Molecular Biology Commons^™

Partitioning Of Minimotifs Based On Function With Improved Prediction Accuracy, Sanguthevar Rajasekaran, Tian Mi, Jerlin Camilus Merlin, Aaron Oommen, Patrick R. Gradie, Martin R. Schiller

Life Sciences Faculty Research

Background

Minimotifs are short contiguous peptide sequences in proteins that are known to have a function in at least one other protein. One of the principal limitations in minimotif prediction is that false positives limit the usefulness of this approach. As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions.

Methodology/Principal Findings

Certain domains and minimotifs are known to be strongly associated with a known cellular process or molecular function. Therefore, we hypothesized that by restricting minimotif predictions to those where the minimotif containing protein and target protein have …

Section Abstracts: Biology With Microbiology And Molecular Biology

Virginia Journal of Science

Abstracts of the Biology with Microbiology and Molecular Biology Section for the 88th Annual Meeting for the Virginia Academy of Science, May 20-21, 2010, James Madison University, Harrisonburg, VA.

An Entrepreneurial Approach To Librarianship, Flora Shrode, Jennifer Duncan, Wendy Holliday

Library Faculty & Staff Publications

Librarians from Utah State University explain recent efforts to encourage subject librarians to take a more holistic view of their roles. We are shifting from a traditional emphasis primarily on collection development and refocusing on natural connections between collections, instruction, liaison, and reference service. The poster provides background about Utah State University’s situation and explains our approach to analyzing local needs and culture to inform development of a new organizational structure. We describe our vision of subject librarianship, the process by which we assessed librarians’ ideas and goals for performing as subject librarians, and the actions we are taking to …

From The Valleys To The Mountains: The Biographic History Of Antelope Squirrels, Bats, And Chipmunks In Western North America, Stacy James Mantooth

UNLV Theses, Dissertations, Professional Papers, and Capstones

Genetic differentiation within and between species often coincides with significant geological or climatic changes that have shaped the sizes and locations of their geographic ranges and altered the connectivity between populations over time. Across western North America, many endemic taxa experienced high levels of initial divergence associated with geological transformations of the Neogene, with subsequent diversification and geographic structuring of populations associated with climatic changes during the Quaternary. As such, we can use a combination of molecular markers and genetic analyses to effectively examine the evolutionary and biogeographic histories of populations, species, and regional biotas whose signatures of differentiation are …

Development Of Ultra-Sensitive Fluorescence Photoamplification Assays For The Detection Of Molecular Recognition Events, Tiffany Priscilla Gustafson

Electronic Theses and Dissertations

During the course of this research a novel method which couples the molecular recognition-triggered photoamplification chain in diaryl ketone adducts of dithiane with a "turn-off" or "turn-on" fluorescence-based assay for the detection of biological targets and ligands, regardless of their nature, through a molecular recognition event has been developed. This research has included several key steps, the most significant being: (1) the design of fluorophore adducts or dyads which recover fluorescence upon photocleavage for a "turn-on" assay and the identification of fluorophores which are quenched upon the photochemical release of a quencher for a "turn off" assay; (2) Optimization of …

Analysis Of Bacterial Diversity In Arctic Soil And Sediment Samples From Ny-Alesund, Norway Using Denaturing Gradient Gel Electrophoresis., Yew Wen Chyin

Student Works (2010-2019)

Bacterial diversity in soil and sediment samples from eighteen sites in and around Dasan Station, Ny-Ålesund, Norway was analyzed using Denaturing Gradient Gel Electrophoresis (DGGE), and was correlated with the environmental variables. Samples analysed included terrestrial soils, beach soil, periglacier soils, inland lake bank sediments, melt lake sediments, and marine sediments. Spearman rank order correlation showed significant correlations (P = 0.001) between conductivity (r = 0.470) and pH (r = 0.294) with the bacterial diversity. Soil from the tundra site (sample 17) appeared to have the most diverse bacterial community while inland lake bank sediment from the …

Analysis Of The Crmp Gene In Drosophila: Determining The Regulatory Role Of Crmp In Signaling And Behavior, Deanna Hardt Morris

