Research Methods in Life Sciences Commons^™

The Temporal Dynamics Of The Tracheal Microbiome In Tracheostomised Patients With And Without Lower Respiratory Infections., Marcos Pérez-Losada, Robert J Graham, Madeline Coquillette, Amenah Jafarey, Eduardo Castro-Nallar, Manuel Aira, Robert J Freishtat, Jonathan M Mansbach

Computational Biology Institute

Background: Airway microbiota dynamics during lower respiratory infection (LRI) are still poorly understood due, in part, to insufficient longitudinal studies and lack of uncontaminated lower airways samples. Furthermore, the similarity between upper and lower airway microbiomes is still under debate. Here we compare the diversity and temporal dynamics of microbiotas directly sampled from the trachea via tracheostomy in patients with (YLRI) and without (NLRI) lower respiratory infections. Methods: We prospectively collected 127 tracheal aspirates across four consecutive meteorological seasons (quarters) from 40 patients, of whom 20 developed LRIs and 20 remained healthy. All aspirates were collected when patients had no …

Red Snapper Distribution On Natural Habitats And Artificial Structures In The Northern Gulf Of Mexico, Mandy Karnauskas, John F. Walter Iii, Matthew D. Campbell, Adam G. Pollack, J. Marcus Drymon, Sean P. Powers

University Faculty and Staff Publications

In 2011, an intensive, multiple-gear, fishery-independent survey was carried out in the northern Gulf of Mexico (GOM) to collect comprehensive age and length information on Red Snapper Lutjanus campechanus. Based on this synoptic survey, we produced a spatial map of Red Snapper relative abundance that integrates both gear selectivity effects and ontogenetically varying habitat usage. Our methodology generated a spatial map of Red Snapper at a 10-km2 grid resolution that is consistent with existing knowledge of the species: Red Snapper occurred in relatively high abundances at depths of 50–90 m along the coasts of Texas and Louisiana and in smaller, …

Determination Of Novel Metabolites Of Therapeutic Agents Used In The Treatment Of Castration-Resistant Prostate Cancer, Mohammad Alyamani

ETD Archive

Despite an array of improved treatment options over the past decade, prostate cancer remains the second leading cause of cancer mortality for men in the United States. Abiraterone and galeterone are oral steroidal compounds that are used to treat metastatic castration-resistant prostate cancer (CRPC). Abiraterone blocks 17a-hydroxylase/17,20-lyase (CYP17A1), an enzyme required for androgen synthesis. Galeteron inhibits CYP17A1, blocks the androgen receptor (AR), and decreases AR protein levels. Both drugs share the same structure with endogenous androgens such as dehydroepiandrosterone, which are substrates for the enzyme, 3ß-hydroxysteroid dehydrogenase (3ßHSD). Metabolites of 3ßHSD undergo further metabolism to produce the AR ligand, testosterone …

Survey Results: Complexities And Overlaps In Existing Citizen Science Mosquito Projects, Yujia He, Elizabeth Tyson

Patterson School of Diplomacy and International Commerce Faculty Publications

Currently, multiple projects worldwide engage the public in the scientific process of learning about mosquito biodiversity or monitoring mosquitoes that carry diseases like Dengue, Chikungunya, Zika and Malaria. These projects are executed at different invasion-stages and different scenarios of epidemiological risk based on their country of origin. Through surveying 12 international research teams, this brief report illuminates the differences and the overlaps in the protocols and tools used by existing citizen science mosquito monitoring projects. The analysis covers project goals, requirements and support for participants, policy impact, digital tools and data privacy.

Genetic Polymorphisms Of The Glucocorticoid Receptor And Interleulin-8 Receptor Genes And Their Relationship To Production Traits And Hair Coat Scores In Crossbred Cattle, Avery B. Deaton, Laura Meyer, Jeremy Powell, Charles F. Rosenkrans Jr.

