Life Sciences Commons^™

Complex Dynamics Of Coral Gene Expression Responses To Low Ph Across Species, Veronica Z. Radice, Ana Martinez, Adina Paytan, Donald C. Potts, Daniel J. Barshis

Biological Sciences Faculty Publications

Coral capacity to tolerate low pH affects coral community composition and, ultimately, reef ecosystem function. Low pH submarine discharges (‘Ojo’; Yucatán, México) represent a natural laboratory to study plasticity and acclimatization to low pH in relation to ocean acidification. A previous >2‐year coral transplant experiment to ambient and low pH common garden sites revealed differential survivorship across species and sites, providing a framework to compare mechanistic responses to differential pH exposures. Here, we examined gene expression responses of transplants of three species of reef‐building corals (Porites astreoides, Porites porites and Siderastrea siderea) and their algal endosymbiont communities …

Exploring The Role Of Microrna-1 (Mir-1) On Skeletal Muscle Hypertrophy, Shengyi Fei

College of Education and Human Sciences: Dissertations, Theses, and Student Research

Skeletal muscle hypertrophy is a complex process that involves a range of signaling pathways and transcriptional regulators. Many hormones and growth factors can activate key signaling pathways, such as the PI3K/AKT/mTOR, MAPK, and cAMP pathways, which play a crucial role in the regulation of muscle hypertrophy. In Chapter 1, we reviewed some of the hormones and growth factors known to be associated with skeletal muscle hypertrophy, as well as the function of these key signaling pathways, and revealed some unresolved issues. In Chapter 2, we explored the role of microRNA-1 (miR-1) in skeletal muscle hypertrophy and aimed to determine the …

Periconceptual Maternal Nutrition Affects Fetal Liver Programming Of Energy- And Lipid-Related Genes, Wellison J. S. Diniz, Alison K. Ward, Kacie L. Mccathy, Cierrah J. Kassetas, Friederike Baumgaertner, Lawrence P. Reynolds, Pawel P. Borowicz, Kevin K. Sedivec, James D. Kirsch, Sheri T. Dorsam, Tammi L. Neville, J. Chris Forcherio, Ronald Scott, Joel S. Caton, Carl R. Dahlen

Department of Animal Science: Faculty Publications

During pregnancy, the fetus relies on the dam for its nutrient supply. Nutritional stimuli during fetal organ development can program hepatic metabolism and function. Herein, we investigated the role of vitamin and mineral supplementation (VTM or NoVTM—at least 71 days pre-breeding to day 83 of gestation) and rate of weight gain (low (LG) or moderate (MG)—from breeding to day 83) on the fetal liver transcriptome and the underlying biological pathways. Crossbred Angus beef heifers (n = 35) were randomly assigned to one of four treatments in a 2 × 2 factorial design (VTM_LG, VTM_MG, NoVTM_LG, and NoVTM_MG). Gene expression …

Genes Involved In Feed Efficiency Identified In A Meta-Analysis Of Rumen Tissue From Two Populations Of Beef Steers, Amanda K. Lindholm-Perry, Allison M. Meyer, Rebecca J. Kern-Lunbery, Hannah C. Cunningham-Hollinger, Taran H. Funk, Brittney N. Keel

Roman L. Hruska U.S. Meat Animal Research Center: Reports

In cattle, the rumen is an important site for the absorption of feed by-products released by bacterial fermentation, and variation in ruminal function plays a role in cattle feed efficiency. Studies evaluating gene expression in the rumen tissue have been performed prior to this. However, validating the expression of genes identified in additional cattle populations has been challenging. The purpose of this study was to perform a meta-analysis of the ruminal transcriptome of two unrelated populations of animals to identify genes that are involved in feed efficiency across populations. RNAseq data from animals with high and low residual feed intake …

Environment-Driven Shifts In Inter-Individual Variation And Phenotypic Integration Within Subnetworks Of The Mussel Transcriptome And Proteome, Richelle L. Tanner, Lani U. Gleason, W. Wesley Dowd

