Biochemistry, Biophysics, and Structural Biology Commons^™

Mapping Molecular Datasets Back To The Brain Regions They Are Extracted From: Remembering The Native Countries Of Hypothalamic Expatriates And Refugees, Khan, Alice Grant, Anais Martinez, Gully Burns, Brendan Thatcher, Vishwanath Anekonda, Benjamin Thompson, Zachary Roberts, Daniel Moralejo, James Blevins

Departmental Papers (Biology)

This article, which includes novel unpublished data along with commentary and analysis,focuses on approaches to link transcriptomic, proteomic, and peptidomic datasets mined frombrain tissue to the original locations within the brain that they are derived from using digital atlasmapping techniques. We use, as an example, the transcriptomic, proteomic and peptidomicanalyses conducted in the mammalian hypothalamus. Following a brief historical overview, wehighlight studies that have mined biochemical and molecular information from the hypothalamusand then lay out a strategy for how these data can be linked spatially to the mapped locations in acanonical brain atlas where the data come from, thereby allowing …

Effect Of Bmp Treatment On Periostin Gene Expression In Pre-Osteoblastic Mc3t3-E1 Mouse Cells, Vincent Lee Khang

UNLV Theses, Dissertations, Professional Papers, and Capstones

Periostin is a secreted, extracellular matrix (ECM) protein widely expressed within collagen-rich fibrous connective tissues of the body including the periodontal ligament (PDL), bone, skin, heart, and cornea. Periostin has been shown to serve many important regulatory functions including cell adhesion, cell motility, wound healing and of particular importance to the dental field, differentiation of osteoblasts. The deletion of periostin compromises osteoblast attachment to bone matrix and induces a reduction in mineralization and expression of bone markers, including type I collagen, osteocalcin, osteopontin and alkaline phosphatase. Periostin has also been shown to play a significant role in collagen fibrillogenesis by …

The Caspase Cascade During Hibernation In The Golden-Mantled Ground Squirrel, Spermophilus Lateralis, Michael David Treat

UNLV Theses, Dissertations, Professional Papers, and Capstones

In several human pathologies like heart attack, stroke, neurodegenerative diseases, and autoimmune disorders, widespread cell death, or apoptosis, is a major cause of organ dysfunction and death. Hibernating golden-mantled ground squirrels, Spermophilus lateralis, experience numerous conditions during the winter that are known to be pro-apoptotic in other mammal systems (e.g. extreme hypothermia, ischemia and reperfusion, acidosis, increased reactive oxygen species, bone and muscle disuse). However, studies suggest that hibernators may invoke a protective phenotype to limit widespread cell damage and loss during the hibernation season. Could regulating apoptosis provide protection against the harmful conditions experienced during the hibernation season? Could …

Muc4 Based Immunotherapy For Pancreatic Cancer, Kasturi Banerjee

Theses & Dissertations

Pancreatic Cancer (PC) is a lethal disease claiming approximately 45000 lives in the US in 2018, and it establishes an elaborate immunosuppressive tumor microenvironment that aids in disease pathogenesis. Immunotherapy has emerged as a strategy to target tumor cells by reprogramming patient’s immune system. Challenges present in PC immunotherapy are: i) identifying a tumor-associated antigen that could be targeted, ii) identifying adjuvants that could efficiently deliver antigens, iii) eliciting robust anti-tumor responses and iv) overcoming peripheral tolerance and immunosuppression elicited by the tumor.

Firstly, we detected circulating autoantibodies to MUC4 present in PC patients and observed that IgM autoantibodies to …

Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Maureen Azar, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants …

Analyzing The Effects Of Site-Directed Mutagenesis On The Structure Of Coxsackievirus B3 Genomic Rna, Erin Dimon

Theses/Capstones/Creative Projects

Coxsackievirus B3 (CVB3) is known to cause myocarditis and pancreatitis in humans. The virus has a single stranded RNA genome that codes for 11 different proteins. CVB3 is found to have two serotypes: 28 (virulent and disease causing) and GA (avirulent and not disease causing). Like other members of the Picornaviridae family, CVB3 utilizes the genomic 5’ untranslated region (5’ UTR) to initiate viral replication mechanisms through interactions with host protein factors. Structural variations of the CVB3 5’ UTR are hypothesized to influence the success of such interactions and consequentially determine viral virulence. The aim of this project was to …

