Life Sciences Commons^™

The Classification Of An Unknown Protein 3h04, Britney Dyszel

Biochemistry and Molecular Biology Presentations

An unclassified protein in the Protein Data Bank, 3H04, was selected as a protein of interest. Research was performed in silico to gain key information on the structure, sequence, and homology of protein 3H04. This research was guided using the BASIL Project’s protocols on in silico research. Several databases were utilized to study protein 3H04. Based on the data gathered, unclassified protein 3H04 is an aminopeptidase that cleaves prolyl-dipeptidyl peptide bonds through alpha beta hydrolase function.

A Review Of Technologies For Malt Flour And Sourdough From Brewery Spent Grain, Zachary Christman

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The utilization of brewer's spent grain for the production of malt flour is the focus of this article. The reader is presented with superheated steam and extrusion as technologies to reduce mycotoxin contamination and improve shelf life. Another option is the fermentation of brewer's spent grain with a cereal grade lactic acid bacteria for the production of sourdough bread. Milling of the brewer's spent grain for the production of bread is also covered.

Multiple Cytosolic Dna Sensors Bind Plasmid Dna After Transfection, Nina Semenova, Masa Bosnjak, Katarina Znidar, Maja Cemazar, Loree Heller

Bioelectrics Publications

Mammalian cells express a variety of nucleic acid sensors as one of the first lines of defense against infection. Despite extensive progress in the study of sensor signaling pathways during the last decade, the detailed mechanisms remain unclear. In our previous studies, we reported increased type I interferon expression and the upregulation of several proposed cytosolic DNA sensors after transfection of several tumor cell types with plasmid DNA (pDNA). In the present study, we sought to reveal the early events in the cytosolic sensing of this nucleic acid in a myoblast cell line. We demonstrated that DNA-dependent activator of interferon …

Investment Of Both Essential Fatty And Amino Acids To Immunity Varies Depending On Reproductive Stage., Taylor V. Pettit, R. John Pettit, Andrew M. Durso, Susannah S. French

Ecology Center Publications

Trade‐offs among the key life‐history traits of reproduction and immunity have been widely documented. However, the currency in use is not well‐understood. We investigated how reproducing female side‐blotched lizards, Uta stansburiana, allocate lipids versus proteins when given an immune challenge. We tested whether lizards would invest more in reproduction or immunity depending on reproductive stage. Females were given stable isotopes (¹⁵N‐leucine and ¹³C‐1‐palmitic acid), maintained on a regular diet and given either a cutaneous biopsy or a sham biopsy (control). Stable isotopes were monitored and analyzed in feces and uric acid, skin biopsies, eggs, and toe …

Time-Restricted Feeding Plus Resistance Training In Active Females: A Randomized Trial, Grant M. Tinsley, M. Lane Moore, Austin J. Graybeal, Trisha A. Vandusseldorp

Faculty and Research Publications

Background A very limited amount of research has examined intermittent fasting (IF) programs, such as time-restricted feeding (TRF), in active populations. Objective Our objective was to examine the effects of TRF, with or without β-hydroxy β-methylbutyrate (HMB) supplementation, during resistance training (RT). Methods This study employed a randomized, placebo-controlled, reduced factorial design and was double-blind with respect to supplementation in TRF groups. Resistance-trained females were randomly assigned to a control diet (CD), TRF, or TRF plus 3 g/d HMB (TRFHMB). TRF groups consumed all calories between 1200 h and 2000 h, whereas the CD group ate regularly from breakfast until …

Computational Analysis Of Large-Scale Trends And Dynamics In Eukaryotic Protein Family Evolution, Joseph Boehm Ahrens

FIU Electronic Theses and Dissertations

The myriad protein-coding genes found in present-day eukaryotes arose from a combination of speciation and gene duplication events, spanning more than one billion years of evolution. Notably, as these proteins evolved, the individual residues at each site in their amino acid sequences were replaced at markedly different rates. The relationship between protein structure, protein function, and site-specific rates of amino acid replacement is a topic of ongoing research. Additionally, there is much interest in the different evolutionary constraints imposed on sequences related by speciation (orthologs) versus sequences related by gene duplication (paralogs). A principal aim of this dissertation is to …

