Life Sciences Commons^™

Applications Of Phylogenetics To Issues In Freshwater Crayfish Biology, Keith A. Crandall

Faculty Publications

Freshwater crayfish have served as model organisms for over 125 years in scientific research, from areas such as neurobiology and vision research to conservation biology and evolution. Recently, evolutionary histories in the form of phylogenies have served as a critical foundation for testing hypotheses in such diverse research areas as well. In this article, I review the amazing diversity of freshwater crayfish, especially in a phylogenetic context and explore how these evolutionary histories have informed crayfish biology and can be used powerfully in the future to guide research in a diversity of areas. Throughout the article, I draw on examples …

Visibility, Visual Awareness, And Visual Masking Of Simple Unattended Targets Are Confined To Areas In The Occipital Cortex Beyond Human V1/V2, Peter U. Tse, Susanna Martinez-Conde, Alexander A. Schlegel, Stephen L. Macknik

Dartmouth Scholarship

In visual masking, visible targets are rendered invisible by modifying the context in which they are presented, but not by modifying the targets themselves. Here, we localize the neuronal correlates of visual awareness in the human brain by using visual masking illusions. We compare monoptic visual masking activation, which we find within all retinotopic visual areas, with dichoptic masking activation, which we find only in those retinotopic areas downstream of V2. Because monoptic and dichoptic masking are equivalent in magnitude perceptually, the present results establish a lower bound for maintenance of visual awareness of simple unattended targets. Moreover, we find …

Growth Factor–Induced Shedding Of Syndecan-1 Confers Glypican-1 Dependence On Mitogenic Responses Of Cancer Cells, Kan Ding, Martha Lopez-Burks, José A. Sánchez-Duran, Murray Korc, Arthur D. Lander

Dartmouth Scholarship

The cell surface heparan sulfate proteoglycan (HSPG) glypican-1 is up-regulated by pancreatic and breast cancer cells, and its removal renders such cells insensitive to many growth factors. We sought to explain why the cell surface HSPG syndecan-1, which is also up-regulated by these cells and is a known growth factor coreceptor, does not compensate for glypican-1 loss. We show that the initial responses of these cells to the growth factor FGF2 are not glypican dependent, but they become so over time as FGF2 induces shedding of syndecan-1. Manipulations that retain syndecan-1 on the cell surface make long-term FGF2 responses glypican …

Seagrass–Pathogen Interactions: ‘Pseudo-Induction’ Of Turtlegrass Phenolics Near Wasting Disease Lesions, Latina Steele, Melanie Caldwell, Anne Boettcher, Tom Arnold

Biology Faculty Publications

Marine protists of the genus Labyrinthula cause the seagrass wasting disease, which is associated with regional die-offs of eelgrass Zostera marina and also infects turtlegrass Thalassia testudinum . The ability of seagrasses to resist pathogen attack is determined by multiple factors, which are poorly understood. One factor hypothesized to influence seagrass disease resistance is the presence of (poly)phenolic natural products such as caffeic acid, which inhibits the growth of L. zosterae in in vitro laboratory bioassays. This hypothesis has been supported by reports of pathogen-induced phenolic accumulations in eelgrass Z. marina. To test the response of T. testudinum to …

Principal Component Analysis For Predicting Transcription-Factor Binding Motifs From Array-Derived Data, Yunlong Liu, Matthew P Vincenti, Hiroki Yokota

Dartmouth Scholarship

The responses to interleukin 1 (IL-1) in human chondrocytes constitute a complex regulatory mechanism, where multiple transcription factors interact combinatorially to transcription-factor binding motifs (TFBMs). In order to select a critical set of TFBMs from genomic DNA information and an array-derived data, an efficient algorithm to solve a combinatorial optimization problem is required. Although computational approaches based on evolutionary algorithms are commonly employed, an analytical algorithm would be useful to predict TFBMs at nearly no computational cost and evaluate varying modelling conditions. Singular value decomposition (SVD) is a powerful method to derive primary components of a given matrix. Applying SVD …

