Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- Microgravity (4)
- Differential gene expression (2)
- Nextflow (2)
- 16S rRNA gene amplicons (1)
- Alzheimer's disease (1)
-
- Alzheimer's treatments. (1)
- Bacterial community composition (1)
- Bisphenol A (BPA) (1)
- Bone loss (1)
- Circadian Rhythm (1)
- Endocrine-disrupting chemical (EDC) (1)
- Endothelial cells (1)
- Gene enrichment analysis (1)
- Immune system. (1)
- MRNA-sequencing (RNA-seq) (1)
- Marine bacteria (1)
- Meta-Analysis (1)
- Microbial oceanography (1)
- Muscle atrophy (1)
- Neurodevelopmental disorders (NDDs) (1)
- Nextflow. (1)
- Palmer LTER (1)
- RNA-Sequencing (RNA-Seq) (1)
- Skeletal Muscle (1)
- Transcription profiling i. (1)
- Transcriptional profiling (1)
- Western Antarctic Peninsula (1)
Articles 1 - 10 of 10
Full-Text Articles in Life Sciences
Effective Cancer Detection Using Higher-Order Genome Architecture And Chromatin Interactions, My Chung
Effective Cancer Detection Using Higher-Order Genome Architecture And Chromatin Interactions, My Chung
Master's Projects
Cancer is a complex disease which requires interactions between cell-intrinsic alterations and tumor microenvironment. The connection between epigenetics and genomic structure plays a key role in chromatin interaction which promotes enhancer-promoter interactions for transcriptional activities. Alterations of chromatin states in oncogenic signaling pathway potentially cause cancer cell-intrinsic changes and inappropriate instructions to normal cell cycles, leading to abnormal cell growth. Resulting phenotypic changes are correlated to underlying changes in higher-order chromatin structure such as topologically associating domains (TADs) and compartments. In cancer cells, TAD structure is usually altered to facilitate the communication between enhancers and promoters in addition to higher …
Spaceflight And Differential Gene Expression Analysis Of Mice Quadriceps Exposed To Microgravity, Tommy Nguyen
Spaceflight And Differential Gene Expression Analysis Of Mice Quadriceps Exposed To Microgravity, Tommy Nguyen
Master's Projects
he trip to Mars and back is planned for the next 20 years. Improvement in technology and research has allowed data analysis, at a larger scale, on spaceflight specimen. However, research involving spaceflight is decentralized, as research is spread across laboratories with different methodologies. NASA’S GeneLab is a public repository for spaceflight-related omics data and promotes centralizing spaceflight RNA-Seq studies using NASA’s RNA-Seq pipeline. Jonathan Oribello, a SJSU’s Bioinformatics graduate and now an employee at GeneLab, has implemented Nextflow to NASA’s RNA-Seq pipeline. The Nextflow RNA-Seq pipeline was ran on San Jose State University’s College of Science High Performance Computing …
An Examination Of Bone Loss During Space Travel With Differential Gene Expression Analysis, Claudia Vo
An Examination Of Bone Loss During Space Travel With Differential Gene Expression Analysis, Claudia Vo
Master's Projects
Spaceflight poses many risks to human health due to the harsh conditions of microgravity, cosmic radiation, and confinement. One of the impacts that spaceflight entails is bone loss, which is a risk to astronauts as future space missions will require long travel durations. To elucidate the role of genetics in spaceflight bone loss, in this study differential gene expression analysis was performed using Nextflow-RCP, an adaptation of NASA Genelab’s RNA-Seq Consensus pipeline. The dataset for this project was GLDS-241, which contained samples from mice femoral skin. To gain a comprehensive understanding of the genes involved in bone loss, the results …
Mrna-Sequencing Pipeline For Differential Gene Expression Analysis, Crystal Han
Mrna-Sequencing Pipeline For Differential Gene Expression Analysis, Crystal Han
Master's Projects
Endothelial cells (ECs) line the insides of blood vessels and play a key role in the coagulation and vascular repair system. Under normal circumstances, ECs are constantly expressing anticoagulants to prevent clots and maintain healthy blood flow. But when there is an injury to the vessel, endothelial cells become centrally involved in orchestrating the complex series of events that would lead to the clotting of the wound. Thus, ECs are dynamic and respond accordingly based on changes in their local environment. Unfortunately, endothelial cells can sometimes misinterpret cues from the environment and initiate coagulation when there is no vessel damage …
Detection Of Antibiotic Resistance Genes In The Wastewater Microbial Metagenome, Alan Caparaz Le
Detection Of Antibiotic Resistance Genes In The Wastewater Microbial Metagenome, Alan Caparaz Le
Master's Projects
