally affects all ages, sexes, and races. As of December 2015, approximately 36.7 million people worldwide are living with HIV. The goal of this study was to (1) sequence the near full length of HIV-1 virus and (2) discover heterogeneity of HIV-1 in the infected individuals, whether the subtypes evolved independently or as evolved as recombinants of subtypes (CRFs). By evaluating samples from Cameroon as a model to study HIV-1 diversity, we used infected plasma samples and characterized near fulllength HIV strains. In order to accomplish this goal, several steps were taken, including nucleic acid extraction, reverse transcription of RNA, polymerase chain reaction (PCR), and gel electrophoresis. Next-Generation Sequencing (NGS) technology was utilized to sequence the DNA. Our results yield that out of the 3 HIV-infected linked samples evaluated: one male sample was infected with CRF02_AG, which includes a CRF and subtypes A and G, and two of his partners were infected with a recombinant known as F2/CRF02. CRF02 virus from the male partner recombined with F2 infected female partners and evolved as F2/CRF02 recombinants. This study provides a useful tool in order to thoroughly understand the HIV epidemiology and pathogenesis, HIV diagnosis, and produce effective vaccine.