Biology Commons^™

Use Of Cre Recombinase And Sb Transposase To Engineer Transgenic Zebrafish, Jie Dong

All-Inclusive List of Electronic Theses and Dissertations

Current transgenesis has become easier for certain species due to the recent development of exogenous non site-specific recombination systems such as Sleeping Beauty (SB) transposon, and site-specific recombination systems such as Cre-loxP. Such recombination systems overcame two major problems caused by conventional transgenesis, position effect and copy number effect. SB is a reconstructed fish transposon that has shown to efficiently insert transgenes into heterologous mammalian chromosomes. The Cre-loxP system is frequently used to delete a given sequence from the genome or to target the integration of foreign DNA. The use of both systems in combination, however, has not yet been …

Ic138 Is A Wd-Repeat Dynein Intermediate Chain Required For Light Chain Assembly And Regulation Of Flagellar Bending, Triscia W. Hendrickson, Catherine A. Perrone, Paul Griffin, Kristin Wuichet, Joshua Mueller, Pinfen Yang, Mary E. Porter, Winfield S. Sale

Biological Sciences Faculty Research and Publications

Increased phosphorylation of dynein IC IC138 correlates with decreases in flagellar microtubule sliding and phototaxis defects. To test the hypothesis that regulation of IC138 phosphorylation controls flagellar bending, we cloned the IC138 gene. IC138 encodes a novel protein with a calculated mass of 111 kDa and is predicted to form seven WD-repeats at the C terminus. IC138 maps near the BOP5 locus, and bop5-1 contains a point mutation resulting in a truncated IC138 lacking the C terminus, including the seventh WD-repeat. bop5-1 cells display wild-type flagellar beat frequency but swim slower than wild-type cells, suggesting that bop5-1 is altered in …

Contractile Responses Of The Rat Gastrocnemius And Soleus Muscles To Isotonic Resistance Exercise, Kris M. Norenberg, Robert H. Fitts

Biological Sciences Faculty Research and Publications

Male rats were divided into control and weight-trained (WT) groups. WT rats performed squattype exercises twice daily, 5 days/wk, for 14 wk. They averaged 36 lifts/day, with an average weight of 555 g. Muscle-to-body weight ratio (mg/g) of the soleus (Sol) was not different from control, but it increased 11 and 6% in the gastrocnemius (Gast) and plantaris, respectively (P < 0.05). The normalized twitch tension of the in situ Sol was elevated by 21%, whereas single-skinned type I fibers from the Sol showed an increased rate constant of tension redevelopment (K_tr) but no other contractile adaptations to WT. In contrast, the Gast type I fibers showed an increase (P < 0.05) in maximal velocity of shortening (25%), peak power (15%), K_tr (18%), and normalized tension (7%). The K_tr and normalized tension of the Gast type IIa fibers increased by …

Density Effects On Growth, Survival And Diet Of June Sucker (Chasmistes Liorus): A Component Allee Effect In An Endangered Species., David Barrett Gonzalez

Theses and Dissertations

Density-dependence is considered one of the most important regulators of population growth, and it has been documented across a wide variety of species. Typically, population growth rate and components thereof decline with increasing density (i.e., negative density-dependence); however, in species that exhibit high population densities and social behavior, positive density-dependence (i.e., Allee effect) may occur at low density. June sucker, a federally endangered lake sucker endemic to Utah Lake, Utah, USA, occurred historically at high density, and it exhibits coordinated feeding behavior. These characteristics indicate a potential for the existence of an Allee effect at current low population densities. To …

Evolution And Phylogeny Of Basal Winged Insects With Emphasis On Mayflies (Ephemeroptera), Thomas H. Ogden

Theses and Dissertations

Ephemeroptera (mayflies) is a monophyletic group of semi-aquatic pterygote insects, comprising 3083 species, 376 genera, and 37 described families and are present on all continents, excluding Antarctica, being associated with freshwater and brackish water habitats. The order is unique among pterygote insects in possessing functional wings at the penultimate molt (subimago stage), prior to the full development of genitalia; in all other insects the presence of functional wings occurs only after the final molt. The purpose of this dissertation is to use molecular and morphological data, in order to investigate the position of the order Ephemeroptera among other insect orders, …