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The environment can alter the magnitude of phenotypic variation among individuals, potentially influencing evolutionary trajectories. However, environmental influences on variation are complex and remain understudied. Populations in heterogeneous environments might exhibit more variation, the amount of variation could differ between benign and stressful conditions, and/or variation might manifest in different ways among stages of the gene-to-protein expression cascade or among physiological functions. Here, we explore these three issues by quantifying patterns of inter-individual variation in both transcript and protein expression levels among California mussels, Mytilus californianus Conrad. Mussels were exposed to five ecologically relevant treatments that varied in the mean …

Changes In Serum Pon1 Activity, Gene Expression And Their Association With Lipid Profile Parameters In Healthy Darehshori Neonatal Foals: A Preliminary Study, Rouzbeh Razavi Dehkordi, Gholam Ali Kojouri, Behnaz Karimi, Ali Mohammad Ahadi

Turkish Journal of Veterinary & Animal Sciences

Paraoxonase 1 (PON1) contributes to the antioxidant mechanisms that prevent lipoprotein oxidation and act as a negative acute-phase protein. This study aimed to evaluate changes in serum PON1 activity, the leukocyte PON1 gene expression, as well as lipid profile tests (LDL, HDL, triglyceride, and cholesterol) in 16 healthy Darehshori newborn foals up to 60 days of life. Blood samples were collected at 1, 7, 15, 30, and 60 days used for detecting biochemical parameters, PON1 activity, and, and its gene expression, using realtime RT-PCR. Low levels of PON1 activity were observed at birth, which increased significantly with increasing age at …

Effects Of Extrinsic And Intrinsic Factors On Meat Quality And Muscle Biology Of Livestock, Yongjie Wang

Graduate Theses and Dissertations

In order to improve the meat quality of livestock, intrinsic and extrinsic factors that impact meat quality have been studied for a long time to optimize production quality. Nutrition, breed, and environment are the three most common factors to improve meat quality and muscle growth. The objective of this thesis is to perform a horizontal comparison of the effects of crude protein levels, breeds, and topsoil on the growth performance, muscle development, and meat quality of livestock, and also a longitudinal analysis using RNA-seq, RT-qPCR, and Western-blot to investigate the changes in genes and proteins related to muscle growth, and …

Effects Of Milk Replacer And Whole Milk Feeding On Rumen Development, Expression Ofgenes Related To Volatile Fatty Acid Absorption, And Rumen Bacteria In Calves, Ahmet Ceylan, Ali̇ Çalik, Burcu Eki̇m, Alev Gürol Bayraktaroğlu, Oğuz Çalişici, Doğukan Özen, Pinar Saçakli

Turkish Journal of Veterinary & Animal Sciences

This research examined the effects of liquid feeds on calf performance, rumen development, rumen cellulolytic bacteria count, and total bacteria diversity. Twenty Holstein bull calves were allocated to 2 groups either fed with milk replacer (MR) or whole milk. Calves fed milk tended to have higher (P = 0.058) average daily weight gain as compared to calves fed with MR during the entire experimental period. Starter mixture intake was not influenced by either milk or milk replacer feeding. Calves fed with milk had higher (P < 0.001) proliferative cells in the rumen papilla. The expressions of MCT1, MCT4, NHE1, NHE3, ACSS1, AceCS2, and ACSM1 genes, which are related to volatile fatty acid absorption, in the dorsal sac of the rumen were similar for calves fed either MR or whole milk. Fibrobacter succinogenes (P = 0.017) and Ruminococcus flavefaciens (P = 0.037) were significantly higher in the rumen of the milkfed calves. Moreover, denaturing gradient gel electrophoresis (DGGE)-derived dendrograms showed noticeable differences in ruminal microbial population between MR-fed and milk-fed calves. In conclusion, feeding calves with whole milk, which contains better quality protein and nutrients, instead of milk replacers, positively affects rumen development, cellulolytic bacteria numbers and total bacteria diversity.

Developmental Regulation Of Sirtuin Genes In Broiler Chicks, Heather L. Winter

Chancellor’s Honors Program Projects

No abstract provided.

