Digital Commons Network^™

Construction, Alignment And Analysis Of Twelve Framework Physical Maps That Represent The Ten Genome Types Of The Genus Oryza, Hyeran Kim, Bonnie Hurwitz, Yeisoo Yu, Kristi Collura, Navdeep Gill, Phillip Sanmiguel, James C. Mullikin, Christopher Maher, William Nelson, Marina Wissotski, Michele Braidotti, David Kudrna, José Luis Goicoechea, Lincoln Stein, Doreen Ware, Scott A. Jackson, Carol Soderlund, Rod A. Wing

Biology Faculty Articles

We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.

Louis Pasteur’S Views On Creation, Evolution, And The Genesis Of Germs, Alan L. Gillen, Frank Sherwin

Faculty Publications and Presentations

“There is no remembrance of men of old, and even those who are yet to come will not be remembered by those who follow.” Ecclesiastes 1:11 (NIV)

In past years revisionist historians have been rewriting the worldview of Christians who have made some of the major discoveries in biology and medicine. It appears that postmodern revisionists are rewriting history to support their agenda of a more “secular” explanation to science. The Judeo-Christian worldview is not politically correct in most universities. This is true in regard to past scientists such as Louis Pasteur who believed in creation. According to reliable, primary …

Effect Of Thyroid Hormone Concentration On The Transcriptional Response Underlying Induced Metamorphosis In The Mexican Axolotl (Ambystoma), Robert B. Page, Stephen R. Voss, Amy K. Samuels, Jeramiah J. Smith, Srikrishna Putta, Christopher K. Beachy

Biology Faculty Publications

Background

Thyroid hormones (TH) induce gene expression programs that orchestrate amphibian metamorphosis. In contrast to anurans, many salamanders do not undergo metamorphosis in nature. However, they can be induced to undergo metamorphosis via exposure to thyroxine (T₄). We induced metamorphosis in juvenile Mexican axolotls (Ambystoma mexicanum) using 5 and 50 nM T₄, collected epidermal tissue from the head at four time points (Days 0, 2, 12, 28), and used microarray analysis to quantify mRNA abundances.

Results

Individuals reared in the higher T₄ concentration initiated morphological and transcriptional changes earlier and completed metamorphosis by …

A Synaptic Basis For Auditory-Vocal Integration In The Songbird, Eric E. Bauer, Melissa J. Coleman, Todd F. Roberts, Arani Roy, Jonathan F. Prather, Richard Mooney

WM Keck Science Faculty Papers

Songbirds learn to sing by memorizing a tutor song that they then vocally mimic using auditory feedback. This developmental sequence suggests that brain areas that encode auditory memories communicate with brain areas for learned vocal control. In the songbird, the secondary auditory telencephalic region caudal mesopallium (CM) contains neurons that encode aspects of auditory experience. We investigated whether CM is an important source of auditory input to two sensorimotor structures implicated in singing, the telencephalic song nucleus interface (NIf) and HVC. We used reversible inactivation methods to show that activity in CM is necessary for much of the auditory-evoked activity …

A New Species Of Giant Sengi Or Elephant-Shrew (Genus Rhynchocyon) Highlights The Exceptional Biodiversity Of The Udzungwa Mountains Of Tanzania, F Rovero, G B. Rathbun, A Perkin, T Jones, David O. Ribble, C Leonard, R R. Mwakisoma, N Doggart

Biology Faculty Research

A new species of sengi, or elephant-shrew, is described. It was discovered in the northern Udzungwa Mountains of Tanzania in 2005. Sengis (Order Macroscelidea, super-cohort Afrotheria) include four genera and 15 species of mammals that are endemic to Africa. This discovery is a significant contribution to the systematics of this small order. Based on 49 camera trap images, 40 sightings and five voucher specimens, the new sengi is diurnal and distinguished from the other three species of Rhynchocyon by a grizzled grey face, pale yellow to cream chest and chin, orange-rufous sides, maroon back and jet-black lower rump and thighs. …

Correlated Evolution Of Genome Size And Cell Volume In Diatoms (Bacillariophyceae), Jessica A. Connolly, Matthew J. Oliver, Jeremy M. Beaulieu, Charles A. Knight, Lars Tomanek, Mark A. Moline

