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The Dynamic Evolutionary History Of The Bananaquit (Coereba Flaveola) In The Caribbean Revealed By A Multigene Analysis, Eva Bellemain, Eldredge Bermingham, Robert Ricklefs

Biology Department Faculty Works

BackgroundThe bananaquit (Coereba flaveola) is a small nectivorous and frugivorous emberizine bird (order Passeriformes) that is an abundant resident throughout the Caribbean region. We used multi-gene analyses to investigate the evolutionary history of this species throughout its distribution in the West Indies and in South and Middle America. We sequenced six mitochondrial genes (3744 base pairs) and three nuclear genes (2049 base pairs) for forty-four bananaquits and three outgroup species. We infer the ancestral area of the present-day bananaquit populations, report on the species' phylogenetic, biogeographic and evolutionary history, and propose scenarios for its diversification and range expansion.ResultsPhylogenetic concordance between …

The Plant Ontology Database: A Community Resource For Plant Structure And Developmental Stages Controlled Vocabulary And Annotations, Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth Kellogg, Susan Mccouch, Anuradha Pujar, Leonore Reiser, Seung Rhee, Martin Sachs, Mary Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Felipe Zapata, Doreen Ware

Biology Department Faculty Works

The Plant Ontology Consortium (POC, http://www.plantontology.org ) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC's principles, existing software and database structure. Over the past year, POC …

Puf1p Acts In Combination With Other Yeast Puf Proteins To Control Mrna Stability, Wendy Olivas, Randi Ulbricht

Biology Department Faculty Works

The eukaryotic Puf proteins bind 3′ untranslated region (UTR) sequence elements to regulate the stability and translation of their target transcripts, and such regulatory events are critical for cell growth and development. Several global genome analyses have identified hundreds of potential mRNA targets of the Saccharomyces cerevisiae Puf proteins; however, only three mRNA targets for these proteins have been characterized thus far. After direct testing of nearly 40 candidate mRNAs, we established two of these as true mRNA targets of Puf-mediated decay in yeast, HXK1 and TIF1. In a novel finding, multiple Puf proteins, including Puf1p, regulate both of these …

The Development Of Caching Behavior, Cache Site And Cache Item Defense Tactics, And Cache Site And Cache Item Sharing In Orphaned Fledgling Blue Jays (Cyanocitta Cristata) At A Songbird Rehabilitation Center, Deanna Martinez

Master's Theses and Doctoral Dissertations

One of the primary goals of songbird rehabilitators is to promote controllable factors that increase survivorship in orphaned songbirds upon to release. As caching serves an important function in corvid life, this study sought to determine if this behavior would develop with or without outside input. Eight orphaned blue jays (consisting of both hatchlings and nestlings) were brought into the care of the Bird Center of Washtenaw County, Inc. in Ann Arbor, Michigan. Birds were videotaped and observed for the development of caching behavior, cache item and cache site sharing, and cache defense tactics. Caching behavior and cache defense tactics …

Estimating Maximum Performance: Effects Of Intraindividual Variation, Stephen C. Adolph, Trevor Pickering '05

All HMC Faculty Publications and Research

Researchers often estimate the performance capabilities of animals using a small number of trials per individual. This procedure inevitably underestimates maximum performance, but few studies have examined the magnitude of this effect. In this study we explored the effects of intraindividual variation and individual sample size on the estimation of locomotor performance parameters. We measured sprint speed of the lizard Sceloporus occidentalis at two temperatures (20 degrees C and 35 degrees C), obtaining 20 measurements per individual. Speed did not vary temporally, indicating no training or fatigue effects. About 50% of the overall variation in speed at each temperature was …

New And Current Microbiological Tools For Ecosystem Ecologists: Towards A Goal Of Linking Structure And Function, Rebecca E. Drenovsky, Kevin P. Ferris, Katharine M. Batten, Krassimira Hristova

Biology

Interest in the relationships between soil microbial communities and ecosystem functions is growing with increasing recognition of the key roles microorganisms play in a variety of ecosystems. With a wealth of microbial methods now available, selecting the most appropriate method can be daunting, especially to those new to the field of microbial ecology. In this review, we highlight those methods currently used and most applicable to ecological studies, including assays to study various aspects of the carbon and nitrogen cycles (e.g., pool dilution, acetylene reduction, enzyme analyses, among others), methods to assess microbial community composition (e.g., phospholipid fatty acid analysis …

