Life Sciences Commons^™

Secondary Structure, A Missing Component Of Sequence- Based Minimotif Definitions, David P. Sargeant, Michael R. Gryk, Mark W. Maciejewsk, Vishal Thapar, Vamsi Kundeti, Sanguthevar Rajasekaran, Pedro Romero, Keith Dunker, Shun-Cheng Li, Tomonori Kaneko, Martin Schiller

Life Sciences Faculty Research

Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis …

Phenotypic Plasticity Of Oral Jaw Dentition In Archosargus Probatocephalus, Cynthia E. Worcester

Masters Theses & Specialist Projects

Phenotypic plasticity, the capacity of a single genotype to exhibit variable phenotypes in different environments, is common in many species. A sample of wild caught Archosargus probatocephalus, also known as sheepshead, from Florida was randomly divided into two treatment groups: one group was fed soft prey, Mercenaria sp. muscle tissue, and the other group was fed hard prey, Mercenaria sp. in the shell, for 365 days. It was hypothesized that the sheepshead fed hard prey would have a thicker tooth enamel layer containing more calcium, and therefore be stronger than the tooth enamel layer of those fed soft prey …

Contour Extraction Of Drosophila Embryos Using Active Contours In Scale Space, Soujanya Siddavaram Ananta

Masters Theses & Specialist Projects

Contour extraction of Drosophila embryos is an important step to build a computational system for pattern matching of embryonic images which aids in the discovery of genes. Automatic contour extraction of embryos is challenging due to several image variations such as size, shape, orientation and neigh- boring embryos such as touching and non-touching embryos. In this thesis, we introduce a framework for contour extraction based on the connected components in the gaussian scale space of an embryonic image. The active contour model is applied on the images to refine embryo contours. Data cleaning methods are applied to smooth the jaggy …

Differential Expression Of Alpha 4 Integrins On Effector Memory T Helper Cells During Bordetella Infections. Delayed Responses In Bordetella Pertussis, Tzvia Abramson, Tuan M. Nguyen, Dipti Ravindra, Brian Kwong, Sana Waheed, Ryan Ferguson, Nicole Tarlton, Victoria Wu, Christopher S. Sequeira, Martina Bremer

Faculty Publications, Biological Sciences

Bordetella pertussis (B. pertussis) is the causative agent of whooping cough, a respiratory disease that is reemerging worldwide. Mechanisms of selective lymphocyte trafficking to the airways are likely to be critical in the immune response to this pathogen. We compared murine infection by B. pertussis, B. parapertussis, and a pertussis toxin-deleted B. pertussis mutant (BpΔPTX) to test the hypothesis that effector memory T-helper cells (emTh) display an altered pattern of trafficking receptor expression in B. pertussis infection due to a defect in imprinting. Increased cell recruitment to the lungs at 5 days post infection (p.i.) with B. parapertussis, and to …

Environmental Groups In Jordan: Cooperating To Avoid Disaster, Laurel Wolf

Student Foreign Language Research

No abstract provided.

Benchmarking Cow Comfort On North American Freestall Dairies: Lameness, Leg Injuries, Lying Time, Facility Design, And Management For High-Producing Holstein Dairy Cows, Marina A.G. Von Keyserlingk, A. K. Barrientos, K. Ito, E. Galo, Daniel M. Weary

Housing and Confinement of Farm Animals Collection

In this paper, we describe a novel approach to corporate involvement in on-farm assessment, driven by the desire to provide a service for dairy producers and to create a vehicle for engagement on issues of dairy cow welfare. This program provides producers with feedback on animal-based (including gait score, leg injuries, and lying time) and facility-based (including freestall design, bedding practices, feed bunk design and management, and stocking density) measures that can be used to better address their management goals. The aim of this paper is to describe variation in the prevalence of lameness and leg injuries, lying behavior, facility …

Species Shout-Outs From Abdul To Zebra: Encouraging Nonmajors To Communicate In The Biology Classroom, Christina P. Colon

Publications and Research

No abstract provided.

Product Pig Production Planner, Scott Williams, Darrell Rothlisberger

Archived Agriculture Publications

There are many factors to consider when selecting a market hog for your 4-H project animal. Seek out reputable hog producers who produce hogs with high quality genetics and growth potential. Discuss the health and feeding program the hogs have received and follow these recommendations to assure your project animal can reach its growth potential.