University of Kentucky Doctoral Dissertations

The mammalian genome encodes five collapsin response mediator protein (CRMP) isoforms. Cell culture studies have shown that the CRMPs mediate growth cone dynamics and neuron polarity through associations with a variety of signal transduction components and cytoskeletal elements. CRMP is also a member of a protein family including the presumably ancestral dihydropyrimidinase (DHP) protein that catalyzes the second step in pyrimidine degradation. In Drosophila, CRMP and DHP proteins are produced by alternatively spliced transcripts of the CRMP gene. The alternative protein forms have a 91% sequence identity, but unique expression patterns. CRMP is found exclusively in neuronal tissues and …

Quantifying And Resolving Multiple Vector Transformants In S. Cerevisiae Plasmid Libraries, Thomas C. Scanlon, Elizabeth C. Gray, Karl E. Griswold

Dartmouth Scholarship

In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the …

Venn, A Tool For Titrating Sequence Conservation Onto Protein Structures, Jay Vyas, Michael R. Gryk, Martin R. Schiller

Life Sciences Faculty Research

Residue conservation is an important, established method for inferring protein function, modularity and specificity. It is important to recognize that it is the 3D spatial orientation of residues that drives sequence conservation. Considering this, we have built a new computational tool, VENN that allows researchers to interactively and graphically titrate sequence homology onto surface representations of protein structures. Our proposed titration strategies reveal critical details that are not readily identified using other existing tools. Analyses of a bZIP transcription factor and receptor recognition of Fibroblast Growth Factor using VENN revealed key specificity determinants. Weblink: http://sbtools.uchc.edu/venn/.

A Proposed Syntax For Minimotif Semantics, Version 1., Jay Vyas, Ronald J. Nowling, Mark W. Maciejewski, Sanguthevar Rajasekaran, Michael R. Gryk, Martin R. Schiller

Life Sciences Faculty Research

BACKGROUND:

One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of …

Section Abstracts: Biology And Microbiology & Molecular Biology

Virginia Journal of Science

Abstracts of the Biology Section and Microbiology & Molecular Biology for the 87th Annual Meeting of the Virginia Academy of Science, May 27th-29th, 2009, Virginia Commonwealth University, Richmond, VA.

Effects Of Estrogen On Muscle Damage In Response To An Acute Resistance Exercise Protocol, Megan R. Wolf

Honors Scholar Theses

Creatine Kinase (CK) is used as a measure of exercise-induced muscle membrane damage. During acute eccentric (muscle lengthening) exercise, muscle sarcolemma, sarcoplasmic reticulum, and Z-lines are damaged, thus causing muscle proteins and enzymes to leak into the interstitial fluid.

Strenuous eccentric exercise produces an elevation of oxygen free radicals, which further increases muscle damage. Muscle soreness and fatigue can be attributed to this membrane damage. Estradiol, however, may preserve membrane stability post-exercise (Brancaccio, Maffulli, & Limongelli, 2007; Carter, Dobridge, & Hackney, 2001; Tiidus, 2001). Because estradiol has a similar structure to Vitamin E, which is known to have antioxidant properties, …

Generation Of An Fsh Inducible Inh-[Alpha]-Flag-Gg-Icer I[Gamma] Ovarian Specific Gene Construct, Goce Bogdanoski

Theses, Dissertations and Culminating Projects

Avian animal models have led to many essential discoveries in molecular biology and biochemistry, including the discovery of vitamins, the chemistry behind vision and the development of transgenic hens as natural bioreactors for pharmaceutically relevant proteins. Hyperovulation in domesticated hens is considered a highly desirable genetic trait, a feature that has been explored in multiple studies and remains the focus of many biotech companies. Unlocking the molecular mechanism that controls ovulation may provide a basis for development in new reproductive technologies.

Previous research done on rodents provided data and identified a single transcription factor, the Inducible cAMP Early Repressor (ICER), …

Characterization Of The Catalytic Mechanism Of The Carboxyltransferase Component Of Escherichia Coli Acetyl-Coa Carboxylase Leading To Rational Inhibitor Identification And The Development Of Enzymatic Mimics, Nabil K. Thalji

Honors Capstones

No abstract provided.