Mutagenesis Of The Tal Gene-Encoding Transaldolase In The Cyanobacterium, Anabaena Sp. Pcc7120, Haydar Karakaya, Nicholas H. Mann

Turkish Journal of Biology

The transaldolase gene (tal) of Anabaena sp. PCC7120 was interrupted by the insertion of the interposon W. Transaldolase assays showed that the tal mutant strain possessed the same activity as the wild-type, indicating that the second copy of the gene complements the enzyme activity. Being coded by a gene (zwf) downstream of tal and probably in the same operon, glucose-6-phosphate dehydrogenase (G6PDH) activity was also analysed. Only 34% of wild-type G6PDH activity was retained in the tal mutant strain. This may have due to the polar affect of tal mutation on the transcription of the zwf gene. Growth of the …

Morphology Of The Inner And Peripheral Ear Of The Loricariid Catfish Pterygoplichthys Gibbiceps K., Brian David Rogers

Mahurin Honors College Capstone Experience/Thesis Projects

The morphology of the peripheral and inner ear structures was studied in the loricariid catfish Pterygoplichthys gibbiceps. Specimens (n=6) were preserved in fixative (4% paraformaldehyde, 2% glutaraldehyde in 0.1M phosphate buffer) and dissected for examination of the gross morphology (using light microscopy) and ultrastructure of the auditory sensory epithelia (using scanning electron microscopy). One additional specimen was cleaned in a dermestid beetle colony in order to examine the osteology of the skull. The swim bladder of P. gibbiceps is divided along the midline of the fish into two reduced but equal lobes residing in two laterally oriented bony encapsulations. Immediately …

What Constitutes A Natural Fire Regime? Insight From The Ecology And Distribution Of Coniferous Forest Birds In North America, Richard L. Hutto, Courtney J. Conway, Victoria A. Saab, Jeffrey R. Walters

Biological Sciences Faculty Publications

Bird species that specialize in the use of burned forest conditions can provide insight into the prehistoric fire regimes associated with the forest types that they have occupied over evolutionary time. The nature of their adaptations reflects the specific post-fire conditions that occurred prior to the unnatural influence of humans after European settlement. Specifically, the post-fire conditions, nest site locations, and social systems of two species (Bachman's sparrow [Aimophila aestivalis] and red-cockaded woodpecker [Picoides borealis]) suggest that, prehistorically, a frequent, low-severity fire regime characterized the southeastern pine system in which they evolved. In contrast, the patterns …

Experimental Confirmation Of Protandric Simultaneous Hermaphroditism In A Caridean Shrimp Outside Of The Genus Lysmata, Helio Laubenheimer, Andrew L. Rhyne

Arts & Sciences Faculty Publications

Caridean shrimps display a variety of sexual systems including gonochorism and various forms of protandry but rarely simultaneous hermaphroditism. Protandric simultaneous hermaphroditism (PSH) has thus far only been demonstrated in the genus Lysmata. The first report of simultaneous hermaphroditism in a caridean shrimp was with Exhippolysmata ensirostris. However, this was not confirmed, since this species was also considered to be strictly protandric. Therefore, inconclusive results about this species’ true sexual system led us to examine Exhippolysmata oplophoroides. Mating between female phase individuals resulted in successful spawning, embryonic development and hatching of viable larvae. Furthermore, we have confirmed that this species …

Cholinergic Neurons Regulate And Utilize Gdnf Secreted By C2c12 Skeletal Muscle Cells In Culture, John-Mary Vianney, John Spitsbergen

Biological Sciences Faculty and Graduate Student Research

Glialcell line-derived neurotrophicfactor (GDNF) has been regarded as a potent survival factor for a subpopulation of neurons. It has been shown that GDNF expression is upregulated in skeletal muscle of patients with early stage of neuromuscular diseases such as amyotrophic lateral sclerosis (ALS). Previous results from our laboratory showed that neural cells regulate GDNF secretion by skeletal muscle; non-innervated skeletal muscle appear to secrete more GDNF compared to innervated skeletal muscle. Two aims were examined in the current study. First, to examine whether neural cells inhibit GDNF through acetylcholine release. Second was to examine whether differentiated NG108-15 neural cells secrete …