Assessing The Nutritional Health Outcomes Of African American Women With Hiv And Substance Abuse Disorders Using A Socioecological Approach, Meena Mahadevan, John Ruzsilla

Department of Nutrition and Food Studies Scholarship and Creative Works

It is well established that poor nutritional status leaves HIV-positive substance abusers especially vulnerable to an increased risk of opportunistic infections and other illnesses. Socioecological frameworks have been useful for identifying multiple influences on health risks, leading to the development and evaluation of promising community-based interventions for diseases such as cancer and diabetes. This article presents a conceptual model, based on the socioecological approach, to examine the mechanisms and pathways by which the various contextual factors unique to HIV-positive African American women with substance abuse disorders intersect to impact their nutritional health outcomes. The mediating effects of the interpersonal, environmental, …

User Taglines: Alternative Presentations Of Expertise And Interest In Social Media, Hemant Purohit, Alex Dow, Omar Alonso, Lei Duan, Kevin Haas

Kno.e.sis Publications

Web applications are increasingly showing recommended users from social media along with some descriptions, an attempt to show relevancy - why they are being shown. For example, Twitter search for a topical keyword shows expert twitterers on the side for 'whom to follow'. Google+ and Facebook also recommend users to follow or add to friend circle. Popular Internet newspaper- The Huffington Post shows Twitter influencers/ experts on the side of an article for authoritative relevant tweets. The state of the art shows user profile bios as summary for Twitter experts, but it has issues with length constraint imposed by user …

Winter Microhabitat Foraging Preferences Of Sympatric Boreal And Black-Capped Chickadees In Michigan's Upper Peninsula, Alec R. Lindsay Ph. D., Zach G. Gayk

Faculty Works

We examined differences in microhab- itat use between Boreal (Poecile hudsonicus) and Black- capped chickadees (P. atricapillus) where they co-occur near Marquette, Michigan, USA. Twenty-four Boreal and 37 Black-capped chickadees were followed during 60 hrs of field observation. Boreal Chickadees foraged only in three conifer species, 76% of which were black spruce (Picea mariana), while Black-capped Chickadees foraged widely across six coniferous and three deciduous tree species. Analysis of foraging data categorized by zones within conifer trees indicated high niche overlap (0.676) between Boreal and Black-capped chickadees across all foraging zones. Individual comparisons on a zone-by-zone basis revealed a significant …

Cues Used By The Black Fly, Simulium Annulus, For Attraction To The Common Loon (Gavia Immer), Meggin L. Weinandt, Michael W. Meyer, R. Mac Strand, Alec R. Lindsay Ph. D.

Faculty Works

The parasitic relationship between a black fly, Simulium annulus, and the common loon (Gavia immer) has been considered one of the most exclusive relationships between any host species and a black fly species. To test the host specificity of this blood-feeding insect, we made a series of bird decoy presentations to black flies on loon-inhabited lakes in northern Wisconsin, U.S.A. To examine the importance of chemical and visual cues for black fly detection of and attraction to hosts, we made decoy presentations with and without chemical cues. Flies attracted to the decoys were collected, identified to species, and quantified. Results …

Determination Of Repetitive Jumping Intensity Relative To Measured Vo2max, Laura Igaune

Masters Theses & Specialist Projects

To regular exercise and a healthy diet, the American Heart Association (AHA) strongly recommends rope jumping, and according to previous studies, rope jumping is considered a very strenuous exercise. Therefore the purpose of this study was to determine the steady state metabolic cost of repetitive jumping on the Digi-Jump machine, and to determine if exercise on this device is more or less strenuous than similar exercise with a jump rope. We also evaluated relative intensity of this type of exercise, based on each person’s VO_2max as measured on a treadmill. Twenty – seven subjects completed two trials, one jumping …

Influences Of A Cladophora Bloom On The Diets Of Amblema Plicata And Elliptio Dilatata In The Upper Green River, Kentucky, Jennifer Maria Yates

Masters Theses & Specialist Projects

Freshwater mussels are the most imperiled group of freshwater invertebrates globally. Recent research suggests a better understanding of mussel feeding ecology may facilitate and improve conservation efforts. The use of stable isotopes is becoming an increasingly common method to study aquatic food webs. Carbon (C) and nitrogen (N) are two of the most frequently employed elements in food web studies. Differences in natural abundance of ¹³C/¹²C can indicate which food sources are the basal sources of carbon incorporated into a consumer’s tissue, while the ratio of ¹⁵N /¹⁴N provides a method of assessing trophic …

Draft Genome Sequence For Pseudomonas Aeruginosa Strain Pao579, A Mucoid Derivative Of Pao381, T. Ryan Withers, Shannon L. Johnson, Hongwei D. Yu

Biochemistry and Microbiology

Pseudomonas aeruginosa is an opportunistic pathogen that establishes a chronic lung infection in individuals afflicted with cystic fibrosis. Here, we announce the draft genome of P. aeruginosa strain PAO579, an alginate-overproducing derivative of strain PAO381.