Dextran Hydrogels By Crosslinking With Amino Acid Diamines And Their Viscoelastic Properties, Naphtali O'Connor, Andrei Jitianu, G Nunez, Quentin Picard, Madeline Wong, D Akpatsu, Adam Negrin, Rajendra Ghardbaran, D Lugo, S Shaker, Mihaela Jitianu, Stephen Redenti

Publications and Research

Amine functionalized polysaccharide hydrogels such as those based on chitosan are widely examined as biomaterials. Here we set out to develop a facile procedure for developing such hydrogels by crosslinking dextran with amino acid diamines. The dextran-amino acid gels were formed by the addition of the amino acid diamines to a dextran and epichlorohydrin solution once it became homogeneous. This was demonstrated with three amino acid diamines, lysine, lysine methyl ester, and cystine dimethyl ester. Hydrogel networks with albumin entrapped were also demonstrated. These hydrogels were characterized by FTIR, SEM, rotational rheometry, swelling studies and cell biocompatibility analysis. These hydrogels …

Role Of Leptin And Dyslipidemia In Chronic Kidney Disease, Sabeela Noor, Faiza Alam, Syeda Sadia Fatima, Mahnur Khan, Rehana Rehman

Department of Biological & Biomedical Sciences

Chronic kidney disease (CKD) patients are at an increased risk of cardiovascular complications and plasma leptin level is elevated in cardio renal syndrome. We wanted to explore leptin levels in patients with different stages of CKD and find its association with risk of cardiovascular disease. This cross-sectional study was conducted in Nephrology Department of Jinnah Post Graduate Medical Centre (JPMC) from January 2014 to September 2014. Group I comprised of controls (GFR=116±8.3, n = 44) acquired from general population, CKD patients were grouped as II, III and IV respectively with GFR; 85.77±9.9 (n = 42), 53.84±9.9 (n=42) and 20.22±8.4 (n …

Determination Of Adamts13 Susceptibility In Type Iia Von Willebrand Disease, Monica Buselli

Dissertations, Masters Theses, Capstones, and Culminating Projects

von Willebrand Disease (vWD) is a bleeding disorder caused by a deficiency in von Willebrand Factor (vWF), a large glycoprotein that assists in coagulation. Specifically, large vWF multimers in the blood stream are key components in starting the coagulation cascade. vWF is cleaved by the metalloprotease ADAMTS13, regulating the multimers size, which hinders vWF’s ability to function properly. The three main types of vWD —Type I, II, and III— are not well defined, and as a result are all similarly treated with plasma-derived vWF replacement therapy. Plasma-derived vWF is a treatment that does not cure the problem but relieves the …

Ph Sensitivity Of Connexin 50 Hemichannels: H95 And Beyond, Leah Volk

Biology Theses

Gap junction channels formed by connexin proteins are critical for the health and function of the vertebrate lens. It is important to understand how these channels are affected by pH because a pH gradient exists in lens tissue. Intracellular pH (pH_i) is a regulator of gap junction coupling, and different connexins show different sensitivities to pH_i. A “Particle-Receptor” model for pH-dependent channel closure involves the intramolecular interaction between the cytoplasmic tail of the connexin and a region near the mouth of the channel dependent on a highly conserved histidine residue at position 95. While this model …

Regulation Of The Tubulin Homolog Ftsz In Escherichia Coli, Monika S. Buczek

Dissertations, Theses, and Capstone Projects

Escherichia coli is a well-known pathogen, and importantly, a widely used model organism in all fields of biological sciences for cloning, protein purification, and as a model for Gram-negative bacterial species. And yet, researchers do not fully understand how this bacterium replicates and divides. Every year additional division proteins are discovered, which adds complexity to how we understand E. coli undergoes cell division. Due to their specific roles in cytokinesis, some of these proteins may be potential targets for development of antibacterials or bacteriostatics, which are much needed for fighting the current global antibacterial deficit. My thesis work focuses on …

