Biochemistry, Biophysics, and Structural Biology Commons^™

Amalgamation Of Nucleosides And Amino Acids In Antibiotic Biosynthesis, Sandra H. Barnard

Theses and Dissertations--Pharmacy

The rapid increase in antibiotic resistance demands the identification of novel antibiotics with novel targets. One potential antibacterial target is the biosynthesis of peptidoglycan cell wall, which is both ubiquitous and necessary for bacterial survival. Both the caprazamycin-related compounds A-90289 and muraminomicin, as well as the capuramycin-related compounds A-503083 and A-102395 are potent inhibitors of the translocase I enzyme, one of the key enzymes required for cell wall biosynthesis. The caprazamycin-related compounds contain a core nonproteinogen b-hydroxy-a-amino acid referred to as 5’-C-glycyluridine (GlyU). Residing within the biosynthetic gene clusters of the aforementioned compounds is a shared open reading ...

Factorbook.Org: A Wiki-Based Database For Transcription Factor-Binding Data Generated By The Encode Consortium, Jie Wang, Jiali Zhuang, Sowmya Iyer, Xinying Lin, Melissa C. Greven, Bong-Hyun Kim, Jill Moore, Brian G. Pierce, Xianjun Dong, Daniel Virgil, Ewan Birney, Jui-Hung Hung, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

The Encyclopedia of DNA Elements (ENCODE) consortium aims to identify all functional elements in the human genome including transcripts, transcriptional regulatory regions, along with their chromatin states and DNA methylation patterns. The ENCODE project generates data utilizing a variety of techniques that can enrich for regulatory regions, such as chromatin immunoprecipitation (ChIP), micrococcal nuclease (MNase) digestion and DNase I digestion, followed by deeply sequencing the resulting DNA. As part of the ENCODE project, we have developed a Web-accessible repository accessible at http://factorbook.org. In Wiki format, factorbook is a transcription factor (TF)-centric repository of all ENCODE ChIP-seq datasets ...

Strand-Specific Libraries For High Throughput Rna Sequencing (Rna-Seq) Prepared Without Poly(A) Selection, Zhao Zhang, William E. Theurkauf, Zhiping Weng, Phillip D. Zamore

Program in Bioinformatics and Integrative Biology Publications and Presentations

BACKGROUND: High throughput DNA sequencing technology has enabled quantification of all the RNAs in a cell or tissue, a method widely known as RNA sequencing (RNA-Seq). However, non-coding RNAs such as rRNA are highly abundant and can consume >70% of sequencing reads. A common approach is to extract only polyadenylated mRNA; however, such approaches are blind to RNAs with short or no poly(A) tails, leading to an incomplete view of the transcriptome. Another challenge of preparing RNA-Seq libraries is to preserve the strand information of the RNAs.

DESIGN: Here, we describe a procedure for preparing RNA-Seq libraries from 1 ...

Networking Development By Boolean Logic, Shikui Tu, Thoru Pederson, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

Eric Davidson at Caltech has spent several decades investigating the molecular basis of animal development using the sea urchin embryo as an experimental system ( 1) (,) ( 2) although his scholarship extends to all of embryology as embodied in several editions of his landmark book. ( 3) In recent years his laboratory has become a leading force in constructing gene regulatory networks (GRNs) operating in sea urchin development. ( 4) This axis of his work has its roots in this laboratory's cDNA cloning of an actin mRNA from the sea urchin embryo (for the timeline see ref. 1)-one of the first eukaryotic ...

Is There A Role For Reactive Oxygen Species In Zebrafish Embryonic Development?, Vivek Krishnan

Biology Master's Theses

Reactive oxygen species (ROS) are generated by many exogenous and endogenous sources. They are highly reactive and can attack biomolecules such as proteins, lipids and DNA, causing damage to living cells. DNA is subjected to constant attack by many damage inducing agents including ROS, but constant repair and maintenance by multiple DNA repair pathways helps to maintain genomic stability. The cell is also protected from the effects of ROS by antioxidants. However, ROS are implicated in cell signaling as important primary and secondary messengers. Many critical transcription factors involved in embryonic development are sensitive to the redox condition in the ...

Ckap2 Ensures Chromosomal Stability By Maintaining The Integrity Of Microtubule Nucleation Sites, Chanelle M. Case, Dan L. Sackett, Danny Wangsa, Tatiana S. Karpova, James G. Mcnally, Thomas Ried, Jordi Camps

Biochemistry and Molecular Medicine Faculty Publications

No abstract provided.

Novel Regulatory Small Rnas In Streptococcus Pyogenes, Rafael A. Tesorero, Ning Yu, Jordan O. Wright, Juan P. Svencionis, Qiang Cheng, Jeong-Ho Kim, Kyu Hong Cho

Biochemistry and Molecular Medicine Faculty Publications

No abstract provided.

