Life Sciences Commons^™

Production Of Bovine Colostrum For Human Consumption To Improve Health, Merve Kaplan, Ayşenur Arslan, Hatice Duman, Melda Karyelioğlu, Barış Baydemir, Bilgetekin Burak Günar, Merve Alkan, Ayşe Bayraktar, Halil İbrahim Tosun, Melih Ertürk, Günay Eskici, Rebbeca M. Duar, Bethany M. Henrick, Steven A. Frese, Sercan Karav

Department of Food Science and Technology: Faculty Publications

Colostrum contains all essential nutrients for the neonate during the first days of life, with impacts that continue far beyond these first days. Bovine colostrum has been used for human consumption due to the high concentrations of bioactive proteins, vitamins, minerals, growth factors, as well as free and conjugated oligosaccharides. Processes involved in the preparation of bovine colostrum for human consumption play a pivotal role in preserving and maintaining the activity of the bioactive molecules. As bovine colostrum is a multifunctional food that offers a myriad of benefits for human health, assessing the main processes used in preparing it with …

The Agricultural Genome To Phenome Initiative (Ag2pi): Creating A Shared Vision Across Crop And Livestock Research Communities, Christopher Tuggle, Jennifer Clarke, Jack C. M. Dekkers, David Ertl, Carolyn J. Lawrence-Dill, Eric Lyons, Brenda M. Murdoch, Nicole M. Scott, Patrick S. Schnable

Department of Food Science and Technology: Faculty Publications

Predicting phenotype from genotype is a central challenge in biology. By understanding genomic information to predict and improve traits, scientists can address the challenges and opportunities of achieving sustainable genetic improvement of complex, economically important traits in agriculturally relevant species. Converting the enormous, recent technical advances in all areas of genomics and phenomics into sustained and ecologically responsible improvements in food and fuel production is complex. It will require engaging agricultural genome to phenome (G2P) experts, drawing from a broad community, including crop and livestock scientists and essential integrative disciplines (e.g., engineers, economists, data and social scientists). To achieve this …

Structural Variant-Based Pangenome Construction Has Low Sensitivity To Variability Of Haplotype-Resolved Bovine Assemblies, Alexander S. Leonard, Danang Crysnanto, Zih-Hua Fang, Michael P. Heaton, Brian L. Vander Ley, Carolina Herrera, Heinrich Bollwein, Derek M. Bickhart, Benjamin D. Rosen, Hubert Pausch

School of Veterinary and Biomedical Sciences: Faculty Publications

Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. …

Does Swab Type Matter? Comparing Methods For Mannheimia Haemolytica Recovery And Upper Respiratory Microbiome Characterization In Feedlot Cattle, William B. Crosby, Lee Pinnell, John T. Richeson, Cory Wolfe, Jake Castle, John Dustin Loy, Sheryl P. Gow, Keun Seok Seo, Sarah F. Capik, Amelia R. Woolums, Paul S. Morley

School of Veterinary and Biomedical Sciences: Faculty Publications

Background: Bovine respiratory disease (BRD) is caused by interactions among host, environment, and pathogens. One standard method for antemortem pathogen identification in cattle with BRD is deep-guarded nasopharyngeal swabbing, which is challenging, costly, and waste generating. The objective was to compare the ability to recover Mannheimia haemolytica and compare microbial community structure using 29.5 inch (74.9 cm) deep-guarded nasopharyngeal swabs, 16 inch (40.6 cm) unguarded proctology swabs, or 6 inch (15.2 cm) unguarded nasal swabs when characterized using culture, real time-qPCR, and 16S rRNA gene sequencing. Samples for aerobic culture, qPCR, and 16S rRNA gene sequencing were collected from the …

Building Digital Twins Of The Human Immune System: Toward A Roadmap, Reinhard Laubenbacher, Anna Niarakis, Tomas Helikar, G. An, B. Shapiro, R. S. Malik-Sheriff, T. J. Sego, P. Macklin, J. A. Glazier

Department of Biochemistry: Faculty Publications

Digital twins, customized simulation models pioneered in industry, are beginning to be deployed in medicine and healthcare, with some major successes, for instance in cardiovascular diagnostics and in insulin pump control. Personalized computational models are also assisting in applications ranging from drug development to treatment optimization. More advanced medical digital twins will be essential to making precision medicine a reality. Because the immune system plays an important role in such a wide range of diseases and health conditions, from fighting pathogens to autoimmune disorders, digital twins of the immune system will have an especially high impact. However, their development presents …