Calvin Avenue Basin Project Description And Analysis, Calvin University

Faculty and Professional Research

The existing detention basin, Calvin Avenue Basin was modified in 2017 to include a two-stage ditch, level spreaders, and micro- and macrotopography with the goal of reducing the volume of stormwater leaving the basin, resulting in less stormwater, less flashiness, and improved water quality in the downstream, impaired waterway of Silver Creek. The total storage increase at a reference elevation of 690 is 348,615 gallons (1.07 acre-feet) for all modifications (two-stage ditch and microtopography). This equates to 4.35 million gallons of stormwater that will be stored and slowly released. Of this, 2.46 million gallons of stormwater will be infiltrated annually. …

A Role Of Vitamin B2 In Reducing Amyloid-Beta Toxicity In A Caenorhabditis Elegans Alzheimer’S Disease Model, Muhammad Tukur Ameen

Electronic Theses and Dissertations

Alzheimer’s disease (AD) is associated with amyloid-beta peptide deposition and loss of mitochondrial function. Using a transgenic C. elegans AD worm model expressing amyloid-beta in body wall muscle, we determined that supplementation with either of the forms of vitamin B₂, flavin mononucleotide (FMN) or flavin adenine dinucleotide (FAD) protected against amyloid-beta mediated paralysis. FMN and FAD were then assayed to determine effects on ATP, oxygen consumption, and reactive oxygen species (ROS) with these compounds not significantly improving any of these mitochondrial bioenergetic functions. Knockdown of the daf-16/FOXO transcriptional regulator or the FAD synthase enzyme completely abrogated the …

Phase Diagram Of Water Confined By Graphene, Zhenghan Gao, Nicolas Giovambattista, Ozgur Sahin

Publications and Research

The behavior of water confined at the nanoscale plays a fundamental role in biological processes and technological applications, including protein folding, translocation of water across membranes, and filtration and desalination. Remarkably, nanoscale confinement drastically alters the properties of water. Using molecular dynamics simulations, we determine the phase diagram of water confined by graphene sheets in slab geometry, at T = 300 K and for a wide range of pressures. We find that, depending on the confining dimension D and density σ, water can exist in liquid and vapor phases, or crystallize into monolayer and bilayer square ices, as observed in …

Evaluating Mutagenicity Of Burned Arginine-Based Heterocyclic Amines And Anti-Mutagenicity Effect Of Chinese Medicinal Herbs, Rayford C. Alva

Honors Theses

From the unexpected finding that cooked grains and meat substitutes elicit a mutagenic response in Salmonella typhimurium TA98, our work has been aimed at deconstructing this finding via a survey of heated binary amino acid combinations, involving arginine, a plant-based amino acid. secondly, our work has looked towards sing phytochemical extracts from traditional Chinese medicinal herbs to inhibit the mutagenic activity of heterocyclic amines (main culprit for mutagenicity in meat). Two fractions from the burned products of arginine and phenylalanine (RF-HCA-06 and -07) were statistically significant inducers of mutagenesis; Scutellaria barbata and Oldenlandia diffusa, both separately and together, were statistically …

Investigation Of Alcohol-Induced Changes In Hepatic Histone Modifications Using Mass Spectrometry Based Proteomics, Crystina Leah Kriss

USF Tampa Graduate Theses and Dissertations

Alcohol liver disease (ALD) is a major health concern throughout the world. Currently, in the United States, 17 million people suffer from alcoholism, of which 1.4 million people are receiving treatment [1, 2]. The link between ethanol metabolism, reactive oxygen species (ROS) and liver injury in ALD has been well characterized over the last couple decades [3-10]. Ethanol metabolism relies on the availability of the cofactor NAD+ for the oxidation of ethanol into acetate, consequently causing alterations in redox potential. Redox dysfunction within the mitochondria can affect multiple pathways important in maintaining cellular homeostasis. Chapter 1 provides an introduction to …

Proteasome Storage Granules Protect Proteasomes From Autophagic Degradation Upon Carbon Starvation, Richard S. Marshall, Richard D. Vierstra

Biology Faculty Research

26S proteasome abundance is tightly regulated at multiple levels, including the elimination of excess or inactive particles by autophagy. In yeast, this proteaphagy occurs upon nitrogen starvation but not carbon starvation, which instead stimulates the rapid sequestration of proteasomes into cytoplasmic puncta termed proteasome storage granules (PSGs). Here, we show that PSGs help protect proteasomes from autophagic degradation. Both the core protease and regulatory particle sub-complexes are sequestered separately into PSGs via pathways dependent on the accessory proteins Blm10 and Spg5, respectively. Modulating PSG formation, either by perturbing cellular energy status or pH, or by genetically eliminating factors required for …