Metabolism And Transcriptional Responses To Asparagine In Arabidopsis Thaliana, Qianyi Zhang

University of Western Ontario - Electronic Thesis and Dissertation Repository

Asparagine aminotransferase transforms asparagine into α-ketosuccinamate, which is further deamidated by an ω-amidase. Serine:glyoxylate aminotransferase, encoded by AGT1 in Arabidopsis, was identified as asparagine aminotransferase. In the roots of 10-day-old Arabidopsis seedlings treated with 20 mM asparagine, AGT1 transcript levels increased by 2-fold while ω-amidase transcripts were decreased by 30%. Recombinant AGT1 had a substrate preference for asparagine when compared with alanine and serine as amino group donors. An ω-amidase candidate gene, AT5G12040, was identified based on amino acid sequence identity with mammalian gene Nitrilase 2. RT-PCR of a T-DNA insertion mutant line showed that ω-amidase expression was abolished ...

Epigenetic Regulation Of Oxysterol Formation, Steve Meaney

Articles

Oxysterols are oxygenated derivatives of cholesterol that may be formed by either enzymatic or non-enzymatic mechanisms. Expression of the genes responsible oxysterol synthesis (GROS) is known to be restricted across different tissues and cell types. Regulation of the transcription of GROS and the activity of their enzyme transcripts has been the subject of intense activity for many years. Recent studies have sought to decipher the mechanism(s) that underpin the restricted expression of the GROS. Available data indicates that epigenetic mechanisms have an important role to play in the control of the expression of GROS. In the current review we ...

Optimizing The Purification Of Wild Type And Mutant Recombinant Phospholipase D: Approaches To Developing A C. Pseudotuberculosis Vaccine, Utsav M. Patwardhan

Biochemistry Student Honors Theses

No abstract provided.

Rapid And Specific Purification Of Argonaute-Small Rna Complexes From Crude Cell Lysates, Carlos Fabian Flores-Jasso, William E. Salomon, Phillip D. Zamore

Biochemistry and Molecular Pharmacology Publications and Presentations

Small interfering RNAs (siRNAs) direct Argonaute proteins, the core components of the RNA-induced silencing complex (RISC), to cleave complementary target RNAs. Here, we describe a method to purify active RISC containing a single, unique small RNA guide sequence. We begin by capturing RISC using a complementary 2'-O-methyl oligonucleotide tethered to beads. Unlike other methods that capture RISC but do not allow its recovery, our strategy purifies active, soluble RISC in good yield. The method takes advantage of the finding that RISC partially paired to a target through its siRNA guide dissociates more than 300 times faster than a fully ...

Endogenous Inhibitor Proteins That Connect Ser/Thr Kinases And Phosphatases In Cell Signaling., Masumi Eto, David L Brautigan

Department of Molecular Physiology and Biophysics Faculty Papers

Protein phosphatase activity acts as a primary determinant of the extent and duration of phosphorylation of cellular proteins in response to physiological stimuli. Ser/Thr protein phosphatase-1 (PP1) belongs to the PPP superfamily, and is associated with regulatory subunits that confer substrate specificity, allosteric regulation, and subcellular compartmentalization. In addition, all eukaryotic cells contain multiple heat-stable proteins that originally were thought to inhibit phosphatase catalytic subunits released from the regulatory subunits, as a fail-safe mechanism. However, discovery of C-kinase-activated PP1 inhibitor, Mr of 17 kDa (CPI-17) required fresh thinking about the endogenous inhibitors as specific regulators of particular phosphatase complexes ...

Establishing The Learning Effect Of Repeated Wingate Anaerobic Tests, Erin Thompson, Natalie Schaeffer, Eric T. Jones, Malcom T. Whitehead

Undergraduate Research Conference

The Wingate anaerobic test (WAnT) is a recognized and well established tool used to measure power output, muscular endurance, and fatigue. While litreature involving WAnT is plentiful, research addressing training effects within WAnT is limited. Previous studies have addressed changes in power output during repeated trials, however, to our knowledge multiple repeated trials over time to establish optimal learned effect has not been addressed. Past published studies using WAnT have incoporated various familiarization trails to account for the learned impact on performance (1, 2, 4). If an optimal number were established to produce a learned response the validity of future ...

