Biology Commons^™

Undergraduate Research. Genomics Education Partnership, D Lopatto, C Alvarez, D Barnard, C Chandrasekaran, H-M Chung, C Du, T Eckdahl, A Goodman, C Hauser, C Jones, O Kopp, G Kuleck, G Mcneil, R Morris, J Myka, A Nagengast, P Overvoorde, J Poet, K Reed, G Regisford, D Revie, A Rosenwald, K Saville, M Shaw, G Skuse, C Smith, M Smith, M Spratt, J Stamm, J Thompson, B Wilson, C Witkowski, J Youngblom, Wilson Leung, Christopher Shaffer, Jeremy Buhler, Elaine Mardis, Sarah C.R. Elgin

Biology Faculty Research

The Genomics Education Partnership offers an inclusive model for undergraduate research experiences incorporated into the academic year science curriculum, with students pooling their work to contribute to international data bases.

Towards The Identification Of Lampreys (Lampetra Spp.) In Archaeological Contexts, Ross E. Smith, Virginia L. Butler

Anthropology Faculty Publications and Presentations

Lampreys were and continue to be an important resource for Native Americans in the Pacific Northwest. Lampreys possess several skeletal structures that are regularly identified in marine mammal and bird stomach contents and fecal samples, suggesting that lamprey elements may preserve in archaeological contexts. However, their remains have not been identified in archaeological faunal samples in the Pacific Northwest. This may be due to the lack of an adequate "search image" for lamprey remains among faunal analysts and limited use of line screen sampling. Descriptions and photographs of lamprey remains that are most likely to survive in archaeological contexts are …

Characterization Of Ten Novel Ty1/Copia-Like Retrotransposon Families Of The Grapevine Genome, Cédric Moisy, Keith Garrison, Carole Meredith, Frédérique Pelsy

School of Science Faculty Works

Background

Retrotransposons make a significant contribution to the size, organization and genetic diversity of their host genomes. To characterize retrotransposon families in the grapevine genome (the fourth crop plant genome sequenced) we have combined two approaches: a PCR-based method for the isolation of RnaseH-LTR sequences with a computer-based sequence similarity search in the whole-genome sequence of PN40024.

Results

Supported by a phylogenic analysis, ten novel Ty1/copia families were distinguished in this study. To select a canonical reference element sequence from amongst the various insertions in the genome belonging to each retroelement family, the following screening criteria were adopted to …

Glandular Secretions Of Male Pteropus (Flying Foxes): Preliminary Chemical Comparisons Among Species, Jamie Wagner

Independent Study Project (ISP) Collection

Chemosignaling – passing information by means of chemical compounds that can be detected by members of the same species – is a very important form of communication for most mammals. Flying fox males have odiferous marking secretions on their neck-ruffs that include a combination of secretion from the neck gland and from the urogenital tract; males use this substance to establish territory, especially during the mating season. The secretions of flying fox males from three Australian species – spectacled (Pteropus conspicillatus), grey-headed (P. poliocephalus), and black (P. alecto) – were compared using high pressure liquid chromatography (HPLC); two spectacled females …

Corallivorous Reef Fishes As Potential Vectors Of Coral Disease Based On A Study Of Dietary Preferences, Tanya Rogers

Independent Study Project (ISP) Collection

The prevalence of coral disease appears to be increasing worldwide, although little is known about how these diseases are transmitted between coral colonies. To examine whether corallivorous fishes could potentially act as disease vectors, this study examined whether and which fish species feed on diseased coral, and whether these fishes actively target diseased coral sections. Branches of Acropora muricata with brown band disease were filmed in the field, and bites taken by fishes on different sections of the coral (live tissue, tissue margin, disease band, dead skeleton, and algae) were recorded. For each fish species, electivity indices were calculated for …

Characteristics Of Oxygen-18 And Deuterium Composition In Waters From The Pecos River In American Southwest, Fasong Yuan, Seiichi Miyamoto

Biological, Geological, and Environmental Faculty Publications

The Pecos River, situated in eastern New Mexico and western Texas, receives snowmelt from winter storms in the headwater region of the southern Rocky Mountains and runoff from warm-season monsoonal rainfall in the lower valley. The isotopic composition of the two water sources differs from each other due to their different geographical origins in the Pacific North and the Gulf of Mexico. To better assess the physical features of the Pecos River, oxygen and hydrogen isotopic compositions (δ¹⁸O and δD), major ion concentrations, and other physical variables (e.g., water temperature and electrical conductivity) were measured on water samples …

