Biology Commons^™

Analysis Of Sry Duplications On The Rattus Norvegicus Y-Chromosome, Jeremy W. Prokop, Adam C. Underwood, Monte E. Turner, Nic Miller, Dawn Pietzrak, Sarah Scott, Chris Smith, Amy Milsted

Biology Faculty Research

Background: Gene copy number variation plays a large role in the evolution of genomes. In Rattus norvegicus and other rodent species, the Y-chromosome has accumulated multiple copies of Sry loci. These copy number variations have been previously linked with changes in phenotype of animal models such as the spontaneously hypertensive rat (SHR). This study characterizes the Y-chromosome in the Sry region of Rattus norvegicus, while addressing functional variations seen in the Sry protein products. Results: Eleven Sry loci have been identified in the SHR with one (nonHMG Sry) containing a frame shift mutation. The nonHMGSry is found and conserved in …

Differences In Temperature Responses Of Achene Types In Centaurea Melitensis, Kandee L. Bain

LUX: A Journal of Transdisciplinary Writing and Research from Claremont Graduate University

Southern California has a Mediterranean climate with wet winters and hot dry summers. This type of environment is associated with irregular temperature patterns and rainfall, which can be unpredictable. Unpredictable environments, can threaten the germination and survival of plants like Centaurea melitensis. To ensure germination and survival under unpredictable environmental conditions, some plants may develop characteristic structures like cleistogamous flower heads, and in some cases they will develop heteromorphic achenes. Morphological differences between peripheral and center achenes may indicate variable responses to temperature. Additionally, unpredictable environmental conditions may lead to differences in the number of peripheral to center achenes …

Mutational Analysis Of The Rotavirus Nsp4 Enterotoxic Domain That Binds To Caveolin-1, Judith M. Ball, Megan E. Schroeder, Cecelia V. Williams, Friedhelm Schroeder, Rebecca D. Parr

Faculty Publications

Background: Rotavirus (RV) nonstructural protein 4 (NSP4) is the first described viral enterotoxin, which induces early secretory diarrhea in neonatal rodents. Our previous data show a direct interaction between RV NSP4 and the structural protein of caveolae, caveolin-1 (cav-1), in yeast and mammalian cells. The binding site of cav-1 mapped to the NSP4 amphipathic helix, and led us to examine which helical face was responsible for the interaction.

Methods: A panel of NSP4 mutants were prepared and tested for binding to cav-1 by yeast two hybrid and direct binding assays. The charged residues of the NSP4 amphipathic helix were changed …

How Migratory Thrushes Conquered Northern North America: A Comparative Phylogeography Approach, Carrie M. Topp, Christin L. Pruett, Kevin G. Mccracken, Kevin S. Winker

Biomedical Engineering and Sciences Faculty Publications

Five species of migratory thrushes (Turdidae) occupy a transcontinental distribution across northern North America. They have largely overlapping breeding ranges, relatively similar ecological niches, and mutualistic relationships with northern woodland communities as insectivores and seed-dispersing frugivores. As an assemblage of ecologically similar species, and given other vertebrate studies, we predicted a shared pattern of genetic divergence among these species between their eastern and western populations, and also that the timing of the coalescent events might be similar and coincident with historical glacial events. To determine how these five lineages effectively established transcontinental distributions, we used mitochondrial cytochrome b sequences to …

Middle Mississippi River Islands: Historical Distribution, Restoration Planning, And Biological Importance, Teresa Cecilia Allen

Dissertations

The Middle Mississippi River’s (MMR’s) hydrology and sedimentation patterns have been altered. These activities contribute to loss of backwaters, islands, secondary channels, and reduced biodiversity. The Fish and Wildlife Service included reasonable and prudent alternatives (RPAs) in its Biological Opinion for the Operation and Maintenance of the Nine-Foot Channel Navigation Project. These RPAs mandate dike notching and island building to increase habitat diversity. My first goal was to examine changes in the number and relative location of islands from 1797 to 2003. I found that the total number of islands increased, the number of central islands decreased, and the number …

