Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards,
2019
Temple University
Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards, Lauren Spirko-Burns, Karthik Devarajan
COBRA Preprint Series
The past two decades have witnessed significant advances in high-throughput ``omics" technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive ``omics" profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential …
Visual Contributions To Balance Control During Gait,
2019
University of Nebraska at Omaha
Visual Contributions To Balance Control During Gait, Kyle Brozek
UNO Student Research and Creative Activity Fair
We propose to isolate the contributions of continuous OF to the orthogonal relationship between balance and gait control during treadmill walking using a series of conditions. Manipulating the direction of OF using a CAREN (Motek Medical, Amsterdam, Netherlands) virtual reality treadmill environment will isolate these visual contributions in human subjects as they walk. We plan to tease out the effect of OF direction on the relationship between gait and balance control by having healthy young adults perform a series of treadmill walking trials while immersed in a VR environment. This will be done by manipulating the direction of walking and …
Day To Day And Leg To Leg Variation In Gene Expression,
2019
University of Nebraska at Omaha
Day To Day And Leg To Leg Variation In Gene Expression, Zohal Alizai
UNO Student Research and Creative Activity Fair
BACKGROUND: Skeletal muscle biopsies are extensively used in research to determine the effects of exercise. Usually, sequential biopsies are taken before and after exercise in order to determine the influence of exercise on gene expression. Often it is not clear if the results are due to exercise or as a result of damage cause by the biopsy to the muscle. Previous studies have proven that multiple biopsies in the same leg cause stress to the muscle and such stress leads to inflammation and other response pathways that alter the gene expression. PURPOSE: The purpose of this study is to determine …
Diversity Of Resistance Mechanisms In Carbapenem-Resistant Enterobacteriaceae At A Health Care System In Northern California, From 2013 To 2016,
2019
Stanford University
Diversity Of Resistance Mechanisms In Carbapenem-Resistant Enterobacteriaceae At A Health Care System In Northern California, From 2013 To 2016, Fiona Senchyna, Rajiv L. Gaur, Johanna Sandlund, Cynthia Truong, Guillaume Tremintin, Dietmar Kültz, Carlos A. Gomez, Fiona B. Tamburini, Tessa Andermann, Ami Bhatt, Isabella A. Tickler, Nancy Watz, Indre Budvytiene, Gongyi Shi, Fred C. Tenover, Niaz Banaei
Biology Faculty Publications
The mechanism of resistance in carbapenem-resistant Enterobacteriaceae (CRE) has therapeutic implications. We comprehensively characterized emerging mechanisms of resistance in CRE between 2013 and 2016 at a health system in Northern California. A total of 38.7% (24/62) of CRE isolates were carbapenemase gene-positive, comprising 25.0% (6/24) blaOXA-48 like, 20.8% (5/24) blaKPC, 20.8% (5/24) blaNDM, 20.8% (5/24) blaSME, 8.3% (2/24) blaIMP, and 4.2% (1/24) blaVIM. Between carbapenemases and porin loss, the resistance mechanism was identified in 95.2% (59/62) of CRE isolates. Isolates expressing blaKPC were 100% susceptible to ceftazidime–avibactam, meropenem–vaborbactam, …
Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis,
2019
Southern Methodist University
Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis, Hongyu Zhou, Zheng Dong, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao
Mathematics, Physics, and Computer Science Faculty Articles and Research
The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an …
Comparative Mito-Genomic Analysis Of Different Species Of Genus Canis By Using Different Bioinformatics Tools,
2019
Institute of Natural and Management Sciences (INAM), Rawalpindi, Pakistan
Comparative Mito-Genomic Analysis Of Different Species Of Genus Canis By Using Different Bioinformatics Tools, Ume Rumman, Ghulam Sarwar, Safia Janjua, Fida Muhammad Khan, Fakhra Nazir
Journal of Bioresource Management
In the current study, the mitochondrial genes sequence for COI, Cyt b and 16s rRNA of seven species found in different parts of the world were retrieved from NCBI Gene Bank while, PCR products of COI, Cyt b and 16s rRNA genes obtained from C. lupus and C.aureus present in Pakistan were sequenced and aligned for comparison. The phylogenetic analysis of mitochondrial COI, Cyt b and 16s rRNA genes showed almost the same results for the extant species of genus Canis. 16s rRNA revealed C. latrans, C. lycaon and C. simensis showed close phylogenetic relation with each other. …
Metabolomics Of Sorghum Roots During Nitrogen Stress Reveals
Compromised Metabolic Capacity For Salicylic Acid Biosynthesis,
2019
Colorado State University