Cardioprotective Signal Transduction To Mitochondria, Casey Lee Quinlan

Dissertations and Theses

Intracellular responses to external stimuli require reception of the message at the plasma membrane followed by encoding and transmission of the message to its effectors downstream. In this process, diverse cellular responses are mediated by many redundant molecular players. The apparent generality and redundancy of many kinases, such as the mitogen-activated protein kinases (MAPKs), suggests that signal transduction must gain specificity through tight regulation. Diffusion and random collisions of relevant signaling components seem insufficient to explain the multilayered complexity observed in cell signaling cascades. Emerging hypotheses suggest that signaling machinery may achieve enhanced specificity and control by exploiting the compartmentalization …

A Large Volume Striped Bass Incubation Chamber: Design And Comparison With A Traditional Method, Chris Harper

All Theses

I conducted a comparative study of a new jar design (experimental chamber) with a standard egg incubation vessel (McDonald jar). Experimental chambers measured 0.4 m in diameter by 1.3 m in height and had a volume of 200 L. McDonald hatching jars measured 16 cm in diameter by 45 cm in height and had a volume of 6 L. Post-hatch survival was estimated at 48, 96 and 144 h. Stocking rates resulted in an average egg density of 21.9 eggs ml-1 (range = 21.6 - 22.1) for McDonald jars and 10.9 eggs ml-1 (range = 7.0 - 16.8) for experimental …

Evolution Of The Holozoan Ribosome Biogenesis Regulon, Seth J. Brown, Michael D. Cole, Albert J. Erives

Dartmouth Scholarship

The ribosome biogenesis (RiBi) genes encode a highly-conserved eukaryotic set of nucleolar proteins involved in rRNA transcription, assembly, processing, and export from the nucleus. While the mode of regulation of this suite of genes has been studied in the yeast, Saccharomyces cerevisiae, how this gene set is coordinately regulated in the larger and more complex metazoan genomes is not understood. Here we present genome-wide analyses indicating that a distinct mode of RiBi regulation co-evolved with the E(CG)-binding, Myc:Max bHLH heterodimer complex in a stem-holozoan, the ancestor of both Metazoa and Choanoflagellata, the protozoan group most closely related to animals. These …

Lis1 And Ndel1 Influence The Timing Of Nuclear Envelope Breakdown In Neural Stem Cells, Sachin Hebbar, Mariano T. Mesngon, Aimee M. Guillotte, Bhavim Desai, Ramses Ayala, Deanna S. Smith

Faculty Publications

Lis1 and Ndel1 are essential for animal development. They interact directly with one another and with cytoplasmic dynein. The developing brain is especially sensitive to reduced Lis1 or Ndel1 levels, as both proteins influence spindle orientation, neural cell fate decisions, and neuronal migration. We report here that Lis1 and Ndel1 reduction in a mitotic cell line impairs prophase nuclear envelope (NE) invagination (PNEI). This dyneindependent process facilitates NE breakdown (NEBD) and occurs before the establishment of the bipolar spindle. Ndel1 phosphorylation is important for this function, regulating binding to both Lis1 and dynein. Prophase cells in the ventricular zone (VZ) …

To Love Your Neighbor: A Christian Perspective On The Study Of Microbiology And Immunology, Joy Doan

Faith Learning Integration Papers

I have been blessed with enough of a sense of adventure to have experienced the awe-inspiring beauty of a rain forest at night, the top of Half Dome at Yosemite National Park, the sheer cliffs and rushing waters of the Narrows at Zion National Park, Plateau Point—which seems suspended in the Grand Canyon, and the top of a 14,000-foot peak in the Rocky Mountains of Colorado. These are the types of places about which one of the characters in Robert Pirsig’s Zen and the Art of Motorcycle Maintenance observes, “This is the hardest stuff in the world to photograph. You …

Emerging Issues In Forensic Dna Profiling: Databases And Advisory Boards, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Many Species In One: Dna Barcoding Overestimates The Number Of Species When Nuclear Mitochondrial Pseudogenes Are Coamplified, Michael F. Whiting, Hojun Song, Keith A. Crandall, Jennifer E. Buhay

Faculty Publications

Nuclear mitochondrial pseudogenes (numts) are nonfunctional copies of mtDNA in the nucleus that have been found in major clades of eukaryotic organisms.