Communication And Common Interest, Peter Godfrey-Smith, Manolo Martínez

Publications and Research

Explaining the maintenance of communicative behavior in the face of incentives to deceive, conceal information, or exaggerate is an important problem in behavioral biology. When the interests of agents diverge, some form of signal cost is often seen as essential to maintaining honesty. Here, novel computational methods are used to investigate the role of common interest between the sender and receiver of messages in maintaining cost-free informative signaling in a signaling game. Two measures of common interest are defined. These quantify the divergence between sender and receiver in their preference orderings over acts the receiver might perform in each state …

Experimental Evolution Of An Alternating Uni- And Multicellular Life Cycle In Chlamydomonas Reinhardtii, William C. Ratcliff, Matthew D. Herron, Kathryn Howell, Jennifer T. Pentz, Frank Rosenzweig, Michael Travisano

Biological Sciences Faculty Publications

The transition to multicellularity enabled the evolution of large, complex organisms, but early steps in this transition remain poorly understood. Here we show that multicellular complexity, including development from a single cell, can evolve rapidly in a unicellular organism that has never had a multicellular ancestor. We subject the alga Chlamydomonas reinhardtii to conditions that favour multicellularity, resulting in the evolution of a multicellular life cycle in which clusters reproduce via motile unicellular propagules. While a single-cell genetic bottleneck during ontogeny is widely regarded as an adaptation to limit among-cell conflict, its appearance very early in this transition suggests that …

Rigidity Analysis Of Protein Biological Assemblies And Periodic Crystal Structures, Filip Jagodzinski, Pamela Clark, Jessica Grant, Tiffany Liu, Samantha Monastra, Ileana Streinu

All Faculty Scholarship for the College of the Sciences

Background

We initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. The goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. We use experimental X-ray crystallography data from the Protein Data Bank (PDB). The analysis relies on an effcient graph-based algorithm. Computational experiments were performed using new protein rigidity analysis tools available in the new release of our KINARI-Web server http://kinari.cs.umass.edu.

Results

We provide two types of results: on biological assemblies and on crystals. We found that when only isolated …

Taxis Toward Hydrogen Gas By Methanococcus Maripaludis, Kristen A. Brileya, James M. Connolly, Carey Downey, Robin Gerlach, Matthew W. Fields

Biology Faculty Publications and Presentations

Knowledge of taxis (directed swimming) in the Archaea is currently expanding through identification of novel receptors, effectors, and proteins involved in signal transduction to the flagellar motor. Although the ability for biological cells to sense and swim toward hydrogen gas has been hypothesized for many years, this capacity has yet to be observed and demonstrated. Here we show that the average swimming velocity increases in the direction of a source of hydrogen gas for the methanogen, Methanococcus maripaludis using a capillary assay with anoxic gas-phase control and time-lapse microscopy. The results indicate that a methanogen couples motility to hydrogen concentration …

Intracellular Recording, Sensory Field Mapping, And Culturing Identified Neurons In The Leech, Hirudo Medicinalis, Josh Titlow, Zana R. Majeed, John G. Nicholls, Robin L. Cooper

Biology Faculty Publications

The freshwater leech, Hirudo medicinalis, is a versatile model organism that has been used to address scientific questions in the fields of neurophysiology, neuroethology, and developmental biology. The goal of this report is to consolidate experimental techniques from the leech system into a single article that will be of use to physiologists with expertise in other nervous system preparations, or to biology students with little or no electrophysiology experience. We demonstrate how to dissect the leech for recording intracellularly from identified neural circuits in the ganglion. Next we show how individual cells of known function can be removed from …

Neural Circuit Recording From An Intact Cockroach Nervous System, Josh Titlow, Zana R. Majeed, H. Bernard Hartman, Ellen Burns, Robin L. Cooper