Espousing Interactions And Fielding Reactions: Addressing Laypeople's Beliefs About Genetic Determinism, David S. Moore

Pitzer Faculty Publications and Research

Although biologists and philosophers of science generally agree that genes cannot determine the forms of biological and psychological traits, students, journalists, politicians, and other members of the general public nonetheless continue to embrace genetic determinism. This article identifies some of the concerns typically raised by individuals when they first encounter the systems perspective that biologists and philosophers of science now favor over genetic determinism, and uses arguments informed by that perspective to address those concerns. No definitive statements can yet be made about why genetic determinism has proven so resilient in the face of empirical evidence pointing up its deficiencies, …

Design Of A Microscopy-Based Screening Method For Stomatal Development Genes In Arabidopsis Thaliana, Mercedes Tatiana Quinteros Perez

Master's Theses and Doctoral Dissertations

Stomata are microscopic pores in the epidermis of plants that regulate gas exchange and transpiration. Regulation of stomatal behavior offers opportunity for crop improvement; stomata are also useful for research into cell patterning, differentiation, and development. The purpose of this project was to create a reverse genetics, microscopy-based screening method to identify Arabidopsis genes important in guard cell development. It was hypothesized that gene coexpression analysis would facilitate identification of gene candidates involved in stomatal development. Plants harboring mutations in the candidate genes were analyzed to detect a stomatal phenotype, using dental resin impressions and light microscopy. Coexpression screening was …

Functional Characterization Of Scn5a, The Cardiac Sodium Channel Gene Associated With Cardiac Arrhythmias And Sudden Death, Ling Wu

ETD Archive

No abstract provided.

Prion Protein As An Infectious Agent Of Transmissible Spongiform Encephalopathies, Wioleta Cyranek

ETD Archive

Transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative diseases of human, animal and yeast caused by an infectious agent designated prion. The "protein only" hypothesis proposed more than three decades ago suggests that the prions are small, infectious pathogens composed of aggregated, abnormal forms of a protein encoded in the host genome. PrPC plays primary role in neurite outgrowth, synaptic function, oxidative stress defense and long term survival of cerebellar neurons. The key event in prion disease is the conversion of the Îł-helical, cellular isoform of the prion protein to the insoluble, Îø-sheet-rich disease- causing isoform. Aggregation of misfolded prion protein …

An Insight Into Gait Complex Mediated Translational Silencing, Purvi Kapasi

ETD Archive

Transcript-specific translational control restricts macrophage inflammatory gene expression. The pero-inflammatory cytokine IFN-Îđ induces the phosphorylation of human ribosomal protein L13a and its subsequent release from 60S ribosome. L13a is a component of the interferon-gamma-activated inhibitor of translation (GAIT). The GAIT complex binds a defined element in the 3'-untranslated region (UTR) of ceruloplasmin (Cp) mRNA and causes delayed silencing of translation. In this research, we elucidate the molecular mechanism underlying L13a translational silencing activity. L13a mediates translational silencing particularly, when driven by internal ribosome entry sites (IRESs) that requires the initiation factor eIF4G, but is resistant to silencing when driven by …

Optimization Of The Conditions Necessary To Show Binding Of The Plasmodium Yoelii Rhop-3 Rhoptry Protein To Mouse Erythrocytes, Latoya T. Myrie

ETD Archive

The Plasmodium Rhop-3 rhoptry protein is an erythrocyte binding protein that is secreted into the RBC membrane during merozoite invasion. Anti-Rhop-3 antibodies inhibit merozoite RBC invasion. The C-terminus of the Rhop-3 protein is highly conserved among Plasmodium species and antisera from endemic areas reacts with recombinant C-terminus of Rhop-3. The binding domain of the Rhop-3 protein is hypothesized to be within the C-terminal region of the protein. In the present study I investigated the conditions necessary for binding of the Rhop-3 protein to RBC by expressing recombinant proteins made from partial fragments of the Rhop-3 gene using the vector pDisplayTM. …

A High Throughput Live Transparent Animal Bioassay To Identify Non-Toxic Small Molecules Or Genes That Regulate Vertebrate Fat Metabolism For Obesity Drug Development, Kevin Jones

