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Spatial And Temporal Dynamics Of Lekking Behavior And Female Mate Choice In The Blue-Crowned Manakin (Lepidothrix Coronata, Aves: Pipridae), Renata Duraes Ribeiro

Dissertations

In lekking species, males aggregate at display grounds (?leks?) that females visit to copulate. Lekking systems are non-resource-based and males vary widely in reproductive output. This dissertation investigates how spatial and temporal factors influence lekking dynamics and female mate choice in the blue-crowned manakin Lepidothrix coronata. The first chapter deals with spatial dynamics of lekking behavior, and investigates whether leks are formed by the establishment of males on sites of high female density (?hotspot hypothesis?). Predictive maps of female spatial distribution were built based on field data and contrasted to the lek distribution. Leks were located in sites where males …

Grassland Birds In Natural And Cultivated Grasslands In The Northern Campos Of Uruguay: Diversity Patterns, Responses To Vegetation Structure, And Nest Survival, Adrian Bruno Azpiroz

Dissertations

Grassland bird populations are declining in many regions of the world as a consequence of habitat modification but research efforts have been concentrated in North America and Europe. In the Neotropics, however, many aspects of grassland bird ecology remain virtually unexplored. The objective of this study was to examine the effects of habitat modification on the distribution, abundance, and reproductive success of grassland birds in the Northern Campos of Uruguay. The study focused on birds that inhabit four grassland habitats which differed in terms of agricultural management in the Northern Campos of Uruguay. First, distance sampling was used to characterize …

A Developmental, Phylogenetic And Taxonomic Study On The Moss Genus Taxithelium Mitt. (Pylaisiadelphaceae), Paulo Saraiva Camara

Dissertations

The family Sematophyllaceae is probably the most diverse Hypnales in the tropics and one of the most complex and taxonomically confused. This thesis comprises three parts: 1, a micromorphological study of papilla development in Taxithelium and relatives; 2, a phylogenetic study of Taxithelium; and 3, a revision of Taxithelium subgenus Vernieri. 1. I present data on the structure and development of leaf cell papillae in different Sematophyllaceae. Two kinds of papillae are recognized. One is dome-shaped to conical tapering to a firmly rounded apex (?conical?), whereas the other presents a more flaccid, baggy appearance, and is often flat-topped and wider …

Population Genetics Of Island Endemics: Neutral And Major Histocompatibility Loci, Jennifer Lynn Bollmer

Dissertations

Island archipelagoes are ideal for the study of microevolutionary forces due to their multiple, closely related but geographically disjunct populations. I used both neutral and major histocompatibility complex (MHC) loci to determine the population genetic structures of bird species endemic to the Galapagos Islands. MHC molecules recognize foreign pathogens in the body, and these loci are known for their high degree of genetic variability maintained by natural selection. Small island populations are predicted to have reduced genetic variability due to the effects of genetic drift; however, selection may be strong enough to prevent the loss of variability at MHC loci. …

Darwin At The Drugstore? Testing The Biological Fitness Of Antibiotic Resistant Bacteria, Alan L. Gillen, Sarah Anderson

Faculty Publications and Presentations

The issue of antibiotic resistance in bacteria is growing. For example, methicillin-resistant Staphylococcus aureus (MRSA) is a leading human pathogen. New strains of MRSA are resistant to methicillin and numerous other antibiotics, placing the patient in significant danger. Indeed, the Centers for Disease Control revealed in 2007 that the number of deaths due to MRSA exceeded that of AIDS in the United States. It is no wonder that antibiotic resistance is one of the most significant and important health care issues. The ability of bacterial pathogens to evade traditional antibiotics is faster than the drug makers’ ability to make new …

Effect Of Rho Kinase Inhibition On Alpha-Actin Remodeling In The Contracting A7r5 Smooth Muscle Cell, Suzette Pike

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 Suzette Pike on July 11, 2008,

Unraveling Protein Networks With Power Graph Analysis, Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder

Faculty Publications, Computer Science

Networks play a crucial role in computational biology, yet their analysis and representation is still an open problem. Power Graph Analysis is a lossless transformation of biological networks into a compact, less redundant representation, exploiting the abundance of cliques and bicliques as elementary topological motifs. We demonstrate with five examples the advantages of Power Graph Analysis. Investigating protein-protein interaction networks, we show how the catalytic subunits of the casein kinase II complex are distinguishable from the regulatory subunits, how interaction profiles and sequence phylogeny of SH3 domains correlate, and how false positive interactions among high-throughput interactions are spotted. Additionally, we …

Do Female Hyaenas Choose Mates Based On Tenure?, Heather E. Watts

Biology Faculty Works

In their investigation into whether female mate-choice drives male dispersal, Höner et al.argue that female spotted hyaenas (Crocuta crocuta) prefer mates whose tenure in the social group is less than the females’ age, to avoid paternal incest, and suggest that male dispersal reflects this preference. However, we are not persuaded that females choose mates on the basis of tenure because Höner et al. overlook the alternative hypothesis that dispersal status itself is important in female mate-choice, such that females prefer immigrants over natal males. Like mate-choice based on tenure, choice based on dispersal status reduces the risk of incest.

Genomic Analysis Of Gene Regulation Complexity, Brandon Barker, Jim Lund

Biology Presentations

With multiple metazoan genomes in each family being sequenced promoter analysis is becoming a useful tool in genomic analysis. Aligning the promoter regions in the DNA of C. elegans and C. briggsae identifies conserved promoter elements. While not all promoter elements are conserved and not all conserved regions are promoter elements, we find that conservation is a useful method for determining promoter complexity. Promoter complexity identifies which genes have particularly interesting regulation, identifying gene groups with a strong promoter complexity signal and cases where a gene's promoter complexity differs from the group's promoter complexity.

We identify potential promoter sequence by …

Identifying Regulatory Elements And Gene Boundaries With Comparative Genomic Sequence Analysis, Jim Lund

Biology Presentations

For several groups of organisms multiple genomes have been sequenced either completely or to the unfinished shotgun sequencing stage. Comparative sequence analysis can identify functional sequence elements for pairs of organisms that diverged far enough in the past to allow mutational drift of non-conserved sequences. While analysis of a pair of genomes identifies many of these functional elements adding additional genomes allows additional information to be elicited.

Additional conserved sequence elements are identified as additional genomes are analyzed. These conserved sequence elements are often regulatory elements although they are difficult to classify with in silico analysis. For an individual gene, …

Phytotoxic Effects Of (+/-)-Catechin In Vitro, In Soil, And In The Field, Inderjit, Jarrod L. Pollock, Ragan M. Callaway, William E. Holben

Biological Sciences Faculty Publications

Background: Exploring the residence time of allelochemicals released by plants into different soils, episodic exposure of plants to allelochemicals, and the effects of allelochemicals in the field has the potential to improve our understanding of interactions among plants. Methodology/Principal Findings: We conducted experiments in India and the USA to understand the dynamics of soil concentrations and phytotoxicity of (+/-)-catechin, an allelopathic compound exuded from the roots of Centaurea maculosa, to other plants in vitro and in soil. Experiments with single and pulsed applications into soil were conducted in the field. Experimental application of (+/-)-catechin to soils always resulted in concentrations …

Computational Design Of Orthogonal Ribosomes, Lon Chubiz, Christopher Rao

Biology Department Faculty Works

Orthogonal ribosomes (o-ribosomes), also known as specialized ribosomes, are able to selectively translate mRNA not recognized by host ribosomes. As a result, they are powerful tools for investigating translational regulation and probing ribosome structure. To date, efforts directed towards engineering o-ribosomes have involved random mutagenesisbased approaches. As an alternative, we present here a computational method for rationally designing o-ribosomes in bacteria. Working under the assumption that base-pair interactions between the 16S rRNA and mRNA serve as the primary mode for ribosome binding and translational initiation, the algorithm enumerates all possible extended recognition sequences for 16S rRNA and then chooses those …

Protecting Migration Corridors: Challenges And Optimism For Mongolian Saiga, Joel Berger, Julie K. Young, Kim Murray Berger

Biological Sciences Faculty Publications

No abstract provided.