Metabolomics Of Sorghum Roots During Nitrogen Stress Reveals Compromised Metabolic Capacity For Salicylic Acid Biosynthesis, Amy M. Sheflin, Dawn Chiniquy, Chaohui Yuan, Emily Goren, Indrajit Kumar, Max Braud, Thomas Brutnell, Andrea L. Eveland, Susannah Tringe, Peng Liu, Stephen Kresovich, Ellen Marsh, Daniel P. Schachtman, Jessica E. Prenni
Nebraska Center for Biotechnology: Faculty and Staff Publications
Sorghum (Sorghum bicolor [L.] Moench) is the fifth most productive cereal crop worldwide with some hybrids having high biomass yield traits making it promising for sustainable, economical biofuel production. To maximize biofuel feedstock yields, a more complete understanding of metabolic responses to low nitrogen (N) will be useful for incorporation in crop improvement efforts. In this study, 10 diverse sorghum entries (including inbreds and hybrids) were field-grown under low and full N conditions and roots were sampled at two time points for metabolomics and 16S amplicon sequencing. Roots of plants grown under low N showed altered metabolic profiles at …
Pretargeted Radioimmunotherapy Utilizing The Inverse Electron Demand Diels-Alder Reaction,
2019
CUNY Graduate Center
Pretargeted Radioimmunotherapy Utilizing The Inverse Electron Demand Diels-Alder Reaction, Rosemery Membreno
Dissertations, Theses, and Capstone Projects
Radioimmunotherapy capitalizes on the specificity and affinity of antibodies for their antigens to localize radioactivity at the tumor site. One limitation in using antibodies is their long circulation time, which can take days to weeks to fully clear from blood circulation. When a radioisotope is directly conjugated to this immunoglobulin vector, the red marrow and other healthy organs are receiving a constant radiation dose while it is in blood circulation. This not only harms healthy organs, but limits the dose of radioactivity that can be administered thus prolonging treatment. A promising alternative to limit the radiation dose to non-tumor tissue …
Mining For Specialized Metabolism Genes In Red Sea Brine Pool Prokaryotic Metagenomes For Antibacterial And Anticancer Activities,
2019
The American University in Cairo AUC
Mining For Specialized Metabolism Genes In Red Sea Brine Pool Prokaryotic Metagenomes For Antibacterial And Anticancer Activities, Laila Ziko
Theses and Dissertations
Antibiotic and anticancer drug resistance are current global health threats, thus new antibiotics and anticancer agents are required to treat the strains and cancers that are currently untreatable with the available drug spectrum. One way to search for new chemotherapeutics is to search nature, particularly metagenomes of un-cultured microbial communities. A subset of specialized metabolites (SMs) produced by microbes confer activities of pharmaceutical importance, such as antibacterial and anticancer effects, and are coded by specialized metabolism gene clusters (SMGCs) in the organisms’ genomes. We aimed to search for SMGCs in the metagenomes of Red Sea brine microbial communities by employing …
Identification And Characterization Of Barrier Insulator Activity In The T-Cell Receptor Alpha Locus Control Region,
2019
CUNY Graduate Center
Identification And Characterization Of Barrier Insulator Activity In The T-Cell Receptor Alpha Locus Control Region, Gayathri Devi Raghupathy
Dissertations, Theses, and Capstone Projects
Genes of different spatiotemporal expression profiles are often juxtaposed in the genome. This organization raises risks of cross-regulatory influences from neighboring genes; for instance heterochromatin can spread over euchromatin or long-range acting enhancers can inappropriately activate genes. Gene regulatory elements such as Locus Control Regions (LCR) and Insulators prevent such cross-communications and allow for normal gene expression patterns. In transgenic systems, LCRs limit influences from surrounding chromatin by providing site-of-integration independent and specific spatiotemporal expression upon a linked transgene. The field’s understanding of the ability of an LCR to overcome chromatin influences and allow site-of-integration independent expression is minimal. Interestingly, …
Histology For Cytotechnologists Ii Mls 568,
2019
University of Rhode Island
Histology For Cytotechnologists Ii Mls 568, Joanna Burkhardt
Library Impact Statements
No abstract provided.
Histology For Cytotechnologists I,
2019
University of Rhode Island
Histology For Cytotechnologists I, Joanna Burkhardt
Library Impact Statements
No abstract provided.
Cytology Practicum Iii Mls 567,
2019
University of Rhode Island
Cytology Practicum Iii Mls 567, Joanna Burkhardt
Library Impact Statements
No abstract provided.
Industry Spotlight: Medical Devices,
2019
Brigham Young University
Industry Spotlight: Medical Devices, Evan D. Poff
Marriott Student Review
Medical devices restore and even redefine health. This Industry Spotlight examines pre-market barriers, medtech business model quirks, current and future developments in the field, and the present-day move to value-based care in the medical device industry.