Biological Sciences

A correlation between genome size and cell volume has been observed across diverse assemblages of eukaryotes. We examined this relationship in diatoms (Bacillariophyceae), a phylum in which cell volume is of critical ecological and biogeochemical importance. In addition to testing whether there is a predictive relationship across extant species, we tested whether evolutionary divergences in genome size were correlated with evolutionary divergences in cell size (using independent contrasts). We estimated total DNA content for 16 diatom species using a flow cytometer and estimated cell volumes using critical dimensions with scaling equations. Our independent contrast analyses indicated a significant correlated evolution …

Biomass And Toxicity Responses Of Poison Ivy (Toxicodendron Radicans) To Elevated Atmospheric Co2: Comment, Stefan A. Schnitzer, Ronald A. Londre, John Klironomos, Peter B. Reich

Biological Sciences Faculty Research and Publications

No abstract provided.

The Cross-Bridge Cycle And Skeletal Muscle Fatigue, Robert H. Fitts

Biological Sciences Faculty Research and Publications

The functional correlates of fatigue observed in both animals and humans during exercise include a decline in peak force (P₀), maximal velocity, and peak power. Establishing the extent to which these deleterious functional changes result from direct effects on the myofilaments is facilitated through understanding the molecular mechanisms of the cross-bridge cycle. With actin-myosin binding, the cross-bridge transitions from a weakly bound low-force state to a strongly bound high-force state. Low pH reduces the number of high-force cross bridges in fast fibers, and the force per cross bridge in both fast and slow fibers. The former is thought …

Computational Prediction And Molecular Confirmation Of Helitron Transposons In The Maize Genome, Chunguang Du, Jason Caronna, Limei He, Hugo K. Dooner

Department of Biology Faculty Scholarship and Creative Works

Background: Helitrons represent a new class of transposable elements recently uncovered in plants and animals. One remarkable feature of Helitrons is their ability to capture gene sequences, which makes them of considerable potential evolutionary importance. However, because Helitrons lack the typical structural features of other DNA transposable elements, identifying them is a challenge. Currently, most researchers identify Helitrons manually by comparing sequences. With the maize whole genome sequencing project underway, an automated computational Helitron searching tool is needed. The characterization of Helitron activities in maize needs to be addressed in order to better understand the impact of Helitrons on the …

Mechanisms Of Ionic Current Changes Underlying Rhythmic Activity Recovery After Decentralization, Olga E. Khorkova Sherman

Dissertations

Neuronal networks capableof generating rhythmic output in the absence of patterned sensory or central inputs are widely represented in the nervous system where they support a variety of functions, from learning and memory to rhythmic motor activity such as breathing. To perfectly function in a living organism, rhythm-generating networks have to combine the capability of producing a stable output with the plasticity needed to adapt to the changing demands of the organism and environment. This dissertation used the pyloric network of the crab Cancer borealis to identify potential mechanisms that ensure stability and adaptation of rhythm generation by neuronal networks …

What Do Students Have To Say About Ecology And Evolution? Using Podcasting To Apply Integrative Biology Themes Across The Tree Of Life, Amy M. Treonis, Malcolm Hill, Theresa Dolson, Sue Mcginnis, Elizabeth Miles

Biology Faculty Publications

We describe a versatile podcasting assignment that requires students to (i) review primary and secondary literature relating to an assigned organism with the goal of identifying the main features of its ecology and evolution, (ii) prepare an enhanced podcast about their organism, and (iii) critique peer podcasts. The goal of this assignment is for each student to gain a fuller appreciation for and understanding of biological diversity. This assignment will enhance students' research, technology, and communication skills while reinforcing the main themes of integrative biology.