Molecular Coevolution Of Pacific Northwest Hantaviruses And Their Host, The Deer Mouse, Peromyscus Maniculatus, Philip Darren Jones

Dissertations and Theses

Sin Nombre virus (SNV, family Bunyaviridae, genus Hantavirus), hosted by the deer mouse, Peromyscus maniculatus (family Cricetidae, Subfamily Neotominae), is the primary etiological agent of Hantavirus pulmonary syndrome (HPS) in the western United States. HPS, with known pathogenicity only to humans and for which there is no cure or prophylaxis, affects the epithelium of the lungs by making the capillaries leaky, thereby resulting in bilateral infiltrates, and eventually leading to respiratory failure and death by drowning in approximately 38% of hospitalized patients.

In the Americas, Peromyscus has been co-evolving with hantaviruses for approximately 12–20 million years, since the first …

Minimotif Miner 2nd Release: A Database And Web System For Motif Search, Sanguthevar Rajasekaran, Sudha Balla, Patrick R. Gradie, Michael R. Gryk, Krishna Kadaveru, Vamsi Kundeti, Mark W. Maciejewski, Tian Mi, Nicholas Rubino, Jay Vyas, Martin R. Schiller

Life Sciences Faculty Research

Minimotif Miner (MnM) consists of a minimotif database and a web-based application that enables prediction of motif-based functions in user-supplied protein queries. We have revised MnM by expanding the database more than 10-fold to approximately 5000 motifs and standardized the motif function definitions. The web-application user interface has been redeveloped with new features including improved navigation, screencast-driven help, support for alias names and expanded SNP analysis. A sample analysis of prion shows how MnM 2 can be used.

Amino Acid Residues Implicated In The Interaction Of Melanocortin Ligands And Their Receptors: A Study Of Mc2r Selectivity, Kristopher D. Veo

Electronic Theses and Dissertations

Melanocortin receptor ligand selectivity has been a question not easily answered. The inability to functionally express melanocortin 2 receptor (MC2R) has inhibited the study of why MC2R is only stimulated by ACTH, a melanocortin hormone. With the recent discovery of the MC2R accessory protein (MRAP), creating a heterologous system is now feasible. Using a general cell line like CHO-K1 cells, which do not express endogenous MCRs, we were able to create a heterologous expression system and test the selectivity of MC2R using analog variants of ACTH(1-24). Our results indicate an amino acid requirement in the C-terminal portion of ACTH(1-24) for …

Molecular Characterisation Of A Bovine-Like Rotavirus Detected From A Giraffe, Emily Mulherin, Jill Bryan, Marijke Beltman, Luke O'Grady, Eugene Pidgeon, Lucie Garon, Andrew Lloyd, John Bainbridge, Helen O'Shea, Paul Whyte, Séamus Fanning

Department of Biological Sciences Publications

Background

Rotavirus (RV), is a member of the Reoviridae family and an important etiological agent of acute viral gastroenteritis in the young. Rotaviruses have a wide host range infecting a broad range of animal species, however little is known about rotavirus infection in exotic animals. In this paper we report the first characterisation of a RV strain from a giraffe calf.

Results

This report describes the identification and detailed molecular characterisation of a rotavirus strain detected from a 14-day-old Giraffe (Giraffa camelopardalis), presenting with acute diarrhea. The RV strain detected from the giraffe was characterized molecularly as G10P[11]. …

Computational Design Of Orthogonal Ribosomes, Lon Chubiz, Christopher Rao

Biology Department Faculty Works

Orthogonal ribosomes (o-ribosomes), also known as specialized ribosomes, are able to selectively translate mRNA not recognized by host ribosomes. As a result, they are powerful tools for investigating translational regulation and probing ribosome structure. To date, efforts directed towards engineering o-ribosomes have involved random mutagenesisbased approaches. As an alternative, we present here a computational method for rationally designing o-ribosomes in bacteria. Working under the assumption that base-pair interactions between the 16S rRNA and mRNA serve as the primary mode for ribosome binding and translational initiation, the algorithm enumerates all possible extended recognition sequences for 16S rRNA and then chooses those …

