Digital Commons Network^™

The Identification Of Rana Ocellata Linnaeus, 1758. Nomenclatural Impact On The Species Currently Known As Leptodactylus Ocellatus (Leptodactylidae) And Osteopilus Brunneus (Gosse, 1851) (Hylidae), Esteban O. Lavilla, José A. Langone, Ulisses Caramaschi, W. Ronald Heyer, Rafael O. De Sá

Biology Faculty Publications

The usage of the name Rana ocellata Linnaeus, 1758, is plagued by misidentifications and misinterpretations. After an exhaustive bibliographic review, we conclude that the Linnaeus 1758 name refers to Osteopilus brunneus (Gosse, 1851) from Jamaica, while the taxon currently known as Leptodactylus ocellatus corresponds to Rana latrans Steffen, 1815. Herein, we designate and provide descriptions of the neotypes of Leptodactylus latrans (Steffen, 1815), revalidated, new combination, and Osteopilus ocellatus (Linnaeus, 1758), new combination, as a senior synonym of Osteopilus brunneus (Gosse, 1851).

Implications Of The Plastid Genome Sequence Of Typha (Typhaceae, Poales) For Understanding Genome Evolution In Poaceae, Mary M. Guisinger, Timothy W. Chumley, Jennifer V. Kuehl, Jeffrey L. Boore, Robert K. Jansen

All Faculty Scholarship for the College of the Sciences

Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including …

Use Of Virtual Cell In Studies Of Cellular Dynamics, Leslie M. Loew, Boris M. Slepchenko

UCHC Articles - Research

The Virtual Cell (VCell) is a unique computational environment for modeling and simulation of cell biology. It has been specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. The models created with VCell can range from the simple, to evaluate hypotheses or to interpret experimental data, to complex multi-layered models used to probe the predicted behavior of spatially resolved, highly non-linear systems. In this Chapter, we discuss modeling capabilities of VCell and demonstrate representative examples of the models published by the Virtual Cell users.

Ducks, Geese, And Swans Of The World: Sources Cited, Paul A. Johnsgard

Ducks, Geese, and Swans of the World by Paul A. Johnsgard

350+ citations

Competition Drives Specialization In Pollination Systems Through Costs To Male Fitness, Nathan Muchhala, Zachary Brown, W. Armbruster, Matthew Potts

Biology Department Faculty Works

No abstract provided.

Waterfowl Of North America: Sources, Paul A. Johnsgard

Waterfowl of North America, Revised Edition (2010) by Paul A. Johnsgard

Approximately 500 citations.

See also the updated bibliography in the 2010 supplement: "North America’s Ducks, Geese and Swans in the 21st Century"

Induction And Regulation Of Autophagy By Novel Prenylation Inhibitors In Sts-26t Malignant Peripheral Nerve Sheath Tumor (Mpnst) Cells, Komal Madhukar Sane

Wayne State University Dissertations

Prenylation pathways have been targeted via several different compounds that inhibit farnesyl transferase (FTase) and/or geranylgeranyl transferase (GGTase) enzymes in many cellular and animal models of cancer. Some of these have also been evaluated in clinical trials with limited success. Multiple mechanisms of action have been elucidated for such compounds, including cell cycle arrest, proteasome inhibition, apoptosis and most recently, autophagy. However, there is still an urgent need of effective agents of this class of anti-tumor therapeutics. In this dissertation, I sought to delve into this issue by characterizing our novel prenylation inhibitors and their potential as anti-tumor agents. Novel …

Mechanisms Of Presynaptic Cav2 Calcium Channel Localization In Caenorhabditis Elegans, Yasunori Saheki

Student Theses and Dissertations

Neurotransmitter release at nerve terminals is a fundamental aspect of communication in the nervous system. Voltage changes in the presynaptic membrane are sensed by presynaptic voltage-gated calcium channels that mediate calcium influx at the nerve terminals to execute exocytosis of various kinds of neurotransmitters. Defects in presynaptic calcium channels lead to many neurological disorders, emphasizing the importance of these channels in the regulation of neuronal activities in the brain. Previous physiological studies have focused on opening kinetics of the channels and their modulation by auxiliary subunits. Cell biological questions such as trafficking and clustering of the channels at the presynaptic …

Distillers Grains And Livestock Are Important To Ethanol Energy And Greenhouse Gas Balance, Virgil R. Bremer, Adam J. Liska, Haishun Yang, Daniel T. Walters, Galen E. Erickson, Terry J. Klopfenstein, Richard K. Koelsch, Kenneth G. Cassman

Nebraska Beef Cattle Reports

A life cycle assessment of the impact of distillers grains plus solubles (DGS) on mitigation of energy and greenhouse gas (GHG) emissions comparing corn ethanol to gasoline demonstrates the importanceof feeding wet DGS (WDGS) to feedlot cattle to optimize the environmental benefit of ethanol production relative to gasoline. Ethanol produced in Nebraska has a superior environmentalimpact compared to ethanol produced in Iowa or Texas.

