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Research Methods in Life Sciences Commons

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Effects Of Grinding Method And Particle Size Of Wheat Grain On Energy And Nutrient Digestibility In Growing And Finishing Pigs, Jesus A. Acosta, Amy L. Petry, Stacie A. Gould, Cassandra K. Jones, Charles R. Stark, Adam Fahrenholz, John F. Patience 2020 Iowa State University

Effects Of Grinding Method And Particle Size Of Wheat Grain On Energy And Nutrient Digestibility In Growing And Finishing Pigs, Jesus A. Acosta, Amy L. Petry, Stacie A. Gould, Cassandra K. Jones, Charles R. Stark, Adam Fahrenholz, John F. Patience

Animal Science Publications

Feed grains are processed to improve their value in pig diets by exposing kernel contents to enzymatic and microbial action. The objective of this study was to quantify the effect of reducing mean particle size (PS) of wheat grain ground with two different grinding methods (GMs) on the apparent total tract digestibility (ATTD) of nutrients and energy in growing and finishing pigs. Forty-eight barrows were housed in individual pens for 11 d for two periods. Pigs were randomly assigned to a 3 × 2 × 2 factorial experimental design: three target mean PS of wheat grain (300, 500, and 700 µm), two ...


Tpr-Containing Proteins Control Protein Organization And Homeostasis For The Endoplasmic Reticulum, Jill Bradley-Graham 2020 University of Massachusetts Amherst

Tpr-Containing Proteins Control Protein Organization And Homeostasis For The Endoplasmic Reticulum, Jill Bradley-Graham

Doctoral Dissertations

The endoplasmic reticulum (ER) is a complex, multifunctional organelle comprised of a continuous membrane and lumen that is organized into several functional regions. It plays various roles including protein translocation, folding, quality control, secretion, calcium signaling, and lipid biogenesis. Cellular protein homeostasis is maintained by a complicated chaperone network, and the largest functional family within this network consists of proteins containing tetratricopeptide repeats (TPRs). TPRs are well-studied structural motifs that mediate intermolecular protein-protein interactions, supporting interactions with a wide range of ligands or substrates. Nine TPR-containing proteins have been shown to localize to the ER and control protein organization and ...


The Effects Of Phosphate On The Metamorphosis Of Larval Western Barred Tiger Salamanders (Ambystoma Mavortium), Lexy Polivanov 2020 University of Nebraska - Lincoln

The Effects Of Phosphate On The Metamorphosis Of Larval Western Barred Tiger Salamanders (Ambystoma Mavortium), Lexy Polivanov

Honors Theses, University of Nebraska-Lincoln

This investigation will collect data to assist in determining if elevated aquatic phosphate levels affects the metamorphosis rate of larval western barred tiger salamanders (Ambystoma mavortium). Monoammonium phosphate fertilizers are being used on crops in Nebraska (NDA, 2017). This area lines up with the area the western barred tiger salamanders are disappearing from (Damme, 2018). Monoammonium phosphate is made up of nitrogen and phosphate. There have been several studies showing how nitrogen is harmful to amphibians such as this salamander (Griffis-Kyle, 2007) (Griffis-Kyle & Richtie, 2007), but there have not been many showing how phosphate affects amphibian’s metamorphosis in the ...


Using Active Learning To Build A Foundation For Bioinformatics Training., Stacey E. Wahl Ph.D., Amy L. Olex MS 2020 Virginia Commonwealth University

Using Active Learning To Build A Foundation For Bioinformatics Training., Stacey E. Wahl Ph.D., Amy L. Olex Ms

Transforming Libraries for Graduate Students

As Health Sciences Libraries evolve, the support they offer graduate students has evolved to incorporate many aspects of the research life cycle. At Tompkins-McCaw Library for the Health Sciences, we have partnered with the Wright Center for Clinical and Translational Research to offer training workshops for graduate students who are interested in using bioinformatics to plan, analyze, or execute scientific experiments. We offer two series: 1) an 8-week, 1-hour per week seminar series providing a general overview of available techniques and 2) a week-long intensive, two hours per session, series on utilizing free databases from the National Center for Biotechnology ...