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

Little is understood about how the diversity of genes, specifically the glucocorticoid receptor (GR) and interleukin-8 receptor (CXCR2), are related to reproductive health and how this affects physical traits in cattle. Glucocorticoid receptors have been positively associated with higher milk yields, lactose content, feed intake, and feed conversion rates. Interleukin-8 genes are part of the innate immune response and help with many aspects of female reproductive health, such as protecting the embryo from the maternal immune system during pregnancy. The objective of this research was to identify polymorphisms in the GR and CXCR2 genes and to associate genotypes between the …

Evolution Of Equine Arteritis Virus During Persistent Infection In The Reproductive Tract Of The Stallion And The Male Donkey, Bora Nam

Theses and Dissertations--Veterinary Science

Equine arteritis virus (EAV) establishes persistent infection in the stallion reproductive tract, and the carrier stallion continues to shed virus in semen for weeks to years or lifelong. The objective of this study was to elucidate the intra-host evolution of EAV during persistent infection in stallions. Seven EAV seronegative stallions were experimentally infected with EAV KY84 strain and followed for 726 days post-infection, and sequential clinical samples including semen were collected for virus isolation and next-generation sequencing (NGS). In addition, archived sequential semen samples from two stallions that were naturally infected with EAV KY84 for a long-period (up to 10 …

Expansion Of Comprehensive Screening Of Male Sexually Transmitted Infection Clinic Attendees With Mycoplasma Genitalium And Trichomonas Vaginalis Molecular Assessment: A Retrospective Analysis, Erik Munson, David Wenten, Sheila Jhansale, Mary Kay Schuknecht, Nicki Pantuso, Joshua Gerritts, Aaron Steward, Kimber L. Munson, Maureen Napierala, Deb Hamer

Clinical Lab Sciences Faculty Research and Publications

Of 1,493 encounters of males at a sexually transmitted infection (STI) clinic in a community with a high prevalence of STI, Chlamydia trachomatis was detected in 8.7% and Neisseria gonorrhoeae was detected in 6.6%. Additional Trichomonas vaginalis and Mycoplasma genitalium screening found 17.4% and 23.9% of the encounters, respectively, to be positive for STI. STI agents were detected in 13.7% of urine specimens; addition of pharyngeal and rectal collections to the analysis resulted in detection of STI agents in 19.0% and 23.9% of encounters, respectively. A total of 101 (23.8%) encounters of identified STI involved sole detection of M. genitalium. …

Effects Of Chromium On Mouse Splenic T Lymphocytes And Effects Of Ethanol Exposure During Early Neurodevelopment On Behaviors In Mice, Lu Dai

Theses and Dissertations--Toxicology and Cancer Biology

The dissertation consists of three major projects with the focus on the immunotoxicity of chromium and the behavior disorders caused by early ETOH exposure respectively.

Hexavalent chromium [Cr(VI)] is widely used in various industrial processes and has been recognized as a carcinogen. As the first line of host defense system, the immune system can be a primary target of Cr(VI). T cell population represents a major arm of the immune system that plays a critical role in host anti-tumor immunity. Dysfunction of T cells compromises host anti-tumor immunity resulting in oncogenesis. Using mouse splenic T cells as an in vitro …

Measuring Bacterial Growth Using A 3d-Printable Spectrometer, Samuel R. Bunting

Williams Honors College, Honors Research Projects

Visible light spectroscopy is a commonly used technique for measuring the growth of bacterial cultures, and growth curves provide broadly important data. However, the equipment and resources required for these experiments has been restricted to higher education and industry due to high cost and sophistication. We have previously reported on an inexpensive, 3D-printable photospectrometer called the SpecPhone. This device utilizes an iPhone as the camera, along with several other, inexpensive additions to make a fully functional spectrometer. Here, the application of the SpecPhone is expanded to the quantification of actively dividing E. coli cultures. Two protocols have been developed; one …

Animal Sentience And The Precautionary Principle, Jonathan Birch

Animal Sentience

In debates about animal sentience, the precautionary principle is often invoked. The idea is that when the evidence of sentience is inconclusive, we should “give the animal the benefit of the doubt” or “err on the side of caution” in formulating animal protection legislation. Yet there remains confusion as to whether it is appropriate to apply the precautionary principle in this context, and, if so, what “applying the precautionary principle” means in practice regarding the burden of proof for animal sentience. Here I construct a version of the precautionary principle tailored to the question of animal sentience together with a …

Refining The Precautionary Framework, Jonathan Birch

Animal Sentience

Most of the commentators so far agree that the precautionary principle can be usefully applied to the question of animal sentience. I consider various ways of refining my proposals in light of the suggestions. I amend BAR to implement C. Brown’s suggestion that the scope of animal welfare law should be extensible by phylogenetic inference from orders in which credible indicators of sentience are found. In response to C. Brown, Mallatt, and Woodruff, I amend ACT to allow that a single credible indicator may sometimes call for urgent further investigation rather than immediate protection. In response …