Feedlot Diets Containing Different Starch Levels And Additives Change The Cecal Proteome Involved In Cattle’S Energy Metabolism And Inflammatory Response, Leone Campos Rocha, Andrey Sávio De Almeida Assunção, Renata Aparecida Martins, Victor Valério De Carvalho, Alexandre Perdigão2, Marília Afonso Rabelo Buzalaf, Jiri Adamec, Camila Pereira Braga, Danilo Domingues Millen, José Cavalcante Souza Vieira, Pedro De Magalhães Padilha

Department of Biochemistry: Faculty Publications

Diets for feedlot cattle must be a higher energy density, entailing high fermentable carbohydrate content. Feed additives are needed to reduce possible metabolic disorders. This study aimed to analyze the post-rumen effects of different levels of starch (25%, 35%, and 45%) and additives (monensin or a blend of essential oils and exogenous α-amylase) in diets for Nellore feedlot cattle. The cecum tissue proteome was analyzed via two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and then differentially expressed protein spots were identified with liquid chromatography–tandem mass spectrometry (LC–MS/MS). The use of blends of essential oils associated with α-amylase as a feed additive promoted …

Increased Signal Complexity Is Associated With Increased Mating Success, Noori Choi, Matt Adams, Kasey Fowler-Finn, Elise Knowlton, Malcolm Rosenthal, Aaron Rundus, Roger D. Santer, Dustin J. Wilgers, Eileen Hebets

Eileen Hebets Publications

The evolution of complex signals has often been explored by testing multiple functional hypotheses regarding how independent signal components provide selective benefits to offset the costs of their production. In the present study, we take a different approach by exploring the function of complexity per se. We test the hypothesis that increased vibratory signal complexity— based on both proportional and temporal patterning—provides selective benefits to courting male Schizocosa stridulans wolf spiders. In support of this hypothesis, all of our quantified metrics of vibratory signal complexity predicted the mating success of male S. stridulans. The rate of visual signalling, which is …

Description Of The Courtship And Copulation Behaviours Of The Wall Spider Oecobius Concinnus (Oecobiidae), Diego Solano-Brenes, Laura Segura-Hernández, Gilbert Barrantes

Eileen Hebets Publications

Courtship and copulation behaviours are yet scantily described in many spider families, and this lack of information limits our understanding of the evolution of such behaviours within and across families. Here, we provide a detailed description of both courtship and copulation behaviour for Oecobius concinnus Simon, 1893. A striking characteristic of the male courtship is the construction of a tubular web (mating web) in which most courtship and copulation occurs. This web likely functions to restrain the female in a reduced space and as a substrate for male pheromones. The courtship consists of a complex web of interactions between both …

Sources Of Variability And Uncertainty In Food-Energy-Water Nexus Systems, Heydi Calderon-Ambelis, Deepak R. Keshwani

Department of Agricultural and Biological Systems Engineering: Faculty Publications

A nexus approach contributes to the strategic allocation of resources to secure food, energy, and water for the world population. Integrated models considering the complex interactions across food, energy, and water (FEW) enhance decision-making and strategic planning towards resilience. However, a significant number of the existing integrated models leave unaddressed the inherent variability and uncertainty present in the FEW sectors. Here, we review the importance of characterizing variability over spatial and temporal scales and the importance of decreasing the uncertainty present within a FEW nexus systems. The review also discusses existing modeling tools that address variability and uncertainty on single …

Modeling The Evolution Of Herbicide Resistance In Weed Species With A Complex Life Cycle, K. Harrison Holmes, John L. Lindquist, Richard Rebarber, Rodrigo Werle, Melinda K. Yerka, Brigitte Tenhumberg

Brigitte Tenhumberg Papers

A growing number of weed species have evolved resistance to herbicides in recent years, which causes an immense financial burden to farmers. An increasingly popular method of weed control is the adoption of crops that are resistant to specific herbicides, which allows farmers to apply the herbicide during the growing season without harming the crop. If such crops are planted in the presence of closely related weed species, it is possible that resistance genes could transfer from the crop species to feral populations of the wild species via gene flow and become stably introgressed under ongoing selective pressure by the …

Reconstructed Evolutionary Patterns For Crocodile-Line Archosaurs Demonstrate Impact Of Failure To Log-Transform Body Size Data, Roger B. J. Benson, Pedro Godoy, Mario Bronzati, Richard J. Butler, William Gearty

School of Biological Sciences: Faculty Publications

No abstract provided.

