Digital Commons Network^™

Is Anthropogenic Cougar Mortality Compensated By Changes In Natural Mortality In Utah? Insight From Long-Term Studies, Michael L. Wolfe, David N. Koons, David C. Stoner, Patricia Terletzky, Eric M. Gese, David M. Choate, Lise M. Aubry

United States Department of Agriculture Wildlife Services: Staff Publications

Understanding the interplay between exploitation and natural mortality is essential to guiding sustainable conservation of wildlife. Exploitation of carnivores by humans has long been thought to result in compensatory reductions of natural mortality among survivors. If rates of human exploitation exceed natural mortality, however, such actions will ‘add’ to overall mortality and could imperil the sustainability of such actions. We applied competing risk analyses to >16 years of data for heavily harvested and semi-protected cougar populations in Utah to test the additive and compensatory mortality hypotheses, while accounting for parameter uncertainty. We additionally tested for presence of the two primary …

Daily Activity Budgets Reveal A Quasi-Flightless Stage During Non-Breeding In Hawaiian Albatrosses, Sarah Gutowsky, Lee Gutowsky, Ian Jonsen, Marty Leonard, Maura Naughton, Marc Romano, Scott A. Shaffer

Faculty Publications, Biological Sciences

Background Animals adjust activity budgets as competing demands for limited time and energy shift across life history phases. For far-ranging migrants and especially pelagic seabirds, activity during breeding and migration are generally well studied but the “overwinter” phase of non-breeding has received less attention. Yet this is a critical time for recovery from breeding, plumage replacement and gaining energy stores for return migration and the next breeding attempt. We aimed to identify patterns in daily activity budgets (i.e. time in flight, floating on the water’s surface and active foraging) and associated spatial distributions during overwinter for the laysan Phoebastria immutabilis …

Caspase-3 Mediates The Pathogenic Effect Of Yersinia Pestis Yopm In Liver Of C57bl/6 Mice And Contributes To Yopm's Function In Spleen, Zhan Ye, Amanda A. Gorman, Annette M. Uittenbogaard, Tanya Myers-Morales, Alan M. Kaplan, Donald A. Cohen, Susan C. Straley

Microbiology, Immunology, and Molecular Genetics Faculty Publications

The virulence protein YopM of the plague bacterium Yersinia pestis has different dominant effects in liver and spleen. Previous studies focused on spleen, where YopM inhibits accumulation of inflammatory dendritic cells. In the present study we focused on liver, where PMN function may be directly undermined by YopM without changes in inflammatory cell numbers in the initial days of infection, and foci of inflammation are easily identified. Mice were infected with parent and ΔyopM-1 Y. pestis KIM5, and effects of YopM were assessed by immunohistochemistry and determinations of bacterial viable numbers in organs. The bacteria were found …

Publication Trends In Model Organism Research, Michael Dietrich, Rachel Ankeny, Patrick Chen

Dartmouth Scholarship

In 1990, the National Institutes of Health (NIH) gave some organisms special status as designated model organisms. This article documents publication trends for these NIH-designated model organisms over the past 40 years. We find that being designated a model organism by the NIH does not guarantee an increasing publication trend. An analysis of model and nonmodel organisms included in GENETICS since 1960 does reveal a sharp decline in the number of publications using nonmodel organisms yet no decline in the overall species diversity. We suggest that organisms with successful publication records tend to share critical characteristics, such as being well …

Study The Quality Of Groundwater Of Al-Zoroup Area In Mahdah State, The Sultanate Of Oman, Fahad Khalifa Rashid Al-Shidi

Theses

The groundwater is the most important source of water in the Sultanate of Oman. Accordingly, the Oman Government has paid great attention commensurate with the importance of water resource in terms of their sources, quality, and ways to rationalize consumption to remain under the term of sustainability and validity of present and future generations. This study was conducted in Al Buraymi at Mahdah State in Al-Zoroub area targete a groundwater quality for 20 wells in private farms. The water samples were taken from these wells and subjected to analysis for microbial and geochemical aspects. For this analysis, the assorted devices …

Documentation Of The Black-Footed Ferret, Mustela Nigripes On The Standing Rock Indian Reservation, Mobridge, South Dakota, Michael P. Gutzmer, Jeffrey C. Kelly

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Since 1991, 19 specific black-footed ferret reintroduction projects have been conducted across 8 States, Canada, and Mexico. All five of the first ferret reintroductions (from 1991 to 1996) continue to be occupied by ferrets. The photographs of October 31 and November 1 are the first unequivocal documentation of black-footed ferrets on the Standing Rock Indian Reservation. Ferrets observed on Standing Rock may be dispersals from the nearby Cheyenne River Sioux Indian Reservation to the south. The nearest re-introduction site for ferrets is approximately 20 miles away, in Whitehorse, South Dakota, and the observation of ferrets on Standing Rock could document …