The Effects Of Methamphetamine Exposure On Cardiovascular Development In Combination With Hypoxia In Danio Rerio, Sarah Donaldson

Williams Honors College, Honors Research Projects

The purpose of this study was to determine the effects of methamphetamine combined with hypoxia on the development and function of the cardiovascular system in Danio rerio embryos. It was hypothesized that the combined effect of the drug and decreased oxygen concentration would result in decreased cardiac parameters due to underdevelopment of the ventricle and vessels resulting from cardiomyopathy and lack of blood flow to tissues. It was found that methamphetamine exposure correlated to an increase in stroke volume, caudal artery and vein diameters and RBC velocities alone, while having a multiplicative effect of increasing arterial RBC velocity when combined …

Biosimp: Using Software Testing Techniques For Sampling And Inference In Biological Organisms, Mikaela Cashman, Jennie L. Catlett, Myra B. Cohen, Nicole R. Buan, Zahmeeth Sakkaff, Massimiliano Pierobon, Christine A. Kelley

School of Computing: Conference and Workshop Papers

Years of research in software engineering have given us novel ways to reason about, test, and predict the behavior of complex software systems that contain hundreds of thousands of lines of code. Many of these techniques have been inspired by nature such as genetic algorithms, swarm intelligence, and ant colony optimization. In this paper we reverse the direction and present BioSIMP, a process that models and predicts the behavior of biological organisms to aid in the emerging field of systems biology. It utilizes techniques from testing and modeling of highly-configurable software systems. Using both experimental and simulation data we show …

The Hidden History Of Humming Frogs, Rafael O. De Sá

Biology Faculty Publications

In the depths of Brazil’s Atlantic Forest, researchers are battling to identify species before they are lost for good. Dr Rafael O de Sá, Professor of Biology at the University of Richmond, Virginia, USA, specialises in a group known as the ‘narrow-mouthed frogs’ and has already found four species new to science.

Mammary Extracellular Matrix Directs Differentiation Of Testicular And Embryonic Stem Cells To Form Functional Mammary Glands In Vivo, Robert D. Bruno, Jodie M. Fleming, Andrea L. George, Corinne A. Boulanger, Pepper Schedin, Gilbert H. Smith

School of Medical Diagnostics & Translational Sciences Publications

Previously, we demonstrated the ability of the normal mammary microenvironment (niche) to direct non-mammary cells including testicular and embryonic stem cells (ESCs) to adopt a mammary epithelial cell (MEC) fate. These studies relied upon the interaction of transplanted normal MECs with non-mammary cells within the mammary fat-pads of recipient mice that had their endogenous epithelium removed. Here, we tested whether acellular mammary extracellular matrix (mECM) preparations are sufficient to direct differentiation of testicular-derived cells and ESCs to form functional mammary epithelial trees in vivo. We found that mECMs isolated from adult mice and rats were sufficient to redirect testicular derived …

Zebrafish (Danio Rerio) As A Model For Orofacial Research, Kevin A. Ghaffari

Theses and Dissertations

Across species, the face and more specifically the mouth, serves as an essential facet of everyday life. Amongst humans the mouth serves as a tool for the ingestion of food, a marker for facial recognition and a medium for communication. In order for the mouth to properly form, a series of precise growth and fusion events are needed. In order to insure that these events are orchestrated properly is a wide array of signals, transcription factors and epigenetic regulators. Due to the needed precision of these events, congenital birth defects of the face such as cleft lip and cleft palate …

Survey Gear Comparisons And Shark Nursery Habitat Use In Southeast Georgia Estuaries, Jeffrey Cohen Carpenter

UNF Graduate Theses and Dissertations

Gill nets and longlines were compared as shark nursery sampling methodologies in inshore waters of Georgia to (1) assess differences in gear selectivity, bias, and stress of capture and (2) determine potential relationships between habitat features and shark distribution and abundance. Gear selectivity varied between gears as a function of both species and life stage resulting in significantly different estimates of species and life stage compositions. Juvenile bonnetheads (Sphyrna tiburo) and young of the year blacktip sharks (Carcharhinus limbatus) experienced significantly higher stress from gill net capture than longline. Major sources of bias are thought to …