Biology Faculty Publications

The cockroach ventral nerve cord preparation is a tractable system for neuroethology experiments, neural network modeling, and testing the physiological effects of insecticides. This article describes the scope of cockroach sensory modalities that can be used to assay how an insect nervous system responds to environmental perturbations. Emphasis here is on the escape behavior mediated by cerci to giant fiber transmission in Periplaneta americana. This in situ preparation requires only moderate dissecting skill and electrophysiological expertise to generate reproducible recordings of neuronal activity. Peptides or other chemical reagents can then be applied directly to the nervous system in solution …

Microtubule Severing At Crossover Sites By Katanin Generates Ordered Cortical Microtubule Arrays In Arabidopsis, Quan Zhang, Erica Fishel, Tyler Bertroche, Ram Dixit

Biology Faculty Research

Highlights

• Severing primarily depolymerizes the overlying CMT at crossover sites
• Severing probability increases nonlinearly with crossover time
• Katanin localizes to crossover sites and is required for severing
• Loss of katanin activity prevents the formation of coaligned CMT arrays

Summary
The noncentrosomal cortical microtubules (CMTs) of land plants form highly ordered parallel arrays that mediate cell morphogenesis by orienting cellulose deposition [1, 2 and 3]. Since new CMTs initiate from dispersed cortical sites at random orientations [4], parallel array organization is hypothesized to require selective pruning of CMTs that are not in the dominant orientation. Severing of CMTs at crossover sites …

Controls Of Phosphorus Loading And Transport In The Cuyahoga River Of Northeastern Ohio, Usa, Fasong Yuan, Jaime A. Quellos, Chaojun Fan

Biological, Geological, and Environmental Faculty Publications

An urban stream differs from a natural stream in that it commonly contains anthropogenic nutrients from a variety of diffuse and point sources (e.g., urban runoff, industrial and municipal effluents). The Cuyahoga River as one of such stream systems receives on average 30% of water from over a dozen wastewater treatment plants (WWTPs) and exports over 300 Mg/yr of total phosphorus (TP) into Lake Erie. Municipal effluents account for at least two thirds of the TP loading and 90% of the effluent TP is in the form of soluble reactive phosphorus (SRP), i.e., the highly bioavailable form in aquatic ecosystems. …

Fluttering Beauty, Jonathan Jeffrey

SCL Faculty and Staff Publications

This article chronicles the efforts of Lillian Iona (Tyne) Pace (1925-2010) in getting the Viceroy butterfly designated as the Kentucky state butterfly.

Phylogeography Of The California Sheephead, Semicossyphus Pulcher: The Role Of Deep Reefs As Stepping Stones And Pathways To Antitropicality, Marloes Poortvliet, Gary C. Longo, Kimberly Selkoe, Paul H. Berber, Crow White, Jennifer E. Caselle, Alejandro Perez-Matus, Steven D. Gaines, Giacomo Bernardi

Biological Sciences

In the past decade, the study of dispersal of marine organisms has shifted from focusing predominantly on the larval stage to a recent interest in adult movement. Antitropical distributions provide a unique system to assess vagility and dispersal. In this study, we have focused on an antitropical wrasse genus, Semicossyphus, which includes the California sheephead, S. pulcher, and Darwin's sheephead, S. darwini. Using a phylogenetic approach based on mitochondrial and nuclear markers, and a population genetic approach based on mitochondrial control region sequences and 10 microsatellite loci, we compared the phylogenetic relationships of these two species, as well …

Filtering Of Ms/Ms Data For Peptide Identification, Jason Gallia, Katelyn Lavrich, Anna Tan-Wilson, Patrick H. Madden

Biological Sciences Faculty Scholarship

Background: The identification of proteins based on analysis of tandem mass spectrometry (MS/MS) data is a valuable tool that is not fully realized because of the difficulty in carrying out automated analysis of large numbers of spectra. MS/MS spectra consist of peaks that represent each peptide fragment, usually b and y ions, with experimentally determined mass to charge ratios. Whether the strategy employed is database matching or De Novo sequencing, a major obstacle is distinguishing signal from noise. Improved ability to distinguish signal peaks of low intensity from background noise increases the likelihood of correctly identifying the peptide, as valuable …