Expression Of Lysine-Mediated Neuropeptide Hormones Controlling Satiety And Appetite In Broiler Chickens, Collins N. Khwatenge, Boniface M. Kimathi, Thyneice Taylor-Bowden, Samuel N. Nahashon

Agricultural and Environmental Sciences Faculty Research

Lysine is the second most limiting amino acid after methionine and is considered the most limiting amino acid for growth in poultry. Lysine requirement for broiler chickens has changed over the years. Leptin and adiponectin represent 2 adipokines that mediate metabolism by eliciting satiety effects whereas ghrelin peptide hormone influences appetite. We hypothesize that this affects growth performance of chicks. This study evaluates the effect of varying dietary lysine homeostasis on performance of broiler chickens through satiety- and appetite-mediating hormones. In 3 replications, 270 one-day-old chicks were reared for 8 wk feeding on diets comprising 0.85, 1.14, and 1.42% lysine …

The Identification Of Differentially Expressed Genes Between Extremes Of Placental Efficiency In Maternal Line Gilts On Day 95 Of Gestation, Shanice K. Krombeen, Vijay Shankar, Rooksana E. Noorai, Christopher A. Saski, Julia L. Sharp, Matthew E. Wilson, Tiffany A. Wilmoth

Faculty & Staff Scholarship

Background: Placental efficiency (PE) describes the relationship between placental and fetal weights (fetal wt/placental wt). Within litters, PE can vary drastically, resulting in similarly sized pigs associated with differently sized placentas, up to a 25% weight difference. However, the mechanisms enabling the smaller placenta to grow a comparable littermate are unknown. To elucidate potential mechanisms, morphological measurements and gene expression profiles in placental and associated endometrial tissues of high PE and low PE feto-placental units were compared. Tissue samples were obtained from eight maternal line gilts during gestational day 95 ovario-hysterectomies. RNA was extracted from tissues of feto-placental units with …

Endotoxin Increases Oxidative Stress And Oxygen Tension While Reducing Milk Protein Gene Expression In The Mammary Gland, Alexander Jonathan Spitzer

Graduate College Dissertations and Theses

Mastitis, the inflammation of the mammary gland by bacterial infection, is one of the costliest diseases to the dairy industry primarily due to a loss in milk production. The aim of this study was to investigate the mechanisms underlying reduced milk production during mastitis. We hypothesized that bacterial endotoxin induces cell apoptosis, oxidative stress and increases hypoxia while inhibiting milk gene expression in the mammary gland. To test this hypothesis, mice were bred to pregnancy, and 3 days post-partum the left and right sides of the 4th pair of mammary glands were alternately injected with either the endotoxin liposaccharide (LPS, …

Acute And Chronic Effects Of Thifluzamide On Daphnia Magna, Feyza İçoğlu Aksakal

Turkish Journal of Zoology

Thifluzamide is a thiazole carboxanilide fungicide used to control a wide range of basidiomycete diseases on maize, potatoes, rice, and other crops. Although this fungicide is found in aquatic environments, there is no information about its acute and chronic toxicity on aquatic invertebrates. In the present study, to investigate acute and chronic toxicity of thifluzamide, daphnids were exposed to 1.25, 1.5, 2, and 2.5 mg/L thifluzamide for 48 h and 21 days, respectively. The expression of four oxidative stress-related genes (CAT, GCLC, GST, and GPX) and life-history parameters such as days to the first brood, days to the first egg …

Novel Approaches To Evaluate And Enhance Neonatal Calf Gastrointestinal Health And Development, Fernanda Trindade Da Rosa

Electronic Theses and Dissertations

Physiological adaptations of the gastrointestinal tract (GIT) epithelial cells as well as methods to manipulate early life GIT microbiota colonization during the neonatal stage, is of great importance to the dairy industry. The first objective of this research was to optimize a method based on evaluation of bovine transcripts in fecal RNA via RTqPCR using L-selectin (SELL) as a marker for polymorphonuclear leukocytes (PMNL), keratin 8 (KRT8) and fatty acid binding protein 2 (FABP2) for GIT enterocytes, and tight junctions in fecal RNA and GIT sections in dairy calves. To test the reliability of the fecal RNA method, fecal and …