Interfacial Stress In The Development Of Biologics: Fundamental Understanding, Current Practice, And Future Perspective, Jinjiang Li, Mary E. Krause, Xiaodong Cheng, Yuan Cheng, Weiguo Dai, John J. Hill, Min Huang, Susan Jordan, Daniel Lacasse, Linda Narhi, Evgenyi Shalaev, Ian C. Shieh, Justin C. Thomas, Raymond Tu, Songyan Zheng, Lily Zhu

Publications and Research

Biologic products encounter various types of interfacial stress during development, manufacturing, and clinical administration. When proteins come in contact with vapor–liquid, solid–liquid, and liquid–liquid surfaces, these interfaces can significantly impact the protein drug product quality attributes, including formation of visible particles, subvisible particles, or soluble aggregates, or changes in target protein concentration due to adsorption of the molecule to various interfaces. Protein aggregation at interfaces is often accompanied by changes in conformation, as proteins modify their higher order structure in response to interfacial stresses such as hydrophobicity, charge, and mechanical stress. Formation of aggregates may elicit immunogenicity concerns; therefore, it …

Predicting Protein Residue-Residue Contacts Using Random Forests And Deep Networks, Joseph Luttrell Iv, Tong Liu, Chaoyang Zhang, Zheng Wang

Faculty Publications

Background: The ability to predict which pairs of amino acid residues in a protein are in contact with each other offers many advantages for various areas of research that focus on proteins. For example, contact prediction can be used to reduce the computational complexity of predicting the structure of proteins and even to help identify functionally important regions of proteins. These predictions are becoming especially important given the relatively low number of experimentally determined protein structures compared to the amount of available protein sequence data.

Results: Here we have developed and benchmarked a set of machine learning methods …

Genome-Wide Association Study Identifies Genomic Loci Affecting Filet Firmness And Protein Content In Rainbow Trout, Ali Ali, Rafet Al-Tobasei, Daniela Lourenco, Tim Leeds, Brett Kenney, Mohamed Saleem

Faculty & Staff Scholarship

Filet quality traits determine consumer satisfaction and affect profitability of the aquaculture industry. Soft flesh is a criterion for fish filet downgrades, resulting in loss of value. Filet firmness is influenced by many factors, including rate of protein turnover. A 50K transcribed gene SNP chip was used to genotype 789 rainbow trout, from two consecutive generations, produced in the USDA/NCCCWA selective breeding program. Weighted single-step GBLUP (WssGBLUP) was used to perform genome-wide association (GWA) analyses to identify quantitative trait loci affecting filet firmness and protein content. Applying genomic sliding windows of 50 adjacent SNPs, 212 and 225 SNPs were associated …

Proprietary Milk Protein Concentrate Reduces Joint Discomfort While Improving Exercise Performance In Non-Osteoarthritic Individuals, Tim N. Ziegenfuss, Chad M. Kerksick, A. William Kedia, Jennifer Sandrock, Betsy Raub, Hector L. Lopez

Faculty Scholarship

Milk and dairy products are known to contain various bioactives with potential anti-inflammatory and immune modulating effects. Previous research has indicated that milk produced from hyperimmunized cows provided meaningful health benefits to individuals suffering from varying degrees of osteoarthritis and rheumatoid arthritis. PURPOSE: To examine the impact of a proprietary milk protein concentrate on joint discomfort and physical function, exercise performance, quality of life and various measures of affect. METHODS: Non-osteoarthritic men (42.5 ± 8.9 years, 176.7 ± 6.7 cm, 89.9 ± 11.5 kg, 28.8 ± 3.5 kg/m2, n = 30) and women (46.4 ± 9.6 years, 163.1 ± 8.2 …

Metabolic Impact Of Protein Feeding Prior To Moderate-Intensity Treadmill Exercise In A Fasted State: A Pilot Study, Bradley T. Gieske, Richard A. Stecker, Charles R. Smith, Kyle E. Witherbee, Patrick S. Harty, Robert Wildman, Chad M. Kerksick

Faculty Scholarship

Background

Augmenting fat oxidation is a primary goal of fitness enthusiasts and individuals desiring to improve their body composition. Performing aerobic exercise while fasted continues to be a popular strategy to achieve this outcome, yet little research has examined how nutritional manipulations influence energy expenditure and/or fat oxidation during and after exercise. Initial research has indicated that pre-exercise protein feeding may facilitate fat oxidation while minimizing protein degradation during exercise, but more research is needed to determine if the source of protein further influences such outcomes.