Reconstitution Of Copii Vesicle Fusion To Generate A Pre-Golgi Intermediate Compartment, Dalu Xu, Jesse C. Hay

Biological Sciences Faculty Publications

What is the first membrane fusion step in the secretory pathway? In mammals, transport vesicles coated with coat complex (COP) II deliver secretary cargo to vesicular tubular clusters (VTCs) that ferry cargo from endoplasmic reticulum exit sites to the Golgi stack. However, the precise origin of VTCs and the membrane fusion step(s) involved have remained experimentally intractable. Here, we document in vitro direct tethering and SNARE-dependent fusion of endoplasmic reticulum-derived COPII transport vesicles to form larger cargo containers. The assembly did not require detectable Golgi membranes, preexisting VTCs, or CON function. Therefore, COPII vesicles appear to contain all of the …

Evaluating Forensic Dna Evidence: Essential Elements Of A Competent Defense Review, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Evidence For And Characterization Of Ca2+ Binding To The Catalytic Region Of Arabidopsis Thaliana Phospholipase Dβ, Xuemin Wang

Biology Department Faculty Works

Most types of plant phospholipase D (PLD) require Ca2+ for activity, but how Ca2+ affects PLD activity is not well understood. We reported previously that Ca2+ binds to the regulatory C2 domain that occurs in the N terminus of the Ca2+-requiring PLDs. Using Arabidopsis thaliana PLDβ and C2-deleted PLDβ (PLDβcat), we now show that Ca2+ also interacts with the catalytic regions of PLD. PLDβcat exhibited Ca2+-dependent activity, was much less active, and required a higher level of Ca2+ than the full-length PLDβ. Ca2+ binding of the proteins was stimulated by phospholipids; phosphatidylserine was the most effective among those tested. Scatchard …

Identification And Phenotypic Characterization Of The Cell-Division Protein Cdpa, Eric Altermann, B. Logan Buck, Raul Cano, Todd R. Klaenhammer

Biological Sciences

Analysis of the automated computer annotation of the early draft phase genome of Lactobacillus acidophilus NCFM revealed the previously discovered S-layer gene slpA and an additional partial ORF with weak similarities to S-layer proteins. The entire gene was sequenced to reveal a 1799-bp gene coding for 599 amino acids with a calculated molecular mass of 64.8 kDa. No transcription or translation signals could be determined in close proximity to the 5′-region. However, a strong putative terminator with a free energy of −16.84 kcal/mol was identified directly downstream of the gene. A PSI-Blast analysis showed similarities to members of S-layer proteins, …

Pyruvate Formate Lyase And Acetate Kinase Are Essential For Anaerobic Growth Of Escherichia Coli On Xylose, A. Hansona, Y. Kim, Frank G. Healy, L. O. Ingram, K. T. Shanmugan

Biology Faculty Research

During anaerobic growth of bacteria, organic intermediates of metabolism, such as pyruvate or its derivatives, serve as electron acceptors to maintain the overall redox balance. Under these conditions, the ATP needed for cell growth is derived from substrate-level phosphorylation. In Escherichia coli, conversion of glucose to pyruvate yields 2 net ATPs, while metabolism of a pentose, such as xylose, to pyruvate only yields 0.67 net ATP per xylose due to the need for one (each) ATP for xylose transport and xylulose phosphorylation. During fermentative growth, E. coli produces equimolar amounts of acetate and ethanol from two pyruvates, and these …

Human Fetal, Cord Blood, And Adult Lymphocyte Progenitors Have Similar Potential For Generating B Cells With A Diverse Immunoglobulin Repertoire, Grant R. Kolar, Takafumi Yokota, Maria Isabel D. Rossi, Swapan K. Nath, J. Donald Capra