Septohippocampal Gabaergic Neurons Mediate The Altered Behaviors Induced By N-Methyl-D-Aspartate Receptor Antagonists., Jingyi Ma, Siew Kian Tai, L Stan Leung

Physiology and Pharmacology Publications

We hypothesize that selective lesion of the septohippocampal GABAergic neurons suppresses the altered behaviors induced by an N-methyl-D-aspartate (NMDA) receptor antagonist, ketamine or MK-801. In addition, we hypothesize that septohippocampal GABAergic neurons generate an atropine-resistant theta rhythm that coexists with an atropine-sensitive theta rhythm in the hippocampus. Infusion of orexin-saporin (ore-SAP) into the medial septal area decreased parvalbumin-immunoreactive (GABAergic) neurons by ~80%, without significantly affecting choline-acetyltransferase-immunoreactive (cholinergic) neurons. The theta rhythm during walking, or the immobility-associated theta induced by pilocarpine, was not different between ore-SAP and sham-lesion rats. Walking theta was, however, more disrupted by atropine sulfate in ore-SAP than …

Sagestep News, Fall 2012, No. 20, Sagestep

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Ecologists Engaging With Communities And Regional Decision-Makers: Organized Oral Session 14 At The 2011 Esa Annual Meeting In Austin, Texas, Nadine Lymn, George Middendorf

Department of Biology Faculty Publications

No abstract provided.

Resistance Screening And Control Options For Glyphosate-Resistant Palmer Amaranth (Amaranthus Palmeri) In Cotton (Gossypium Hirsutum), Ryan Christopher Doherty

Graduate Theses and Dissertations

In the mid-2000's, glyphosate-resistant Palmer amaranth biotypes began to emerge in many southern states. In 2006, glyphosate-resistant Palmer amaranth was identified in a field in Mississippi County, Arkansas. A greenhouse experiment was conducted in 2008 to screen Palmer amaranth accessions, collected in this survey, for glyphosate resistance. Inflorescence were collected from a total of 276 plants from fields were glyphosate failure occurred, representing 74 accessions in 14 counties, including Clay, Craighead, Crittenden, Greene, Jackson, Jefferson, Lawrence, Lee, Mississippi, Phillips, Poinsett, Randolph, St. Francis, and White Counties. Eight of the 74 accessions did not produce viable seed. In the greenhouse, 32 …

A Symbiotic View Of Life: We Have Never Been Individuals, Scott F. Gilbert, J. Sapp, A. I. Tauber

Biology Faculty Works

The notion of the "biological individual" is crucial to studies of genetics, immunology, evolution, development, anatomy, and physiology. Each of these biological subdisciplines has a specific conception of individuality, which has historically provided conceptual contexts for integrating newly acquired data. During the past decade, nucleic acid analysis, especially genomic sequencing and high-throughput RNA techniques, has challenged each of these disciplinary definitions by finding significant interactions of animals and plants with symbiotic microorganisms that disrupt the boundaries that heretofore had characterized the biological individual. Animals cannot be considered individuals by anatomical or physiological criteria because a diversity of symbionts are both …

Review Of "Fifty Animals That Changed The Course Of History" By E. Chaline, John B. Jenkins

Biology Faculty Works

No abstract provided.

Cd4+ Regulatory And Effector/Memory T Cell Subsets Profile Motor Dysfunction In Parkinson’S Disease, Jessica A. Hutter Saunders, Katherine A. Estes, Lisa M. Kosloski, Heather E. Allen, Kathryn Dempsey Cooper, Diego R. Torres-Russotto, Jane L. Meza, Pamela M. Santamaria, John M. Bertoni, Daniel L. Murman, Hesham Ali, David G. Standaert, R. Lee Mosley, Howard E. Gendelman

Interdisciplinary Informatics Faculty Publications

Animal models and clinical studies have linked the innate and adaptive immune system to the pathology of Parkinson’s disease (PD). Despite such progress, the specific immune responses that influence disease progression have eluded investigators. Herein, we assessed relationships between T cell phenotype and function with PD progression. Peripheral blood lymphocytes from two separate cohorts, a discovery cohort and a validation cohort, totaling 113 PD patients and 96 age- and environment-matched caregivers were examined by flow cytometric analysis and T cell proliferation assays. Increased effector/memory T cells (Tem), defined as CD45RO+ and FAS+ CD4+ T cells and decreased CD31+ and α4β7+ …

Nullomer Derived Anticancer Peptides (Nullops): Differential Lethal Effects On Normal And Cancer Cells In Vitro, Abdelkrim Alileche, Jayita Goswami, William Bourland, Mike Davis, Greg Hampikian