Recruitment Of Coastal Fishes And Oceanographic Variability In Central California, J. R. Wilson, B. R. Broitman, J. E. Caselle, D. E. Wendt

Biological Sciences

Recruitment of pelagic larval fishes to the nearshore environment is dependent on a suite of biological and physical processes operating at many spatial and temporal scales. Nearshore circulation processes associated with coastal upwelling are widely upheld as major determinants of year class strength for many rockfishes (Sebastes spp.), but the mechanism by which these processes drive recruitment is largely unknown. We used Standard Monitoring Units for the Recruitment of Fishes (SMURFs) to monitor recruitment of two rockfish complexes (Sebastes spp.) and cabezon (Scorpaenichthys marmoratus) from March to September of 2004 and 2005 at 3 sites along …

Caspase-Cleaved Tar Dna Binding Protein-43 Is A Major Pathological Finding In Alzheimer’S Disease, Troy T. Rohn

Biology Faculty Publications and Presentations

The TAR DNA binding protein-43 (TDP-43) has been identified as a major constituent of inclusions found in frontotemporal dementia with ubiquitin-positive inclusions (FTLD-U) and amyotrophic lateral sclerosis (ALS). To determine a possible role for TDP-43 in Alzheimer’s disease (AD), a site-directed caspase-cleavage antibody to TDP-43 based upon a known caspase-3 cleavage consensus site within TDP-43 at position D219 was designed. In vitro, this antibody labeled the predicted 25 kDa caspase-cleavage fragment of TDP-43 without labeling full-length TDP-43 following digestion of recombinant TDP-43 with caspase-3 or treatment of Hela cells with staurosporine. Application of this antibody in postmortem brain sections …

Application Of Shortest-Path Network Analysis To Identify Genes That Modulate Longevity In Saccharomyces Cerevisiae, Jr Managbanag

Theses and Dissertations

Shortest-path network analysis was employed to identify novel genes that modulate longevity in the baker’s yeast Saccharomyces cerevisiae. Based upon a set of previously reported genes associated with increased life span, a shortest path network algorithm was applied to a pre-existing protein-protein interaction dataset in order to construct a shortest-path longevity network. To validate this network, the replicative aging potential of 88 single gene deletion strains corresponding to predicted components of the shortest path longevity network was determined. The 88 single-gene deletion strains identified by a network approach are significantly enriched for mutation conferring both increased and decreased replicative life …

Breakdown And Invertebrate Colonization Of Dead Wood In Wetland, Upland, And River Habitats, Amy Braccia, Darold P. Batzer

Biological Sciences Faculty and Staff Research

Breakdown of woody debris in river and upland habitats as well as the interactions between wood and invertebrates have been well described. Studies of wood in wetlands are rare, and far less is known about breakdown and invertebrate use of wood in these transitional habitats. This study experimentally assessed breakdown and invertebrate colonization of wood in a floodplain wetland and directly related patterns in the wetland to adjacent river and upland habitats. Over a 2.7 year period, we monitored breakdown and invertebrate presence in 10 cm diameter × 150 cm long sweetgum (Liquidambar styraciflua L.) logs in a floodplain wetland …

Population Structure Of Coyote (Canis Latrans) In The Urban Landscape Of The Cleveland, Ohio Area, Rebecca M. Rashleigh, Robert A. Krebs, Harry Van Keulen

Biological, Geological, and Environmental Faculty Publications

To obtain information on the population structure of coyote (Canis latrans) in an urban setting, a non-invasive genetic sampling technique was applied that consisted of DNA isolation from scat collected around the Cleveland metropolitan area. Muscle tissue was provided from two other coyotes. Amplifying the mitochondrial D-loop or control region produced 33 haplotypes from just 57 coyote sequences and two additional dog sequences from putative coyote-dog hybrids. The mitochondrial DNA genetic diversity in the Cleveland area was high, π 0.02, and composed of six distinct haplotype lineages. In addition, Fst values ranged from 0.07 between collections east and west of …

Synergistic Applications Of Autonomous Underwater Vehicles And Regional Ocean Modeling System In Coastal Ocean Forecasting, Yi Chao, Zhijin Li, John D. Farrara, Mark A. Moline, Oscar M.E. Schofield, Sharanya J. Majumdar

Biological Sciences

The potential for using synergistic combinations of measurements from autonomous underwater vehicles (AUVs) and output from three-dimensional numerical models for studying the central California coastal region is demonstrated. Two case studies are used to illustrate the approach. In the first, propeller-driven AUV observations revealed a subsurface salinity minimum in northern Monterey Bay. A Regional Ocean Modeling System (ROMS) reanalysis of the three-dimensional flow in the region suggested an offshore source for this water and particular propagation pathways from the south and west into the bay. In the second case study, the effectiveness of assimilating observations in improving the ROMS reanalysis …