The Effect Of Soil Regimes And Topography On Tree Community Composition In The Gordon Natural Area, Calen Daugherty, William Hochella, Kyle Houser, Sarah Johnson, Carolyn Keene

Gordon Natural Area Soils Studies Documents

No abstract provided.

Soydb: A Knowledge Database Of Soybean Transcription Factors, Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry T. Nguyen, Dong Xu, Gary Stacey, Jianlin Cheng

Department of Agronomy and Horticulture: Faculty Publications

Background: Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors.

Description: The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI) and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database …

Science Based Authentication Of Dietary Supplements: Studies On The Chemical Constituents, Analytical Method And Biological Activities Of Scutellaria Spp And Pfaffia Paniculata, Jing Li

Electronic Theses and Dissertations

During the last decade, the use of herbal medicine has expanded globally and gained popularity. With the tremendous expansion in the use of herbal medicine worldwide, safety and efficacy as well as quality control of herbal medicines have become more and more issues of concern for both health authorities and the public. Although herbal medicine has been in use for hundreds to thousands years, very limited science-based data exist to explicit its chemical constituents, pharmacological activities and toxicity. Therefore, lack of scientific evidence for herbal medicine usage elicits the need for systematic studies of herbal medicine, including phytochemical, analytical, and …

Relationship Of Climate And Growth Of Quaking Aspen (Populus Tremuloides) In Yellowstone National Park, Erik S. Jules, Allyson L. Carroll, Matthew J. Kauffman

Aspen Bibliography

Quaking aspen is a widespread tree that is in decline across wide areas of western North America, and is predicted to experience a large range shift if future climate predictions are realized. The purpose of our study was to determine what climate factors have influenced aspen growth in Yellowstone National Park, USA, and to determine whether these climatic influences vary across a heterogeneous landscape. We extracted increment cores from 10-12 aspen in each of 16 stands spread across a 1,526 km2 area. Using ring widths, we created a182-year standardized chronology from 1821 to 2003 A.D. composed of 151 series. We …

Elucidating The Structure Of Protein Aggregates By Raman Spectroscopy, Ludmila A. Popova

Legacy Theses & Dissertations (2009 - 2024)

The structures and properties of amyloid fibrils are of considerable interest due to their associations with numerous neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease and transmissible spongiform encephalopaties (prion diseases). Understanding fibrillogenesis at a molecular level requires detailed structural characterization of amyloid fibrils. However amyloid fibrils are difficult objects to study due to their non-crystalline and insoluble nature. These properties make the application of classical tools of structural biology, such as X-Ray crystallography and solution Nuclear Magnetic Resonance spectroscopy, impractical for structural characterization of protein fibrils.

Automated Isolation Of Translational Efficiency Bias That Resists The Confounding Effect Of Gc(At)-Content, Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer

Kno.e.sis Publications

Genomic sequencing projects are an abundant source of information for biological studies ranging from the molecular to the ecological in scale; however, much of the information present may yet be hidden from casual analysis. One such information domain, trends in codon usage, can provide a wealth of information about an organism's genes and their expression. Degeneracy in the genetic code allows more than one triplet codon to code for the same amino acid, and usage of these codons is often biased such that one or more of these synonymous codons is preferred. Detection of this bias is an important tool …

Density Based Pruning For Identification Of Differentially Expressed Genes From Microarray Data, Jianjun Hu, J. Xu

Faculty Publications

Motivation

Identification of differentially expressed genes from microarray datasets is one of the most important analyses for microarray data mining. Popular algorithms such as statistical t-test rank genes based on a single statistics. The false positive rate of these methods can be improved by considering other features of differentially expressed genes.

Results

We proposed a pattern recognition strategy for identifying differentially expressed genes. Genes are mapped to a two dimension feature space composed of average difference of gene expression and average expression levels. A density based pruning algorithm (DB Pruning) is developed to screen out potential differentially expressed genes usually …

Automated Interpretation Of The Tandem Mass Spectra Of Peptides Using Artificial Neural Networks, Timothy Patrick Manning

Theses

The manual interpretation of mass spectra is a complex and time consuming task. The problem of manually interpreting this data is further exacerbated by the large numbers of mass spectra which can potentially be produced in a single proteoniics experiment. This shows the need for high throughput approaches to the interpretation of mass spectra. Existing automated approaches are however error prone due to the complexity of the task. Accordingly, this thesis discusses and evaluates the application of neural networks to improving the sensitivity, specificity and robustness of current approaches to the automated interpretation of such mass spectral data.