The Cosm Newsletter

COSM Newsletter

• The College of Science and Mathematics Welcomes New Administration in the Dean’s Office
• COSM Faculty and Staff Recognized at College and University Levels
• College Awards
• University Awards
• Summer SOAR Project: Books for Back Pack Buddies
• COSM Alum Honored in Promotion Ceremony at the Pentagon
• Altrusa partners with Georgia Southern Pre-Vet Students for First Annual Dog Wash
• Two COSM Undergrads selected for Prestigious Summer Research Programs
• The Department of Biology Welcomes New Faculty
• Dr. Ed Mondor Named 2014 Outstanding Advocate for First Year Students
• Distinguished Alumnus Chosen
• Honor’s Day Ceremony Resumes
• Professor Gives Talk at 11th Congress on the Biology of …

Characterization Of Metal-Reducing Microorganisms In Walker Lake: A Terminal Saline Desert Lake, Memona Khan

Honors College Theses

Metal-reducing microorganisms are increasingly being recognized as an essential component of aquatic microbial ecosystems involved in decomposition of organic matter. Alkaliphilic microbial reduction from alkaline lakes is a little studied field and one particular ecosystem, Walker Lake, presents the opportunity to investigate alkaliphilic metal reducers in their native ecological setting. Walker lake is a terminal, saline, desert lake with pH 9.4, Walker Lake samples of surface and deep sediments and water column samples from 0, 10, 5, 15, 17.5, 19 m depths were cultured by serial dilution in synthetic Walker Lake medium and supplemented separately with Hydrous Ferric Oxide (HFO), …

The Cosm Newsletter, Georgia Southern University

College of Science & Mathematics: News & Publications (2012-2022)

• The College of Science and Mathematics Welcomes New Administration in the Dean’s Office
• COSM Faculty and Staff Recognized at College and University Levels
• College Awards
• University Awards
• Summer SOAR Project: Books for Back Pack Buddies
• COSM Alum Honored in Promotion Ceremony at the Pentagon
• Altrusa partners with Georgia Southern Pre-Vet Students for First Annual Dog Wash
• Two COSM Undergrads selected for Prestigious Summer Research Programs
• The Department of Biology Welcomes New Faculty
• Dr. Ed Mondor Named 2014 Outstanding Advocate for First Year Students
• Distinguished Alumnus Chosen
• Honor’s Day Ceremony Resumes
• Professor Gives Talk at 11th Congress on the Biology of …

Component Trees For The Exploration Of Macromolecular Structures In Biology, Lucas Oliveira

Dissertations, Theses, and Capstone Projects

Understanding the three-dimensional structure of a macromolecular complex is essential for understanding its function. A component tree is a topological and geometric image descriptor that captures information regarding the structure of an image based on the connected components determined by different grayness thresholds. This dissertation presents a novel interactive framework for visual exploration of component trees of the density maps of macromolecular complexes, with the purpose of improved understanding of their structure. The interactive exploration of component trees together with a robust simplification methodology provide new insights in the study of macromolecular structures. An underlying mathematical theory is introduced and …

Mapping Regions Of Rnf168 Required For Its Degradation By Icp0, Andrea Cyr, Matthew Weitzman

e-Research: A Journal of Undergraduate Work

Viruses establish infection by overtaking host cell processes and developing mechanisms that promote viral replication. Herpes simplex virus undergoes lytic and latent cycles of infection throughout the lifespan of its host. The viral genome is transcriptionally silent during latency, but viral proteins are produced upon reactivation. Herpes simplex virus type 1 encodes the ICP0 protein, an E3 ubiquitin ligase required for reactivation from latency of the infectious virus. The immediate-early protein ICP0 regulates the herpes simplex virus by activating viral gene expression thereby initiating lytic infection. Cellular proteins are degraded by ICP0, promoting the virus to enter the lytic cycle. …

Use Of Cysteine-Reactive Crosslinkers To Probe Conformational Flexibility Of Human Dj-1 Demonstrates That Glu18 Mutations Are Dimers, Janani Prahlad, David N. Hauser, Nicole M. Milkovic, Mark R. Cookson, Mark A. Wilson