Loss Of Editing Activity During The Evolution Of Mitochondrial Phenylalanyl-Trna Synthetase, Hervé Roy, Jiqiang Ling, Juan D. Alfonzo, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Accurate selection of amino acids is essential for faithful translation of the genetic code. Errors during amino acid selection are usually corrected by the editing activity of aminoacyl-tRNA synthetases such as phenylalanyl-tRNA synthetases (PheRS), which edit misactivated tyrosine. Comparison of cytosolic and mitochondrial PheRS from the yeast Saccharomyces cerevisiae suggested that the organellar protein might lack the editing activity. Yeast cytosolic PheRS was found to contain an editing site, which upon disruption abolished both cis and trans editing of Tyr-tRNA^Phe. Wild-type mitochondrial PheRS lacked cis and trans editing and could synthesize Tyr-tRNA^Phe, an activity enhanced in …

The Role Of Phosducin-Like Protein And The Cytosolic Chaperonin Cct In G Beta Gamma Dimer Assembly, Ting Hu

Theses and Dissertations

Phosducin-like protein (PhLP), a G protein beta gamma subunit dimer binder and G protein signaling regulator, was suggested to regulate the activity of cytosolic chaperonin CCT by their high affinity interaction. In the present study, the three-dimensional structure of PhLP:CCT complex has been solved by cryoelectron microscopy. PhLP was found to bind only one of the chaperonin rings with both N- and C-terminal domains. It spans the central folding cavity of CCT and interacts with two opposite sides of the top apical region, inducing the constraining of the entry of the folding cavity. These findings support a putative role of …

An Introduction To Low-Level Analysis Methods Of Dna Microarray Data, Wolfgang Huber, Anja Von Heydebreck, Martin Vingron

Bioconductor Project Working Papers

This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of nucleic acid abundance in a set of tissues or cell populations for thousands of transcripts or loci simultaneously. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. This includes the design of probes, the experimental design, the image analysis of microarray scanned images, the normalization of fluorescence intensities, the assessment of the quality of microarray …

Cortical Regions Associated With Autonomic Cardiovascular Regulation During Lower Body Negative Pressure In Humans., Derek S Kimmerly, Deborah D O'Leary, Ravi S Menon, Joseph S Gati, J Kevin Shoemaker

Kinesiology Publications

The purpose of the present study was to determine the cortical structures involved with integrated baroreceptor-mediated modulation of autonomic cardiovascular function in conscious humans independent of changes in arterial blood pressure. We assessed the brain regions associated with lower body negative pressure (LBNP)-induced baroreflex control using functional magnetic resonance imaging with blood oxygen level-dependent (BOLD) contrast in eight healthy male volunteer subjects. The levels of LBNP administered were 5, 15 and 35 mmHg. Heart rate (HR; representing the cardiovascular response) and LBNP (representing the baroreceptor activation level) were simultaneously monitored during the scanning period. In addition, estimated central venous pressure …

Hybridization Of Lythrurus Fasciolaris (Cope) And Lythrurus Umbratilis (Girard) (Cypriniformes: Cyprinidae) In The Ohio River Basin, Robert L. Hopkins Ii

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science and Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science by Robert L. Hopkins, II on November 14, 2005.

Hispanic Physicians' Tobacco Intervention Practices: A Cross-Sectional Survey Study, Francisco G. Soto Mas, Richard L. Papenfuss, Holly E. Jacobson, Chiehwen E. Hsu, William M. Kane

Faculty, Staff and Student Publications

Background U.S. Hispanic physicians constitute a considerable professional collective, and they may be most suited to attend to the health education needs of the growing U.S. Hispanic population. These educational needs include tobacco use prevention and smoking cessation. However, there is a lack of information on Hispanic physicians' tobacco intervention practices, their level of awareness and use of cessation protocols, and the type of programs that would best address their tobacco training needs. The purpose of this study was to assess the tobacco intervention practices and training needs of Hispanic physicians.