Zebrafish: Modeling For Herpes Simplex Virus Infections, Kevin Jones

Department of Biology Faculty Publications

Abstract For many years, zebrafish have been the prototypical model for studies in developmental biology. In recent years, zebrafish has emerged as a powerful model system to study infectious diseases, including viral infections. Experiments conducted with herpes simplex virus type-1 in adult zebrafish or in embryo models are encouraging as they establish proof of concept with viral-host tropism and possible screening of antiviral compounds. In addition, the presence of human homologs of viral entry receptors in zebrafish such as 3-O sulfated heparan sulfate, nectins, and tumor necrosis factor receptor superfamily member 14-like receptor bring strong rationale for virologists to test …

Evaluating The Efficacy Of Land Snail Survey Techniques In Hawaii: Implications For Conservation Throughout The Pacific, Torsten Durkan, Norine Yeung, Wallace Meyer, Kenneth Hayes, Robert Cowie

Department of Biology Faculty Publications

Terrestrial micromolluscs (snails with an adult maximum shell dimension <5 mm) constitute a considerable proportion of the land snail fauna of the Pacific. However, micromolluscs are often underestimated in biological surveys because of size bias. It has been argued that visual searches are preferable on Pacific islands because: (1) size biases are limited based on the understanding that most native Pacific island land snails are very small, and (2) amount of labor is less than other methods such as soil surveys and adequate for inventory purposes (though not for abundance assessments). To test whether visual surveys and soil surveys were accurately recording all taxa, land snail inventories were completed in three forest reserves (5 sampling sites in each) on the island of Oahu, Hawaii. Visual surveys involved 30-min visual search in a 10 m2 site; soil surveys involved sieving leaf litter and topsoil from four 0.3 m2 quadrats and extracting snails with the aid of a microscope. The data indicate a size and microhabitat bias associated with both techniques. Visual surveys consistently collected large arboreal and litter-dwelling species but missed a significant portion of micromolluscs, while soil surveys collected micromolluscs but missed larger snails. Because of such biases, employing both methods is critical for collecting all taxa at a survey location. As such, we recommend that future land snail surveys on Pacific Islands incorporate both survey techniques. Obtaining a complete inventory is critical if we are to understand species distributions and patterns of diversity and make well-informed conservation recommendations.

Reflections On The Cost Of "Low-Cost" Whole Genome Sequencing: Framing The Health Policy Debate, Timothy Caulfield, Jim Evans, Amy Mcguire, Christopher Mccabe, Tania M. Bubela, Robert Cook-Deegan, Jennifer Fishman, Stuart Hogarth, Fiona A. Miller, Vardit Ravitsky

Office of the Provost

The cost of whole genome sequencing is dropping rapidly. There has been a great deal of enthusiasm about the potential for this technological advance to transform clinical care. Given the interest and significant investment in genomics, this seems an ideal time to consider what the evidence tells us about potential benefits and harms, particularly in the context of health care policy. The scale and pace of adoption of this powerful new technology should be driven by clinical need, clinical evidence, and a commitment to put patients at the centre of health care policy.

Protargol Synthesis: An In-House Protocol, Xuming Pan, William A. Bourland, Weibo Song

Biology Faculty Publications and Presentations

The protargol staining method has proved to be indispensable for revealing the cellular structures of a variety of protozoa, especially the flagellates and ciliates. Protargol provides permanent stains of a variety of cellular structures: nuclei, extrusomes, basal bodies, and microfilamentous constituents of cells. Together with the older silver nitrate methods, protargol impregnations have provided the basis for the detailed descriptions of nearly all ciliates to date. The performance of commercially available preparations has varied widely. Recently, suppliers have stopped stocking the effective forms of protargol resulting in a worldwide shortage. Thus, it has become necessary for protistologists to explore on-site …

High-Throughput Amplicon Sequencing Of Rrna Genes Requires A Copy Number Correction To Accurately Reflect The Effects Of Management Practices On Soil Nematode Community Structure, B. J. Darby, T. C. Todd, M. A. Herman