Biology Faculty Publications and Presentations

We demonstrate the first use of the nullomer (absent sequences) approach to drug discovery and development. Nullomers are the shortest absent sequences determined in a species, or group of species. By identifying the shortest absent peptide sequences from the NCBI databases, we screened several potential anti-cancer peptides. In order to improve cell penetration and solubility we added short poly arginine tails (5Rs), and initially solubilized the peptides in1M trehalose. The results for one of the absent sequences 9R (RRRRRNWMWC), and its scrambled version 9S1R (RRRRRWCMNW) are reported here. We refer to these peptides derived from nullomers as PolyArgNulloPs. A control …

Artifacts And Noise In Dna Profiling, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Knockout Of The 15 Kda Selenoprotein Protects Against Chemically-Induced Aberrant Crypt Formation In Mice, Petra A. Tsuji, Bradley A. Carlson, Salvador Naranjo-Suarez, Min-Hyuk Yoo, Xue-Ming Xu, Dmitri E. Fomenko, Vadim Gladyshev, Dolph L. Hatfield, Cindy D. Davis

Department of Biochemistry: Faculty Publications

Evidence suggests that selenium has cancer preventive properties that are largely mediated through selenoproteins. Our previous observations demonstrated that targeted down-regulation of the 15 kDa selenoprotein (Sep15) in murine colon cancer cells resulted in the reversal of the cancer phenotype. The present study investigated the effect of Sep15 knockout in mice using a chemically-induced colon cancer model. Homozygous Sep15 knockout mice, and wild type littermate controls were given four weekly subcutaneous injections of azoxymethane (10 mg/kg). Sep15 knockout mice developed significantly (pGBP-1 in humans has been associated with a highly significant, increased five-year survival rate in colorectal cancer patients. In …

51/2 | ‘Akko I. The 1991–1998 Excavations: The Crusader-Period Pottery Part 2: Plates, Edna J. Stern

IAA Reports—Monograph Series of the Israel Antiquities Authority

This volume, which comprises two parts: text and plates, is the first of the series documenting the results of the large-scale IAA excavations at ‘Akko during the years 1991–1998. It presents the Crusader-period pottery (12th–13th centuries CE), the largest pottery assemblage of the Latin Kingdom of Jerusalem to be studied from a site in the Levant to date. An important component of this assemblage is the wide variety of imported ceramic wares from regions throughout the western and eastern Mediterranean, some not previously identified in Crusader-period contexts in the Levant. This assemblage is important for the study of trade and …

Sagestep News, Winter 2012, No. 17, Sagestep

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Mechanisms And Signal Transduction Pathways Involved In Bovine Oocyte Activation, Ammon Hanson Bayles

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Being able to create a genetically identical, living replicate of a prized animal sounds impossible. Through advanced scientific methods and the wonders of mother nature it can be accomplished by a process called cloning. In 2003, the USU Animal, Dairy, and Veterinary Science department and Dr. Kenneth L. White gained world wide recognition when they, along with a team for Idaho, cloned the first equine species.

Cloning certain animals could be very advantageous to the agricultural industry. Prized animals that have died could be cloned, producing the best meat and milk supply. Animals that are sterile or endangered could be …

Modulation Of The Host Response To Tacaribe Arenavirus Infection In Ag129 Mice By My-24, Eric Sefing

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

MY-24 is a new antiviral compound recently shown to protect immunocompromised mice from lethal challenge with Tacaribe virus (TCRV). Tacaribe virus is incapable of causing disease to humans, but is closely related to the highly pathogenic New World arenaviruses that cause often-fatal viral hemorrhagic fever syndromes. Remarkably, MY-24 prevents mortality without reducing virus burden in the circulation or tissues. To investigate the mechanism by which MY-24 protects AG129 mice against Tacaribe virus infection, we first characterized the natural history of disease in the model with an emphasis on host immune response and blood vessel function to establish the best times …

Process And Domain Specificity In Regions Engaged For Face Processing: An Fmri Study Of Perceptual Differentiation, Heather R. Collins, Xun Zhu, Ramesh S. Bhatt, Jonathan D. Clark, Jane E. Joseph

Psychology Faculty Publications

The degree to which face-specific brain regions are specialized for different kinds of perceptual processing is debated. This study parametrically varied demands on featural, first-order configural, or second-order configural processing of faces and houses in a perceptual matching task to determine the extent to which the process of perceptual differentiation was selective for faces regardless of processing type (domain-specific account), specialized for specific types of perceptual processing regardless of category (process-specific account), engaged in category-optimized processing (i.e., configural face processing or featural house processing), or reflected generalized perceptual differentiation (i.e., differentiation that crosses category and processing type boundaries). ROIs were …