Methods Data was collected through a validated survey instrument …

Palladium-Imidazolium Carbene Catalyzed Heck Coupling Reactions And Synthesis Of A Novel Class Of Fluoroanthracenylmethyl Ptc Catalysts, Jiuqing Zhang

Theses and Dissertations

Palladium catalyzed Heck coupling with aryl and alkenyl halides has become a powerful means of carbon-carbon bond formation. This standard synthetic method has been developed to a high level of utility using various catalysts, conditions and substrates. Yet significant drawbacks remain, including poor reactivity, the need for high temperatures and base, limited substrate generality, and selectivity. Mixed products often suffer from olefin migration following insertion. N-Heterocyclic carbenes (NHC) have proven to be electron-rich donors which provide higher stability and reactivity than phosphines. In a previous paper reported by our research group the imidazolium-palladium carbene has proven to be highly efficient …

The Tree-Thinking Challenge, David A. Baum, Stacey Dewitt Smith, Samuel S.S. Donovan

School of Biological Sciences: Faculty Publications

The preferred interpretation of a phylogenetic tree is as a depiction of lines of descent. That is, trees communicate the evolutionary relationships among elements, such as genes or species, that connect a sample of branch tips. Under this interpretation, the nodes (branching points) on a tree are taken to correspond to actual biological entities that existed in the past: ancestral populations or ancestral genes. However, tree diagrams are also used in many nonevolutionary contexts, which can cause confusion. For example, trees can depict the clustering of genes on the basis of their expression profiles from microarrays, or the clustering of …

A Novel Cysteine-Rich Domain Of Sep15 Mediates The Interaction With Udp-Glucose:Glycoprotein Glucosyltransferase, Vyacheslav M. Labunskyy, Andrew D. Ferguson, Dmitri E. Fomenko, Yogarany Chelliah, Dolph L. Hatfield, Vadim N. Gladyshev

Vadim Gladyshev Publications

Selenium is an essential trace element with potent cancer prevention activity in mammals. The 15-kDa selenoprotein (Sep15) has been implicated in the chemopreventive effect of dietary selenium. Although the precise function of Sep15 remains elusive, Sep15 copurifies with UDP-glucose:glycoprotein glucosyltransferase (GT), an essential regulator of quality control mechanisms within the endoplasmic reticulum. Recent studies identified two GT and two Sep15 homologues in mammals. We characterize interactions between these protein families in this report. Sep15 and GT form a tight 1:1 complex, and these interactions are conserved between mammals and fruit flies. In mammalian cells, Sep15 co-immunoprecipitates with both GT isozymes. …

Increased Demand For Wool Apparel In Western European Markets: Effect On Australian Wool Auctions, Nazrul Islam, John Stanton, Emma Kopke

Agriculture reports

The need for marketing activities in retail markets for wool apparel is a current and reoccurring industry debate. This paper reports on the impact of these activities, as a change of demand for pure wool apparels at retail, on the price and quantity of raw wool cleared through Australian wool auctions. The analysis uses a world wool trade model developed by the Department of Agriculture Western Australian and the University of Western Australia which tracks global flows of wool and wool products from production to retail in 10 regional markets. The impact of demand is presented for selected wool garments …

2005 Oregon Harvest Report, Oregon Wine Board

Oregon Wine Board Documents

This harvest report for the Oregon wine industry from 2005 discusses how the cooler temperatures and lower alcohol levels affected the vintages. The harvests were later and difficulties arose with autumn rains, but excellent wines were still made.