Microbes And The Days Of Creation, Alan L. Gillen

Faculty Publications and Presentations

The world of germs and microbes has received much attention in recent years. But where do microbes fit into the creation account? Were they created along with the rest of the plants and animals in the first week of creation, or were they created later, after the Fall? These are some questions that creation microbiologists have been asking in recent years. Ongoing research, based on the creation paradigm, appears to provide some answers to these puzzling questions. The answers to these questions are not explicit in Scripture, so the answers cannot be dogmatic. However, a reasonable extrapolation from biological data …

Antiretroviral Pre-Exposure Prophylaxis Prevents Vaginal Transmission Of Hiv-1 In Humanized Blt Mice, Paul W. Denton, Jacob D. Estes, Zhifeng Sun, Florence A. Othieno, Bangdong L. Wei, Anja K. Wege, Daniel A. Powell, Deborah A. Payne, Ashley T. Haase, J. Victor Garcia

Biology Faculty Publications

Background: Worldwide, vaginal transmission now accounts for more than half of newly acquired HIV-1 infections. Despite the urgency to develop and implement novel approaches capable of preventing HIV transmission, this process has been hindered by the lack of adequate small animal models for preclinical efficacy and safety testing. Given the importance of this route of transmission, we investigated the susceptibility of humanized mice to intravaginal HIV-1 infection.

Methods and Findings: We show that the female reproductive tract of humanized bone marrow–liver–thymus (BLT) mice is reconstituted with human CD4þ T and other relevant human cells, rendering these humanized mice …

First Male Sperm Precedence In Multiply-Mated Females Of The Cooperative Spider Anelosimus Studiosus (Araneae, Theridiidae), Thomas Jones, Patricia Parker

Biology Department Faculty Works

No abstract provided.

Plant Succession On Gopher Mounds In Western Cascade Meadows: Consequences For Species Diversity And Heterogeneity, Chad C. Jones, Charles B. Halpern, Jessica Niederer

Botany Faculty Publications

Pocket gophers have the potential to alter the dynamics of grasslands by creating mounds that bury existing vegetation and locally reset succession. Gopher mounds may provide safe sites for less competitive species, potentially increasing both species diversity and vegetation heterogeneity (spatial variation in species composition). We compared species composition, diversity and heterogeneity among gopher mounds of different ages in three montane meadows in the Cascade Range of Oregon. Cover of graminoids and forbs increased with mound age, as did species richness. Contrary to many studies, we found no evidence that mounds provided safe sites for early successional species, despite their …

A Watershed Analysis Of Pattee Pond: Implications For Water Quality And Land Use Management, Problems In Environmental Science Course (Biology 493), Colby College, Colby Environmental Assessment Team, Colby College

Colby College Watershed Study: Pattee Pond (2008, 1992)

The Colby Environmental Assessment Team (CEAT) investigated the impact of land use patterns on the water quality of Pattee Pond in Winslow, Maine, during the summer and fall of 2008. Physical, chemical, and biological characteristics of water quality were analyzed to evaluate the current health of the lake. Data collected were compared with previous studies conducted by the Maine Department of Environmental Protection (DEP) and CEAT to examine changes in water quality and land use over time. Trends in Pattee Pond water quality suggest an improvement since the 1970s. However, the lake is still experiencing algal blooms resulting from phosphorus …

Effects Of Aging And Gender On Regulators Of Muscle Adaptation In F344/Bn Rat Model, Satyanarayana Paturi

Theses, Dissertations and Capstones

Sarcopenia is the loss of muscle mass and strength that occurs with aging. Here we examine the effects of aging and gender on the regulation of molecules believed to regulate muscle growth and adaptation in the F344/BN rat. In male animals, soleus and EDL muscle/body weight ratio declined continuously with aging while muscle atrophy in female animals plateaued at 26-months and remained constant thereafter. Aging increased the phosphorylation of protein kinase-B (Akt) and the mammalian target of rapamycin (mTOR) in the female but not male soleus muscle. This finding was associated with the attenuation of muscle atrophy observed in female …

Studying Gene Function In Caenorhabditis Elegans Using Rna-Mediated Interference, Eleanor M. Maine

Biology - All Scholarship

The RNA interference (RNAi) method for targeted gene silencing is widely used in Caenorhabditis elegans for large-scale functional genomic studies, analysis of limited gene sets and detailed analysis of individual gene function. The application of RNAi has identified genes that participate in various aspects of development, physiology and cell biology. In addition, RNAi has been used to identify interacting genes and to study functionally redundant genes. This review discusses the various applications of RNAi in C. elegans, focusing particularly on the analysis of developmental processes.