Department of Biochemistry: Faculty Publications

The oxidation of a key cysteine residue (Cys106) in the parkinsonism-associated protein DJ-1 regulates its ability to protect against oxidative stress and mitochondrial damage. Cys106 interacts with a neighboring protonated Glu18 residue, stabilizing the Cys106-SO₂ ⁻ (sulfinic acid) form of DJ-1. To study this important post-translational modification, we previously designed several Glu18 mutations (E18N, E18D, E18Q) that alter the oxidative propensity of Cys106. However, recent results suggest these Glu18 mutations cause loss of DJ-1 dimerization, which would severely compromise the protein’s function. The purpose of this study was to conclusively determine the oligomerization state of these mutants using X-ray …

Biophysical Interactions In The Straits Of Florida: Turbulent Mixing Due To Diel Vertical Migrations Of Zooplankton, Cayla Whitney Dean

HCNSO Student Theses and Dissertations

Diel vertical migrations (DVM) comprise the largest animal migration on the planet and are a phenomenon present in all bodies of water on Earth. A strong sound scattering layer undergoing DVM was observed in the Straits of Florida via a bottom-mounted Acoustic Doppler current profiler (ADCP) Workhorse Longranger 75 kHz (Teledyne RD Instruments) located at the 244 m isobath. ADCP average backscatter showed a clear periodicity corresponding with sunrise and sunset times indicating the presence of a nocturnal DVM. Analysis of the ADCP backscatter data indicated zooplankton swimming velocities were faster during sunrise than sunset times. In several cases the …

Particle Swarm Optimization Using Multiple Neighborhood Connectivity And Winner Take All Activation Applied To Biophysical Models Of Inferior Colliculus Neurons, Brandon S. Coventry

Open Access Theses

Age-related hearing loss is a prevalent neurological disorder, affecting as many as 63% of adults over the age of 70. The inability to hear and understand speech is a cause of much distress in aged individuals and is becoming a major public health concern as age-related hearing loss has also been correlated with other neurological disorders such as Alzheimer's dementia. The Inferior Colliculus (IC) is a major integrative auditory center, receiving excitatory and inhibitory inputs from several brainstem nuclei. This complex balance of excitation and inhibition gives rise to complex neural responses, which are measured in terms of firing rate …

Evaluating The Utility Of Natural History Collections In Research And For The Public, Bethany L. Abrahamson

Biology ETDs

Natural history collections (NHCs) are useful in many fields of study, but knowledge about how they are used in the modern day is poor. The first part of this study, focused on the collections data held by the Museum of Southwestern Biology (MSB), analyzes specimen-based publications, specimen loan records, and guestbook information to determine how NHCs have been used in scientific study over time. Using a novel methodology, I objectively sorted the publications into ten research subjects via particular phrases found in publication titles, places of publication, and keywords. I observed from this dataset the proportions of particular subjects for …

Branching Into Rnai: Synthesis, Characterization And Biology Of Branch And Hyperbranch Sirnas, Anthony Muriithi Maina

Seton Hall University Dissertations and Theses (ETDs)

The cancer epidemic continues to afflict millions of humans world-wide each year and despite a renewed hope with the development of new and improved forms of therapy, a cure for cancer remains an elusive goal. This is partly related to the rise of resilient forms of tumors that have evolved with resistance towards conventional chemotherapy and radiation treatments. Moreover, these non-specific therapeutic regimens are highly toxic, leading to severe immunosuppressive effects which poisons the body and compromises the road towards remission. In an effort to mitigate these limitations, cancer-targeting approaches are currently experiencing a renaissance in the translation of new …

On Individual, Sex And Age Differentiation Of Indian House Crow (Corvus Splendens) Call: A Preliminary Study In Potohar, Pakistan, Waqas Hameed, Inayat Ullah, Safia Janjua, Fakhar -I- Abbas, Afsar Mian

Journal of Bioresource Management

Considering importance of acoustics studies in population biology, 500 calls of the Indian House Crow (Corvus splendens) were recorded in morning - mid-afternoon hours (January-February, 2009) from 23 sites of urban areas of Potahar (Punjab, Pakistan). Calls were recorded using Sony CFS 1030 S sound records (sampling rate = 48 KHz) and edited using Sound Analysis Pro (Version 1.02). software using FFT method rate 50%, data window 9.27 ms, advanced window 1.36 ms. Through editing of calls, we selected 60 (37 ♂♂, 17 ♀♀, 6 Juvenile ♂♂) good quality spectrograms for detailed analysis. Spectrograms were characterized by rapid frequency modulations …

Status Of Demersal Finfish Stocks On The West Coast Of Australia, David V. Fairclough, Brett W. Molony, Brett M. Crisafulli, Ian S. Keay, Sybrand Alexander Hesp, Ross J. Marriott