Effects Of Native Species Diversity And Resource Additions On Invader Impact, John L. Maron, Marilyn Marler

Biological Sciences Faculty Publications

Theory and empirical work have demonstrated that diverse communities can inhibit invasion. Yet, it is unclear how diversity influences invader impact, how impact varies among exotics, and what the relative importance of diversity is versus extrinsic factors that themselves can influence invasion. To address these issues, we established plant assemblages that varied in native species and functional richness and crossed this gradient in diversity with resource (water) addition. Identical assemblages were either uninvaded or invaded with one of three exotic forbs: spotted knapweed (Centaurea maculosa), dalmatian toadflax (Linaria dalmatica), or sulfur cinquefoil (Potentilla recta). To determine impacts, we measured the …

Is The Effect Of Forest Structure On Bird Diversity Modified By Forest Productivity?, Jacob P. Verschuyl, Andrew J. Hansen, David B. Mcwethy, Rex Sallabanks, Richard L. Hutto

Biological Sciences Faculty Publications

Currently, the most common strategy when managing forests for biodiversity at the landscape scale is to maintain structural complexity within stands and provide a variety of seral stages across landscapes. Advances in ecological theory reveal that biodiversity at continental scales is strongly influenced by available energy (i.e., climate factors relating to heat and light and primary productivity). This paper explores how available energy and forest structural complexity may interact to drive biodiversity at a regional scale.

We hypothesized that bird species richness exhibits a hump-shaped relationship with energy at the regional scale of the northwestern United States. As a result, …

African Genetic Diversity: Implications For Human Demographic History, Modern Human Origins, And Complex Disease Mapping, Michael Campbell, Sarah Tishkoff

Department of Biology Faculty Publications

Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the …

A Microcosm Of The Biomedical Research Experience For Upper-Level Undergraduates, Daryl D. Hurd

Biology Faculty/Staff Publications

The skill set required of biomedical researchers continues to grow and evolve as biology matures as a natural science. Science necessitates creative yet critical thinking, persuasive communication skills, purposeful use of time, and adeptness at the laboratory bench. Teaching these skills can be effectively accomplished in an inquiry-based, active-learning environment at a primarily undergraduate institution. Cell Biology Techniques, an upper-level cell biology laboratory course at St. John Fisher College, features two independent projects that take advantage of the biology of the nematode Caenorhabditis elegans, a premier yet simple model organism. First, students perform a miniature epigenetic screen for novel phenotypes …

Phylogeography And Geographical Variation Of Behavioral And Morphological Characteristics In Paruroctonus Boreus, Abraham Miller

Biology Dissertations - Archive

Specimens of Paruroctonus boreus were collected from twenty-four sites to assess the geographic variation in behavioral, morphological and molecular traits. Statistical analyses showed males demonstrated a positive response to females from the same population but not females from different populations, and that males exhibit a negative response to males from the same population. Pectine morphology was measured with SEM and demonstrated sexual dimorphism among and within populations. This difference was most apparent in mature individuals. Sequence data from 16S and COI genes suggest there is structure among the populations but this structure does not support a north and south clades …

Promoter Library Designed For Fine-Tuned Gene Expression In Pichia Pastoris, Franz S. Hartner, Claudia Ruth, David Langenegger, Sabrina N. Johnson, Petr Hyka, Geoff P. Lin-Cereghino, Joan Lin-Cereghino, Karin Kovar, James Cregg, Anton Glieder

College of the Pacific Faculty Articles

Although frequently used as protein production host, there is only a limited set of promoters available to drive the expression of recombinant proteins in Pichia pastoris. Fine-tuning of gene expression is often needed to maximize product yield and quality. However, for efficient knowledge-based engineering, a better understanding of promoter function is indispensable. Consequently, we created a promoter library by deletion and duplication of putative transcription factor-binding sites within the AOX1 promoter (P_AOX1) sequence. This first library initially spanned an activity range between ∼6% and >160% of the wild-type promoter activity. After characterization of the promoter library employing …