Several neural …

The Role Of The Ca2+-Dependent Protein Kinase, Camk-Ii, In Heart And Kidney Development In The Zebrafish, Danio Rerio, Sarah Rothschild

Theses and Dissertations

Ca2+/calmodulin-dependent protein kinase type II (CaMK-II) is a multifunctional serine/threonine kinase that is ubiquitously expressed throughout the lifespan of metazoans. Mammals encode four genes (α, β, γ, δ) that generate over forty splice-variants. CaMK-II is important in a myriad of functions, including ion channel regulation, cell-cycle progression, and long term potentiation. In adults, alterations in activation of CaMK-II induce cardiac arrhythmias and heart failure. Developmental roles for CaMK-II are not as well understood since mouse knockouts are embryonic lethal. Therefore the identification of other vertebrate CaMK-II genes will add to our understanding of development. Zebrafish encode seven catalytically active CaMK-II …

Heterologous Expression Studies Of Saccharomyces Cerevisiae Reveal Two Distinct Trypanosomatid Caax Protease Activities And Identify Their Potential Targets, David Z. Mokry, Surya P. Manandhar, Kristen A. Chicola, George M. Santangelo, Walter K. Schmidt

Faculty Publications

The CaaX tetrapeptide motif typically directs three sequential posttranslational modifications, namely, isoprenylation, proteolysis, and carboxyl methylation. In all eukaryotic systems evaluated to date, two CaaX proteases (Rce1 and Ste24/Afc1) have been identified. Although the Trypanosoma brucei genome also encodes two putative CaaX proteases, the lack of detectable T. brucei Ste24 activity in trypanosome cell extracts has suggested that CaaX proteolytic activity within this organism is solely attributed to T. brucei Rce1 (J. R. Gillespie et al., Mol. Biochem. Parasitol. 153: 115-124. 2007). In this study, we demonstrate that both T. brucei Rce1 and T. brucei Ste24 are enzymatically active when …

Characterization And Functional Regulation Of Bioactive Peptides In Avian Macrophages And Heterophils, Lakshmi Kannan

Graduate Theses and Dissertations

Oligopeptides and low molecular weight polypeptides play central roles as effectors and signal transducers acting as hormones, neurotransmitters, growth factors, toxins, and antimicrobial factors that are important for the survival of the organism. Owing to the ubiquitous involvement of peptides in many key regulatory processes, we have been interested to identify native peptides in different cells and tissues and understand their functions. To conduct our studies, we used avian macrophages and heterophils as models of specialized cells which constitute central components of innate immunity. These studies involved (a) qualitative identification and characterization of the peptides associated with high intensity mass …

Exploring Red-Tailed Hawk Migration Using Stable Isotope Analysis And Dna Sexing Techniques, Kara Clare Donohue

Boise State University Theses and Dissertations

Understanding the movements of migratory birds and connecting the different stages of their annual cycle is necessary for the conservation and management of migratory bird species. Stable isotope technology has the potential to shed light on the movements of migratory species and to help us better understand their population dynamics. Several studies use stable hydrogen isotopes in particular to predict origins of birds sampled during migration or in winter. However, recent work on stable hydrogen isotopes in feathers (δD_f) draws into question the utility of this technology in estimating origins of migrants. My objective was to determine whether …

Genome 10k: A Proposal To Obtain Whole-Genome Sequence For 10000 Vertebrate Species, David Haussler, Stephen J. O'Brien, Oliver A. Ryder, F. Keith Barker, Michele Clamp, Andrew J. Crawford, Robert Hanner, Olivier Hanotte, Warren E. Johnson, Jimmy A. Mcguire, Webb Miller, Robert W. Murphy, William J. Murphy, Frederick H. Sheldon, Barry Sinervo, Byrappa Venkatesh, Edward O. Wiley, Fred W. Allendorf, George Amato, C. Scott Baker, Aaron Bauer, Albano Beja-Pereira, Eldredge Bermingham, Giacomo Bernardi, Cibele R. Bonvicino, Sydney Brenner, Terry Burke, Joel Cracraft, Mark Diekhans

Biology Faculty Articles

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16203 representative vertebrate species spanning evolutionary diversity across living …

Genome 10k: A Proposal To Obtain Whole-Genome Sequence For 10 000 Vertebrate Species, Tony Gamble, Genome 10k Community Of Scientists

Biological Sciences Faculty Research and Publications

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10 000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G₁₀KCOS), will assemble and allocate a biospecimen collection of some 16 203 representative vertebrate species spanning …

Time's Arrow Flies Like A Bird: Two Paradoxes For Avian Circadian Biology, Vincent M. Cassone, Jiffin K. Paulose, Melissa G. Whitfield-Rucker, Jennifer L. Peters

