Research Methods in Life Sciences Commons^™

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 …

Analyzing And Modeling The Dysfunction Of Inhibitory Neurons In Alzheimer’S Disease, Carlos Perez, Jokubas Ziburkus, Ghamim Ullah

Physics Faculty Publications

Alzheimer’s disease (AD) is characterized by the abnormal proteolytic processing of amyloid precursor protein, resulting in increased production of a self-aggregating form of beta amyloid (Aβ). Several lines of work on AD patients and transgenic mice with high Aβ levels exhibit altered rhythmicity, aberrant neuronal network activity and hyperexcitability reflected in clusters of hyperactive neurons, and spontaneous epileptic activity. Recent studies highlight that abnormal accumulation of Aβ changes intrinsic properties of inhibitory neurons, which is one of the main reasons underlying the impaired network activity. However, specific cellular mechanisms leading to interneuronal dysfunction are not completely …

Act On The Registration And Evaluation Of Chemicals (K-Reach) And Replacement, Reduction Or Refinement Best Practices, Soojin Ha, Troy Seidle, Kyung-Min Lim

Legal Regulation of Animal Research Collection

Objectives - Korea’s Act on the Registration and Evaluation of Chemicals (K-REACH) was enacted for the protection of human health and the environment in 2015. Considering that about 2000 new substances are introduced annually across the globe, the extent of animal testing requirement could be overwhelming unless regulators and companies work proactively to institute and enforce global best practices to replace, reduce or refine animal use. In this review, the way to reduce the animal use for K-REACH is discussed. Methods - Background of the enforcement of the K-REACH and its details was reviewed along with the papers and regulatory …

Animal-Friendly Affinity Reagents: Replacing The Needless In The Haystack, A. C. Gray, S. S. Sidhu, P. C. Chandrasekera, C. F.M. Hendriksen, C. A.K. Borrebaeck

Biomedicine and Animal Models in Research Collection

The multibillion-dollar global antibody industry produces an indispensable resource but that is generated using millions of animals. Despite the irrefutable maturation and availability of animal-friendly affinity reagents (AFAs) employing na€ive B lymphocyte or synthetic recombinant technologies expressed by phage display, animal immunisation is still authorised for antibody production. Remarkably, replacement opportunities have been overlooked, despite the enormous potential reduction in animal use. Directive 2010/63/EU requires that animals are not used where alternatives exist. To ensure its implementation, we have engaged in discussions with the EU Reference Laboratory for alternatives to animal testing (EURL ECVAM) and the Directorate General for Environment …

Arkansas Animal Science Department Report 2016, Paul Beck, Jason Apple, Shane Gadberry, Beth Kegley, Charles Rosenkrans Jr.

Arkansas Agricultural Experiment Station Research Series

No abstract provided.

Photography-Based Taxonomy Is Inadequate, Unnecessary, And Potentially Harmful For Biological Sciences, Luis M. P. Ceríaco, Eliécer E. Gutiérrez, Alain Dubois, Rafael O. De Sá, Et Al.

Biology Faculty Publications

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per …

Guidelines To Avoid Typical Difficulties According To The Rubric For Experimental Design (Red), Annwesa Dasgupta, Nancy Pelaez

PIBERG Publications

Experimental design is an important component of undergraduate biology education as it generates knowledge of biology. Despite its importance, there is limited information about what students actually learn from designing experiments. Dasgupta et al (2014) reported on the development and validation of a Rubric for Experimental Design (RED), informed by a literature review and empirical analysis of thousands of undergraduate biology students’ responses to three published assessments. The RED is a useful probe for five major areas of experimental design abilities: the variable properties of an experimental subject; the manipulated variables; measurement of outcomes; accounting for variability; and the scope …

Nemo-Like Kinase (Nlk) Is A Pathological Signaling Effector In The Mouse Heart, Ruijie Liu