Species Limits And Phylogenetic Systematic Of The Diurnal Geckos Of The Genus Gonatodes (Squamata: Sphaerodactylidae), Walter E. Schargel

Biology Dissertations - Archive

The genus Gonatodes (family Sphaerodactylidae) is a diverse of group of about 20 species currently recognized of mostly diurnal geckos that are collectively distributed from southern Mexico to Brazil and Bolivia, and also including most of the Caribbean Islands. The systematics of this group remains poorly studied with published contributions limited mostly to the original species descriptions, natural history notes, and a recent, yet largely incomplete, molecular phylogeny. In this work, several contributions to the systematics of this genus are made. The first chapter is a general introduction to the group. Chapter 2 is a phylogeographic study of the G. …

How Herbivores Affect Plant Growth, Community Structure And Litter Decomposition In Alaskan Tundra: Implications For Responses To Climate Change, David R. Johnson

Biology Dissertations - Archive

Increasing atmospheric carbon dioxide (CO2) concentrations have caused higher air temperatures in the Arctic. Because arctic organisms are temperature limited, warmer conditions lead to higher decomposition and nutrient cycling rates by soil microorganisms resulting in positive feedbacks; more CO2 is released from warmer soils thus increasing global atmospheric CO2 concentrations. Higher decomposition and nutrient cycling rates increase soil nutrient availability for plants resulting in increased net primary productivity (NPP) and shifts in community structure. If these "warmer" communities contain more woody shrubs, they may store more carbon in plant tissue, potentially offsetting increases in CO2 from decomposition. However, little is …

Proteasomal Gene Duplications And Recruitment Of Testis Specific Expression In Drosophila, Mehran Sorourian

Biology Theses - Archive

Proteasome is a large multisubunit complex that degrades ubiquitinated proteins in a highly regulated manner in all eukaryotes. Two subcompartments of this subunit are the 19Scap and the 20S core particle with 19S acting as regulatory subunit, it attaches at both ends of the 20Score particle harboring the catalytic domains. In D. melanogaster one third of the genes encoding for this subunit were recognized to have many male specific duplicates. In this work, we make use of the new 12 genomes sequences and show that the majority of the genes encoding for the 20S particle gave rise to at least …

The Control Of Gene Expression By High Light Stress In Cyanobacteria Through The Apparent Two-Component Nbls-Rpab Signal Transduction Pair, Anthony David Kappell

Biology Dissertations - Archive

In nature photosynthetic organisms including cyanobacteria are dependent upon their ability to acclimate to changes in environmental conditions including light and nutrient levels. The NblS sensor kinase of the cyanobacterium Synechococcus elongatus PCC 7942 regulates gene expression in response to a number of stress conditions including high-intensity light and nutrient limitation. NblS is known as DspA or Hik33 in the cyanobacterium Synechocystis PCC 6803. We determined that the high light-inducible hliA gene from S. elongatus is under negative control through NblS. We have identified the High Light Regulatory 1 (HLR1) sequence (two direct repeats of (G/T)TTACA(T/A)(T/A) separated by two nucleotides) …

Mojave Applied Ecology Notes Summer 2008, Doug Merkler, Scott R. Abella, Dianne N. Bangle, Donovan J. Craig, Jessica E. Spencer, Alex Suazo

Mojave Applied Ecology Notes

Soil climate project, rare plant monitoring, JFS update, granivory and Sahara mustard

Weak Competition Among Tropical Tree Seedlings: Implications For Species Coexistence, C.E. Timothy Paine, Kyle E. Harms, Stefan A. Schnitzer, Walter P. Carson

Biological Sciences Faculty Research and Publications

The intensity of competition among forest tree seedlings is poorly understood, but has important ramifications for their recruitment and for the maintenance of species diversity. Intense competition among seedlings could allow competitively dominant species to exclude subordinate species. Alternatively, the low density and small stature of forest tree seedlings could preclude intense interseedling competition. In this case, other processes, such as size‐asymmetric competition with adults, interactions with consumers, or neutral dynamics would prevail as those structuring the forest understory. We tested the intensity of, and potential for, intraspecific competition among tree seedlings of three species (Brosimum alicastrum, Matisia …