Methods

Eleven healthy, college-aged males (23.5 ± 2.1 years, 86.0 ± 15.6 kg, 184 …

The Evolution Of Molecular Compatibility Between Bacteriophage Φx174 And Its Host, Alexander Kula, Joseph Saelens, Jennifer Cox, Alyxandria M. Schubert, Michael Travisano, Catherine Putonti

Biology: Faculty Publications and Other Works

Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic …

Animal Agriculture And American Health: The Search For Sustainable Protein, Britta Brinkmann

Biology: Student Scholarship & Creative Works

This study examines the impact large-scale animal agriculture has on the environment. It links the environment and health. The goal is to find protein sources that are sustainable and nutritious in order to replace typical meat and dairy products. A study is proposed to measure the impact of the typical American diet, a vegan diet, an insect-supplemented diet and a diet heavy in seafood.

Neuromuscular Adaptations Following Training And Protein Supplementation In A Group Of Trained Weightlifters, Christopher B. Taber, Kevin Carroll, Brad H. Deweese, Kimitake Sato, Charles Stuart, Mary Howell, Kenton Hall, Caleb D. Bazyler, Michael H. Stone

ETSU Faculty Works

The purpose of this study was to examine the effects of a recovery supplement compared with a placebo on muscle morphology in trained weightlifters. Vastus lateralis and muscle fiber cross sectional area of type I and type II fibers were compared between groups using a series of 2 × 2 (group × time) repeated measure ANOVAs. Both groups on average improved cross-sectional area of the vastus lateralis, type I and type II muscle fibers from pre-to-post but individual response varied within both groups. Greater magnitude of changes in type I and type II muscle fibers were observed for the placebo …

Neuromuscular Adaptations Following Training And Protein Supplementation In A Group Of Trained Weightlifters, Christopher B. Taber, Kevin M. Carroll, Brad H. Deweese, Kimitake Sato, Charles A. Stuart, Mary Howell, Kenton Hall, Caleb Bazyler, Michael H. Stone

Exercise Science Faculty Publications

The purpose of this study was to examine the effects of a recovery supplement compared with a placebo on muscle morphology in trained weightlifters. Vastus lateralis and muscle fiber cross sectional area of type I and type II fibers were compared between groups using a series of 2 × 2 (group × time) repeated measure ANOVAs. Both groups on average improved cross-sectional area of the vastus lateralis, type I and type II muscle fibers from pre-to-post but individual response varied within both groups. Greater magnitude of changes in type I and type II muscle fibers were observed for the placebo …

Mobilization And Role Of Starch, Protein, And Fat Reserves During Seed Germination Of Six Wild Grassland Species, Ming Zhao, Hongxiang Zhang, Hong Yan, Lu Qiu, Carol C. Baskin

Biology Faculty Publications

Since seed reserves can influence seed germination, the quantitative and qualitative differences in seed reserves may relate to the germination characteristics of species. The purpose of our study was to evaluate the correlation between germination and seed reserves, as well as their mobilization during germination of six grassland species (Chloris virgata, Kochia scoparia, Lespedeza hedysaroides, Astragalus adsurgens, Leonurus artemisia, and Dracocephalum moldavica) and compare the results with domesticated species. We measured starch, protein, and fat content in dry seeds and the initial absorption of water during imbibition. Starch, soluble protein, fat, and soluble …

Hard-Sphere-Like Dynamics In Highly Concentrated Alpha-Crystallin Suspensions, Preeti Vodnala, Laurence Lurio, Michael C. Vega, Elizabeth Gaillard

Faculty Peer-Reviewed Publications

The dynamics of concentrated suspensions of the eye-lens protein alpha crystallin have been measured using x-ray photon correlation spectroscopy. Measurements were made at wave vectors corresponding to the first peak in the hard-sphere structure factor and volume fractions close to the critical volume fraction for the glass transition. Langevin dynamics simulations were also performed in parallel to the experiments. The intermediate scattering function f(q,τ) could be fit using a stretched exponential decay for both experiments and numerical simulations. The measured relaxation times show good agreement with simulations for polydisperse hard-sphere colloids.