Content And Performance Of The Minimuga Genotyping Array, A New Tool To Improve Rigor And Reproducibility In Mouse Research [Preprint], John Sebastian Sigmon, Christopher M. Sassetti, Clare M. Smith, Martin T. Ferris, Leonard McMillan, Fernando Pardo-Manuel de Villena 2020 University of North Carolina

Content And Performance Of The Minimuga Genotyping Array, A New Tool To Improve Rigor And Reproducibility In Mouse Research [Preprint], John Sebastian Sigmon, Christopher M. Sassetti, Clare M. Smith, Martin T. Ferris, Leonard Mcmillan, Fernando Pardo-Manuel De Villena

University of Massachusetts Medical School Faculty Publications

The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well annotated genome, wealth of genetic resources and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost effective, informative and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole genome sequencing. Here we describe the content and performance of a new Mouse Universal Genotyping Array (MUGA). MiniMUGA, an ...


Canine Models Of Inherited Musculoskeletal And Neurodegenerative Diseases, Brett D. Story, Matthew E. Miller, Allison M. Bradbury, Emily D. Million, Dongsheng Duan, Toloo Taghian, Dominik Faissler, Deborah Fernau, Sidney J. Beecy, Heather Gray-Edwards 2020 Auburn University

Canine Models Of Inherited Musculoskeletal And Neurodegenerative Diseases, Brett D. Story, Matthew E. Miller, Allison M. Bradbury, Emily D. Million, Dongsheng Duan, Toloo Taghian, Dominik Faissler, Deborah Fernau, Sidney J. Beecy, Heather Gray-Edwards

Open Access Publications by UMMS Authors

Mouse models of human disease remain the bread and butter of modern biology and therapeutic discovery. Nonetheless, more often than not mouse models do not reproduce the pathophysiology of the human conditions they are designed to mimic. Naturally occurring large animal models have predominantly been found in companion animals or livestock because of their emotional or economic value to modern society and, unlike mice, often recapitulate the human disease state. In particular, numerous models have been discovered in dogs and have a fundamental role in bridging proof of concept studies in mice to human clinical trials. The present article is ...


Activation Of The Sonic Hedgehog Effector Smoothened Counteracts L-Dopa Induced Dyskinesia By Restoring Cholinergic Interneuron Function, Lauren Malave 2020 The Graduate Center, City University of New York

Activation Of The Sonic Hedgehog Effector Smoothened Counteracts L-Dopa Induced Dyskinesia By Restoring Cholinergic Interneuron Function, Lauren Malave

Dissertations, Theses, and Capstone Projects

Many types of neurons act as multimodal signaling centers. Yet, we have only limited insight into the regulation and functional consequences of neuronal co-transmission. For example, dopamine (DA) neurons, whose degeneration causes motor deficits characteristic of Parkinson’s Diseases (PD), communicate with all their targets by DA but only a selective subset of their targets using GABA, Glutamate, and the secreted cell signaling protein Sonic Hedgehog (Shh). It is unknown whether Levo-dopamine (L-Dopa) induced dyskinesia (LIDs), a severely debilitating side effect of DA supplementation in PD, might appear because DA neuron targets are exposed to high DA- but low Shh- ...


Pgc-1Α Overexpression Increases Transcription Factor Eb Nuclear Localization And Lysosome Abundance In Dystrophin-Deficient Skeletal Muscle, Hannah R. Spaulding, Amanda K. Ludwig, Katrin Hollinger, Matthew B. Hudson, Joshua T. Selsby 2020 Iowa State University

Pgc-1Α Overexpression Increases Transcription Factor Eb Nuclear Localization And Lysosome Abundance In Dystrophin-Deficient Skeletal Muscle, Hannah R. Spaulding, Amanda K. Ludwig, Katrin Hollinger, Matthew B. Hudson, Joshua T. Selsby

Animal Science Publications

Duchenne muscular dystrophy (DMD) is caused by the absence of functional dystrophin protein and results in progressive muscle wasting. Dystrophin deficiency leads to a host of dysfunctional cellular processes including impaired autophagy. Autophagic dysfunction appears to be due, at least in part, to decreased lysosomal abundance mediated by decreased nuclear localization of transcription factor EB (TFEB), a transcription factor responsible for lysosomal biogenesis. PGC‐1α overexpression decreased disease severity in dystrophin‐deficient skeletal muscle and increased PGC‐1α has been linked to TFEB activation in healthy muscle. The purpose of this study was to determine the extent to which PGC ...