Biological Sciences Faculty Research & Creative Works

Several characteristics of the immunoglobulin (Ig) repertoire in fetuses and adults set them apart from each other. Functionally, this translates into differences in the affinity and effectiveness of the humoral immune response between adults and the very young. At least 2 possibilities could explain these differences: (1) fetal and adult lymphocyte progenitors differ significantly in their potential to form a diverse repertoire, and (2) factors extrinsic to the immunoglobulin locus are more influential to the character of the repertoire. To address this, we used nonobese diabetic-severe combined immunodeficient- β2 microglobulin knockout (NOD/SCID/β2m ^-/-) mice reconstituted with human B-cell progenitors …

Application Of Genotypic And Phenotypic Analyses To Commercial Probiotic Strain Identity And Relatedness, P. S. M. Yeung, Christopher L. Kitts, Phillip S. Tong, M. E. Sanders

Biological Sciences

Aims: The objective of this study was to generate strain-specific genomic patterns of a bank of 67 commercial and reference probiotic strains, with a focus on probiotic lactobacilli.
Methods and Results: Pulsed-field gel electrophoresis (PFGE) was used as the primary method for strain differentiation. This method was compared with carbohydrate fermentation analysis. To supplement visual comparison, PFGE patterns were analysed quantitatively by cluster analysis using unweighted pair group method with arithmetic averages. SmaI, NotI and XbaI were found to effectively generate clear and easy-to-interpret PFGE patterns of a range of probiotic strains. Some probiotic strains from different sources shared highly …

Sex Differences In Metabolic Rates In Field Crickets And Their Dipteran Parasitoids, Gita R. Kolluru, Mark A. Chappell, Marlene Zuk

Biological Sciences

Sex differences in metabolic rate (MR) can result from dimorphism in the performance of energetically demanding activities. Male crickets (Teleogryllus oceanicus) engage in costly calling and aggressive activity not performed by females. Consistent with this difference, we found higher maximal MR, factorial scope, and fat content in males than females. T. oceanicus song is also costly because it attracts the parasitoid fly Ormia ochracea. Parasitized crickets had reduced maximal MR consistent with a metabolic cost to harboring larvae. This cost was greater for females, either because females invest more heavily into reproduction at the expense of metabolic …

Alteration Of The Food Web Along The Antarctic Peninsula In Response To A Regional Warming Trend, Mark A. Moline, Herve Claustre, Thomas K. Frazer, Oscar Schofield, Maria Vernet

Biological Sciences

In the nearshore coastal waters along the Antarctic Peninsula, a recurrent shift in phytoplankton community structure, from diatoms to cryptophytes, has been documented. The shift was observed in consecutive years (1991–1996) during the austral summer and was correlated in time and space with glacial melt-water runoff and reduced surface water salinities. Elevated temperatures along the Peninsula will increase the extent of coastal melt-water zones and the seasonal prevalence of cryptophytes. This is significant because a change from diatoms to cryptophytes represents a marked shift in the size distribution of the phytoplankton community, which will, in turn, impact the zooplankton assemblage. …

Application Of Genotypic And Phenotypic Analyses To Commerical Probiotic Strain Identity And Relatedness, P.S.M. Yeung, C. L. Kitts, R. Cano, P. Tong

Biological Sciences

Aims: The objective of this study was to generate strain-specific genomic patterns of a bank of 67 commercial and reference probiotic strains, with a focus on probiotic lactobacilli.

Methods and Results: Pulsed-field gel electrophoresis (PFGE) was used as the primary method for strain differentiation. This method was compared with carbohydrate fermentation analysis. To supplement visual comparison, PFGE patterns were analysed quantitatively by cluster analysis using unweighted pair group method with arithmetic averages. SmaI, NotI and XbaI were found to effectively generate clear and easy-to-interpret PFGE patterns of a range of probiotic strains. Some probiotic strains from different sources …

The Effects Of Postfire Salvage Logging On Aquatic Ecosystems In The American West, J. R. Karr, Jj Rhodes, Gw Minshall, F. Richard Hauer, R. L. Beschta, C. A. Frissell, D. A. Perry

Biological Sciences Faculty Publications

Recent changes in the forest policies, regulations, and laws affecting public lands encourage postfire salvage logging, an activity that all too often delays or prevents recovery. In contrast, the 10 recommendations proposed here can improve the condition of watersheds and aquatic ecosystems.