The Depressive Effect Of PI On The Force-Pca Relationship In Skinned Single Muscle Fibers Is Temperature Dependent, Edward Patrick Debold, Janell Romatowski, Robert H. Fitts

Biological Sciences Faculty Research and Publications

Increases in P_i combined with decreases in myoplasmic Ca2+ are believed to cause a significant portion of the decrease in muscular force during fatigue. To investigate this further, we determined the effect of 30 mM P_ion the force-Ca²⁺ relationship of chemically skinned single muscle fibers at near-physiological temperature (30°C). Fibers isolated from rat soleus (slow) and gastrocnemius (fast) muscle were subjected to a series of solutions with an increasing free Ca²⁺ concentration in the presence and absence of 30 mM P_iat both low (15°C) and high (30°C) temperature. In slow fibers, 30 mM …

Ego-1, A Putative Rna-Dependent Rna Polymerase, Is Required For Heterochromatin Assembly On Unpaired Dna During C. Elegans Meiosis, Eleanor M. Maine, Jessica Hauth, Thomas Ratliff, Valarie E. Vought, Xingyu She, William G. Kelly

Biology - All Scholarship

During meiosis in C. elegans, unpaired chromosomes and chromosomal regions accumulate high levels of histone H3 lysine 9 dimethylation (H3K9me2), a modification associated with facultative heterochromatin assembly and the resulting transcriptional silencing [1, 2]. Meiotic silencing of unpaired DNA may be a widely conserved genome defense mechanism [3–5]. The mechanisms of meiotic silencing remain unclear, although both transcriptional and posttranscriptional processes are implicated [3–5]. Cellular RNA-dependent RNA polymerases (RdRPs) function in development and RNA-mediated silencing in many species [3, 6, 7] and in heterochromatin assembly in S. pombe [3, 8]. There are four C. elegans RdRPs, including two with known …

Semantics For Scientific Experiments And The Web: The Implicit, The Formal And The Powerful, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Mypyramid.Gov, Ann Y. Mcdermott

Kinesiology and Public Health

The US Department of Agriculture (USDA) has un-unveiled a new symbol and an interactive "food guidance system" called "MyPyramid: Steps to a Healthier You," which replaces the 13-year-old Food Guide Pyramid. The new program aims to support the eating and physical activity habits necessary to promote health and prevent such common diseases as obesity, cardiovascular disease, diabetes, osteoporosis, and some cancers. Over the past few decades, population-specific scientific evidence of the effects of nutrition, activity, and body weight on health outcomes has become available. The scientific literature allowed the formulation of new and more detailed recommendations. The USDA's new system …

Muscle Biochemistry And The Ontogeny Of Flight Capacity During Behavioral Development In The Honey Bee, Apis Mellifera, Stephen P. Roberts, Michelle M. Elekonich

Biological Sciences Faculty Research & Creative Works

A Fundamental Issue in Physiology and Behavior is Understanding the Functional and Genetic Mechanisms that Underlie Major Behavioral Shifts in Organisms as They Adopt New Environments or Life History Tactics. Such Transitions Are Common in Nature and Include the Age-Related Switch from Nest/hive Work to Foraging in Social Insects Such as Honeybees (Apis Mellifera). Because of their Experimental Tractability, Recently Sequenced Genome and Well Understood Biology, Honeybees Are an Ideal Model System for Integrating Molecular, Genetic, Physiological and Sociobiological Perspectives to Advance Understanding of Behavioral and Life History Transitions. When Honeybees (Apis Mellifera) Transition from Hive Work to Foraging, their …

Plumage Convergence In Picoides Woodpeckers Based On A Molecular Phylogeny, With Emphasis On Convergence In Downy And Hairy Woodpeckers, Amy C. Weibel, William S. Moore

Biological Sciences Faculty Research Publications

Adult and juvenile plumage characters were traced onto a well-resolved molecular based phylogeny for Picoides woodpeckers, and a simple phylogenetic test of homology, parallelism, and convergence of plumage characters was performed. Reconstruction of ancestral character states revealed multiple events of independent evolution of derived character states in most characters studied, and a concentrated changes test revealed that some plumage characters evolved in association with habitat type. For example, there was a statistically significant association between loss of dorsal barring and use of densely vegetated habitats among Picoides species. Two analyses indicated that convergence, as opposed to parallel evolution or shared …

Production And Handling Practices For Safe Produce, Pamela L. Brady, Justin R. Morris

AAES Research Reports and Research Bulletins

The University of Arkansas Division of Agriculture received a grant from the USDA’s Initiative for Future Agriculture and Food Systems program to help small- and medium-sized farms become more profitable and to therefore add stability to the family farm. One approach to doing this is to help farmers growing produce reduce or eliminate safety hazards which may be associated with their products.