Nuclear Localization Of Cpi-17, A Protein Phosphatase-1 Inhibitor Protein, Affects Histone H3 Phosphorylation And Corresponds To Proliferation Of Cancer And Smooth Muscle Cells., Masumi Eto, Jason A Kirkbride, Rishika Chugh, Nana Kofi Karikari, Jee In Kim

Department of Molecular Physiology and Biophysics Faculty Papers

CPI-17 (C-kinase-activated protein phosphatase-1 (PP1) inhibitor, 17kDa) is a cytoplasmic protein predominantly expressed in mature smooth muscle (SM) that regulates the myosin-associated PP1 holoenzyme (MLCP). Here, we show CPI-17 expression in proliferating cells, such as pancreatic cancer and hyperplastic SM cells. Immunofluorescence showed that CPI-17 was concentrated in nuclei of human pancreatic cancer (Panc1) cells. Nuclear accumulation of CPI-17 was also detected in the proliferating vascular SM cell culture and cells at neointima of rat vascular injury model. The N-terminal 21-residue tail domain of CPI-17 was necessary for the nuclear localization. Phospho-mimetic Asp-substitution of CPI-17 at Ser12 attenuated the nuclear ...

Evolutionary And Molecular Analysis Of Conserved Vertebrate Immunity To Fungi, Erin Carter

Honors College

The innate immune system is highly conserved amongst all multicellular organisms. Yet a constant battle exists between host cells and pathogens due to the rapid evolution of immune system components. Functional genomics and in silico methods can be employed to elucidate the evolutionary patterns of vertebrate immunity to pathogenic fungi such as Candida albicans, an opportunistic fungal pathogen that can cause lethal candidiasis in the immunocompromised. Mammals such as humans and mice possess conserved C-type lectin receptors that recognize the C. albicans cell wall. However, these receptors have not been identified in fish. Here I describe how we identified potential ...

Investigation Of The Mechanism Underlying Arsenic Disruption Of Mast Cell Degranulation, Alejandro Velez

Honors College

Exposure to arsenic (As) is a global health concern, according to the World Health Organization and Agency for Toxic Substances and Disease Registry. Prolonged exposure to this naturally occurring chemical has been linked to hyperkeratosis, type II diabetes, developmental abnormalities, and cancer. Some of the adverse health effects of As may be linked to its ability to alter cellular signal transduction. Recently, published work from the Gosse laboratory has shown that inorganic arsenite inhibits the signaling cascade leading to mast cell degranulation, a vital immune function, through an as-yet unknown mechanism.
Further work in the Gosse lab has suggested that ...

Structural And Functional Characterization Of Mulitdrug Resistance Transporter And Regulator, Linliang Yu

Theses and Dissertations--Chemistry

Drug resistant bacteria pathogen poses a severe threat to human health. Bacterial drug efflux pumps are transporter proteins involved in the export of antibiotics out of cells. Efflux by transporters is one of the major drug resistant mechanisms. Multidrug efflux pumps can transport multiple classes of antibiotics and are associated with bacteria multiple drug resistance (MDR). Overproduction of these pumps reduces susceptibility of bacteria to a variety of antibiotics. MDR regulators are cytoplasmic proteins that control the expression level of MDR transporters in response to the cellular concentration of antibiotics. This thesis research focuses on three main directions in the ...

Defending Your Dna: Combating Threats Both Foreign And Domestic, James Mcisaac

Undergraduate Review

We are under constant assault from forces capable of damaging our DNA. The genetic code of DNA is made up of four nucleotides: adenine (A) which bonds with thymine (T) and guanine (G) which bonds with cytosine (C). If something happens to upset this normal pairing or the nucleotides themselves, our body must spring to action and respond to the damage. When damage to nucleotides prevents the normal replication machinery from doing its job, enzymes like the Y-family polymerases are called in. A special mechanism allows them to identify damage and insert the correct nucleotide or bypass the lesion to ...

Expression Of Itgb8 In Epicardial Adipose Tissue Is Highly And Directly Correlated With The Severity Of Coronary Atherosclerosis, Nancy Lee, Sarah M. Nicoloro, Juerg R. Straubhaar, Melinda Darrigo, Stanley Tam, Michael P. Czech, Timothy P. Fitzgibbons

Senior Scholars Program

Background: In patients with coronary artery disease (CAD), epicardial adipose tissue (EAT) has been shown to express increased levels of inflammatory cytokines (IL-1β, IL-6, MCP-1, TNFα) and decreased levels of anti-inflammatory and cardioprotective adipokines. However, it is not known whether or not inflammation in EAT is a primary cause or a secondary response to atherosclerosis. In order to better understand this pathophysiology, we tested the hypothesis that expression of certain genes in EAT would correlate with the degree of coronary atherosclerosis.

Purpose: The purpose of this study was to determine whether there is a difference in gene expression in epicardial ...

Diterpene Modulator Of Macrophage Phagosomal Maturation, Reuben J. Peters, David G. Russell, Francis M. Mann

Iowa State University Patents

Novel uses for diterpene modulators of macrophage phagosomal maturation are provided. The diterpene isotuberculosinol is used as an immune modulator, assay for pharmaceutical compositions and an isolated Mycobacterium tuberculosis labdane-related diterpenoid virulence factor. A method of treating Mycobacterium tuberculosis infectivity is further provided.