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Research Methods in Life Sciences Commons

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Bird Abundance At Bird Feeders In Response To Temperature, Wind Speed And Precipitation During The Winter Season, Siddhant Kahal 2018 California Polytechnic State University, San Luis Obispo

Bird Abundance At Bird Feeders In Response To Temperature, Wind Speed And Precipitation During The Winter Season, Siddhant Kahal

Master's Theses and Project Reports

The goal of this project is to explore how 23 different bird species respond to 3 climatic attributes. These attributes are lower than average temperatures, wind speed and precipitation level. Information about the bird species and all of the data associated with them is provided by Project FeederWatch (PFW). This is a citizen based survey study that provides key information about bird species abundance through the use of backyard and community feeders. The study volunteers from across the United States and Canada monitor these bird feeders and note important information about the species such as the number of individuals seen ...


Recta: Regulon Identification Based On Comparative Genomics And Transcriptomics Analysis, Xin Chen, Anjun Ma, Adam McDermaid, Hanyuan Zhang, Chao Liu, Huansheng Cao, Qin Ma 2018 Tianjin University,

Recta: Regulon Identification Based On Comparative Genomics And Transcriptomics Analysis, Xin Chen, Anjun Ma, Adam Mcdermaid, Hanyuan Zhang, Chao Liu, Huansheng Cao, Qin Ma

CSE Journal Articles

Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to ...


The Wide Utility Of Rabbits As Models Of Human Diseases, Pedro J. Esteves, Yuxing Chen, Shuying Liu, Shan Lu, Michael Vaine, Shixia Wang, Rose Mage 2018 Universidade do Porto, Portugal

The Wide Utility Of Rabbits As Models Of Human Diseases, Pedro J. Esteves, Yuxing Chen, Shuying Liu, Shan Lu, Michael Vaine, Shixia Wang, Rose Mage

Open Access Articles

Studies using the European rabbit Oryctolagus cuniculus contributed to elucidating numerous fundamental aspects of antibody structure and diversification mechanisms and continue to be valuable for the development and testing of therapeutic humanized polyclonal and monoclonal antibodies. Additionally, during the last two decades, the use of the European rabbit as an animal model has been increasingly extended to many human diseases. This review documents the continuing wide utility of the rabbit as a reliable disease model for development of therapeutics and vaccines and studies of the cellular and molecular mechanisms underlying many human diseases. Examples include syphilis, tuberculosis, HIV-AIDS, acute hepatic ...


Digital Tools For Managing Different Steps Of The Systematic Review Process, Wendy Wu, Katherine Akers, Ella Hu, Alexandra Sarkozy, Patricia Vinson 2018 Wayne State University

Digital Tools For Managing Different Steps Of The Systematic Review Process, Wendy Wu, Katherine Akers, Ella Hu, Alexandra Sarkozy, Patricia Vinson

Library Scholarly Publications

Performing systematic reviews (SR) and meta-analyses is an arduous and time-consuming process that involves not only comprehensive literature searching but also record de-duplication, title/abstract and full-text screening, data extraction, quality assessment, statistical analysis, data visualization, report writing, and the creation of a bibliography. In the past several years, several digital tools and software have become available to facilitate different steps of the systematic review process. However, due to the growing number of tools, it can be difficult for systematic reviewers to make fully informed decisions about which tool(s) to use. Here, we (1) compile a comprehensive list of ...


Differential Tissue Response To Growth Hormone In Mice, Ryan Berry, Graham R. McGinnis, Ronadip R. Banerjee, Martin E. Young, Stuart J. Frank 2018 University of Alabama

Differential Tissue Response To Growth Hormone In Mice, Ryan Berry, Graham R. Mcginnis, Ronadip R. Banerjee, Martin E. Young, Stuart J. Frank

Kinesiology and Nutrition Sciences Faculty Publications

Growth hormone (GH) has been shown to act directly on multiple tissues throughout the body. Historically, it was believed that GH acted directly in the liver and only indirectly in other tissues via insulin‐like growth hormone 1 (IGF‐1). Despite extensive work to describe GH action in individual tissues, a comparative analysis of acute GH signaling in key metabolic tissues has not been performed. Herein, we address this knowledge gap. Acute tissue response to human recombinant GH was assessed in mice by measuring signaling via phospho‐STAT5 immunoblotting. STAT5 activation is an easily and reliably detected early marker of ...