Peer Reviewed Articles

Nemo-like kinase (NLK) is an evolutionary conserved serine/threonine protein kinase implicated in development, proliferation and apoptosis regulation. Here we identified NLK as a gene product induced in the hearts of mice subjected to pressure overload or myocardial infarction injury, suggesting a potential regulatory role with pathological stimulation to this organ. To examine the potential functional consequences of increased NLK levels, cardiac-specific transgenic mice with inducible expression of this gene product were generated, as well as cardiac-specific Nlk gene-deleted mice. NLK transgenic mice demonstrated baseline cardiac hypertrophy, dilation, interstitial fibrosis, apoptosis and progression towards heart failure in response to two surgery-induced …

A Murine Model Of Inflammation-Induced Cerebral Microbleeds, Rachita K. Sumbria, Mher Mahoney Grigoryan, Vitaly Vasilevko, Tatiana B. Krasieva, Miriam Scadeng, Alexandra K. Dvornikova, Annlia Paganini-Hill, Ronald Kim, David H. Cribbs, Mark J. Fisher

Pharmacy Faculty Articles and Research

Background: Cerebral microhemorrhages (CMH) are tiny deposits of blood degradation products in the brain and are pathological substrates of cerebral microbleeds. The existing CMH animal models are β-amyloid-, hypoxic brain injury-, or hypertension-induced. Recent evidence shows that CMH develop independently of hypoxic brain injury, hypertension, or amyloid deposition and CMH are associated with normal aging, sepsis, and neurodegenerative conditions. One common factor among the above pathologies is inflammation, and recent clinical studies show a link between systemic inflammation and CMH. Hence, we hypothesize that inflammation induces CMH development and thus, lipopolysaccharide (LPS)-induced CMH may be an appropriate model to …

Inducing Application Of Interdisciplinary Frameworks: Experiences From The Domains Of Information Literacy And Responsible Conduct Of Research, Anne E. Leonard, Jean E. Hillstrom

Publications and Research

Constructivist frameworks for information literacy and research ethics can be developed and nurtured in the context of an interdisciplinary course. Using the frameworks of two disciplines, students went on an experiential journey in support of ethics foundations through guest lectures and active learning exercises. This study describes the development and content of the responsible conduct of research and information literacy modules and discusses the role of each in an interdisciplinary course. Learning goals for both modules were evaluated by examining student responses in a free-writing exercise at the end of the semester, concluding with a discussion of the structural and …

Nasp: An Accurate, Rapid Method For The Identification Of Snps In Wgs Datasets That Supports Flexible Input And Output Formats, Jason Sahl, Darrin Lemmer, Jason Travis, James Schupp, John Gillece, Maliha Aziz, +Several Additional Authors

Environmental and Occupational Health Faculty Publications

Whole-genome sequencing (WGS) of bacterial isolates has become standard practice in many laboratories. Applications for WGS analysis include phylogeography and molecular epidemiology, using single nucleotide polymorphisms (SNPs) as the unit of evolution. NASP was developed as a reproducible method that scales well with the hundreds to thousands of WGS data typically used in comparative genomics applications. In this study, we demonstrate how NASP compares with other tools in the analysis of two real bacterial genomics datasets and one simulated dataset. Our results demonstrate that NASP produces similar, and often better, results in comparison with other pipelines, but is much more …

Telonicher Marine Laboratory, Hsu Telonicher Marine Laboratory

Newsletters

No abstract provided.

The Influence Of Juncus-Rhizosphere Dissolved Organic Matter On Coastal Plankton Communities, Brittany Zepernick, Robert Michael Mckay, George S. Bullerjahn, Jeffrey W. Krause, Behzad Mortazavi

Honors Projects

Many aquatic plants produce copious amounts of dissolved organic matter (DOM) which enters surrounding waters and potentially stimulates planktonic activity. In the northern Gulf of Mexico, Juncus roemarianus (i.e. black needlerush) is a dominant marsh grass species residing in coastal zones and barrier islands. The below-ground biomass i.e. rhizosphere, can be consistently submerged, serving as a potential source of DOM to the surrounding waters. The lability and possible stimulatory effect of J. roemarianus DOM was examined for three plankton communities collected within the discharge region of Mobile Bay and adjacent waters of Gulf Shores, Alabama (less affected by Mobile Bay). …

Pain And Laboratory Animals: Publication Practices For Better Data Reproducibility And Better Animal Welfare, Larry Carbone, Jamie Austin