Introduction To The Limnology And Oceanography Special Issue On Autonomous And Lagrangian Platforms And Sensors (Alps), Mark A. Moline, T. D. Dickey, E. C. Itsweire, M. J. Perry

Biological Sciences

This issue is devoted to recent developments of autonomous and Lagrangian platforms and sensors (ALPS) and their uses for solving a broad range of interdisciplinary aquatic problems. The collective papers treat a variety of problems that generally require measurements spanning a continuum of temporal and spatial scales. ALPS platforms in this issue include surface drifters, profiling and other types of subsurface floats, gliders, unmanned boats, autonomous underwater vehicles, and instrumented animals. ALPS platforms can provide access in difficult environments (e.g., under ice and in high-sea states). They are also important for emerging networked ocean and lake observing systems that require …

Genome Size Is A Strong Predictor Of Cell Size And Stomatal Density In Angiosperms, Jeremy M. Beaulieu, Ilia J. Leitch, Sunil Patil, Arjun Pendharkar, Charles A. Knight

Biological Sciences

• Across eukaryotes phenotypic correlations with genome size are thought to scale from genome size effects on cell size. However, for plants the genome/cell size link has only been thoroughly documented within ploidy series and small subsets of herbaceous species. • Here, the first large-scale comparative analysis is made of the relationship between genome size and cell size across 101 species of angiosperms of varying growth forms. Guard cell length and epidermal cell area were used as two metrics of cell size and, in addition, stomatal density was measured. • There was a significant positive relationship between genome size and …

Shrub-Interspace Dynamics Alter Relationships Between Microbial Community Composition And Belowground Ecosystem Characteristics, Rebecca E. Drenovsky, Z. T. Aanderud, M. I. Shuldman, J. H. Richards

Biology

In desert ecosystems, belowground characteristics are influenced chiefly by the formation and persistence of “shrub-islands of fertility” in contrast to barren plant interspaces. If soil microbial communities are exclusively compared between these two biogeochemically distinct soil types, the impact of characteristics altered by shrub species, especially soil C and N, are likely to be overemphasized and overshadow the role of other characteristics in structuring microbial composition. To determine how belowground characteristics influence microbial community composition, and if the relative importance of these characteristics shifts across the landscape (i.e., between and within shrub and interspace soils), changes in microbial communities across …

Weed-Biocontrol Insects Reduce Native-Plant Recruitment Through Second-Order Apparent Competition, Dean E. Pearson, Ragan M. Callaway

Biological Sciences Faculty Publications

Small-mammal seed predation is an important force structuring native-plant communities that may also influence exotic-plant invasions. In the intermountain West, deer mice (Peromyscus maniculatus) are prominent predators of native-plant seeds, but they avoid consuming seeds of certain widespread invasives like spotted knapweed (Centaurea maculosa). These mice also consume the biological-control insects Urophora spp. introduced to control C. maculosa, and this food resource substantially increases deer mouse populations. Thus, mice may play an important role in the invasion and management of C. maculosa through food-web interactions. We examined deer mouse seed predation and its effects on …

Toxic Introns And Parasitic Intein In Coxiella Burnetii: Legacies Of A Promiscuous Past, Rahul Raghavan, Linda D. Hicks, Michael F. Minnick

Biological Sciences Faculty Publications

The genome of the obligate intracellular pathogen Coxiella burnetii contains a large number of selfish genetic elements, including two group I introns (Cbu.L1917 and Cbu.L1951) and an intervening sequence that interrupts the 23S rRNA gene, an intein (Cbu.DnaB) within dnaB and 29 insertion sequences. Here, we describe the ability of the intron-encoded RNAs (ribozymes) to retard bacterial growth rate (toxicity) and examine the functionality and phylogenetic history of Cbu.DnaB. When expressed in Escherichia coli, both introns repressed growth, with Cbu.L1917 being more inhibitory. Both ribozymes were found to associate with ribosomes of Coxiella and E. coli. In addition, ribozymes significantly …

Phylogenetic Relationships Of Crown Conchs (Melongena Spp.): The Corona Complex Simplified, Kenneth Hayes, Stephen Karl

Department of Biology Faculty Publications

The larval stages of marine taxa are often assumed to have an overriding influence on the phylogeographical structure of a species as well as on rates of speciation. Phylogeographical disjunctions in high-dispersal marine taxa are generally attributed to historical events or contemporary ecological factors. The lack of genetic structure in low-dispersal marine taxa is often ascribed to rafting by juveniles, yet few studies discuss the effects of historical conditions. Around peninsular Florida, there are three species of the crown conch, Melongena, which have direct-developing, crawl-away larvae. One of these species, M. corona, is subdivided into three subspecies. We refer to …