Biology Faculty Publications

Biological timekeeping in birds is a fundamental feature of avian physiology, behavior and ecology. The physiological basis for avian circadian rhythmicity has pointed to a multi-oscillator system of mutually coupled pacemakers in the pineal gland, eyes and hypothalamic suprachiasmatic nuclei (SCN). In passerines, the role of the pineal gland and its hormone melatonin is particularly important. More recent molecular biological studies have pointed to a highly conserved mechanism involving rhythmic transcription and translation of "clock genes". However, studies attempting to reconcile the physiological role of pineal melatonin with molecular studies have largely failed. Recent work in our laboratory has suggested …

Reversed-Phase Hplc Determination Of Alliin In Diverse Varieties Of Fresh Garlic And Commercial Garlic Products., Aaron Kwaku Apawu

Electronic Theses and Dissertations

Alliin is a predominant flavor precursor in garlic cloves. It interacts with the enzyme alliinase when garlic cloves are crushed, cut, or chewed to produce allicin, an unstable thiosulfinate that is the main biologically active component of fresh crushed garlic. Biological functions and health benefits of garlic include reduction of cancer risk in humans, improving immune system, and anti-microbial, anti-oxidant, and anti-hypertensive activities. The quality of fresh garlic and garlic products is usually related to its alliin content and allicin release potential. This research presents a simple, rapid, and precise HPLC method for alliin determination. It involves the use of …

Population Ecology Of The Floodplain Herb Macbridea Caroliniana (Lamiaceae) With Investigations On The Species' Habitat, Breeding System And Genetic Diversity, Katherine Weeks

All Dissertations

The perennial herbaceous mint Macbridea caroliniana is known from 36 locations in discrete watersheds of the Carolinas and Georgia. It is one of relatively few conspicuously flowering herbs that occupy bottomland hardwood forests. The general project goal was to gain knowledge that is applicable to the species' conservation both at the Congaree National Park (CNP) where the largest known population of this species occurs and range-wide. Specific objectives were to (1) quantify the population size and describe the distribution of M. caroliniana within CNP, and determine the extent of co-occurrence with wild hogs and the non-native Murdannia keisak; (2) identify …

Assessment Of Pre-Pcr Whole Genome Amplification Of Single Pollen Grains Using Flowering Dogwood (Cornus Florida), Candace Dillon

Theses and Dissertations

Studies of gene flow in natural plant populations often focus on either historical or abiotic dispersal methods (e.g. wind, water, gravity), but there is little information available on contemporary, animal-mediated pollen dispersal patterns. Emerging molecular laboratory techniques allow unprecedented insights into spatial patterns of pollen-mediated gene flow. However, to date, technical challenges have limited their widespread application. The genome of a pollen grain can be amplified via whole genome amplification (WGA) prior to traditional amplification via polymerase chain reaction (PCR) to prevent the stochastic effects associated with low copy number amplification. Even still, WGA can suffer from low success rates …

Temporal Shifts In Demography And Life History Of An Anadromous Alewife Population In Connecticut, Justin P. Davis, Eric T. Schultz

EEB Articles

Populations of anadromous alewives (Alosa pseudoharengus) are declining throughout much of their range, particularly in southern New England where fishery moratoriums have recently been instituted in three states. The alewife run at Bride Brook, a coastal stream in East Lyme, Connecticut, was studied from 2003-06 to assess shifts in demography and life history. Annual censuses of abundance, along with sampling for size, age, and spawning history structure were conducted. These data were compared to similar data in 1966-67 at this site. Recent alewife runs at Bride Brook featured lower abundance and younger, smaller fish that were less likely to be …

Hair Identification: The Mammalian Fingerprint, E. Santana

Wildlife Damage Management Conference

Microscopic hair identification has been used as an analysis tool in a broad range of biological studies and has diverse applications in the fields of wildlife biology, anthropology, forensics, and natural resource management. Examining differences in cortex patterns, medulla characteristics, cuticular scale anatomy, shape, size, and color can be used to reliably identify mammalian guard hairs. Microscopic hair identification provides a diagnostic tool for identifying mammalian hair and has broad applications in the field of wildlife damage management. Hair collected from scent stations can provide presence confirmation and population density estimates on carnivores and ungulates, while hairs extracted from scats …

Investigations Into Earthworm Control On Airports, T. Seamans, G. Bernhardt, D. Steyer

Wildlife Damage Management Conference

Earthworms, though generally considered beneficial for soil conditioning, can become a hazard at airports. When found in large numbers on runways or taxiways after heavy rainfall, they create slippery conditions for aircraft rolling over them. Additionally, earthworms attract birds, especially gulls, thereby increasing the risk of bird strikes to aircraft that are landing or taking off. For example, during a 35-minute period on 3 September 2004 at Calgary International Airport (YYC), a B737 of Westjet and an A319 of Air Canada aborted takeoffs after multiple strikes with gulls attracted to the runways to feed on earthworms. The B737 had strikes …