Functional Genomics And Immunologic Tools: The Impact Of Viral And Host Genetic Variations On The Outcome Of Zika Virus Infection, Sang-Im Yun, Byung-Hak Song, Jordan C. Frank, Justin G. Julander, Aaron L. Olsen, Irina A. Polejaeva, Christopher J. Davies, Kenneth L. White, Young-Min Lee

Animal, Dairy, and Veterinary Science Faculty Publications

Zika virus (ZIKV) causes no-to-mild symptoms or severe neurological disorders. To investigate the importance of viral and host genetic variations in determining ZIKV infection outcomes, we created three full-length infectious cDNA clones as bacterial artificial chromosomes for each of three spatiotemporally distinct and genetically divergent ZIKVs: MR-766 (Uganda, 1947), P6-740 (Malaysia, 1966), and PRVABC-59 (Puerto Rico, 2015). Using the three molecularly cloned ZIKVs, together with 13 ZIKV region-specific polyclonal antibodies covering nearly the entire viral protein-coding region, we made three conceptual advances: (i) We created a comprehensive genome-wide portrait of ZIKV gene products and their related species, with several previously …

Investigating The Potential Of Plant-Derived Antimicrobials For Controlling Campylobacter Jejuni In Poultry And Poultry Products, Basanta Raj Wagle

Graduate Theses and Dissertations

Campylobacter jejuni infection in humans is strongly associated with the handling and consumption of contaminated poultry products. Interventions reducing C. jejuni contamination in poultry would reduce the risk of subsequent human infections. In the first study, the efficacy of a Generally Recognized as Safe (GRAS) compound, eugenol (EG; derived from cloves), as an antimicrobial dip treatment to reduce C. jejuni in postharvest poultry was evaluated. The antimicrobial efficacy of EG was studied in suspension, emulsion and nanoemulsion delivery systems. EG suspension reduced C. jejuni counts with the greatest reduction of >2.0 Log CFU/sample for the 2% dose of EG (P<0.05). Eugenol emulsions or nanoemulsions did not provide any additional Campylobacter reduction when compared with suspension alone. In the second study, the efficacy of pectin or chitosan coatings fortified with eugenol to reduce C. jejuni on chicken wingettes was investigated. Inoculated wingettes were randomly assigned to controls, eugenol (0.5, 1 or 2%), pectin (3%), chitosan (2%) or their combinations. Following 1 min of coating, wingettes were air dried (1 h) and sampled on d 0, 1, 3, 5, and 7. The incorporation of 0.5, 1 or 2% eugenol in the pectin improved coating efficacy against C. jejuni whereas the efficacy of chitosan coating was improved by 2% eugenol treatment (P<0.05). Exposure of C. jejuni to eugenol, chitosan or combination significantly modulated select genes encoding for motility, quorum sensing and stress response. In the third study, the efficacy of eugenol, trans-cinnamaldehyde and carvacrol in inhibiting C. jejuni biofilm formation and inactivating mature biofilm was evaluated. For the inhibition study, C. jejuni was grown either in the presence or absence of sub-inhibitory concentrations of phytochemicals and biofilm formation was quantified at 24 h intervals by enumeration. For the inactivation study, mature C. jejuni biofilms were exposed to the phytochemicals (0, 0.25, 0.5, or 1%) for 1, 5, or 10 min, and surviving C. jejuni in the biofilms were enumerated. All phytochemicals reduced C. jejuni biofilm formation as well as inactivated mature biofilm at both temperatures (P<0.05). Moreover, scanning electron microscopy revealed disruption of biofilm architecture and loss of extracellular polymeric substances after treatment.

