Structural Biology Commons^™

Molecular Mechanisms Of Neuropilin-Ligand Binding, Matthew W. Parker

Theses and Dissertations--Molecular and Cellular Biochemistry

Neuropilin (Nrp) is an essential cell surface receptor with dual functionality in the cardiovascular and nervous systems. The first identified Nrp-ligand family was the Semaphorin-3 (Sema3) family of axon repulsion molecules. Subsequently, Nrp was found to serve as a receptor for the vascular endothelial growth factor (VEGF) family of pro-angiogenic cytokines. In addition to its physiological role, VEGF signaling via Nrp directly contributes to cancer stemness, growth, and metastasis. Thus, the Nrp/VEGF signaling axis is a promising anti-cancer therapeutic target. Interestingly, it has recently been shown that Sema3 and VEGF are functionally opposed to one another, with Sema3 possessing potent …

Germline Transgenic Methods For Tracking Cells And Testing Gene Function During Regeneration In The Axolotl, Shahryar Khattak, Maritta Schuez, Tobias Richter, Dunja Knapp, Saori L. Haigo, Tatiana Sandoval-Guzmán, Kristyna Hradlikova, Annett Duemmler, Ryan R. Kerney, Elly M. Tanaka

Biology Faculty Publications

The salamander is the only tetrapod that regenerates complex body structures throughout life. Deciphering the underlying molecular processes of regeneration is fundamental for regenerative medicine and developmental biology, but the model organism had limited tools for molecular analysis. We describe a comprehensive set of germline transgenic strains in the laboratory-bred salamander Ambystoma mexicanum(axolotl) that open up the cellular and molecular genetic dissection of regeneration. We demonstrate tissue-dependent control of gene expression in nerve, Schwann cells, oligodendrocytes, muscle, epidermis, and cartilage. Furthermore, we demonstrate the use of tamoxifen-induced Cre/loxP-mediated recombination to indelibly mark different cell types. Finally, we inducibly …

Isoflurane Increases Neuronal Cell Death Vulnerability By Downregulating Mir-214, Hailiang Yan, Tao Xu, Hongfeng Zhao, Kuo-Chieh Lee, Hoau-Yan Wang, Yan Zhang

Publications and Research

Since accumulating evidence suggests the application of anesthetics may increase the risk of Alzheimer’s disease (AD), we investigated the cytotoxicity of inhaled general anesthesia in neurons and its underlying mechanism. Using primary cultured rat hippocampal neurons as the study model, here we show that isoflurane increases vulnerability to intracellular or extracellular amyloid b with or without serum deprivation. This isoflurane-induced effect is mediated by the downregulation of miR-214 level that lead to an elevated expression of Bax, a prominent target for miR-214. We conclude that isoflurane increases cell death in the presence of amyloid b by increasing Bax level through …

The Effect Of Visual Wulst Lesions And Trigeminal Nerve Sectioning On The Discrimination Of Magnetic Inclination In The Homing Pigeon (Columba Livia), Merissa Acerbi

Honors Projects

The ability of homing pigeons to return to their loft from unknown places has fascinated scientists for centuries. It is well established that homing pigeons, like migratory birds, posses an innate magnetic inclination compass to determine direction by measuring the angle between the magnetic field vector and the Earth's surface. Recent work has indicated that the avian magnetic compass is light mediated and appears to mediate magnetic information to the brain. This occurs via a visual pathway with processing in the visual Wulst area of the forebrain. There is, however, also evidence from other avian species that magnetic direction may …

Secondary Structure, A Missing Component Of Sequence- Based Minimotif Definitions, David P. Sargeant, Michael R. Gryk, Mark W. Maciejewsk, Vishal Thapar, Vamsi Kundeti, Sanguthevar Rajasekaran, Pedro Romero, Keith Dunker, Shun-Cheng Li, Tomonori Kaneko, Martin Schiller

Life Sciences Faculty Research

Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis …

Achieving High Accuracy Prediction Of Minimotifs, Tian Mi, Sanguthevar Rajasekaran, Jerlin Camilus Merlin, Michael R. Gryk, Martin Schiller

Life Sciences Faculty Research

The low complexity of minimotif patterns results in a high false-positive prediction rate, hampering protein function prediction. A multi-filter algorithm, trained and tested on a linear regression model, support vector machine model, and neural network model, using a large dataset of verified minimotifs, vastly improves minimotif prediction accuracy while generating few false positives. An optimal threshold for the best accuracy reaches an overall accuracy above 90%, while a stringent threshold for the best specificity generates less than 1% false positives or even no false positives and still produces more than 90% true positives for the linear regression and neural network …