The Candida Albicans Stress Response Gene Stomatin-Like Protein 3 Is Implicated In Ros-Induced Apoptotic-Like Death Of Yeast Phase Cells, Karen A. Conrad, Ronald Rodriguez, Eugenia C. Salcedo, Jason M. Rauceo

Publications and Research

The ubiquitous presence of SPFH (Stomatin, Prohibitin, Flotillin, HflK/HflC) proteins in all domains of life suggests that their function would be conserved. However, SPFH functions are diverse with organism-specific attributes. SPFH proteins play critical roles in physiological processes such as mechanosensation and respiration. Here, we characterize the stomatin ORF19.7296/SLP3 in the opportunistic human pathogen Candida albicans. Consistent with the localization of stomatin proteins, a Slp3p-Yfp fusion protein formed visible puncta along the plasma membrane. We also visualized Slp3p within the vacuolar lumen. Slp3p primary sequence analyses identified four putative S-palmitoylation sites, which may facilitate membrane localization and are conserved features …

An Investigation Of Atomic Structures Derived From X-Ray Crystallography And Cryo-Electron Microscopy Using Distal Blocks Of Side-Chains, Lin Chen, Jing He, Salim Sazzed, Rayshawn Walker

Computer Science Faculty Publications

Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2-4 Å resolutions. The results show that the normalized probability density function of block …

Create Myplate Youth Curriculum, Gaelynn Peterson, Sharmi Crowther, Suzanne Prevedel

All Current Publications

This curriculum is divided into two sections: kindergarten through second grade and third grade through sixth grade. This curriculum was adopted by Utah’s Food $ense Program as part of the Supplemental Nutrition Assistance Program-Education (SNAP-Ed) and was introduced and delivered to all Nutrition Education assistants and Extension agents in Utah.

Constrained Sequence Alignment, Kyle Daling

WWU Honors College Senior Projects

Constrained Sequence Alignment: A new algorithm designed to help biologists produce better alignment for protein sequences.

Effect Of Bm-Hpme® Free Protein On Hbm-Mscs In Benchtop Bioreactor With Microcarriers, Adam Talbot

Biology Posters

Mesenchymal stem cell (MSC)-based therapies have great potential for treating many age-related diseases. When harvested from human bone marrow (hBM), these cells are relatively scarce and thus is is necessary for the cells to be expanded to achieve the necessary numbers needed for any therapeutic application and for many research applications. In order for the potential of MSCs to be unlocked, a strategy must be developed to expand these cells in the most efficient and effective way possible. Here we present a method to expand MSCs in a benchtop bioreactor with microcarriers and quantify the effect of the addition of …

Identification Of Hydrated And Dehydrated Lipids And Protein Secondary Structures In Seeds Of Cotton (Gossypium Hirsutum) Line, Diwas Kumar Silwal, Nsoki Phambu, Bharat Pokharel, Ahmad Naseer Aziz

Chemistry Faculty Research

Cottonseeds from two parents (TM-1 and 3-79) and their 17 progeny (chromosomal substitution) lines were analyzed for various secondary structures of proteins and moisture content of lipids, separately in hulls and kernels. Fourier transform infrared spectroscopy (FTIR) was used on mature seeds from Upland cotton (G. hirsutum) progeny lines and parents. Based on secondary structures of proteins and hydration levels of lipids, differences were observed among the cottonseeds. The two progeny lines – CS-B12sh and CS-B22sh retained lipid moisture content and protein secondary structures similar to both parents, while CS-B06, CS-B15sh and CS-B16 remained distinct from either parent. On the …

Testing The Independence Hypothesis Of Accepted Mutations For Pairs Of Adjacent Amino Acids In Protein Sequences, Jyotsna Ramanan, Peter Revesz

School of Computing: Faculty Publications

Evolutionary studies usually assume that the genetic mutations are independent of each other. However, that does not imply that the observed mutations are independent of each other because it is possible that when a nucleotide is mutated, then it may be biologically beneficial if an adjacent nucleotide mutates too. With a number of decoded genes currently available in various genome libraries and online databases, it is now possible to have a large-scale computer-based study to test whether the independence assumption holds for pairs of adjacent amino acids. Hence the independence question also arises for pairs of adjacent amino acids within …

Protocols And Pitfalls In Obtaining Fatty Acid-Binding Proteins For Biophysical Studies Of Ligand-Protein And Protein-Protein Interactions, Qian Wang, Samar Rizk, Cédric Bernard, May Poh Lai, David Kam, Judith Storch, Ruth E. Stark