Juvenile Amphibian Response To Oak And Maple Leaf Litter, Benjamin Breslau 2018 University of Connecticut - Storrs

Juvenile Amphibian Response To Oak And Maple Leaf Litter, Benjamin Breslau

Honors Scholar Theses

The composition of tree species within New England forests has changed significantly in recent decades, with an increase in maple (Acer spp.) abundance and a decrease in oak (Quercus spp.) abundance. Changing forest structure results in changing leaf litter composition of the forest floor, which influences the ground-dwelling amphibians that live in the litter. To better understand how changes to forest composition alters amphibian habitat quality, we recorded the growth and survival of 27 juvenile wood frogs (Lithobates sylvaticus or Rana sylvatica) and 27 juvenile American toads (Anaxyrus americanus) in response to leaf litter type. Between early August and late ...


Isolation, Sequencing, And Characterization Of Four Transmissible Antibiotic Resistance Plasmids Captured From Bacteria In Stream Sediments, Curtis J. Kapsak 2018 James Madison University

Isolation, Sequencing, And Characterization Of Four Transmissible Antibiotic Resistance Plasmids Captured From Bacteria In Stream Sediments, Curtis J. Kapsak

Masters Theses

Self-transmissible plasmids are key vectors in the transfer of resistance, catabolic, and other genes among bacteria native to environments such as streams and wetlands. The evolution of antibiotic resistance in particular is known to be powerfully affected by conjugative plasmid transfer due to the ease in which some plasmids can be horizontally transferred into a broad range of host bacteria and their ability to exchange mobile genetic elements that often contain antibiotic resistance genes.

In this study, we captured tetracycline resistance plasmids from stream sediments impacted by agricultural runoff. We selected for resistance plasmids using tetracycline, an antibiotic commonly used ...


The Effect Of Diet On Craniofacial Growth In Osteogenesis Imperfecta Mouse Model, Summer H. Ladd 2018 University of North Texas Health Science Center at Fort Worth

The Effect Of Diet On Craniofacial Growth In Osteogenesis Imperfecta Mouse Model, Summer H. Ladd

Theses and Dissertations

Osteogenesis imperfecta (OI, or “brittle bone disease”) is a rare disorder that is caused by genetic point mutations (COL1A1/COL1A2) that affect type 1 collagen. In OI type III (severe) patients, limb bones are more susceptible to skeletal fractures and the bones of the craniofacial region are underdeveloped. Some OI type III patients also suffer from dental malocclusions or fractures (dentinogenesis imperfecta, DI). The goals of this project are 1) to describe the facial phenotype in an OI mouse model, to see if this model can be used to test potential behavioral and pharmaceutical interventions; and 2) to determine if ...


Evolutionary Competition As Religion: A Religio-Biological Model Of The Maori And Vaisnava Sahajiya Traditions, Benjamin Highland 2018 William & Mary

Evolutionary Competition As Religion: A Religio-Biological Model Of The Maori And Vaisnava Sahajiya Traditions, Benjamin Highland

Undergraduate Honors Theses

Within the modern field of Religious Studies, there exists an epistemological divide between structuralist and post-structuralist thought. Structuralists seek to find underlying and universally applicable knowledge about religion, while post-structuralists argue that traditions must be studied within their own specific geographic, temporal, and cultural contexts. In an aim to reconcile these two disparate paradigms, I introduce the Religio-Biological Model and apply it to two distinct religious traditions: the Maori and the Vaisnava Sahajiya. Drawing from both religious and biological theory (specifically multilevel selection theory), this thesis seeks to create an interdisciplinary framework for the future study of religion that cohesively ...


Pyruvate Kinase Isoform M2 Influences Autophagy And Related Processes In Hepatocellular Carcinoma Cells, Matthew Lin 2018 University of Connecticut

Pyruvate Kinase Isoform M2 Influences Autophagy And Related Processes In Hepatocellular Carcinoma Cells, Matthew Lin

University Scholar Projects

Hepatocellular carcinoma (HCC) is the most common form of liver cancer that affects ~14 million people in the world. Like all cancers, HCC is a disease that arises from unstinted cellular growth initiated by genetic alterations, metabolic changes, and dysregulation in key cellular pathways. Of interest is the relationship between metabolism and cell proliferation/degradation for therapeutic targeting. Pyruvate kinase M2 is a dimeric, glycolytically inactive isoform of the final enzyme involved in glycolysis, that is often upregulated in cancerous tissue. It is thought that the enzymatic function of PKM2 outside of glycolysis contributes to the biosynthesis of anabolic intermediates ...