Raccoon (Procyon Lotor) Harvesting On And Near The U.S. Department Of Energy’S Savannah River Site, Karen F. Gaines, James M. Novak

Faculty Research & Creative Activity

Understanding the toxicodynamics of wildlife populations in contaminated ecosystems is one of the greatest challenges in ecotoxicology today. The goal is to manage these populations to minimize risk to ecosystem integrity as well as human health. Ecological risk assessments (ERAs) in the United States are designed to meet the regulatory mandates of the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) and the Resource Conservation and Recovery Act. According to the U.S. Environmental Protection Agency, an ERA evaluates the potential adverse effects that human activities have on the ' ora and fauna that de( ne an ecosystem (U.S. Environmental Protection …

Of Mice And Men: A Comparative Study Assessing Behavioral Indicators Of Sugar Addiction In Mice And College Students, Kahlilia Morris

Capstone Research Projects

No abstract provided.

Sustainability In A Time Of Climate Change: Developing An Intensive Research Framework For The Platte River Basin And The High Plains Proceedings From The 2008 Climate Change Workshop, Monica Norby, Ashley Washburn

Office of Research and Economic Development: Publications

Proceedings from the 2008 Climate change Workshop, Nebraska Sandhills, May 19-22, 2008. Hosted by the University of Nebraska–Lincoln and the U.S. Geological Survey

Accelerated Exchange Of Exon Segments In Viperid Three-Finger Toxin Genes (Sistrurus Catenatus Edwardsii; Desert Massasauga), Robin Doley, Susanta Pahari, Stephen P. Mackessy, Manjunatha Kini

Biological Sciences Faculty Publications

BACKGROUND: Snake venoms consist primarily of proteins and peptides showing a myriad of potent biological activities which have been shaped by both adaptive and neutral selective forces. Venom proteins are encoded by multigene families that have evolved through a process of gene duplication followed by accelerated evolution in the protein coding region. RESULTS: Here we report five gene structures of three-finger toxins from a viperid snake, Sistrurus catenatus edwardsii. These toxin genes are structured similarly to elapid and hydrophiid three-finger toxin genes, with two introns and three exons. Both introns and exons show distinct patterns of segmentation, and the insertion/deletion …

Lack Of Assortative Mating For Tail, Body Size, Or Condition In The Elaborate Monomorphic Turquoise-Browed Motmot (Eumomota Superciliosa), Troy G. Murphy

Biology Faculty Research

Elaborate male and female plumage can be maintained by mutual sexual selection and function as a mate-choice or status signal in both sexes. Both male and female Turquoise-browed Motmot (Eumomota superciliosa) have long tails that terminate in widened blue-and-black rackets that appear to hang, unattached, below the body of the bird. I tested whether mutual sexual selection maintains the Turquoise-browed Motmot’s elaborate tail plumage by testing the prediction that mating occurs in an assortative manner for tail plumage. I also tested whether assortative mating occurs for body size, a potential measure of dominance, and for phenotypic condition, a …

Purinergic Receptors In The Circumvallate Papillae Of Rats, Alana Marselle Montoya

Electronic Theses and Dissertations

P2X2 receptors and P2Y4 receptors are ATP-activated cell surface receptors that gate movement of K+, Na+, and Ca2+. We used immunocytochemistry for P2X2 and P2Y4 receptors as well as taste cell type markers to learn if P2X2 immunoreactivity (IR) is present in nerve processes in close apposition to Type II and/or Type III taste cells. We also tested to see if P2Y4 IR is present in Type II and/or Type III taste cells. Our results indicate that P2X2 is present only in intragemmal nerve processes. P2X2-LIR nerve processes form close contacts with Type II and Type III taste cells. P2Y4 …

Methods For Detection Of Matrix Metalloproteinases As Biomarkers In Cardiovascular Disease, Viorica Lopez-Avila, Juliet Spencer

Biology Faculty Publications

Matrix metalloproteinases (MMPs) are a family of zinc-dependent proteolytic enzymes that degrade extracellular matrix (ECM) components like collagen, fibronectin, and laminin. While this activity is important for normal development, morphogenesis, and wound healing, deregulation of MMP activity has been implicated in a number of cardiovascular diseases, including congenital heart defects, atherosclerosis, myocardial infarction, and congestive heart failure. MMPs are good potential diagnostic indicators of cardiovascular disease, but current detection methods are time consuming and quite laborious. This review will discuss MMP biology, current methods for detection of MMPs from patient samples, and potential new developments in multiplexed analysis of MMPs.