A Neural Mechanism For Capnotaxis In The Naked Mole-Rat, Michael Zions 2020 The Graduate Center, City University of New York

A Neural Mechanism For Capnotaxis In The Naked Mole-Rat, Michael Zions

Dissertations, Theses, and Capstone Projects

A Neural Mechanism for Capnotaxis in the Naked Mole-Rat

The Naked Mole-Rat (NM-R) is a small hairless rodent that has thrived underground in the Horn of Africa for the past 40 million years. It was first discovered in 1847, but has only been maintained in captivity and studied as a laboratory animal over the past 40 years. To date, more than 400 scientific papers have been published on this species. This is relatively few compared to established lab animals like rats and mice, but those papers contain a trove of information that has changed our understanding of the constraints of ...


Demarcation Of Sepsis-Induced Peripheral And Central Acidosis With Ph (Low) Insertion Cycle Peptide, Kelly E. Henry, Aisling M. Chaney, Veronica L. Nagle, Haley C. Cropper, Saghar Mozaffari, Chip Slaybaugh, Keykavous Parang, Oleg A. Andreev, Yana K. Reshetnyak, Michelle L. James, Jason S. Lewis 2020 Memorial Sloan Kettering Cancer Center

Demarcation Of Sepsis-Induced Peripheral And Central Acidosis With Ph (Low) Insertion Cycle Peptide, Kelly E. Henry, Aisling M. Chaney, Veronica L. Nagle, Haley C. Cropper, Saghar Mozaffari, Chip Slaybaugh, Keykavous Parang, Oleg A. Andreev, Yana K. Reshetnyak, Michelle L. James, Jason S. Lewis

Pharmacy Faculty Articles and Research

Acidosis is a key driver for many diseases, including cancer, sepsis, and stroke. The spatiotemporal dynamics of dysregulated pH across disease remain elusive, and current diagnostic strategies do not provide localization of pH alterations. We sought to explore if PET imaging using hydrophobic cyclic peptides that partition into the cellular membrane at low extracellular pH (denoted as pH [low] insertion cycles, or pHLIC) can permit accurate in vivo visualization of acidosis. Methods: Acid-sensitive cyclic peptide c[E4W5C] pHLIC was conjugated to bifunctional maleimide-NO2A and radiolabeled with 64Cu (half-life, 12.7 h). C57BL/6J mice were ...


A Review Of The Scientific Rigor, Reproducibility, And Transparency Studies Conducted By The Abrf Research Groups., Sheenah M Mische, Nancy C Fisher, Susan M Meyn, Katia Sol Church, Rebecca L Hegstad-Davies, Frances Weis-Garcia, Marie Adams, John M Ashton, Kym M Delventhal, Julie A Dragon, Laura Holmes, Pratik Jagtap, Christopher E Mason, Magnus Palmblad, Brian C Searle, Christoph W Turck, Kevin L Knudtson 2020 Institute for Systems Biology, Seattle, Washington, USA.

A Review Of The Scientific Rigor, Reproducibility, And Transparency Studies Conducted By The Abrf Research Groups., Sheenah M Mische, Nancy C Fisher, Susan M Meyn, Katia Sol Church, Rebecca L Hegstad-Davies, Frances Weis-Garcia, Marie Adams, John M Ashton, Kym M Delventhal, Julie A Dragon, Laura Holmes, Pratik Jagtap, Christopher E Mason, Magnus Palmblad, Brian C Searle, Christoph W Turck, Kevin L Knudtson

Articles, Abstracts, and Reports

Shared research resource facilities, also known as core laboratories (Cores), are responsible for generating a significant and growing portion of the research data in academic biomedical research institutions. Cores represent a central repository for institutional knowledge management, with deep expertise in the strengths and limitations of technology and its applications. They inherently support transparency and scientific reproducibility by protecting against cognitive bias in research design and data analysis, and thedy have institutional responsibility for the conduct of research (research ethics, regulatory compliance, and financial accountability) performed in their Cores. The Association of Biomolecular Resource Facilities (ABRF) is a FASEB-member scientific ...