Evaluation Of Oocyte Developmental Competence And Potential Strategies To Improve Oocyte Quality, Min Yang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Assisted reproductive technologies (ARTs) have now been extensively used to promote reproductive efficiency as a fertility treatment not only in human medicine but also animal reproduction. ARTs serve as an important tool to advance the fundamental knowledge of reproductive processes. The quality of female’s eggs defines its ability to undergo maturation, fertilization, and development. This quality is determined by various factors and is crucial for the success of ARTs. Any alternations happening during the egg growth and maturation process can result in the decreased quality, which could have long-lasting effects on development. Improving the developmental efficiency of the egg is …

Gene Expression Levels In Some Candidate Genes For Mastitis Resistance, Milk Yield, And Milk Quality Of Goats Reared Under Different Feeding Systems, Akin Yakan, Hüseyi̇n Özkan, Aysel Eraslan Şakar, Necmetti̇n Ünal, Ceyhan Özbeyaz

Turkish Journal of Veterinary & Animal Sciences

This study aimed to identify the expression levels of some candidate genes for mastitis resistance (LTF and BRCA1), milk yield (POU1F1 and IGF-1), and milk quality (PPARγ and CSN2) in different feeding systems (pen- and pasture-based) used for Damascus goats. Milk samples were taken from all goats in both pen and pasture groups at 4 times, at the 1st, 3rd, 5th, and 7th months of the study. It was found that, compared to the pen group, the LTF and CSN2 genes in the pasture group had significant levels of upregulation in the 7th month of lactation (3.538- and 5.436-fold, respectively), …

Transcriptional Analysis Of Abdominal Fat In Chickens Divergently Selected On Bodyweight At Two Ages Reveals Novel Mechanisms Controlling Adiposity: Validating Visceral Adipose Tissue As A Dynamic Endocrine And Metabolic Organ, Christopher W. Resnyk, Wilfrid Carré, Xiaofei Wang, Tom E. Porter, J. Simon, Elisabeth Le Bihan-Duval, Michel J. Duclos, Sammy E. Aggrey, Larry A. Cogburn

Biology Faculty Research

Background

Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today’s broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and disorders of metabolism and reproduction). The present descriptive analysis of the abdominal fat transcriptome aimed to identify functional genes and biological pathways that likely contribute to an extreme difference in visceral fatness of divergently selected broiler chickens.

Methods

We used the Del-Mar 14 K Chicken Integrated Systems microarray to take time-course snapshots of global gene transcription …

Transcriptomic Analysis Of Maternally Provisioned Cues For Phenotypic Plasticity In The Annual Killifish, Austrofundulus Limnaeus, Amie L. Romney, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Background: Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifsh Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause. Alternately, embryos can be programmed to “escape” from diapause and develop directly by both maternal …

Transcriptome Analysis Reveals Potential Mechanisms Underlying Differential Heart Development In Fast- And Slow-Growing Broilers Under Heat Stress, Jibin Zhang, Carl J. Schmidt, Susan J. Lamont

Jibin Zhang

Pag 2017 Poster _ Jibin Zhang.Pdf, Jibin Zhang, Michael G. Kaiser, Melissa S. Herrmann, Rodrigo A. Gallardo, David A. Bunn, Terra R. Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont

Jibin Zhang

Identification Of Thyroid Hormone Receptors α And β Genes And Their Expression Profiles During Metamorphosis In Rana Chensinensis, Chuan-Chuan Du, Xin-Yi Li, Hua-Xin Wang, Kai Liang, Hong-Yuan Wang, Yuhui Zhang

Turkish Journal of Zoology

To explore the role of thyroid hormones in organ remodeling during the metamorphosis of amphibians, the cDNAs of two thyroid hormone receptors (TRα and TRβ) in Rana chensinensis were identified. The 1257 bp of rcTRα cDNA encoding 418 amino acids and the 1122 bp of rcTRβ cDNA encoding 373 amino acids were cloned. Their polypeptide sequences contain two highly conserved cysteine-rich zinc fingers in the DNA-binding domain, while rcTRβ is 42 amino acids shorter in its A/B domain when compared with rcTRα. Fifty-five amino acids differed between the TRα and TRβ domains. The rcTRα and rcTRβ mRNA levels in the …

Monkey-Based Research On Human Disease: The Implications Of Genetic Differences, Jarrod Bailey

Jarrod Bailey, PhD

Assertions that the use of monkeys to investigate human diseases is valid scientifically are frequently based on a reported 90–93% genetic similarity between the species. Critical analyses of the relevance of monkey studies to human biology, however, indicate that this genetic similarity does not result in sufficient physiological similarity for monkeys to constitute good models for research, and that monkey data do not translate well to progress in clinical practice for humans. Salient examples include the failure of new drugs in clinical trials, the highly different infectivity and pathology of SIV/HIV, and poor extrapolation of research on Alzheimer’s disease, Parkinson’s …

