Life Sciences Commons^™

Rhodococcus Opacus Pd630 Genetic Tool Development To Enable The Conversion Of Biomass, Drew Michael Delorenzo

McKelvey School of Engineering Theses & Dissertations

The discovery of fossil fuels facilitated a new era in human history and allowed many firsts, such as the mass production of goods, the ability to travel and communicate long distances, the formation of population dense cities, and unprecedented improvements in quality of life. Alternative sources of energy and chemicals are needed, however, as hydrocarbon reserves continue to deplete and the effects of burning fossils on the planet become better understood. Lignocellulosic biomass is the most abundant raw material in the world and a viable alternative to petroleum-derived products. The pre-treatment of lignocellulose (e.g., thermocatalytic depolymerization, enzymatic hydrolysis, pyrolysis, etc.) …

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 …

Transcriptional Responses Of Soybean Aphids To Sublethal Insecticide Exposure, Laramy S. Enders, Leslie C. Rault, Tiffany Heng-Moss, Blair Siegfried, Nicholas J. Miller

Department of Entomology: Faculty Publications

Insecticides are a key tool in the management of many insect pests of agriculture, including soybean aphids. The selection imposed by insecticide use has often lead to the evolution of resistance by the target pest through enhanced detoxification mechanisms. We hypothesised that exposure of insecticide-susceptible aphids to sublethal doses of insecticides would result in the up-regulation of genes involved in detoxification of insecticides, revealing the genes upon which selection might act in the field. We used the soybean aphid biotype 1 reference genome, version 6.0 as a reference to analyze RNA-Seq data. We identified multiple genes with potential detoxification roles …

The Role Of Multidrug Resistance Regulators Mara, Soxs, Rob And Rama In Regulating Virulence Traits In Salmonella Enterica, Srinivas Thota

Dissertations

Enteric pathogens sense numerous signals specific to the anatomical location in the intestine and integrate them with the complex regulatory networks to temporally and spatially regulate their virulence genes. MarA, SoxS, Rob and RamA are homologous transcription factors that belong to AraC family of proteins in Salmonella enterica that primarily were thought to be involved in rendering antibiotic resistance to bacteria by up regulating efflux pumps and down regulating outer membrane porins. The fact that these transcription factors respond to the same intestinal compounds that regulate virulence genes in Salmonella motivated us to look for other roles of these transcription …

Thermal Stress Responses Of Sodalis Glossinidius, An Indigenous Bacterial Symbiont Of Hematophagous Tsetse Flies, Jose Santinni Roma, Shaina D’Souza, Patrick J. Somers, Leah F. Cabo, Ruhan Farsin, Serap Aksoy, Laura J. Runyen-Janecky, Brian L. Weiss

Biology Faculty Publications

Tsetse flies (Diptera: Glossinidae) house a taxonomically diverse microbiota that includes environmentally acquired bacteria, maternally transmitted symbiotic bacteria, and pathogenic African trypanosomes. Sodalis glossinidius, which is a facultative symbiont that resides intra and extracellularly within multiple tsetse tissues, has been implicated as a mediator of trypanosome infection establishment in the fly’s gut. Tsetse’s gut-associated population of Sodalis are subjected to marked temperature fluctuations each time their ectothermic fly host imbibes vertebrate blood. The molecular mechanisms that Sodalis employs to deal with this heat stress are unknown. In this study, we examined the thermal tolerance and heat shock response of …

Gene Expression Of Endangered Coral (Orbicella Spp.) In Flower Garden Banks National Marine Sanctuary After Hurricane Harvey, Rachel M. Wright, Adrienne M.S. Correa, Lucinda A. Quigley, Lory Z. Santiago-Vázquez, Kathryn E.F. Shamberger, Sarah W. Davies

Biological Sciences: Faculty Publications

About 190 km south of the Texas–Louisiana border, the East and West Flower Garden Banks (FGB) have maintained > 50% coral cover with infrequent and minor incidents of disease or bleaching since monitoring began in the 1970s. However, a mortality event, affecting 5.6 ha (2.6% of the area) of the East FGB, occurred in late July 2016 and coincided with storm-generated freshwater runoff extending offshore and over the reef system. To capture the immediate effects of storm-driven freshwater runoff on coral and symbiont physiology, we leveraged the heavy rainfall associated with Hurricane Harvey in late August 2017 by sampling FGB corals …

Implication Of Spiritual Network Support System In Epigenomic Modulation And Health Trajectory, Laurens Holmes Jr., Chinacherem Chinaka, Hikma Elmi, Kerti Deepika, Lavisha Palaez, Michael Enwere, Olumuyiwa T. Akinola, Kirk W. Dabnet

Community & Environmental Health Faculty Publications

With challenges in understanding the multifactorial etiologies of disease and individual treatment effect heterogeneities over the past four decades, much has been acquired on how physical, chemical and social environments a ffect human health, predisposing certain subpopulations to adverse health outcomes, especially the socio-environmentally disadvantaged (SED). Current translational data on gene and adverse environment interaction have revealed how adverse gene-environment interaction, termed aberrant epigenomic modulation, translates into impaired gene expression via messenger ribonucleic acid (mRNA) dysregulation, reflecting abnormal protein synthesis and hence dysfunctional cellular differentiation and maturation. The environmental influence on gene expression observed in most literature includes physical, chemical, …