Dune And Vegetation Stability At South Padre Island, Texas, United States Of America, Frank W. Judd, Kenneth R. Summy, Robert I. Lonard, Ruben A. Mazariegos

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Padre Island is the longest of five barrier islands occurring along the Texas Gulf Coast. South Padre Island is separated from the northern two-thirds of the island by the Mansfield Channel. The composition and pattern of vegetation on South Padre Island are relatively well known, but data on the interrelationship of dune and vegetation stability are lacking. We hypothesized that (1) there should be an inverse relationship between elevation change and percent cover on transects across the nearshore dunes of South Padre Island; and (2) percent cover, species composition, and species importance should be most stable where elevation change was …

Species Limits And Phylogeography Of North American Cricket Frogs (Acris: Hylidae), Tony Gamble, Peter B. Berendzen, H. Bradley Shaffer, David E. Starkey, Andrew M. Simons

Biological Sciences Faculty Research and Publications

Cricket frogs are widely distributed across the eastern United States and two species, the northern cricket frog (Acris crepitans) and the southern cricket frog (A. gryllus) are currently recognized. We generated a phylogenetic hypothesis for Acris using fragments of nuclear and mitochondrial genes in separate and combined phylogenetic analyses. We also used distance methods and fixation indices to evaluate species limits within the genus and the validity of currently recognized subspecies of A. crepitans. The distributions of existing A. crepitans subspecies, defined by morphology and call types, do not match the distributions of evolutionary lineages recovered using …

Out Of The Blue: A Novel, Trans‐Atlantic Clade Of Geckos (Gekkota, Squamata), Tony Gamble, Aaron M. Bauer, Eli Greenbaum, Todd R. Jackman

Biological Sciences Faculty Research and Publications

Phylogenetic relationships among gekkotan lizards were estimated from five nuclear protein-coding genes in separate and combined analyses using maximum parsimony, maximum likelihood and Bayesian analyses. All analyses recovered a monophyletic trans-Atlantic gecko clade (Phyllodactylidae) consisting of the genera Asaccus, Haemodracon, Homonota, Phyllodactylus, Phyllopezus, Ptyodactylus, Tarentola and Thecadactylus. No other phylogenetic or taxonomic hypotheses have proposed linking these genera, which have been consistently grouped with other taxa outside of the clade. In this paper, we determine the relationships of this new clade to other major gekkotan groups, evaluate previous phylogenetic hypotheses regarding constituent members of this novel clade, and critically …

Cloning Of The Neurodegeneration Gene Drop-Dead And Characterization Of Additional Phenotypes Of Its Mutation, Edward M. Blumenthal

Biological Sciences Faculty Research and Publications

Mutations in the Drosophila gene drop-dead (drd) result in early adult lethality and neurodegeneration, but the molecular identity of the drd gene and its mechanism of action are not known. This paper describes the characterization of a new X-linked recessive adult-lethal mutation, originally called lot's wife (lwf¹) but subsequently identified as an allele of drd (drd^lwf); drd^lwf mutants die within two weeks of eclosion. Through mapping and complementation, the drd gene has been identified as CG33968, which encodes a putative integral membrane protein of unknown function. The drd^lwf allele is associated …

Reproductive And Social Dynamics Of A Lek Breeding Bird, Thomas Brandt Ryder

Dissertations

Sociality and the unequal apportionment of reproductive success among social individuals is a common characteristic of many vertebrate taxa. To date, our understanding of what factors drive high variance in reproductive success (i.e., intra vs. inter-sexual selection) and which male attributes contribute to that variance, are still fragmentary for most species. Moreover, how social structure interacts with individual behavior and fitness remains understudied despite its potential importance to the evolution of cooperation. This dissertation research focused on understanding this complex synergistic interplay between social and reproductive dynamics in a lek-breeding bird, the wire-tailed manakin. The first chapter examines the complex …