Predator Induction Of Spine Length In Larval Leucorrhinia Intacta (Odonata), Shannon Mccauley, Christopher J. Davis, Earl E. Werner

Biological Sciences

Questions: Do larvae of a dragonfly with a broad habitat distribution have longer abdominal spines when they co-exist with fish, and are these differences the result of phenotypic plasticity?
Hypothesis: Phenotypic plasticity will result in larvae having longer spines when they are exposed to cues from predatory fish.
Organism: Larvae of Leucorrhinia intacta (Odonata: Libellulidae).
Research site: Natural ponds and cattle tanks on the E.S. George Reserve in southeast Michigan.
Methods: We compared the morphology of larvae collected from two natural ponds before and after a drought resulted in the extirpation of fish from one pond. We also compared …

Denaturing Gradient Gel Electrophoresis As A Tool To Determine Batch Similarity Of Probiotic Cultures Of Porcine Cecal Bacteria, Michael Hume, Charles M. Scanlan, Roger B. Harvey, Kathleen Andrews, James D. Snodgrass, Armen Nalian, Alexandra Martynova-Van Kley, David Nisbet

Faculty Publications

A continuous-flow porcine cecal bacterial culture has been used experimentally as treatment against enterotoxigenic Escherichia coli in weanling pigs. Periodically, the cultures must be started from frozen stock. Our results indicate that denaturing gradient gel electrophoresis can be applied as an indirect indication of culture similarity for each new batch generated from frozen stock.

Sexual Selection And Alternative Reproductive Tactics In Cyprinodon Elegans, Jennifer M. Gumm

Faculty Publications

In systems with alternative reproductive tactics (ARTs), males have discrete behaviors and morphologies that allow them to optimize their reproductive success in relation to others in the population. Males with different phenotypes directly compete with one another for mates, providing unique opportunities for studying social interactions within a species. Using the Comanche Springs pupfish, Cyprinodonelegans, a species with three alternative reproductive tactics, I examine how male behaviors and social interactions influence the reproductive success of each tactic.

Previous studies suggest that large territorial males have high reproductive success, while satellite males and female mimics must intrude into territories in order …

The Ecology Of Fear: Colonization And Oviposition In Aquatic Systems [Poster], Leeanna Pletcher, Johanna Kraus, James R. Vonesh

Biology Presentations

Introduction

Amphibians and aquatic invertebrates have complex life histories that link aquatic and terrestrial food webs. It has been suggested that amphibian reproduction is an important source of carbon to some aquatic systems. Movement of organisms across the aquatic-terrestrial habitat boundary can represent important subsidies to the receiving habitat. Subsidies are organisms, nutrients, or detritus that cross habitat boundaries and are consumed, and these allochthonous inputs can affect food web structure. Predators can alter subsidies by consuming organisms that would otherwise move across habitat boundaries. Predator induced shifts in habitat selection are a well known non-lethal effect in aquatic systems. …

Mitochondria In Energy-Limited States: Mechanisms That Blunt The Signaling Of Cell Death, Steven C. Hand, Michael A. Menze

Faculty Research & Creative Activity

Cellular conditions experienced during energy-limited states – elevated calcium, shifts in cellular adenylate status, compromised mitochondrial membrane potential – are precisely those that trigger, at least in mammals, the mitochondrion to initiate opening of the permeability transition pore, to assemble additional protein release channels, and to release pro-apoptotic factors. These proapototic factors in turn activate initiator and executer caspases. How is activation of mitochondria-based pathways for the signaling of apoptotic and necrotic cell death avoided under conditions of hypoxia, anoxia, diapause, estivation and anhydrobiosis? Functional trade-offs in environmental tolerance may have occurred in parallel with the evolution of diversified pathways …