Altering Social Cue Perception Impacts Honey Bee Aggression With Minimal Impacts On Aggression-Related Brain Gene Expression, James W. Harrison, Joseph H. Palmer, Clare C. Rittschof

Entomology Faculty Publications

Gene expression changes resulting from social interactions may give rise to long term behavioral change, or simply reflect the activity of neural circuitry associated with behavioral expression. In honey bees, social cues broadly modulate aggressive behavior and brain gene expression. Previous studies suggest that expression changes are limited to contexts in which social cues give rise to stable, relatively long-term changes in behavior. Here we use a traditional beekeeping approach that inhibits aggression, smoke exposure, to deprive individuals of aggression-inducing olfactory cues and evaluate whether behavioral changes occur in absence of expression variation in a set of four biomarker genes …

Treatment Of Hiv-Infected Individuals With The Histone Deacetylase Inhibitor Panobinostat Results In Increased Numbers Of Regulatory T Cells And Limits Ex Vivo Lipopolysaccharide-Induced Inflammatory Responses, Christel Rothe Brinkmann, Jesper Falkesgaard Højen, Thomas Aagaard Rasmussen, Anne Sofie Kjær, Rikke Olesen, Paul W. Denton, Lars Østergaard, Zhengyu Ouyang, Mathias Lichterfeld, Xu Yu, Ole Schmeltz Søgaard, Charles Dinarello, Martin Tolstrup

Paul W. Denton

Histone deacetylase inhibitors (HDACi) modulate the transcriptional activity of all cells, including innate and adaptive immune cells. Therefore, we aimed to evaluate immunological effects of treatment with the HDACi panobinostat in HIV-infected patients during a clinical phase IIa latency reversal trial. Using flow cytometry, we investigated changes in T cell activation (CD69, CD38, HLA-DR) and the expression of CD39 and CTLA4 on regulatory T cells (Tregs). Whole-blood stimulations were performed and cytokine responses measured using Luminex. Gene expression in purified peripheral blood mononuclear cells (PBMCs) was evaluated using an Affymetrix HTA 2.0 gene chip. We found that proportions of CD4+ …

Multigene Signatures Of Responses To Chemotherapy Derived By Biochemically-Inspired Machine Learning., Peter K. Rogan

Biochemistry Publications

Pharmacogenomic responses to chemotherapy drugs can be modeled by supervised machine learning of expression and copy number of relevant gene combinations. Such biochemical evidence can form the basis of derived gene signatures using cell line data, which can subsequently be examined in patients that have been treated with the same drugs. These gene signatures typically contain elements of multiple biochemical pathways which together comprise multiple origins of drug resistance or sensitivity. The signatures can capture variation in these responses to the same drug among different patients.

Characterization Of Early Biofilm Formation And Physiology In Neisseria Gonorrhoeae, Kelly Eckenrode

Dissertations, Theses, and Capstone Projects

Many bacteria rely on the dynamics of their extracellular appendages to perform important tasks, like motility and biofilm formation. Interestingly, these dynamics have been linked to physiological responses in some pathogenic bacteria; therefore, it is important to understand more about the role of physical forces in bacteria. I used the causative agent of the human disease gonorrhea, Neisseria gonorrhoeae, as a model system to study the role of physical force on early biofilm formation. The advantage of this system is that cell-cell interactions are controlled by extracellular filaments called type IV pili (tfp). Tfp is composed of monomers that give …

Advances In Gene Ontology Utilization Improve Statistical Power Of Annotation Enrichment, Eugene Waverly Hinderer Iii, Robert M. Flight, Rashmi Dubey, James N. Macleod, Hunter N. B. Moseley

Maxwell H. Gluck Equine Research Center Faculty Publications

Gene-annotation enrichment is a common method for utilizing ontology-based annotations in gene and gene-product centric knowledgebases. Effective utilization of these annotations requires inferring semantic linkages by tracing paths through edges in the ontological graph, referred to as relations. However, some relations are semantically problematic with respect to scope, necessitating their omission or modification lest erroneous term mappings occur. To address these issues, we created the Gene Ontology Categorization Suite, or GOcats—a novel tool that organizes the Gene Ontology into subgraphs representing user-defined concepts, while ensuring that all appropriate relations are congruent with respect to scoping semantics. Here, we demonstrate the …

Biological Pathway Involvement In Melanoma Heterogeneity And Drug-Induced Resistance, Sarah V. Pack

STAR Program Research Presentations

Tumors develop resistance to numerous drug therapies, and this remains a major obstacle in treating many types of non-surgical cancers. Melanoma provides a good model system for studying drug resistance in cancer due to its high propensity to incur resistance after a significant initial response to a drug. Genes that are highly expressed in melanoma cancer cells have been studied, but in order to further understand the collective function of these highly expressed genes we must analyze gene sets, or pathways. A single gene’s function is rarely independent of other genes, and pathway analysis takes this into account.