Soluble Factors From Plasmodium Falciparum-Infected Erythrocytes Induce Apoptosis In Human Brain Vascular Endothelial And Neuroglia Cells, Winston Anderson

Department of Biology Faculty Publications

The severity of malaria is multi-factorial. It is associated with parasite-induced alteration in pro-inflammatory and anti-inflammatory cytokine and chemokine levels in host serum and cerebrospinal fluid. It is also associated with sequestration and cytoadherence of parasitized erythrocytes (pRBCs) in post-capillary venules and blood-brain barrier (BBB) dysfunction. The role of these factors in development of vascular injury and tissue damage in malaria patients is unclear. While some studies indicate a requirement for pRBC adhesion to vascular endothelial cells (ECs) in brain capillaries to induce apoptosis and BBB damage, others show no role of apoptosis resulting from adhesion of pRBC to EC. …

Sex- And Gonad-Affecting Scent Compounds And 3 Male Pheromones In The Rat, Jian-Xu Zhang, Lixing Sun, Jin-Hua Zhang, Zhi-Yong Feng

All Faculty Scholarship for the College of the Sciences

This study was aimed at identifying sex pheromones of the rat (Rattus norvegicus). We characterized the volatiles and semivolatiles of rat preputial gland and voided urine by using gas chromatography–mass spectrometry (GC–MS) and quantified them by their GC areas (abundances) and percentage of GC areas (relative abundances). Although all the compounds other than 4-heptanone and phenol detected were shared by males and females, the quantities for some of these sex-common compounds exhibited sexual dimorphism and decreased with gonadectomy. Thus, these compounds might be sex pheromones. Among them, squalene from preputial glands and 2-heptanone and 4-ethyl phenol from urine …

Shifts In Southern Wisconsin Forest Canopy And Understory Richness, Composition, And Heterogeneity, David A. Rogers, Thomas P. Rooney, Daniel Olson, Donald M. Waller

Biological Sciences Faculty Publications

We resurveyed the under- and overstory species composition of 94 upland forest stands in southern Wisconsin in 2002–2004 to assess shifts in canopy and understory richness, composition, and heterogeneity relative to the original surveys in 1949–1950. The canopy has shifted from mostly oaks (Quercus spp.) toward more mesic and shade-tolerant trees (primarily Acer spp.). Oak-dominated early-successional stands and those on coarse, nutrient-poor soils changed the most in canopy composition. Understories at most sites (80%) lost native species, with mean species density declining 25% at the 1-m² scale and 23.1% at the 20-m² scale. Woody species have increased …

The Indirect Effects Of Cheatgrass Invasion: Grasshopper Herbivory On Native Grasses Determined By Neighboring Cheatgrass, Julie Beckstead, Susan E. Meyer, Carol K. Augsperger

Biology Faculty Scholarship

Invasion biology has focused on the direct effects of plant invasion and has generally overlooked indirect interactions. Here we link theories of invasion biology and herbivory to explore an indirect effect of one invading species on associational herbivory (the effect of neighboring plants on herbivory) of native species. We studied a Great Basin shadscale (Atriplex confertifolia)-bunchgrass community in western Utah, U.S.A.This community is dominated by native bunchgrasses, invaded by cheatgrass (Bromus tectorum), and home to large populations of grasshoppers (Xanthippus corallipes and Melanoplus confusus). Observations of associational herbivory provided support for the attractant-source hypothesis for one of two native species …

The Yeast Aac2 Protein Exists In Physical Association With The Cytochrome Bc1-Cox Supercomplex And The Tim23 Machinery, Mary Kathryn Dienhart, Rosemary A. Stuart

Biological Sciences Faculty Research and Publications

The ADP/ATP carrier (AAC) proteins play a central role in cellular metabolism as they facilitate the exchange of ADP and ATP across the mitochondrial inner membrane. We present evidence here that in yeast (Saccharomyces cerevisiae) mitochondria the abundant Aac2 isoform exists in physical association with the cytochrome c reductase (cytochrome bc₁)-cytochrome c oxidase (COX) supercomplex and its associated TIM23 machinery. Using a His-tagged Aac2 derivative and affinity purification studies, we also demonstrate here that the Aac2 isoform can be affinity-purified with other AAC proteins. Copurification of the Aac2 protein with the TIM23 machinery can occur independently …