Pea Aphid Winged And Wingless Males Exhibit Reproductive, Gene Expression, And Lipid Metabolism Differences, Omid Saleh Ziabari, Qingyi Zhong, Swapna R. Purandare, Joel Reiter, Anthony J. Zera, Jennifer A. Brisson

School of Biological Sciences: Faculty Publications

Alternative, intraspecific phenotypes offer an opportunity to identify the mechanistic basis of differences asso- ciated with distinctive life history strategies. Wing dimorphic insects, in which both flight-capable and flight- incapable individuals occur in the same population, are particularly well-studied in terms of why and how the morphs trade offflight for reproduction. Yet despite a wealth of studies examining the differences between fe- male morphs, little is known about male differences, which could arise from different causes than those acting on females. Here we examined reproductive, gene expression, and biochemical differences between pea aphid ( Acyrthosiphon pisum ) winged and wingless …

Social Networks In The Single Cell, Moira Rodriguez, Ana Martinez-Hottovy, Alan C. Christensen

School of Biological Sciences: Faculty Publications

Plant mitochondrial DNA (mtDNA) can become damaged in many ways. A major repair mechanism is homologous recombination, which requires an undamaged DNA template. Presumably, this template comes from a different mitochondrion in the same cell. Plant mitochondria undergo fission and fusion to form transient networks which could allow the exchange of genetic information. To test this hypothesis, Chustecki et al. (2022) used msh1 mutants with defective DNA repair, and showed that mitochondrial interactions increased, revealing a link between the physical and genetic behavior of mitochondria.

Towards An Integrative View Of Virus Phenotypes, John P. Delong, Maitham A. Al-Sammak, Zeina Al-Ameeli, David Dunigan, Kyle F. Edwards, Jeffry J. Fuhrmann, Jason P. Gleghorn, Hanqun Li, Kona Haramoto, Amelia O. Harrison, Marcia F. Marston, Ryan M. Moore, Shawn W. Polson, Barbra D. Ferrell, Miranda E. Salsbery, Christopher R. Schvarcz, Jasmine Shirazi, Grieg F. Steward, James L. Van Etten, K. Eric Wommack

School of Biological Sciences: Faculty Publications

Understanding how phenotypes emerge from genotypes is a foundational goal in biology. As challenging as this task is when considering cellular life, it is further complicated in the case of viruses. During replication, a virus as a discrete entity (the virion) disappears and manifests itself as a metabolic amalgam between the virus and the host (the virocell). Identifying traits that unambiguously constitute a virus’s phenotype is straightforward for the virion, less so for the virocell. Here, we present a framework for categorizing virus phenotypes that encompasses both virion and virocell stages and considers functional and performance traits of viruses in …

Phenotypic And Genomic Diversification In Complex Carbohydrate-Degrading Human Gut Bacteria, Nicholas A. Pudlo, Karthik Urs, Ryan Crawford, Ali Pirani, Todd Atherly, Roberto Jimenez, Nicolas Terrapon, Bernard Henrissat, Daniel Peterson, Cherie Ziemer, Evan Snitkin, Eric C. Martens

Department of Food Science and Technology: Faculty Publications

Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central for defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability …

Experimental Evaluation Of Ecological Principles To Understand And Modulate The Outcome Of Bacterial Strain Competition In Gut Microbiomes, Rafael R. Segura Munoz, Sara Mantz, Ines Martinez, Fuyong Li, Robert J. Schmaltz, Nicholas A. Pudlo, Karthik Urs, Eric C. Martens, Jens Walter, Amanda Ramer-Tait

Department of Food Science and Technology: Faculty Publications

It is unclear if coexistence theory can be applied to gut microbiomes to understand their characteristics and modulate their composition. Through experiments in gnotobiotic mice with complex microbiomes, we demonstrated that strains of Akkermansia muciniphila and Bacteroides vulgatus could only be established if microbiomes were devoid of these species. Strains of A. muciniphila showed strict competitive exclusion, while B. vulgatus strains coexisted but populations were still influenced by competitive interactions. These differences in competitive behavior were reflective of genomic variation within the two species, indicating considerable niche overlap for A. muciniphila strains and a broader niche space for B. vulgatus …

Large-Scale Analyses Of Heat Shock Transcription Factors And Database Construction Based On Whole-Genome Genes In Horticultural And Representative Plants, Tong Yu, Yun Bai, Zhuo Liu, Zhiyuan Wang, Qihang Yang, Tong Wu, Shuyan Feng, Yu Zhang, Shaoqin Shen, Quang Li, Liqiang Gu, Xiaoming Song