Influenza D Virus M2 Protein Exhibits Ion Channel Activity In Xenopus Laevis Oocytes, Evan Daniel Kesinger

School of Biological Sciences: Dissertations, Theses, and Student Research

The Influenza virus M2 ion channel has good potential as a target for antiviral drugs, as the channel is necessary for viral replication. M2 of Influenza A and B viruses has beenstudied extensively, and is understood to function as a proton channel. Antiviral drugs like amantadine and rimantadine have been used to block the function of Influenza A virus M2. Influenza C virus M2 has also been researched and is understood to act as a chloride ion channel. However, the M2 channel of Influenza D virus (DM2) has been studied very little, and the activity and mechanism of the channel …

Anti-Colon Cancer Effect Of Origanum Majorana Essential Oil, Asma Nasser Rashed Alrashedi

Biology Theses

Plants have been shown to be an excellent source of new drugs, including anticancer agents. Origanum majorana commonly known as marjoram is a plant that is known to possess different therapeutic values including antioxidant andantimicrobial activities.

Our research team has previously tested the ethanolic extract of O. majorana on triple negative breast cancer and published the findings. The ethanolic extract promoted mitotic arrest at G2/M phase, induced apoptosis as well as inhibition of migration and metastasis. The promising potential of the ethanolic extract encouraged us to test the effects of O. majorana essential oil on human colon cancer cell lines. …

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

Valued readers, it is with a heavy heart that I inform you that this is the last issue of Killi-Data News. The good news is that we will be back as Killifish Research Review. The dissolution of Killi-Data International created a prob- lem: how can the newsletter of a defunct organization live on without that organization? But other additional problems were building in the background. The first issue numbered 15 pages. The previous issue was 28 pages. The number of killifish related papers is increasing while time on our end (the editorial team) is running out. It takes a lot …

Killi-Data News (Fall), Tyrone Genade

Killifish Research Review

Many interesting papers have been published over the last three months. The large volume of papers coupled with the start of the new college semester (and the workload it brings) delayed this issue of Killi-Data News. But better late than never—or so I hope! In this issue Richard van der Laan provides an insightful review of the recent Aphanius papers as to their taxonomic implications and questions. The systematic issues he raises show the importance of the Molecular project: we need to get more samples of the various cyprinodontiforme families to resolve unsettled systematic and taxonomic issues. In the Next …

Killi-Data News (Summer), Tyrone Genade

Killifish Research Review

Over the last three months several interesting and exciting pa- pers have been published. By now most of you have heard the Nothobranchius fish poo news emanating from the Valenzano lab. That paper is reviewed and certainly has repercussions for the health of our captive fish. Polaçik et al have published interesting data with ramifications as to how we breed and incubate annual killifish. The big news in this issue is the paper from the Reznick lab which Jean Huber reviews. The contents of that paper goes to the heart of the question of just what a killifish is. The …

Killi-Data News (Spring), Tyrone Genade

Killifish Research Review

This is the start of Killi-Data News’ second year. In this first issue of the year we have the usual review of research pub- lications as well as input from Martin Reichard on his lab’s Nothobranchius research. Martin is responding to my reviews of his lab’s work in the previous edition. I am serious about making sure the content in this newsletter is reliable but I erred in the previous edition and Martin has written extensively to correct my mistake in the section “Erratum”. This reply is welcomed and owed to readers. I must confess that I don’t know everything …

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

This is the fourth edition, and concluding issue of the first volume, of Killi-Data News and I am happy that it has been well received by readers. At 25 pages this issue is a bit thin- ner than the last but this is because we agreed to make the cut-off for submissions the 1 st of December so we could get this edition out by the New Year. This is an exciting edition full of new species descrip- tions and analyses that will keep taxonomists busy for years to come. Costa has given us two molecular phylogenies on Melanorivulus as …