Department of Biology Faculty Publications

The alarming rise in the obesity epidemic and growing concern for the pathologic consequences of the metabolic syndrome warrant great need for development of obesity-related pharmacotherapeutics. The search for such therapeutics is severely limited by the slow throughput of animal models of obesity. Amenable to placement into a 96 well plate, zebrafish larvae have emerged as one of the highest throughput vertebrate model organisms for performing small molecule screens. A method for visually identifying non-toxic molecular effectors of fat metabolism using a live transparent vertebrate was developed. Given that increased levels of nicotinamide adenine dinucleotide (NAD) via deletion of CD38 …

Biocontrol In Hawaii: A Response To Messing (2007), Brenden Holland, Carl Christensen, Kenneth Hayes, Robert Cowie

Department of Biology Faculty Publications

Commentary. In recent decades, disagreement regarding the role of biocontrol in causing ecological damage versus its agricultural benefit has increased. Because of the historical importance of biocontrol in its agriculture and the high recent extinction rates of its endemic wildlife, Hawaii has been termed the “crucible of the debate”. A number of biocontrol programs in Hawaii and the Pacific not only failed to control target pests, but have backfired spectacularly, leading directly to range reductions and extinctions of endemic taxa. We agree with Messing that rigorous biological review is important, that minimizing inefficiency, irrationality, lack of transparency and lack of …

Measuring Knowledge Of Natural Selection: A Comparison Of The C.I.N.S., An Open-Response Instrument, And An Oral Interview, Ross Nehm, Irvin Sam Schonfeld

Publications and Research

Growing recognition of the central importance of fostering an in-depth understanding of natural selection has, surprisingly, failed to stimulate work on the development and rigorous evaluation of instruments that measure knowledge of it. We used three different methodological tools, the Conceptual Inventory of Natural Selection (CINS), a modified version of Bishop and Anderson's (Bishop and Anderson [1990] Journal of Research in Science Teaching 27: 415-427) open-response test that we call the Open Response Instrument (ORI), and an oral interview derived from both instruments, to measure biology majors' understanding of and alternative conceptions about natural selection. We explored how these instruments …

Combating Amphibian Population Declines: An Investigation Of The Pathophysiology And Possible Treatments Of Batrachochytrium Dendrobatidis, Christopher A. Gaulke

Undergraduate Honors Theses

The fungus Batrachochytrium dendrobatidis has been linked to the decline of amphibians worldwide. Research has been devoted to examining the range of B. dendrobatidis and various physiological aspects of the fungus; however, little is known about how it causes mortality in individuals. Subsequently, we investigated the potential mechanisms of mortality by examining the pathogen's effect on metabolic rate and osmotic balance. In addition, we attempted to develop a field treatment for the pathogen using Itraconazol. Metabolic rates, mass, pathogen symptoms and osmotic concentrations were measured in Rana pipiens and Hyla rigilla. Results suggest symptoms are variable and individuals survive for …

More Evidence That Mutation Rate In The Chloroplast Genome Depends On Copy Number, Ashley Dutton

Undergraduate Honors Theses

The conservative nature of the copy variable region (CVR) of the chloroplast genome, also known as the inverted repeat (IR) region, is well established; however the basis for the lower mutation rate has been debated. Two ideas have been proposed to explain the reduced rate: 1) genes in the region are inherently slow to evolve; or 2) the presence of two copies reduces the rate via copy correction. Comparisons of eighty-three genes and twenty introns were made estimating mutation rates, from both the CVR region and single copy (SC) regions in legumes and gymnosperms. In gene and intron comparisons, CVR …

Validation Of A Bioelectrical Impedance Analysis Equation Predicting Body Composition Using Conductor Length Instead Of Height, Jessica Dawn Nye

Undergraduate Honors Theses

Bioelectrical impedance analysis (BIA) is widely used in predicting body composition. Impedance of an electrical current that passes through the body is related to the composition of the body and the length of the conductor, conventionally estimated using height. The purpose of this study was to compare a BIA equation prediction fat-free mass (FFM) that utilized actual conductor length (Parsons) with a conventional BIA equation (NHANES), using hydrodensitometry as the reference method. Thirty-nine male and 53 female subjects were studied. For both sexes, FFM predicted by both Parsons and NHANES equations were equally and highly correlated with FFM measured using …