Fisheries Research Reports

Assessments of the key indicator species for the West Coast Demersal Scalefish Resource (WCDSR; West Australian dhufish Glaucosoma hebraicum, Snapper Pagrus auratus and Baldchin groper Choerodon rubescens) in 2007 and 2009 demonstrated that the stocks were experiencing overfishing. Thus, between late 2007 and early 2010, substantial changes were made to the management of the commercial and recreational fisheries that exploit the WCDSR. These were designed to reduce catches of the entire suite of demersal scalefish species (and of each indicator species) by both the commercial and recreational sectors in the West Coast Bioregion (WCB) by at least 50 % of …

Investigations Of Cho 1-15 And Silk Gland Cell Line Development, Susan Kathleen Robinson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The BioProcessing Demonstration and Training Laboratory was established with a collaboration between Utah State University and Thermo Fisher-Scientific, Inc. This lab was developed into a fully functioning tissue culture facility. Demonstration of tissue culture procedures were necessary for the lab to be industry-fully qualified. The CHO 1-15 cell line protocols were optimized by establishing conditions for reproducibility in shaker flasks and bioreactors (2 to 250 L capacity). CHO 1-15 is the cell line of choice for protein production in the bio-manufacturing industry. Oxidative stress is a problem in the industry because it can cause a decrease in protein production. Mesobiliverdin …

An Evaluation Of The East Indianapolis Food Desert, Angelina Qin

Undergraduate Honors Thesis Collection

The Indy East Food Desert (IEFD) appears to suffer from many common conditions noted by various scholars as food desert identifiers. Yet, its situation still remains unique. Though there is a prevalence of minority populations, low-income households, and low-education attainment levels, there are also factors of low-access, poor food options (within the limited food outlets in the neighborhoods), and poor eating habits which shape the situation of the community. In an attempt to alleviate the food desert problems, the Indy East Food Desert Coalition (IEFDC) was formed. IEFDC partnered with Butler University's Center for Urban Ecology in order to assess …

Analysis Of Social Dominance In The Green Anole, Jordan Mckenzie Bush

Biology Honors Theses

Dominance relationships are an important aspect of the social organization of many species. Male dominance often results in successful territory defense and/or access to potential mates, and thus is a central component in establishing social rank. In this study, I used mathematical models to consider social interactions of the green anole lizard (Anolis carolinensis) in both territorial and hierarchical contexts. I then identified the behavioral and morphological traits associated with dominance in this species.

I first analyzed a series of ranking algorithms to evaluate their effectiveness as a novel approach to quantifying animal social status. I found that all eight …

Acetobixan, An Inhibitor Of Cellulose Synthesis Identified By Microbial Bioprospecting, Ye Xia, Lei Lei, Chad Brabham, Jozsef Stork, James R. Strickland, Adam Ladak, Ying Gu, Ian Wallace, Seth Debolt

Horticulture Faculty Publications

In plants, cellulose biosynthesis is an essential process for anisotropic growth and therefore is an ideal target for inhibition. Based on the documented utility of small-molecule inhibitors to dissect complex cellular processes we identified a cellulose biosynthesis inhibitor (CBI), named acetobixan, by bio-prospecting among compounds secreted by endophytic microorganisms. Acetobixan was identified using a drug-gene interaction screen to sift through hundreds of endophytic microbial secretions for one that caused synergistic reduction in root expansion of the leaky AtcesA6prc1-1 mutant. We then mined this microbial secretion for compounds that were differentially abundant compared with Bacilli that failed to mimic CBI action …

A Novel Three Degree-Of-Freedoms Oscillation System Of Insect Flapping Wings, Yi Qin

Open Access Theses

We propose an oscillation system to replicate the dynamic behavior of flapping wings, inspired by insect flight muscles. In particular, we study the flight of the fruit fly Drosophila virilis . We model the wing as a rigid body with three degree-of-freedom, described by three Euler angles: the stroke angle, the rotation angle and the deviation angle. Insect flight muscles are separated into two types: power muscles and control muscles. One actuator and one torsional spring at the stroke angle act as the power muscles. Two torsional springs at the rotation angle and the deviation angle mimic the control muscles. …

Modeling Stem Cell Population Dynamics, Samiur Arif

Computer Science Theses & Dissertations

Because of the stochastic nature of biological systems, mathematical and computational modeling approaches have become more acceptable to experimentalists and clinicians in recent years as contributing to new understandings of complicated cell mechanisms and tissue physiology. Indeed, even single cell or small tissue samples are complex dynamic systems that adapt to environmental challenges in space and time which is poorly understood. Mathematical models and computer simulations can explain and uncover unknown aspects of cell behavior and tissue functions. Models based on key biological mechanisms can give interesting insights and formulate predictions that cannot be derived from physical experiments or statistical …

Strad Pseudokinases Regulate Axogenesis And Lkb1 Stability, Biliana O. Veleva-Rotse, James L. Smart, Annette F. Baas, Benjamin Edmonds, Zi-Ming Zhao, Allyson Brown, Lillian R. Klug, Kelly Hansen, Gabrielle Rielly, Alexandria P. Gardner, Krishnaveni Subbiah, Eric A. Gaucher, Hans Clevers, Anthony P. Barnes

Faculty Publications - Department of Biological & Molecular Science

No abstract provided.