Effects Of Hypoxia On Swimming And Sensing In A Weakly Electric Fish, Kerri Lynn Ackerly, Rüdiger Krahe, Christopher P. Sanford, Lauren J. Chapman 2018 McGill University

Effects Of Hypoxia On Swimming And Sensing In A Weakly Electric Fish, Kerri Lynn Ackerly, Rüdiger Krahe, Christopher P. Sanford, Lauren J. Chapman

Faculty Publications

Low dissolved oxygen (hypoxia) can severely limit fish performance, especially aerobically expensive behaviours including swimming and acquisition of sensory information. Fishes can reduce oxygen requirements by altering these behaviours under hypoxia, but the underlying mechanisms can be difficult to quantify. We used a weakly electric fish as a model system to explore potential effects of hypoxia on swim performance and sensory information acquisition, which enabled us to non-invasively record electric signalling activity used for active acquisition of sensory information during swimming. To quantify potential effects of hypoxia, we measured critical swim speed (Ucrit) and concurrent electric signalling activity under highand ...


Iteratively Improving Hi-C Experiments One Step At A Time, Rosela Golloshi, Jacob T. Sanders, Rachel Patton McCord 2018 University of Tennessee, Knoxville

Iteratively Improving Hi-C Experiments One Step At A Time, Rosela Golloshi, Jacob T. Sanders, Rachel Patton Mccord

Faculty Publications and Other Works -- Biochemistry, Cellular and Molecular Biology

The 3D organization of eukaryotic chromosomes affects key processes such as gene expression, DNA replication, cell division, and response to DNA damage. The genome-wide chromosome conformation capture (Hi-C) approach can characterize the landscape of 3D genome organization by measuring interaction frequencies between all genomic regions. Hi-C protocol improvements and rapid advances in DNA sequencing power have made Hi-C useful to study diverse biological systems, not only to elucidate the role of 3D genome structure in proper cellular function, but also to characterize genomic rearrangements, assemble new genomes, and consider chromatin interactions as potential biomarkers for diseases. Yet, the Hi-C protocol ...


Diversity, Structure And Sources Of Bacterial Communities In Earthworm Cocoons., Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez 2018 George Washington University

Diversity, Structure And Sources Of Bacterial Communities In Earthworm Cocoons., Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez

Computational Biology Institute

Animals start interactions with the bacteria that will constitute their microbiomes at embryonic stage. After mating, earthworms produce cocoons externally which will be colonized with bacteria from their parents and the environment. Due to the key role bacterial symbionts play on earthworm fitness, it is important to study bacterial colonization during cocoon formation. Here we describe the cocoon microbiome of the earthworms Eisenia andrei and E. fetida, which included 275 and 176 bacterial species, respectively. They were dominated by three vertically-transmitted symbionts, Microbacteriaceae, Verminephrobacter and Ca. Nephrothrix, which accounted for 88% and 66% of the sequences respectively. Verminephrobacter and Ca ...


Respiratory Disease, Behavior, And Survival Of Mountain Goat Kids, Julie A. Blanchong, Christopher A. Anderson, Nicholas Clark, Robert W. Klaver, Paul J. Plummer, Mike Cox, Caleb Mcadoo, Peregrine L. Wolff 2018 Iowa State University

Respiratory Disease, Behavior, And Survival Of Mountain Goat Kids, Julie A. Blanchong, Christopher A. Anderson, Nicholas Clark, Robert W. Klaver, Paul J. Plummer, Mike Cox, Caleb Mcadoo, Peregrine L. Wolff

Natural Resource Ecology and Management Publications

Bacterial pneumonia is a threat to bighorn sheep (Ovis canadensis) populations. Bighorn sheep in the East Humboldt Mountain Range (EHR), Nevada, USA, experienced a pneumonia epizootic in 2009–2010. Testing of mountain goats (Oreamnos americanus) that were captured or found dead on this range during and after the epizootic detected bacteria commonly associated with bighorn sheep pneumonia die‐offs. Additionally, in years subsequent to the bighorn sheep epizootic, the mountain goat population had low kid:adult ratios, a common outcome for bighorn sheep populations that have experienced a pneumonia epizootic. We hypothesized that pneumonia was present and negatively affecting mountain ...


The Subject Librarian Newsletter, Biology, Spring 2017, Sandy Avila 2018 University of Central Florida

The Subject Librarian Newsletter, Biology, Spring 2017, Sandy Avila

Sandy Avila

No abstract provided.