Department of Food Science and Technology: Faculty Publications

Heat shock transcription factor (Hsf) plays a critical role in regulating heat resistance. Here, 2950 Hsf family genes were identified from 111 horticultural and representative plants. More Hsf genes were detected in higher plants than in lower plants. Based on all Hsf genes, we constructed a phylogenetic tree, which indicated that Hsf genes of each branch evolved independently after species differentiation. Furthermore, we uncovered the evolutionary trajectories of Hsf genes by motif analysis. There were only six motifs (M1–M6) in lower plants, and then four novel motifs (M7–M10) appeared in higher plants. However, the motifs of some Hsf genes were …

Thermal Inactivation Of Salmonella On Chicken Wings Cooked In Domestic Convection And Air Fryer Ovens, Carmen Cano, Xinyao Wei, Cyril A. Etaka, Byron D. Chaves

Department of Food Science and Technology: Faculty Publications

Chicken wings are among the most popular poultry products for home and foodservice consumption. Poultry products must be handled and cooked safely to decrease the risk of foodborne salmonellosis for consumers. This study aims to validate the use of domestic appliances (convection and air fryer ovens) for the thermal inactivation of Salmonella on chicken wings. Wings (n = 3, 46.5 ± 4.3 g) were inoculated with a five-strain cocktail of Salmonella (ca. 8 log₁₀ CFU/wing) and cooked in a convection oven (179.4ºC) or an air fryer (176, 190, or 204ºC) for 2, 5, 10, 15, 20, 22, or 25 …

Small Bowel Stomas Are Associated With Higher Risk Of Circulating Food-Specific-Igg Than Patients With Organic Gastrointestinal Conditions And Colostomies, Walker K. Carson, Joseph L. Baumert, Jennifer Clarke, Jacques Izard

Department of Food Science and Technology: Faculty Publications

Objective The effects of food sensitivity can easily be masked by other digestive symptoms in ostomates and are unknown. We investigated food-specific-IgG presence in ostomates relative to participants affected by other digestive diseases.

Design Food-specific-IgG was evaluated for 198 participants with a panel of 109 foods. Immunocompetency status was also tested. Jejunostomates, ileostomates, and colostomates were compared with individuals with digestive tract diseases with inflammatory components (periodontitis, eosinophilic esophagitis, duodenitis, ulcerative colitis, Crohn’s disease, and appendicitis), as well as food malabsorption due to intolerance. A logistic regression model with covariates was used to estimate the effect of the experimental data …

Improving Taxonomic Delimitation Of Fungal Species In The Age Of Genomics And Phenomics, Ashley Stengel, Kimberly M. Stanke, Amanda C. Quattrone, Joshua R. Herr

Department of Plant Pathology: Faculty Publications

Species concepts have long provided a source of debate among biologists. These lively debates have been important for reaching consensus on how to communicate across scientific disciplines and for advancing innovative strategies to study evolution, population biology, ecology, natural history, and disease epidemiology. Species concepts are also important for evaluating variability and diversity among communities, understanding biogeographical distributions, and identifying causal agents of disease across animal and plant hosts. While there have been many attempts to address the concept of species in the fungi, there are several concepts that have made taxonomic delimitation especially challenging. In this review we discuss …

Determining The Novel Pathogen Neodothiora Populina As The Causal Agent Of The Aspen Running Canker Disease In Alaska, Loretta M. Winton, Gerard C. Adams, Roger W. Ruess

Department of Plant Pathology: Faculty Publications

Neodothiora populina Crous, G.C. Adams & Winton was determined to be a new pathogen of trembling aspen (Populus tremuloides) growing in Alaska, based on completion of Koch's Postulates in replicated forest and growth chamber inoculation trials. The pathogen is responsible for severe damage and widespread rapid mortality of sapling to mature aspen (≥ 80 years) in the boreal forests of interior Alaska, due to large diffuse annual (1–2 years) cankers. Isolation of the pathogen was challenging, and identification based on cultural characters was difficult. Fruiting bodies were not found on wild diseased trees, but erumpent pycnidia were found …

Creating A Pre-Illness Covid-19 Action Plan: A Web-Based Public Education Initiative, Brian S. Hustad

DNP Research Projects

Abstract

Background: The COVID-19 pandemic took the world by storm in the beginning stages of 2020. Public health agencies were overwhelmed, undermanned, and therefore slow to respond. Information began to flow at an unprecedented rate. Yet, very limited resources were put into place to present this information or to instruct the public on evidence-based prevention, treatment, or care at home during active infection.