Is There An Antipredator Blood-Squirting Defense In The Bull Horned Lizard, Phrynosoma Taurus?, George Middendorf

Department of Biology Faculty Publications

No abstract provided.

Filarial Genomics, Steven A. Williams

Biological Sciences: Faculty Publications

No abstract provided.

Law, Evolution, And The Brain: Applications And Open Questions, Owen D. Jones

Vanderbilt Law School Faculty Publications

This essay discusses several issues at the intersection of law and brain science. If focuses principally on ways in which an improved understanding of how evolutionary processes affect brain function and human behavior may improve law's ability to regulate behavior. It explores sample uses of such "evolutionary analysis in law" and also raises questions about how that analysis might be improved in the future. Among the discussed uses are: 1) clarifying cost-benefit analyses; 2) providing theoretical foundation and potential predictive power; 3) assessing comparative effectiveness of legal strategies; and 4) revealing deep patterns in legal architecture. Throughout, the essay emphasizes …

Patterns Of Fitness And Fluctuating Asymmetry Across A Broad Hybrid Zone, Mitchell B. Cruzan

Biology Faculty Publications and Presentations

We estimated levels of developmental instability in leaves, as indicated by fluctuating asymmetry (i.e., random deviations from perfect bilateral symmetry), across a broad hybrid zone between two taxa in the Piriqueta caroliniana complex. Previous studies have indicated that this hybrid zone was initiated in southern Florida and has expanded northward. We found that plants from the hybrid zone generally had higher levels of leaf developmental instability than plants from allopatric regions, but the increase in asymmetry was not substantial. Although it is usually assumed that developmental instability is associated with lower fitness, these Piriqueta hybrids from central Florida are similar …

The Yeast Rrna Biosynthesis Factor Ebp2p Is Also Required For Efficient Nuclear Division, Costin N. Ionescu, Sofia Origanti, Michael A. Mcalear

Biological Sciences Faculty Research and Publications

Molecular genetic analysis of the yeast Ebp2 protein has revealed that it is an essential, nucleolar protein that functions in the rRNA biosynthesis pathway. Temperature-sensitive ebp2-1 mutants are defective in the processing of the 27 SA precursor rRNA, and the point substitutions that disrupt this activity cluster towards the central, more highly conserved region of the Ebp2 protein. We report here that other ebp2 mutants exhibit deficiencies associated with defects in chromosome segregation. Yeast cells bearing a 50 amino acid C-terminal truncation allele (ebp2ΔC50) display a slow-growth phenotype and exhibit an increased percentage of cells with …

Evaluating Forensic Dna Evidence, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Forensic Dna Evidence: Collection, Mixtures, And Degradation, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Relationship Among Genes Conferring Partial Resistance To Leaf Rust (Puccinia Triticina) In Wheat Lines Ci 13227 And L-574-1, Jeffrey Lehman

Biology and Earth Science Faculty Scholarship

This study describes the segregation of genes for resistance to the fungus Puccinia triticina in a cross between partially resistant wheat lines L-574-1 and CI 13227 with two and four genes for resistance, respectively. The objectives of this study were to use parental, F1, F2, and backcross populations to quantify maternal effects, degree of dominance, and transgressive segregation, and to determine whether CI 13227 and L-574- 1 share any resistance genes for long latent period or small uredinia. In two experiments conducted in the greenhouse, the uppermost leaf of adult wheat plants was inoculated prior to heading with P. triticina. …

Two Drosophila Suppressors Of Cytokine Signaling (Socs) Differentially Regulate Jak And Egfr Pathway Activities, Jason S. Rawlings, Gabriela Rennebeck, Susan M.W. Harrison, Rongwen Xi, Douglas A. Harrison