Emptying And Refilling Of Slime Glands In Atlantic (Myxine Glutinosa) And Pacific (Eptatretus Stoutii) Hagfishes, Sarah Schorno, Todd E. Gillis, Douglas S. Fudge 2018 University of Guelph

Emptying And Refilling Of Slime Glands In Atlantic (Myxine Glutinosa) And Pacific (Eptatretus Stoutii) Hagfishes, Sarah Schorno, Todd E. Gillis, Douglas S. Fudge

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Hagfishes are known for their unique defensive slime, which they use toward off gill-breathing predators. Although much is known about the slime cells (gland thread cells and gland mucous cells), little is known about how long slime gland refilling takes, or how slime composition changes with refilling or repeated stimulation of the same gland. Slime glands can be individually electrostimulated to release slime, and this technique was used to measure slime gland refilling times for Atlantic and Pacific hagfish. The amount of exudate produced, the composition of the exudate and the morphometrics of slime cells were analyzed during refilling, and ...


Whole Tart Cherry Improves Disease Activity Index In Rat Model Of Dextran Sulfate Solution – Induced Ulcerative Colitis By Downregulating The Janus 1 And Janus 3 Kinases And Tnf - Alpha, Johana Alexandra Coronel 2018 Louisiana State University and Agricultural and Mechanical College

Whole Tart Cherry Improves Disease Activity Index In Rat Model Of Dextran Sulfate Solution – Induced Ulcerative Colitis By Downregulating The Janus 1 And Janus 3 Kinases And Tnf - Alpha, Johana Alexandra Coronel

LSU Master's Theses

Ulcerative colitis (UC) is a disabling inflammatory bowel disease. UC is characterized by chronic, relapsing inflammation of the colon and rectum. Current treatments such as monoclonal antibodies against TNF-α, IL-6, IL-12/p40, adhesion molecules, Janus kinases (JAK) inhibitors have side effects or lose their effects over time. Alternative approaches with fewer side effects for patients are needed. Montmorency tart cherries (Prunus cerasus) are a good source of anti-inflammatory flavonoids. We hypothesized that regular consumption whole tart cherry (TC) standardized to its major anthocyanin content, namely cyanidin-3-glucosyl-rutinoside, would be effective in reducing inflammation in UC. The aim of this research was ...


Glucocorticoids Modulate Gastrointestinal Microbiome In A Wild Bird., José C Noguera, Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez, Alberto Velando 2018 George Washington University

Glucocorticoids Modulate Gastrointestinal Microbiome In A Wild Bird., José C Noguera, Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez, Alberto Velando

Computational Biology Institute

It has recently been hypothesized that stress exposure (e.g. via glucocorticoid secretion) may dysregulate the bacterial gut microbiome, a crucial 'organ' in animal health. However, whether stress exposure (e.g. via glucocorticoid secretion) affects the bacterial gut microbiome of natural populations is unknown. We have experimentally altered the basal glucocorticoid level (corticosterone implants) in a wild avian species, the yellow-legged gull


Disruption Of Female Reproductive Function By Endotoxins, K. L. Bidne, M. J. Dickson, J. W. Ross, L. H. Baumgard, A. F. Keating 2018 Iowa State University

Disruption Of Female Reproductive Function By Endotoxins, K. L. Bidne, M. J. Dickson, J. W. Ross, L. H. Baumgard, A. F. Keating

Animal Science Publications

Endotoxemia can be caused by obesity, environmental chemical exposure, abiotic stressors, and bacterial infection. Circumstances that deleteriously impact intestinal barrier integrity can induce endotoxemia and controlled experiments have identified negative impacts of lipopolysaccharide (LPS; an endotoxin mimetic) on folliculogenesis, puberty onset, estrus behavior, ovulation, meiotic competence, luteal function and ovarian steroidogenesis. In addition, neonatal LPS exposures have transgenerational female reproductive impacts, raising concern about early life contacts to this endogenous reproductive toxicant. Aims of this review are to identify physiological stressors causing endotoxemia, to highlight potential mechanism(s) by which LPS compromises female reproduction, and identify knowledge gaps regarding how ...


Developing New Apparatus For In-Situ Vermicomposting And Varying Diet Parameters To Understand Optimal Conditions For Soil Fertilization., Nataliya Ryzhenko 2018 Lesley University

Developing New Apparatus For In-Situ Vermicomposting And Varying Diet Parameters To Understand Optimal Conditions For Soil Fertilization., Nataliya Ryzhenko

Lesley University Community of Scholars Day

Vermicomposting is the process of decomposing vegetable and other food waste using earthworms.

We investigate apparatus for in-situ vermicomposting and vary diet parameters to understand optimal conditions for soil fertilization.

As a pilot project, we created a small in-situ vermicomposting apparatus which can be used in a home or at a small farm. In this setting, we need to ensure that the setup does not produce repulsive odor, since it is meant to be kept indoors. Also, the setup should be easily maintained: the food waste easily added, and the bedding kept moist.

Based on results seen, in-situ vermicomposting farm ...


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