Intervention: A project website was created and accessed through a QR code on the project flyer or by entering the URL into any browser. Participants were able to access three evidence- based video modules, which introduced the …

Desired Properties Of Recycling-Derived Fertilisers From An End-User Perspective, Aoife Egan, Niamh Power

Grey Literature

The Interreg North-West (NW) Europe ReNu2Farm project aims to increase the recycling rates of the plant nutrients nitrogen (N), phosphorous (P) and potassium (K). Currently, farmers predominantly use mineral fertilisers that are a finite resource and in the case of nitrogen are energy-intensive to produce. Then again, there are several regions in NW Europe with a nutrient surplus and there have been many advances in technology that can recover these nutrients. However, there has been very little up-take overall, with these recycling derived fertilisers (RDFs). To explore the reason behind the reluctance of farmers to use these sustainable recycled products, …

The Challenges Of Growing Orchids From Seeds For Conservation: An Assessment Of Asymbiotic Techniques, Devani Jolman, Martín I. Batalla, Alexis Hungerford, Pryce Norwood, Noah Tait, Lisa E. Wallace

Biological Sciences Faculty Publications

Lewis Knudson first successfully germinated orchid seeds asymbiotically on artificial medium in 1922. While many orchid species have since been grown asymbiotically, the tremendous variation in how species respond to artificial medium and growth conditions ex situ has also become apparent in the past century. In this study, we reviewed published journal articles on asymbiotic orchid seed germination to provide a summary of techniques used and to evaluate if these differ between terrestrial and epiphytic species, to identify areas where additional research is needed, and to evaluate whether asymbiotic germination could be used more often in ex situ conservation. We …

A Lims-Less System For Genotyping Data In Marker-Assisted Selection, Alex Rios

Master's Projects

Climate change and feeding the growing human population are two tightly intertwined problems we face now. Innovations across several agricultural sectors are needed to meet these challenges as we proceed into the future. Seed companies and plant breeders are at the forefront of producing new plant varieties that must survive under the unique stresses of extreme weather patterns caused by changing climates. This project aims to provide breeders with faster marker results by streamlining the data process of marker-assisted selection (MAS). Manually managing genotyping data in MAS can take several hours or days to compile results for breeders. Although some …

Differential Gene Expression Analysis Of Zebrafish Embryos Exposed To Simulated Microgravity And Insights Into Cellular Effects, Nicholas Lien

Master's Projects

Spaceflight consists of many dangers which adversely affects the health of astronauts through hazards such as microgravity and cosmic radiation. One area that is still poorly understood is how spaceflight impacts human reproductive health. This study aims to shed insight into how microgravity may impact the development of embryos. Differential gene expression analysis was performed via Jupyter Notebook and SLURM scripts and run on SJSU’s HPC server as a method of implementing NASA GeneLab’s RNA-Seq Consensus Pipeline. Data for this project utilized RNA-Seq files for early-stage embryonic zebrafish (Danio rerio), stored under GLDS-373. Gene Set Enrichment Analysis was performed to …

Impact Of Sleep And Training On Game Performance And Injury In Division-1 Women’S Basketball Amidst The Pandemic, Samah Senbel, S. Sharma, S. M. Raval, Christopher B. Taber, Julie K. Nolan, N. S. Artan, Diala Ezzeddine, Kaya Tolga

School of Computer Science & Engineering Faculty Publications

We investigated the impact of sleep and training load of Division - 1 women’s basketball players on their game performance and injury prediction using machine learning algorithms. The data was collected during a pandemic-condensed season with unpredictable interruptions to the games and athletic training schedules. We collected data from sleep monitoring devices, training data from coaches, injury reports from medical staff, and weekly survey data from athletes for 22 weeks.With proper data imputation, interpretable feature set, data balancing, and classifiers, we showed that we could predict game performance and injuries with more than 90% accuracy. More importantly, our F1 and …

Childhood Trauma And Chronic Disease, Breanna Urena

Graduate Research Projects

No abstract provided.

Contents, Discovery Editors

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

No abstract provided.

Featured Faculty Mentor And Student Explore The Dynamics Of This Research Relationship, Matt Bertucci, Gracie Morrison

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

No abstract provided.