Sound Production In Two Loricariid Catfishes, Amanda Lynn Webb

Masters Theses & Specialist Projects

Many families of catfish produce sounds via pectoral spine stridulation and/or swim bladder compression using sonic muscles attached to the swim bladder. The sound production capabilities and characteristics in Loricariidae, the largest catfish family, have not been well examined. Sounds produced by two loricariid catfish species, Macrotocinclus affinis and Pterygoplichthys gibbiceps were recorded. Both species produce broad band calls via pectoral spine stridulation. These species produce sounds by rubbing the ridges of the dorsal process of the pectoral spine base against the groove of the pectoral girdle. Call duration was generally shorter in M. affinis (2-15 ms) as opposed to …

Hivtoolbox, An Integrated Web Application For Investigating Hiv, David P. Sargeant, Sandeep Deverasetty, Yang Luo, Angel Villahoz Baleta, Stephanie Zobrist, Viraj Rathnayake, Jacqueline C. Russo, Jay Vyas, Mark A. Muesing, Martin Schiller

Life Sciences Faculty Research

Many bioinformatic databases and applications focus on a limited domain of knowledge federating links to information in other databases. This segregated data structure likely limits our ability to investigate and understand complex biological systems. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and allows virologists and structural biologists to access sequence, structure, and functional relationships in an intuitive web application. HIV-1 integrase protein was used as a case study to show the utility of this application. We show how data integration facilitates identification of new questions and hypotheses much more rapid …

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 …

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 …

Assessing Crosstalk Between Calcium And Camp In Pancreatic Alpha Cells, Julianne Michelle Imseis

Electronic Theses and Dissertations

Blood glucose levels are regulated by the interactions between insulin and glucagon. Pancreatic alpha cells release glucagon in response to a drop in blood sugar. Pancreatic alpha cells appear to be regulated through multiple signaling pathways. One potential method of regulation occurs from α-MSH or epinephrine stimulated production of the intracellular messenger cyclic AMP. Exocytosis of dense core vesicles containing glucagon ultimately requires an increase in cytosolic calcium. This study focused on the link between cyclic AMP and calcium in pancreatic alpha cells which allows alpha cell regulation. Interactions between calcium and cyclic AMP in pancreatic alpha cells consists of …

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.

Effects Of Antimetabolites On Sclerotium Rolfsii Growth And Oxalic Acid Production, Ezikiel Okafor-Agilo

Seton Hall University Dissertations and Theses (ETDs)

.

Determining The Phylogenetic Relationships Among The Northern Pike (Esox Lucius), The Muskellunge (Esox Masquinongy), And The Silver Pike, Steven W. Foster

Theses, Dissertations and Capstones

Prioritization of taxa has become a necessity due to limited resources available for conservation. Conservation efforts are often concentrated on those threatened and endangered species with the highest taxonomic importance. The silver pike is a rare game fish, often accounting for less than 1% of a total pike population where it is found. Although silver pike are normally found in association with northern pike, they have distinct morphological characteristics and have not been shown to hybridize with the northern pike. Still, many fisheries biologists consider the silver pike to be a color variant of the northern pike, and to date …

The Holliday Junction In An Inverted Repeat Dna Sequence: Sequence Effects On The Structure Of Four-Way Junctions, Brandt F. Eichman, Jeff Vargason, Blaine H.M. Mooers, P. Shing Ho

Faculty Publications - Department of Biological & Molecular Science

Holliday junctions are important structural intermediates in recombination, viral integration, and DNA repair. We present here the single-crystal structure of the inverted repeat sequence d(CCGGTACCGG) as a Holliday junction at the nominal resolution of 2.1 Å. Unlike the previous crystal structures, this DNA junction has B-DNA arms with all standard Watson–Crick base pairs; it therefore represents the intermediate proposed by Holliday as being involved in homologous recombination. The junction is in the stacked-X conformation, with two interconnected duplexes formed by coaxially stacked arms, and is crossed at an angle of 41.4° as a right-handed X. A sequence comparison with previous …

Benthic Biodiversity And Physico-Chemical Parameters Of Acid Mine Drainage, Acid Impacted And Nonimpacted Streams, Stephen D. Greene

Theses, Dissertations and Capstones

South Fork of Sand Lick Creek, Logan County, West Virginia, drains an abandoned coal strip mine which had exploited Pottsville series coalbeds (Pennsylvania strata). These strata outcrop throughout southwestern West Virginia. North Fork watershed is relatively unchanged, save a small roadcut throughout. South Fork benthic community had not recovered although mining activity had ceased about 20 years earlier. Benthic communities were analyzed with detrended correspondence analysis (DCA). Family Chironomidae predominated South Fork benthic community throughout the study. North Fork’s benthic community had as major contributors acid resistant caddisfly family Hydropsychidae, mayfly family Baetidae, and stonefly families Perlodidae and Nemouridae. Family …