Generating Broadly Protective Immune Responses To Viral Influenza, Evan Engelhardt 2020 Iowa State University

Generating Broadly Protective Immune Responses To Viral Influenza, Evan Engelhardt

Creative Components

Modern influenza vaccines are very effective against the strains they are composed of. However, variations between flu strains easily bypasses the induced immunity, rendering the vaccine outdated by the time the next flu season comes around. Current research into a “universal” influenza vaccine that can elicit a broadly protective response from the immune system has made great progress. Most methods are designed to induce broadly neutralizing antibodies to conserved sequences within surface glycoproteins. These methods can be adapted to induce broad cellular immunity as well. Memory to conserved sequences grants the immune system protection against divergent strains of influenza that ...


Vaccine Development For Respiratory Syncytial Virus, Lakshmi sravya Konakanchi 2020 Iowa State University

Vaccine Development For Respiratory Syncytial Virus, Lakshmi Sravya Konakanchi

Creative Components

The respiratory syncytial virus (RSV) is a human pathogen that causes a lower respiratory infection in infants and healthy adults. The first incidence of RSV was recorded in the 1960s. The greatest success against viruses has always been by increasing immunity through vaccination like in smallpox, measles, influenza, polio. Though RSV spread its roots almost six decades ago, the creation of a vaccine against RSV is still an ongoing challenge. The structural proteins of RSV, mainly F and G, play an essential role in pathogenicity. Structural instability of the F protein is responsible for making the vaccine discovery an uncertain ...


Optimizing Animal Welfare In Commercial Laying Hens Through Novel Management Practices And Farm Manager Evaluation, John R. Brunnquell 2020 University of Kentucky

Optimizing Animal Welfare In Commercial Laying Hens Through Novel Management Practices And Farm Manager Evaluation, John R. Brunnquell

Theses and Dissertations--Animal and Food Sciences

The commercial production of pasture and free-range eggs in the United States is expanding rapidly. According to the United States Department of Agriculture Agricultural Management Assistance, in May of 2019 there were 2.6M pasture hens and 4.5M free-range hens representing 1.9% of the nation’s laying flock. There is little industry and/or academic experience with this style of production in the United States. Programs such as the European Layer Training Initiative (ELTI), which emerged in 2019, have tried to fill this void but participation from the US was low. The principal sources for guidance of commercial ...


Effect Of The Prospect Of Transport On Captive Tiger Behavior And Fecal Cortisol In Naïve And Experienced Tigers, Callan Lichtenwalter 2020 University of Arkansas, Fayetteville

Effect Of The Prospect Of Transport On Captive Tiger Behavior And Fecal Cortisol In Naïve And Experienced Tigers, Callan Lichtenwalter

Theses and Dissertations

With close to 5,000 captive tigers in the United States, it is vital to ensure that these tigers are receiving adequate welfare whether they are in an accredited facility, or privately owned. The goal of this study was to assess whether captive tigers at a rescue facility with experience being transported outside of the facility would respond differently to the presentation of their transport vehicle than their naïve counterparts who had only been transported within the facility. The behavior of 5 naïve and 7 experienced tigers (n = 12) located at Turpentine Creek Wildlife Refuge in Eureka Springs, Arkansas was ...


Frontal Brain Injury: Effects On Flexibility, Impulse Control, And Attention, Christopher Matthew O'Hearn 2020 WVU

Frontal Brain Injury: Effects On Flexibility, Impulse Control, And Attention, Christopher Matthew O'Hearn

Graduate Theses, Dissertations, and Problem Reports

Traumatic Brain Injury (TBI) is defined as an impact to the head, penetration of the skull, or rapid deceleration of the skull, resulting in an alteration of brain function or neurological deficit. Cognitive deficits are common following TBI and often go unresolved due to a lack of effective treatments. These deficits often perseverate into the chronic post injury phase, so the development of rehabilitative strategies is imperative. Behavioral flexibility, impulse control, and attention are a few cognitive processes that are commonly affected by TBI. The current research compares these processes between rats with and without a severe frontal brain injury ...