The existential threat of emerging antibiotic resistance in microbial communities poses significant risks to public health. In particular, wastewater can serve as a point of confluence for pharmaceuticals and antibiotic-resistant bacteria from urban and agricultural settings. While this is a prime environment for genetic drift and horizontal transfer of antibiotic resistance genes (ARGs) and mobile genetic elements, it also presents an opportunity for resistome monitoring via shotgun metagenomic sequencing and downstream analysis. This project reports the application of a hybrid assembly approach for the detection of ARGs within DNA derived from a wastewater sample collected from the San José-Santa Clara …
Transcriptional Profiling Of Neurological Development Of Drosophila Following Bisphenol A Exposure, Eden Johnson
Transcriptional Profiling Of Neurological Development Of Drosophila Following Bisphenol A Exposure, Eden Johnson
Master's Projects
The ubiquitous environmental chemical bisphenol A (BPA) is an emerging risk factor for neurodevelopmental disorders (NDDs). BPA is an endocrine-disrupting chemical (EDC) that is thought to interfere with neuron development by changing neuronal gene expression. Impacting neurodevelopment in this manner can cause lasting changes in behavior and potentially lead to the development of NDDs. Delineating the molecular processes that incur changes in gene expression following BPA exposure will advance our understanding of how BPA impacts neurodevelopmental pathways and affects the pathophysiology of NDDs. An RNA-Sequencing (RNA-Seq) analysis pipeline was created for transcriptional profiling of neurological development in wild-type Drosophila melanogaster …
Differential Gene Expression Analysis Of Mice Thymi After Spaceflight, Roshani Codipilly
Differential Gene Expression Analysis Of Mice Thymi After Spaceflight, Roshani Codipilly
Master's Projects
With increases in space travel and a desire to inhabit the moon and Mars comes a pressing need to understand the impact of spaceflight on the body. Some effects are already known, such as reduced cardiac function and bone loss, but one area that needs to be further explored is the immune system. Differential gene expression analysis of mice thymi was performed to determine the impact of spaceflight on the immune system. The dataset that was analyzed, GLDS-289, was obtained from GeneLab, a space-omics database developed by NASA. Differential gene expression analysis was accomplished using a Nextflow implementation of GeneLab’s …
Summer Marine Bacterial Community Composition Of The Western Antarctic Peninsula, Codey Phoun
Summer Marine Bacterial Community Composition Of The Western Antarctic Peninsula, Codey Phoun
Master's Projects
The Western Antarctic Peninsula has experienced dramatic warming due to climate change over the last 50 years and the consequences to the marine microbial community are not fully clear. The marine bacterial community are fundamental contributors to biogeochemical cycling of nutrients and minerals in the ocean. Molecular data of bacteria from the surface waters of the Western Antarctic Peninsula are lacking and most existing studies do not capture the annual variation of bacterial community dynamics. In this study, 15 different 16S rRNA gene amplicon samples covering 3 austral summers were processed and analyzed to investigate the marine bacterial community composition …
Meta-Analysis Of Natural Vs Pharmaceutical Interventions For Alzheimer's Disease, Tamara Vrublevskaya
Meta-Analysis Of Natural Vs Pharmaceutical Interventions For Alzheimer's Disease, Tamara Vrublevskaya
Master's Projects
The purpose of this research is to present a way to compare interventions by collecting all available drug clinical trials for a disease of interest. The assessment is done using Meta-Analysis, a method for evaluating data from several studies to arrive at a combined estimate of treatment effect. The evaluation is done in R on a given set of studies to answer the question – which Alzheimer's Disease intervention (pharmaceutical vs. natural) show better outcomes and fewer adverse effects. The research covers many types of interventions across diverse patient populations. On a small subset of papers, natural treatments showed better …
Differential Gene Expression Analysis Of Rodents Exposed To Long-Term Space Flight And Insights Into Physiological Effects, Jonathan Oribello
Differential Gene Expression Analysis Of Rodents Exposed To Long-Term Space Flight And Insights Into Physiological Effects, Jonathan Oribello
Master's Projects
Space travel presents inherent risks to human health and a better understanding of space biology is required to mitigate harm in an oncoming age of increased space travel. Omics analysis will play a central role in better understanding human health in space. In this project, differential gene expression analysis was performed on GLDS-104, an open science dataset provided by NASA’s GeneLab. GeneLab’s RNA-Seq Consensus Pipeline was implemented using Nextflow, performed on San Jose State University’s College of Science High Performance Computing Cluster, and optimized for computational resource efficiency. Comparison of the Nextflow implemention developed in this project to GeneLab’s posted …