School of Biological Sciences: Faculty Publications

Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. …

Survivorship Of Ploidy-Variable Unisexual Ambystoma Aalamanders Across Developmental Stages, Christina Marie Casto

Master's Theses and Doctoral Dissertations

Unisexual Ambystoma produce ploidy-variable offspring that differ in survivorship to adulthood. These populations reproduce through kleptogenesis, persisting by stealing genetic material from males of compatible bisexual Ambystoma species (e.g., Jefferson's Salamander A. jeffersonianum, and the Blue-Spotted Salamander A. laterale). Kleptogenesis can result in ploidy-variable embryos within an egg mass because the female may or may not incorporate the male ambystomatid genome. Little is known about the survivorship of ploidy-variable individuals. In previous studies, triploid individuals are the most abundant class, suggesting a greater mortality in high-ploidy (tetraploid and pentaploid) individuals. We assessed the frequency of ploidy levels (determined …

Gene Expression Studies For The Analysis Of Domoic Acid Production In The Marine Diatom Pseudo-Nitzschia Multiseries, Katie R. Boissonneault, Brooks M. Henningsen, Stephen S. Bates, Deborah L. Robertson, Sean Milton, Jerry Pelletier, Deborah A. Hogan, David E. Housman

Biology

Background: Pseudo-nitzschia multiseries Hasle (Hasle) (Ps-n) is distinctive among the ecologically important marine diatoms because it produces the neurotoxin domoic acid. Although the biology of Ps-n has been investigated intensely, the characterization of the genes and biochemical pathways leading to domoic acid biosynthesis has been limited. To identify transcripts whose levels correlate with domoic acid production, we analyzed Ps-n under conditions of high and low domoic acid production by cDNA microarray technology and reverse-transcription quantitative PCR (RT-qPCR) methods. Our goals included identifying and validating robust reference genes for Ps-n RNA expression analysis under these conditions. Results: Through microarray analysis of …

Filopodia As Sensors, Carol A. Heckman, H. K. Plummer

Biological Sciences Faculty Publications

Filopodia are sensors on both excitable and non-excitable cells. The sensing function is well documented in neurons and blood vessels of adult animals and is obvious during dorsal closure in embryonic development. Nerve cells extend neurites in a bidirectional fashion with growth cones at the tips where filopodia are concentrated. Their sensing of environmental cues underpins the axon's ability to "guide," bypassing non-target cells and moving toward the target to be innervated. This review focuses on the role of filopodia structure and dynamics in the detection of environmental cues, including both the extracellular matrix (ECM) and the surfaces of neighboring …

The Glucose Signaling Network In Yeast, Jeong-Ho Kim, Adhiraj Roy, David Jouandot Ii, Kyu Hong Cho

Faculty Publications

Background

Most cells possess a sophisticated mechanism for sensing glucose and responding to it appropriately. Glucose sensing and signaling in the budding yeast Saccharomyces cerevisiae represent an important paradigm for understanding how extracellular signals lead to changes in the gene expression program in eukaryotes.

Scope of review

This review focuses on the yeast glucose sensing and signaling pathways that operate in a highly regulated and cooperative manner to bring about glucose-induction of HXT gene expression.

Major conclusions

The yeast cells possess a family of glucose transporters (HXTs), with different kinetic properties. They employ three major glucose signaling pathways—Rgt2/Snf3, …

Morphological Divergence And Flow-Induced Phenotypic Plasticity In A Native Fish From Anthropogenically Altered Stream Habitats, Nathan R. Franssen, Laura K. Stewart, Jacob F. Schaefer

Faculty Publications

Understanding population-level responses to human-induced changes to habitats can elucidate the evolutionary consequences of rapid habitat alteration. Reservoirs constructed on streams expose stream fishes to novel selective pressures in these habitats. Assessing the drivers of trait divergence facilitated by these habitats will help identify evolutionary and ecological consequences of reservoir habitats. We tested for morphological divergence in a stream fish that occupies both stream and reservoir habitats. To assess contributions of genetic-level differences and phenotypic plasticity induced by flow variation, we spawned and reared individuals from both habitats types in flow and no flow conditions. Body shape significantly and consistently …