Biology Faculty Publications

BACKGROUND: The Janus kinase (JAK) cascade is an essential and well-conserved pathway required to transduce signals for a variety of ligands in both vertebrates and invertebrates. While activation of the pathway is essential to many processes, mutations from mammals and Drosophila demonstrate that regulation is also critical. The SOCS (Suppressor Of Cytokine Signaling) proteins in mammals are regulators of the JAK pathway that participate in a negative feedback loop, as they are transcriptionally activated by JAK signaling. Examination of one Drosophila SOCS homologue, Socs36E, demonstrated that its expression is responsive to JAK pathway activity and it is capable of downregulating …

Skeletal Muscle Fiber Atrophy: Altered Thin Filament Density Changes Slow Fiber Force And Shortening Velocity, Danny A. Riley, J. L. W. Bain, Janell Romatowski, Robert H. Fitts

Biological Sciences Faculty Research and Publications

Single skinned fibers from soleus and adductor longus (AL) muscles of weight-bearing control rats and rats after 14-day hindlimb suspension unloading (HSU) were studied physiologically and ultrastructurally to investigate how slow fibers increase shortening velocity (V₀) without fast myosin. We hypothesized that unloading and shortening of soleus during HSU reduces densities of thin filaments, generating wider myofilament separations that increase V₀ and decrease specific tension (kN/m²). During HSU, plantarflexion shortened soleus working length 23%. AL length was unchanged. Both muscles atrophied as shown by reductions in fiber cross-sectional area. For AL, the 60% atrophy …

A Comparison Of Behavioural Change In Drosophila During Exposure To Thermal Stress, Angel G. Fasolo, Robert A. Krebs

Biological, Geological, and Environmental Faculty Publications

In order to understand how adaptive tolerance to stress has evolved, we compared related species and populations of Drosophila for a variety of fitness relevant traits while flies directly experienced the stress. Two main questions were addressed. First, how much variation exists in the frequency of both courtship and mating among D. melanogaster, D. simulans, and D. mojavensis when each are exposed to a range of temperatures? Second, how does variation in these same behaviours compare among four geographically isolated populations of D. mojavensis, a desert species with a well defined ecology? Our hierarchical study demonstrated that mating success under …

Correction [To Maurakis And Grimes Article, V. 54, #3&4]

Virginia Journal of Science

This page is a correction to an article by Eugene G. Maurakis and David V. Grimes: Predicting Fish Species Diversity in Lotic Freshwaters of Greece, published in Virginia Journal of Science Volume 54, numbers 3 and 4. Amended table 2a owed to a printing corruption.

Subterranean Loss And Gain Of Water In Mountain Lake, Virginia: A Hydrologic Model, Martin Jansons, Bruce C. Parker, Jacob E. Waller

Virginia Journal of Science

Mountain Lake, Virginia is a small, unique, oligotrophic, subalpine ecosystem in the southern Appalachians. Previous studies have disclosed that this lake has manifested periodic prolonged low water levels during the several thousand years of its existence. The most recent low water level occurred during the drought years of 1999-2002. Measurements of lake level, precipitation, and other meteorological data including calculated evapotranspiration in the lake basin from 2/19/02 to 8/31/03 have enabled estimation of net subterranean water losses presumably through cracks between Clinch sandstone boulders and/or the recently discovered deep hole at the northwest end of Mountain Lake. These net losses …

Germination Of Silene Regia Seeds From Four Sites In Lawrence County, Illinois, Following Scarification Or Stratification, Nicolette L. Flocca, Janice M. Coons, Henry R. Owen, Brian J. Fischer, Bob E. Edgin

Faculty Research & Creative Activity

Silene regia Sims is an endangered prairie forb in Illinois where small isolated colonies are scattered. In La·wrence County, two sites (Allison Prairie and Chauncey Marsh) have fewer plants (6-23) than two other sites (Cmmty Road and Cemetery) with 26-45 plants. Information on seed germination in these isolated colonies is needed. Our goal was to evaluate seed germination of S. regia from colonies in Lawrence County, illinois. S. regia fruits were collected from these four sites on August 9 and 19, 1999. Seeds were scarified by cutting the seed coat, or they were stratified at 2 C for 12 or …