Publications and Research

Adipocyte fatty acid-binding protein (AFABP: FABP4) is a member of the intracellular lipid-binding protein family that is thought to target long-chain fatty acids to nuclear receptors such as peroxisome proliferatoractivated receptor gamma (PPARγ), which in turn plays roles in insulin resistance and obesity. A molecular understanding of AFABP function requires robust isolation of the protein in liganded and free forms as well as characterization of its oligomerization state(s) under physiological conditions. We report development of a protocol to optimize the production of members of this protein family in pure form, including removal of their bound lipids by mixing with hydrophobically …

Evaluation Of Protein And Fiber From Distillers Grains Plus Solubles In Finishing Beef Cattle Diets, Zachary E. Carlson

Department of Animal Science: Dissertations, Theses, and Student Research

Four studies were conducted to evaluate the components of distillers grains plus solubles in finishing beef cattle diets. Experiment 1 evaluated the effects of five composites of feedstuffs formulated to be similar in nutrient composition to DDGS on finishing performance of cattle. Experiment 2 evaluated isolating the protein from distillers grains using a feedstuff from the wet milling ethanol industry to determine the impacts of protein on the feeding value of WDGS in finishing performance of cattle. Experiments 3 and 4 evaluated the effects of protein from distillers grains with the diets used in Exp. 2 on site of digestion, …

Ticks Elicit Variable Fibrinogenolytic Activities Upon Feeding On Hosts With Different Immune Backgrounds, Ashish Vora, Vikas Taank, John F. Anderson, Durland Fish, Daniel E. Sonenshine, John D. Catravas, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Ticks secrete several anti-hemostatic factors in their saliva to suppress the host innate and acquired immune defenses against infestations. Using Ixodes scapularis ticks and age-matched mice purchased from two independent commercial vendors with two different immune backgrounds as a model, we show that ticks fed on immunodeficient animals demonstrate decreased fibrinogenolytic activity in comparison to ticks fed on immunocompetent animals. Reduced levels of D-dimer (fibrin degradation product) were evident in ticks fed on immunodeficient animals in comparison to ticks fed on immunocompetent animals. Increased engorgement weights were noted for ticks fed on immunodeficient animals in comparison to ticks fed on …

Growing Yeast For Livestock, Zachary Christman

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Over 500,000 tons of organic materials such as food scraps are disposed of each year in Wisconsin. A large percentage of this material could be composted or turned into useful products. The purpose of this article is to educate farmers and organizations on how to turn food waste into a high value food source for livestock. Yeast can be grown at any time of the year without the large inputs of agricultural chemicals and machinery that is common with other feed production methods. A yeast growing facility can be scalable to any size the producer wants such as a small …

An Effective Computational Method Incorporating Multiple Secondary Structure Predictions In Topology Determination For Cryo-Em Images, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al Nasr, Jing He

Computer Science Faculty Publications

A key idea in de novo modeling of a medium-resolution density image obtained from cryo-electron microscopy is to compute the optimal mapping between the secondary structure traces observed in the density image and those predicted on the protein sequence. When secondary structures are not determined precisely, either from the image or from the amino acid sequence of the protein, the computational problem becomes more complex. We present an efficient method that addresses the secondary structure placement problem in presence of multiple secondary structure predictions and computes the optimal mapping. We tested the method using 12 simulated images from alpha-proteins and …

Prediction Of Human Dietary Δ15N Intake From Standardized Food Records: Validity And Precision Of Single Meal And 24-H Diet Data, Frank Hülsemann, Karsten Koehler, Jürgen Wittsiepe, Michael Wilhelm, Annett Hilbig, Mathilde Kersting, Hans Braun, Ulrich Flenker, Wilhelm Schänzer

Department of Nutrition and Health Sciences: Faculty Publications

Natural stable isotope ratios (δ15N) of humans can be used for nutritional analyses and dietary reconstruction of modern and historic individuals and populations. Information about an individual’s metabolic state can be obtained by comparison of tissue and dietary δ¹⁵N. Different methods have been used to estimate dietary δ¹⁵N in the past; however, the validity of such predictions has not been compared to experimental values. For a total of 56 meals and 21 samples of 24-h diets, predicted and experimental δ¹⁵N values were compared. The δ¹⁵N values were predicted from self-recorded food intake …