Facile Synthesis, Characterization, And Antimicrobial Activity Of Cellulose-Chitosan-Hydroxyapatite Composite Material: A Potential Material For Bone Tissue Engineering, Tamutsiwa M. Mututuvari, April L. Harkins, Chieu D. Tran

Clinical Lab Sciences Faculty Research and Publications

Hydroxyapatite (HAp) is often used as a bone-implant material because it is biocompatible and osteoconductive. However, HAp possesses poor rheological properties and it is inactive against disease-causing microbes. To improve these properties, we developed a green method to synthesize multifunctional composites containing: (1) cellulose (CEL) to impart mechanical strength; (2) chitosan (CS) to induce antibacterial activity thereby maintaining a microbe-free wound site; and (3) HAp. In this method, CS and CEL were co-dissolved in an ionic liquid (IL) and then regenerated from water. HAp was subsequently formed in situ by alternately soaking [CEL+CS] composites in aqueous solutions of CaCl_{2 …}

Insights Into The Carboxyltransferase Reaction Of Pyruvate Carboxylase From The Structures Of Bound Product And Intermediate Analogs, Adam D. Lietzan, Martin St. Maurice

Biological Sciences Faculty Research and Publications

Pyruvate carboxylase (PC) is a biotin-dependent enzyme that catalyzes the MgATP- and bicarbonate-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. The carboxyltransferase (CT) domain of PC catalyzes the transfer of a carboxyl group from carboxybiotin to the accepting substrate, pyruvate. It has been hypothesized that the reactive enolpyruvate intermediate is stabilized through a bidentate interaction with the metal ion in the CT domain active site. Whereas bidentate ligands are commonly observed in enzymes catalyzing reactions proceeding through an enolpyruvate intermediate, no bidentate interaction has yet been observed in the CT domain of PC. Here, we …

Liana Impacts On Carbon Cycling, Storage And Sequestration In Tropical Forests, Geertje M. Van Der Heijden, Stefan A. Schnitzer, Jennifer S. Powers, Oliver L. Phillips

Biological Sciences Faculty Research and Publications

Mature tropical forests sequester large quantities of atmospheric CO2, which they store as plant biomass. These forests are changing however, including an increase in liana abundance and biomass over recent decades in Neotropical forests. We ask here how this increase in lianas might impact the tropical forest carbon cycle and their capacity for carbon storage and sequestration. Lianas reduce tree growth, survival, and leaf productivity; however, lianas also invest significantly in leaf production, and the increase in lianas could conceivably offset liana‐induced reductions in tree canopy productivity with no adverse effects to the forest‐level canopy productivity. By contrast, lianas decrease …

Novel Neuroprotective Function Of Apical-Basal Polarity Genecrumbs In Amyloid Beta 42 (Aβ42) Mediated Neurodegeneration, Andrew Steffensmeier, Meghana Tare, Oorvashi Roy Puli, Rohan Modi, Jaison Nainaparampil, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Alzheimer's disease (AD, OMIM: 104300), a progressive neurodegenerative disorder with no cure to date, is caused by the generation of amyloid-beta-42 (Aβ42) aggregates that trigger neuronal cell death by unknown mechanism(s). We have developed a transgenic Drosophilaeye model where misexpression of human Aβ42 results in AD-like neuropathology in the neural retina. We have identified an apical-basal polarity gene crumbs (crb) as a genetic modifier of Aβ42-mediated-neuropathology. Misexpression of Aβ42 caused upregulation of Crb expression, whereas downregulation of Crb either by RNAi or null allele approach rescued the Aβ42-mediated-neurodegeneration. Co-expression of full length Crb with Aβ42 increased severity of Aβ42-mediated-neurodegeneration, …