Building The Vertebrate Codex Using The Gene Breaking Protein Trap Library, Noriko Ichino, Gaurav K. Varshney, Ying Wang, Hsin-kai Liao, Maura McGrail, Jeffrey J. Essner, Shawn M. Burgess, et al. 2020 Mayo Clinic

Building The Vertebrate Codex Using The Gene Breaking Protein Trap Library, Noriko Ichino, Gaurav K. Varshney, Ying Wang, Hsin-Kai Liao, Maura Mcgrail, Jeffrey J. Essner, Shawn M. Burgess, Et Al.

Genetics, Development and Cell Biology Publications

One key bottleneck in understanding the human genome is the relative under-characterization of 90% of protein coding regions. We report a collection of 1200 transgenic zebrafish strains made with the gene-break transposon (GBT) protein trap to simultaneously report and reversibly knockdown the tagged genes. Protein trap-associated mRFP expression shows previously undocumented expression of 35% and 90% of cloned genes at 2 and 4 days post-fertilization, respectively. Further, investigated alleles regularly show 99% gene-specific mRNA knockdown. Homozygous GBT animals in ryr1b, fras1, tnnt2a, edar and hmcn1 phenocopied established mutants. 204 cloned lines trapped diverse proteins, including 64 orthologs of human disease-associated ...


Non-Invasive Method For Leptin Supplementation In Zebrafish (Danio Rerio), Regan McNamara 2020 The University of Akron

Non-Invasive Method For Leptin Supplementation In Zebrafish (Danio Rerio), Regan Mcnamara

Williams Honors College, Honors Research Projects

I tested the hypothesis that recombinant leptin protein can be introduced to zebrafish in vivo through non-invasive soaking in a solution containing the protein. One way to study various molecules’ effects in vivo is through intraperitoneal or intracerebroventricular injections during the embryonic or larval stage, which is invasive, difficult to administer, and can have a high mortality rate. 48 hours post fertilization (hpf) zebrafish were soaked in a His-tagged recombinant leptin protein solution at 10 nM and 100 nM concentrations (produced by Genscript). After soaking, zebrafish larvae were washed extensively to remove all recombinant protein on their exterior before homogenization ...


Investigating The Morphology Of Iprgcs In Control Vs. Glaucomatous Retinas, Samantha Cook 2020 The University of Akron

Investigating The Morphology Of Iprgcs In Control Vs. Glaucomatous Retinas, Samantha Cook

Williams Honors College, Honors Research Projects

Glaucoma is a build-up of pressure in the eye that leads to the gradual loss of sight. The intention of this study was to investigate how glaucoma affects intrinsically photosensitive Retinal Ganglion Cells (ipRGCs). These cells contain melanopsin, a photopigment, that enables the cells to react to light. Four-month-old control and five-month-old glaucoma mice retinas were dissected, stained using primary and secondary antibodies, then traced using ImageJ’s Simple Neurite Tracer. There were no significant differences in soma size, total dendritic length, dendritic field size, and dendritic field diameter between control and glaucoma ipRGCs. However, further research is needed to ...


Physiological Response Of Elasmobrachs During Propofol Immersion, Matthew Levendosky 2020 Georgia Southern University

Physiological Response Of Elasmobrachs During Propofol Immersion, Matthew Levendosky

Electronic Theses and Dissertations

Sensory experiments require anesthesia so the animal is immobilized, however fish anesthetics have shown to depress sensory responses. Newer anesthetics may offer similar anesthetic relief, but differ in means of action so sensory responses may be unaffected. Propofol has been used intravenously on small elasmobranchs but may provide prolonged effects if used as an immersion anesthetic. Objectives of this study were 1. Determine appropriate concentration of anesthetic to minimize induction and recovery for animals anesthetized at a surgical plane of anesthesia and 2. Measure physiological response of the pupil to light stimuli during anesthetic immersion. To address these objectives, I ...


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