Epigenetic Regulation Of Gene Expression During Spermatogenesis, Karishma Nayak

Senior Honors Projects

In the US livestock production industry, improving reproductive efficiency will improve animal welfare and maintain reasonable costs of meat and milk for consumers. In recent research, abnormalities in epigenetic markers in sperm during spermatogenesis, has been linked to male subfertility in many species. Epigenetics is the study of changes in organisms caused by modifications of gene expression, including DNA methylation, rather than alteration of the genetic code itself. When this process is disturbed, it can negatively impact semen therefore decreasing its fertility. Through further research on how DNA methylation influences gene expression during spermatogenesis and its impact on sperm quality, …

Distinct Cardiac Responses To Heat Stress Between Two Broiler Lines Identified By Transcriptome Analysis, Jibin Zhang, Carl J. Schmidt, Susan J. Lamont

Jibin Zhang

Investigation Of The Promoter Polymorphisms Of The Growth Hormone (Gh1), Growth Hormone Receptor (Ghr), Insulin-Like Growth Factor (Igf-I), And Prolactin (Prl) Genes And The Correlation Between Gene Expression And Milk Yields In Holstein Cattle Raised In Central Anatolia, Korhan Arslan, Serpi̇l Taheri̇, Eli̇f Funda Şener, Bi̇lal Akyüz, Aytaç Akçay, Yusuf Özkul, Kaan Muhsi̇n İşcan

Turkish Journal of Veterinary & Animal Sciences

The aim of this study was to investigate the promoter polymorphisms of the growth hormone (GH1), growth hormone receptor (GHR), insulin-like growth factor (IGF-I), and prolactin (PRL) genes, and the correlation of the expression levels of these genes with lactation and daily milk yields in Holstein cattle. A total of 154 lactating Holstein cows raised in the Central Anatolia Region of Turkey, with a mean age of 5.4 years and a mean body weight of 571.7 kg, constituted the study material. Each blood sample was examined by real-time PCR for mRNA expression levels and the promoter polymorphisms of the GH1, …

Differential Expression Of Cyb5a In Chinese And European Pig Breeds Due To Genetic Variations In The Promoter Region..Pdf, Ying Bai, Jibin Zhang, Y Xue, Yl Peng, Gang Chen, Meiying Fang

Jibin Zhang

Developmental Mechanisms That Support Genome Stability And Embryonic Survival In Stress-Tolerant Embryos Of The Annual Killifish Austrofundulus Limnaeus, Josiah Tad Wagner

Dissertations and Theses

In order to complete their life cycles, vertebrates require oxygen and water. However, environments are not always forgiving when it comes to constantly providing these basic needs for vertebrate life. The annual killifish Austrofundulus limnaeus is possibly the most well described extremophile vertebrate and its embryos have been shown to tolerate extremes in oxygen, salinity, and water availability. This phenotype is likely a result of the annual killifish life history, which includes periods of temporary habitat desiccation and oxygen deprivation, and requires the production of stress-tolerant embryos that depress metabolism in a state of suspended animation, known as diapause. Over …

Plasticity Of Boldness In Rainbow Trout, Oncorhynchus Mykiss: Do Hunger And Predation Influence Risk-Taking Behaviour?, Jack S. Thomson, Phillip C. Watts, Tom G. Pottinger, Lynne U. Sneddon

Lynne U. Sneddon, Ph.D.

Boldness, a measure of an individual's propensity for taking risks, is an important determinant of fitness but is not necessarily a fixed trait. Dependent upon an individual's state, and given certain contexts or challenges, individuals may be able to alter their inclination to be bold or shy in response. Furthermore, the degree to which individuals can modulate their behaviour has been linked with physiological responses to stress. Here we attempted to determine whether bold and shy rainbow trout, Oncorhynchus mykiss, can exhibit behavioural plasticity in response to changes in state (nutritional availability) and context (predation threat). Individual trout were initially …