Vines For Utah Landscape, Larry A. Sagers

All Archived Publications

No abstract provided.

Performance Of Binary-Encounter-Bethe (Beb) Theory For Electron-Impact Ionization Cross Sections Of Molecules Containing Heavy Elements (Z > 10), Gregory E. Scott, Karl K. Irikura

Chemistry and Biochemistry

The binary-encounter-Bethe (BEB) theory developed by Kim and coworkers has been successful for computing electron-impact ionization cross sections of many molecules. However, some recent publications have stated that BEB theory performs poorly for molecules that contain heavier elements such as chlorine and sulfur. We have found that the BEB calculations in those publications were performed incorrectly. When performed correctly, BEB predictions are as good for heavy-element molecules as for light-element molecules. We recommended recently that an alternative, less-confusing procedure be used for molecules that contain heavier elements. The alternative procedure, based upon effective core potentials (ECPs), does not require explicit …

Optimal Adaptation In Autonomic Web Processes With Inter-Service Dependencies, Kunal Verma, Prashant Doshi, Karthik Gomadam, John A. Miller, Amit P. Sheth

Kno.e.sis Publications

We present methods for optimally adapting Web processes to exogenous events while preserving inter-service dependencies. For example, in a supply chain process, orders placed by the manufacturer may get delayed in arriving. In response to this event, the manufacturer has the choice of either waiting out the delay or changing the supplier.

Kentucky Warbler (Vol. 81, No. 4), Kentucky Library Research Collections

The Kentucky Warbler

No abstract provided.

Chimpanzee Theory Of Mind: Looking In All The Wrong Places?, Kristin Andrews

Sentience Collection

I respond to an argument presented by Daniel Povinelli and Jennifer Vonk that the current generation of experiments on chimpanzee theory of mind cannot decide whether chimpanzees have the ability to reason about mental states. I argue that Povinelli and Vonk’s proposed experiment is subject to their own criticisms and that there should be a more radical shift away from experiments that ask subjects to predict behavior. Further, I argue that Povinelli and Vonk’s theoretical commitments should lead them to accept this new approach, and that experiments which offer subjects the opportunity to look for explanations for anomalous behavior should …

Cortical Complexity In Cetacean Brains, Patrick R. Hof, Rebecca Chanis, Lori Marino

Veterinary Science and Medicine Collection

Cetaceans (dolphins, whales, and porpoises) have a long, dramatically divergent evolutionary history compared with terrestrial mammals. Throughout their 55–60 million years of evolution, cetaceans acquired a compelling set of characteristics that include echolocation ability (in odontocetes), complex auditory and communicative capacities, and complex social organization. Moreover, although cetaceans have not shared a common ancestor with primates for over 90 million years, they possess a set of cognitive attributes that are strikingly convergent with those of many primates, including great apes and humans. In contrast, cetaceans have evolved a highly unusual combination of neurobiological features different from that of primates. As …

In Situ Examination Of Boldness–Shyness Traits In The Tropical Poeciliid, Brachyraphis Episcopi, Culum Brown, Felicity Jones, Victoria Braithwaite

Sentience Collection

Explaining consistent variation in the behaviour of individuals in terms of personality differences is one of the cornerstones of understanding human behaviour but is seldom discussed in behavioural ecology for fear of invoking anthropomorphism. Recently, however, interest has begun to focus on identifying personality traits in animals and examining their possible evolutionary consequences. One major axis used to define personality traits is the shyness–boldness continuum. We examined boldness in an in situ experiment using fish from eight populations of the poeciliid Brachyraphis episcopi (also referred to as Brachyrhaphis episcopi). Fish from high- and low-predation regions within four streams that run …