The Ipocamp Pressure Incubator For Deep-Sea Fauna, Bruce Shillito, Françoise Gaill, Juliette Ravaux

Journal of Marine Science and Technology–Taiwan

Animal Biology studies have always benefited from the achievement of experiments on live animals, which obviously provide data on dynamic aspects of physiology. When it comes to deep-sea fauna, in vivo experiments are impaired, and in some cases impossible, due to the severe and often lethal stress experienced by animals throughout the sampling process. However, freshly collected deep fauna may be maintained alive and in good condition, by using specific aquaria which restore environmental conditions prevailing at depth in situ. Here we describe the pressure device named “Incubateur Pressurisé pour l’Observation et la Culture d’Animaux Marins Profonds”, or IPOCAMP, and …

Copy Number Variation In Chickens: A Review And Future Prospects, Xiaofei Wang, Shannon Byers

Biology Faculty Research

DNA sequence variations include nucleotide substitution, deletion, insertion, translocation and inversion. Deletion or insertion of a large DNA segment in the genome, referred to as copy number variation (CNV), has caught the attention of many researchers recently. It is believed that CNVs contribute significantly to genome variability, and thus contribute to phenotypic variability. In chickens, genome-wide surveys with array comparative genome hybridization (aCGH), SNP chip detection or whole genome sequencing have revealed a large number of CNVs. A large portion of chicken CNVs involves protein coding or regulatory sequences. A few CNVs have been demonstrated to be the determinant factors …

An Ethnobotanical, Ecological And Lc-Ms-Based Chemometric Investigation Of Phaleria Nisidai, A Traditional Adaptogen Containing Diterpene Esters From Palau, Micronesia, Daniel Kulakowski

Dissertations, Theses, and Capstone Projects

An ethnobotanical, ecological and LC-MS-based chemometric investigation of Phaleria nisidai, a traditional adaptogen containing diterpene esters from Palau, Micronesia

Palau is a country with a rich heritage of traditional medicine still being practiced. One of the most popular and respected remedies in Palau is a tea made from fresh leaves of Phaleria nisidai Kaneh. (Thymelaeaceae). Interviews conducted to determine the use of this plant revealed that it is employed non-specifically to treat a variety of general health concerns. Its use as a prophylactic to keep away sickness, as a 'system cleaner', as well as for strength and energy indicate …

Serpentine Soils, Nishanta Rajakaruna, R. S. Boyd

Faculty Publications, Biological Sciences

Serpentine soils are weathered products of a range of ultramafic rocks composed of ferromagnesian silicates. Serpentine more accurately refers to a group of minerals, including antigorite, chrysotile, and lizardite, in hydrothermally altered ultramafic rocks. Common ultramafic rock types include peridotites (dunite, wehrlite, harzburgite, lherzolite) and the secondary alteration products formed by their hydration within the Earth’s crust, including serpentinite, the primary source of serpentine soil. Serpentine soils are generally deficient in plant essential nutrients such as nitrogen, phosphorus, potassium, and sulfur; have a calcium-to-magnesium (Ca:Mg) molar ratio of less than 1; and have elevated levels of heavy metals such as …

Investigation Into The Binding Interactions Of Klenow Fragment To Dna Modified With Carcinogens Af And Aaf Using Surface Plasmon Resonance, Ashley M. Floyd

Wayne State University Dissertations

The two major forms of DNA adducts from the carcinogen N-acetoxyacetyl-2-aminofluorene, N-(deoxygunanonsin-8-yl)-2-acetylaminofluorene (dG-C8-AAF) and N-(deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF), are both known to impede replication, though in different ways. AAF is a strong block to replication leading to frameshift mutations, while the AF adduct is more easily bypassed, causing base substitutions. Surface plasmon resonance (SPR) was used to study the binding of exonuclease deficient E. coli polymerase I, Klenow fragment (KF), to DNA modified with AF or AAF at two locations: as a templating base or in the last formed base pair. KF binding to the modified DNA bases was also monitored to …