Biotechnological Application In Aquaculture And Its Sustainability Constraints,
2019
Embry-Riddle Aeronautical University
Biotechnological Application In Aquaculture And Its Sustainability Constraints, Olaganathan Rajee, Tang Kar Mun Alicia
Publications
The valuable nutritional and biochemical properties have made fisheries products one of the most vital high-quality protein sources for human consumption. Aquaculture has become the great alternative to substitute wild catches when the yield from fishing are no longer sufficient to sustain the massive food demand of the human population which is constantly burgeoning. However, aquaculture requires multidisciplinary approaches with holistic and environmental-friendly management measures to ensure its long term success and sustainability. Biotechnological applications have enhanced the effectiveness and cost-efficiencies of aquaculture by augmenting the productivity of aquaculture to meet global needs. Despite the benefits, the biotechnological application in …
Method Development For Structural Assessment Of Nanolipoprotein Particles With And Without Cross-Linked Lipids,
2019
University of Oregon
Method Development For Structural Assessment Of Nanolipoprotein Particles With And Without Cross-Linked Lipids, Emma J. Mullen, Wei He, Sean Gilmore, Matthias Frank, Matthew Coleman, Megan Shelby
STAR Program Research Presentations
Membrane proteins make up approximately 30% of the cellular proteome and account for over 60% of pharmaceutical targets.1 Determining the structures of this class of proteins is critical to our understanding of disease states and will advance rational drug design. But membrane proteins have limited solubility, rarely form large crystals that diffract well, and often misfold outside of a bilayer, hindering crystallographic studies.1 Nanolipoprotein particles (NLPs) have arisen as a platform to readily solubilize membrane proteins while mimicking a native lipid environment. NLPs consist of a discoidal phospholipid bilayer encircled by an apolipoprotein belt. In an effort to optimize and …
Amelioration Of Alzheimer's Disease Pathology In 12-Month-Old Happ(Sweind) Transgenic Mice After Treatment With A Cysteine Rich Whey Supplement, Immunocal®,
2019
University of Denver
Amelioration Of Alzheimer's Disease Pathology In 12-Month-Old Happ(Sweind) Transgenic Mice After Treatment With A Cysteine Rich Whey Supplement, Immunocal®, Srivalli Puttagunta
Electronic Theses and Dissertations
Deficits in Reelin expression and signaling play a pathogenic role in Alzheimer’s disease (AD). Thus, strategies aimed at correcting Reelin deficits may provide a novel therapeutic approach to treating AD. The cysteine-rich, whey protein supplement, Immunocal®, has recently been shown to rescue Reelin expression in a mouse model of Schizophrenia. Given that Reelin-expressing neurons of the entorhinal cortex region are a highly vulnerable population of cells that are lost early in AD, we examined the effects of Immunocal® in the hippocampal-entorhinal cortex formation in a mouse model of AD. Glutathione levels and Reelin expression in the hippocampal-entorhinal cortex formation (entorhinal …
Characterization Of Vps41 And Its Role In The Regulated Secretory Pathway,
2019
University of Denver
Characterization Of Vps41 And Its Role In The Regulated Secretory Pathway, Christian Henry Burns
Electronic Theses and Dissertations
Insulin secretory granules (SGs) mediate the regulated secretion of insulin, which is essential for glucose homeostasis. The basic machinery responsible for this regulated exocytosis consists of specific membrane proteins present both at the plasma membrane and on insulin SGs. The protein composition of insulin SGs thus dictates their release properties, yet the mechanisms controlling insulin SG formation, which determines this molecular composition, remain poorly understood. VPS41, a component of the endolysosomal tethering HOPS complex, was recently identified as a cytosolic factor involved in the formation of neuroendocrine/neuronal granules. We now find that a stable pool of VPS41 exists outside of …
Investigation Of Transient Expression System In Nicotiana Bethamiana To Produce Novel Tales And The Development Of (Ds)Dna Detection With Quantum Dot-Labeled Proteins In Graphene Oxide Quenching Arrays,
2019
Western Kentucky University
Investigation Of Transient Expression System In Nicotiana Bethamiana To Produce Novel Tales And The Development Of (Ds)Dna Detection With Quantum Dot-Labeled Proteins In Graphene Oxide Quenching Arrays, Colleen Jackson
Mahurin Honors College Capstone Experience/Thesis Projects
Our objective was to develop a faster method of quantitively detecting double stranded (ds)DNA of pathogenic bacteria such as the Shiga Toxin 2 gene present in E. coli O157. Transcription Activator-Like Effectors (TALEs) are a new class of DNA-binding proteins which selectively bind to dsDNA with the 12th and 13th amino acids of each repeat, called repeat variable diresidues (RVDs). Novel TALE proteins were designed to target the stx2 gene and were cloned into existing AvrBs3 TALE protein in the pMAL c2x vector system for bacterial BL-21 E. Coli expression. The protein’s DNA-binding region was then subcloned pEAQ vectors for …
Structure/Function Analysis Of Fega And Fhua In Bradyrhizobium Sp.,
2019
James Madison University
Structure/Function Analysis Of Fega And Fhua In Bradyrhizobium Sp., Alexander James Herd
Senior Honors Projects, 2010-2019
Bradyrhizobium japonicum is a Gram-negative soil bacterium commonly known for its agriculturally significant mutualistic relationship with soybean. In this symbiosis, the bacteria and plant undergo complex molecular signaling characterized by sent and received signals resulting in the formation of infection threads and root nodules. This research aimed to compare two related bacterial outer membrane proteins, FegA and FhuA, associated with the molecular signaling between the bacteria and plant. Previous work has led to the hypothesis that the N-terminal domain (NTD) of FegA in B. japonicum is needed for a functional symbiosis to occur. Recombinant bacterial strains expressing altered FegA proteins …