Laboratory Research and Animal Welfare Collection

Scientists who perform major survival surgery on laboratory animals face a dual welfare and methodological challenge: how to choose surgical anesthetics and post-operative analgesics that will best control animal suffering, knowing that both pain and the drugs that manage pain can all affect research outcomes. Scientists who publish full descriptions of animal procedures allow critical and systematic reviews of data, demonstrate their adherence to animal welfare norms, and guide other scientists on how to conduct their own studies in the field. We investigated what information on animal pain management a reasonably diligent scientist might find in planning for a successful …

Single-Cell Transcriptional Analysis Of Normal, Aberrant, And Malignant Hematopoiesis In Zebrafish, Finola E. Moore, Elaine G. Garcia, Riadh Lobbardi, Esha Jain, Qin Tang, John C. Moore, Mauricio Cortes, Aleksey Molodtsov, Melissa Kasheta, Christina C. Luo, Amaris J. Garcia, Ravi Mylvaganam, Jeffrey A. Yoder, Jessica S. Blackburn, Ruslan I. Sadreyev, Craig J. Ceol, Trista E. North, David M. Langenau

Molecular and Cellular Biochemistry Faculty Publications

Hematopoiesis culminates in the production of functionally heterogeneous blood cell types. In zebrafish, the lack of cell surface antibodies has compelled researchers to use fluorescent transgenic reporter lines to label specific blood cell fractions. However, these approaches are limited by the availability of transgenic lines and fluorescent protein combinations that can be distinguished. Here, we have transcriptionally profiled single hematopoietic cells from zebrafish to define erythroid, myeloid, B, and T cell lineages. We also used our approach to identify hematopoietic stem and progenitor cells and a novel NK-lysin 4⁺ cell type, representing a putative cytotoxic T/NK cell. Our platform …

Alzheimer Disease Research In The 21st Century: Past And Current Failures, New Perspectives And Funding Priorities, Francesca Pistollato, Elan L. Ohayon, Ann Lam, Gillian R. Langley, Thomas J. Novak, David Pamies, George Perry, Eugenia Trushina, Robin S.B. Williams, Alex E. Roher, Thomas Hartung, Stevan Harnad, Neal D. Barnard, Martha Clare Morris, Mei-Chun Lai, Ryan Merkley, P. Charukeshi Chandrasekera

Experimentation Collection

Much of Alzheimer disease (AD) research has been traditionally based on the use of animals, which have been extensively applied in an effort to both improve our understanding of the pathophysiological mechanisms of the disease and to test novel therapeutic approaches. However, decades of such research have not effectively translated into substantial therapeutic success for human patients. Here we critically discuss these issues in order to determine how existing human-based methods can be applied to study AD pathology and develop novel therapeutics. These methods, which include patient-derived cells, computational analysis and models, together with large-scale epidemiological studies represent novel and …

Detecting Cardio-Respiratory Instability In Neonates, Joshua Todd Carroll, Shahrokh Sani

Celebration of Student Scholarship Poster Sessions Archive

No abstract provided.

Bringing Silicon Valley To Thailand, Krating Poonpol

Asian Management Insights

Searching for unicorns.

Annotated Bibliography: Attitudes Toward Animal Research (2014-2015), Erich Yahner

BIBLIOGRAPHIES

No abstract provided.

The Ethics Of Animal Research: A Survey Of The Public And Scientists In North America, Ari R. Joffe, Meredith Bara, Natalie Anton, Nathan Nobis

Morality and Ethics of Animal Experimentation Collection

Background: To determine whether the public and scientists consider common arguments (and counterarguments) in support (or not) of animal research (AR) convincing.

Methods: After validation, the survey was sent to samples of public (Sampling Survey International (SSI; Canadian), Amazon Mechanical Turk (AMT; US), a Canadian city festival and children’s hospital), medical students (two second-year classes), and scientists (corresponding authors, and academic pediatricians). We presented questions about common arguments (with their counterarguments) to justify the moral permissibility (or not) of AR. Responses were compared using Chi-square with Bonferonni correction.

Results: There were 1220 public [SSI, n = 586; AMT, n = …