Killi-Data News (Spring), Tyrone Genade

Killifish Research Review

This is the start of Killi-Data News’ second year. In this first issue of the year we have the usual review of research pub- lications as well as input from Martin Reichard on his lab’s Nothobranchius research. Martin is responding to my reviews of his lab’s work in the previous edition. I am serious about making sure the content in this newsletter is reliable but I erred in the previous edition and Martin has written extensively to correct my mistake in the section “Erratum”. This reply is welcomed and owed to readers. I must confess that I don’t know everything …

Studies Of Amino Acid Mutations In Drug Resistance Of The Smo Protein, Eunice Wintona

UNO Student Research and Creative Activity Fair

Smoothened receptor (SMO) is a protein that in humans, is encoded by the SMO gene. A systemic mutation in its binding pocket helps predict the sensitivity of mutant proteins to different drugs. Known as a GPCR-like receptor, it is a component of the hedgehog signaling pathway; a pathway involved in body patterning and the regulation of adult stem cells. An uncontrolled or inappropriate activation of the Hedgehog pathway drives tumor progression in cancers and a number of birth defects. To achieve these goals, the molecular modeling software MOE was used to build small molecules and drug molecules like Vismodegib and …

Investigating The Response Of Magnetotactic Bacteria To Varying Field Strength And Developing Autonomous Analysis Of Spatial Dispersal, Madeleine D. Pasco

Rose-Hulman Undergraduate Research Publications

Magnetotactic bacteria (MTB) are single-celled organisms which contain organelles called “magnetosomes,” membrane-bound ferrous nanocrystals. These organelles allow for magnetotaxis, which is movement guided by magnetic fields. MTB are generally found in the top layers of sediment of aqueous environments, and magnetotaxis is thought to help guide these microbes to ideal oxygen concentrations in the water after they may have been displaced by turbulent waters. In this we study the effect of the strength of a magnetic field on magnetotaxis.

Curcumin Potentiates The Function Of Human Α7-Nicotinic Acetylcholine Receptors Expressed In Sh-Ep1 Cells, Eslam El Nebrisi, Lina T. Al Kury, Keun-Hang Susan Yang, Petrilla Jayaprakash, Frank Christopher Howarth, Nadine Kabbani, Murat Oz

Mathematics, Physics, and Computer Science Faculty Articles and Research

Effects of curcumin, a biologically active ingredient of turmeric, were tested on the Ca²⁺transients induced by the activation of α₇ subunit of the human nicotinic acetylcholine (α₇nACh) receptor expressed in SH-EP1 cells. Curcumin caused a significant potentiation of choline (1 mM)-induced Ca²⁺ transients with an EC₅₀ value of 133 nM. The potentiating effect of curcumin was not observed in Ca²⁺ transients induced by high K⁺ (60 mM) containing solutions or activation of α₄β₂ nACh receptors and the extent of curcumin potentiation was not altered in the presence of …

Crosstalk Among Lncrnas, Micrornas And Mrnas In The Muscle ‘Degradome’ Of Rainbow Trout, Bam Paneru, Ali Ali, Rafet Al-Tobasei, Brett Kenney, Mohamed Salem

Faculty & Staff Scholarship

In fish, protein-coding and noncoding genes involved in muscle atrophy are not fully characterized. In this study, we characterized coding and noncoding genes involved in gonadogenesis-associated muscle atrophy, and investigated the potential functional interplay between these genes. Using RNA- Seq, we compared expression pattern of mRNAs, long noncoding RNAs (lncRNAs) and microRNAs of atrophying skeletal muscle from gravid females and control skeletal muscle from age-matched sterile individuals. A total of 852 mRNAs, 1,160 lncRNAs and 28 microRNAs were differentially expressed (DE) between the two groups. Muscle atrophy appears to be mediated by many genes encoding ubiquitin- proteasome system, autophagy related …

Audiobook Of A World From Dust, Ben Mcfarland

Faculty Open Access Books

A World From Dust is a popular science book about the chemical sequence behind the evolution of creation.

It’s about how geology, biology, and chemistry worked together over billions of years, providing a hidden order under the random flow of genes and lava and water.

It’s about the chemical job that each element takes up in life, and how that job is predictable from its place on the periodic table.

It can be told as the story of many elements: how iron and sulfur gave a spark of life; how manganese was a key for oxygen; and how copper and …