Ontogenetic Changes In Feeding Morphology And Diet In The Chiselmouth Minnow, Acrocheilus Alutaceus, Corrie Murray

Undergraduate Honors Theses

The chiselmouth minnow (Acrocheilus alutaceus) is an herbivorous fish endemic to freshwater systems of the Pacific Northwest and abundant in mid-reaches of the Yakima River, WA. Uncommon in temperate streams, herbivorous fish are ecologically important because they provide a direct link between primary production and fish biomass. Chiselmouth minnows undergo ontogenetic morphological changes as they transform from insectivore to herbivore, the lower jaw becomes flattened, calcified and hardened for scraping algae and the intestine grows long for digestion. The timing of these changes in relation to diet and ecological status are poorly understood. By quantifying changes in jaw …

Open Circuit Potential Shifts Of Activated Carbon In Aqueous Solutions During Chemical And Adsorption Interactions, Mikhail M. Goldin, Vladimir A. Kolesnikov, Mogely Sh. Khubutiya, Alexander G. Volkov, Gary J. Blanchard, Anatoly K. Evseev, Mark M. Goldin

Faculty Publications and Presentations

Interaction of certain inorganic and organic compounds with activated carbon and the effect of such interaction on open circuit potential of activated carbon were studied. Open circuit potential shifts were observed for an overwhelming majority of the substances and brands of activated carbons investigated. Both negative and positive potential shifts were observed. It was shown that open circuit potential shifts for organic substances depend on degree of coverage of the activated carbon surface. Whereas adsorption of investigated organic compound on activated carbon led to positive potential shifts, desorption of adsorbates from the activated carbon surface led to potential shifts in …

Rapid Bursts Of Androgen-Binding Protein (Abp) Gene Duplication Occurred Independently In Diverse Mammals, Christina M. Laukaitis, Andreas Heger, Tyler D. Blakely, Pavel Munclinger, Chris P. Ponting, Robert C. Karn

Scholarship and Professional Work - LAS

Background

The draft mouse (Mus musculus) genome sequence revealed an unexpected proliferation of gene duplicates encoding a family of secretoglobin proteins including the androgen-binding protein (ABP) α, β and γ subunits. Further investigation of 14 α-like (Abpa) and 13 β- or γ-like (Abpbg) undisrupted gene sequences revealed a rich diversity of developmental stage-, sex- and tissue-specific expression. Despite these studies, our understanding of the evolution of this gene family remains incomplete. Questions arise from imperfections in the initial mouse genome assembly and a dearth of information about the gene family structure in other rodents …

The Pholcid Spiders Of Micronesia And Polynesia (Araneae, Pholcidae), Joseph A. Beatty, James W. Berry, Bernhard A. Huber

Scholarship and Professional Work - LAS

Records of pholcid spiders from Micronesia and Polynesia are presented, along with records from Indonesia and parts of Melanesia. Nineteen species representing eleven genera are included. An illustrated key for Pacific pholcids is provided. Two species and one genus are not yet known from Micronesia or Polynesia, but are included in the key because they may occur there. Seven species are widespread synanthropic or anthropophilic species, two species are widespread native species, and nine species are endemics of one or several neighboring islands. Distribution maps include only specimens we have seen, not literature records.

Plaster Creek Watershed Management Plan, Fishbeck, Thompson, Carr, & Huber, Inc.

Watershed Reports

The quality of Plaster Creek is influenced by many factors, such as human activities within the Plaster Creek Watershed (Watershed), physical and biological characteristics of the natural resources, and the management of those resources. This document provides an overview of these diverse aspects of the Watershed, including detailed information about the sources and causes of watershed pollution, recommendations needed to address impairments, and steps to implement the recommendations.

"Broadening The Coverage Of Biodiversity Assessments" , Ben Collen, Mala Ram, Nadia Dewhurst, Viola Clausnitzer, Vincent Kalkman, Neil Cumberlidge, Jonathan Em Baillie

Journal Articles

No abstract provided.

A Global Assessment Of Freshwater Crab Diversity , Darren Cj Yeo, Pkl Ng, Neil Cumberlidge, Celio Magalhães, Savel Regan Daniels Phd, Martha R. Campos

Journal Articles

No abstract provided.