Clarification Of The Hybrid Origin Of Carex X Deamii Herm. (Cyperaceae) Based On Macro And Micro Morphological Characters, Paul B. Marcum

Theses, Dissertations and Capstones

The origin of Carex x deamii Herm. has been in question ever since it was named to science in 1938. Collections of the hybrid have always been associated with C. shortiana Dewey and either C. typhina Michx. or C. squarrosa L.. C. typhina and C. squarrosa are closely related taxa (Section Squarrosae) and often are morphologically similar. Because of this similarity, determining the correct parental species to the hybrid has been extremely difficult. It is known that the hybrid is sterile and only reproduces asexually. Pollen was analyzed to ascertain the viability of all four taxa. This study utilizes both …

Effects Of Creatine Supplementation On Muscular Strength And Power Development In Well-Trained Football Players, Josef D. Mcquain

Theses, Dissertations and Capstones

The purpose of this study was to determine the effects of creatine supplementation on strength and power performance in well-trained football players. Twenty-one subjects were randomly assigned to three treatment groups: 1) creatine monohydrate, 2) creatine monohydrate+dextrose, or 3) placebo utilizing a double-blind design. Prior to assignment, subjects were matched according to lean body mass. After a five day loading dose, a maintenance dose was administered for 12 days. Test protocols included three anaerobic work bouts: l) two 30 s Wingate bike tests interspersed with five minutes recovery were used to ascertain relative and absolute power, 2) two 100 yard …

Description Of Tadpoles Of Three Species Of Scinax (Anura: Hylidae), Rafael O. De Sá, Rocjard Wassersig, Arturo I. Kehr

Biology Faculty Publications

Larval morphological characteristics have been used to cluster species of Scinax in seven species groups and to support the monophyly of some of these groups. However, our present knowledge of Scinax tadpoles is incomplete; currently, tadpoles of only 21 of the approximately 80 recognized species have been described. Herein, we describe and illustrate the external morphology and oral disc characteristics of larval Scinax berthae, S. nebulosa, and S. boesemani. The presence of a "labial arm" supporting the P3 tooth row in S. boesemani, and its absence from S. nebulosa, is discussed in the light of our limited knowledge of tadpoles …

Morfología Y Moléculas: Bases Complementarias De La Sistemática Moderna, Rafael O. De Sá, David M. Hillis

Biology Faculty Publications

RESUMEN

El auge de las técnicas moleculares en las últimas dos décadas ha traído nuevos enfoques en los estudios sistemáticos. Aquí presentaremos una revisión del uso, las aplicaciones, y los problemas de las principales metodologías de trabajo. Cada una de estas técnicas es aplicable a algunos problemas e inapropiada para otros, y es importante entender las suposiciones y limitaciones de cada técnica. Concluimos que el uso combinado de los enfoques morfológicos y moleculares otorga mejor resolución a los problemas sistemáticos.

ABSTRACT

The development of molecular techniques during the last two decades has brought new approaches to the analysis of systematic …

Spermatogenesis And Histology Of The Testes Of The Caecilian, Chthonerpeton Indistinctum, Rafael O. De Sá, Nibia Berois

Biology Faculty Publications

Macroscopically, the testes of Chthonerpeton indistinctum consist of a series of oval lobes. The number and size of lobes is variable in Chthonerpeton indistinctum. Histologically, the testes are divided into structural units, locules separated by septa of connective tissue. Inside of each locule spermatogenesis takes place in cysts of germinal cells that divide synchronically. Chthonerpeton indistinctum is divided chronologically into four stages of development based on the shape of the nuclei of the spermatids and their arrangement in the cyst: (1) round, (2) kidney shaped, (3) attenuate, and (4) bouquet arrangement.

Anatomy And Histology Of The Digestive Tract Of A Deep-Sea Fish Coelorhynchus Carminatus, Elly M. Jacobsen

University Studies (University of Nebraska) (1888–1984)

This paper deals with the anatomy and histology of the digestive tube of one of the grenadiers or rat-tails, Coelorhynchus carminatus (Goode), as classified by Jordan & Evermann (1896).1 Many studies on the structure of the digestive tracts of fishes have been made in the past, and pioneer work in the teleost group was done by Valatour in 1861, Pillet in 1894 on the Pleuronectidae, and Gulland in 1898 on the salmon. More recent studies have been made by Greene (1912) on the king salmon, Blake 2 (1930) on the sea bass, and Rogick (1931) on the minnow.

The species …