Promoter Library Designed For Fine-Tuned Gene Expression In Pichia Pastoris, Franz S. Hartner, Claudia Ruth, David Langenegger, Sabrina N. Johnson, Petr Hyka, Geoff P. Lin-Cereghino, Joan Lin-Cereghino, Karin Kovar, James Cregg, Anton Glieder

College of the Pacific Faculty Articles

Although frequently used as protein production host, there is only a limited set of promoters available to drive the expression of recombinant proteins in Pichia pastoris. Fine-tuning of gene expression is often needed to maximize product yield and quality. However, for efficient knowledge-based engineering, a better understanding of promoter function is indispensable. Consequently, we created a promoter library by deletion and duplication of putative transcription factor-binding sites within the AOX1 promoter (P_AOX1) sequence. This first library initially spanned an activity range between ∼6% and >160% of the wild-type promoter activity. After characterization of the promoter library employing …

Intracellular Levels Of Centrin2, Xpc, & Hhr23b Increase After Dna Damage, Nicholas A. Rowland

Honors Capstones

Capstone submitted as a graduate requirement for the BSU Honors Program.

A Watershed Analysis Of Pattee Pond: Implications For Water Quality And Land Use Management, Problems In Environmental Science Course (Biology 493), Colby College, Colby Environmental Assessment Team, Colby College

Colby College Watershed Study: Pattee Pond (2008, 1992)

The Colby Environmental Assessment Team (CEAT) investigated the impact of land use patterns on the water quality of Pattee Pond in Winslow, Maine, during the summer and fall of 2008. Physical, chemical, and biological characteristics of water quality were analyzed to evaluate the current health of the lake. Data collected were compared with previous studies conducted by the Maine Department of Environmental Protection (DEP) and CEAT to examine changes in water quality and land use over time. Trends in Pattee Pond water quality suggest an improvement since the 1970s. However, the lake is still experiencing algal blooms resulting from phosphorus …

Development Of An In Vitro Protocol To Study The Effect Of Estrogen On Osteoblast Activity, Sourik Ganguly

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science & Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science by Sourik Ganguly on July 7, 2006.

Alternative Assay Techniques For Protein Kinase A, Justin Brink

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

The Effect Of Rooibos Tea (Aspalathus Linearis) On The Survival And Transformation Of C3h-Bt1 Mouse Fibroblasts, Krista M. Beach, Paul J. Smith

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

Condensed Protocol For Competent Cell Preparation And Transformation Of The Methylotrophic Yeast Pichia Pastoris, Joan Lin-Cereghino, William Wong, See Xiong, William Giang, Linda Luong, Jane Vu, Sabrina Johnson, Geoff P. Lin-Cereghino

College of the Pacific Faculty Articles

No abstract provided.

Pcr And 16s Rdna Sequencing For Identifying And Comparing Gram-Negative Bacteria, Molly Truax

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

Core Concepts In Biochemistry And Molecular Biology In An Integrated Mbbs Curriculum, M P. Iqbal

Department of Biological & Biomedical Sciences

No abstract provided.

Mer1p Is A Modular Splicing Factor Whose Function Depends On The Conserved U2 Snrnp Protein Snu17p, Marc Spingola, Javier Armisen, Manuel Ares

Biology Department Faculty Works

Mer1p activates the splicing of at least three pre‐mRNAs (AMA1, MER2, MER3) during meiosis in the yeast Saccharomyces cerevisiae. We demonstrate that enhancer recognition by Mer1p is separable from Mer1p splicing activation. The C‐terminal KH‐type RNA‐binding domain of Mer1p recognizes introns that contain the Mer1p splicing enhancer, while the N‐terminal domain interacts with the spliceosome and activates splicing. Prior studies have implicated the U1 snRNP and recognition of the 5′ splice site as key elements in Mer1p‐activated splicing. We provide new evidence that Mer1p may also function at later steps of spliceosome assembly. First, Mer1p can activate splicing of introns …

Comparison Of Tnf-A Levels Produced By Macrophages Treated With Brucella Abortus And Escherichia Coli Lps, Tajie Harris

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.