Our objective …

Response Of Early Life Stage Homarus Americanus To Ocean Warming And Acidification: An Interpopulation Comparison, Maura K. Niemisto

Electronic Theses and Dissertations

Anthropogenic carbon released into the atmosphere is driving rapid, concurrent increases in temperature and acidity across the world’s oceans, most prominently in northern latitudes. The geographic range of the iconic American lobster (Homarus americanus) spans a steep thermal gradient and one of the most rapidly warming oceanic environments. Understanding the interactive effects of ocean warming and acidification on this species’ most vulnerable early life stages is important to predict its response to climate change on a stage-specific and population level. This study compares the responses of lobster larvae from two sub-populations spanning New England’s north-south temperature gradient (southern …

The Effect Of Metal Composition And Particle Size On Nanostructure-Toxicity In Plants, Natalie Lynn Smith

MSU Graduate Theses

Silver nanoparticles (AgNPs) have consistently been shown to have a detrimental effect on bacteria, fungi, and plants. The interaction of AgNPs with plants has received considerable scientific attention, because it is potentially through plants that these structures can enter the food chain and bioaccumulate in humans and animals. To determine the effects of AgNPs on plants, Arabidopsis thaliana seedlings were chronically exposed to sublethal levels of AgNPs using a standardized method. To gain insight on mechanism of phytotoxicity, the seedlings were exposed to low concentrations of Ag⁺ (in the form of silver nitrate), AgNPs, or gold nanoparticles (AuNPs). To …

Adversarial Deep Neural Networks Effectively Remove Nonlinear Batch Effects From Gene-Expression Data, Jonathan Bryan Dayton

Theses and Dissertations

Gene-expression profiling enables researchers to quantify transcription levels in cells, thus providing insight into functional mechanisms of diseases and other biological processes. However, because of the high dimensionality of these data and the sensitivity of measuring equipment, expression data often contains unwanted confounding effects that can skew analysis. For example, collecting data in multiple runs causes nontrivial differences in the data (known as batch effects), known covariates that are not of interest to the study may have strong effects, and there may be large systemic effects when integrating multiple expression datasets. Additionally, many of these confounding effects represent higher-order interactions …

Estimation And Testing Of Gene Expression Heterosis, Tieming Ji, Peng Liu, Dan Nettleton

Dan Nettleton

Heterosis, also known as the hybrid vigor, occurs when the mean phenotype of hybrid offspring is superior to that of its two inbred parents. The heterosis phenomenon is extensively utilized in agriculture though the molecular basis is still unknown. In an effort to understand phenotypic heterosis at the molecular level, researchers have begun to compare expression levels of thousands of genes between parental inbred lines and their hybrid offspring to search for evidence of gene expression heterosis. Standard statistical approaches for separately analyzing expression data for each gene can produce biased and highly variable estimates and unreliable tests of heterosis. …

Substantial Contribution Of Genetic Variation In The Expression Of Transcription Factors To Phenotypic Variation Revealed By Erd-Gwas, Hung-Ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Background: There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits.

Results: The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes. In contrast, transcription factors are depleted among genes whose expression is either highly stable or highly variable across genotypes. We developed a …

Cell Wall Enzymes In Zygnema Circumcarinatum Utex 1559 Respond To Osmotic Stress In A Plant-Like Fashion, Elisabeth Fitzek, Lauren Orton, Sarah Entwistle, W. Scott Grayburn, Catherine Ausland, Melvin R. Duvall, Yanbin Yin

Department of Food Science and Technology: Faculty Publications

Previous analysis of charophyte green algal (CGA) genomes and transcriptomes for specific protein families revealed that numerous land plant characteristics had already evolved in CGA. In this study, we have sequenced and assembled the transcriptome of Zygnema circumcarinatum UTEX 1559, and combined its predicted protein sequences with those of 13 additional species [five embryophytes (Emb), eight charophytes (Cha), and two chlorophytes (Chl) as the outgroup] for a comprehensive comparative genomics analysis. In total 25,485 orthologous gene clusters (OGCs, equivalent to protein families) of the 14 species were classified into nine OGC groups. For example, the ChaCEmb group contains 4,174 OGCs …

Investigation Of Even-Skipped, A Developmentally-Regulated Gene Controlling Neural Segmentation In Dragonflies, Kathryn Bangser

Honors Theses

A comprehensive understanding of the genetic mechanisms underlying pattern formation and neurogenesis is necessary in order to trace the evolutionary history of insect embryogenesis.

One of the most important processes of embryogenesis is the organized pattern formation that allows for proper body segmentation and neural development. Proper segmentation, which relies on a series of specific gene expressions, is necessary for the development of an operational nervous system. Even-skipped (eve), one such regulatory gene, has been studied extensively in certain model organisms, and theories regarding the evolution of its functional role could be further elucidated by visualizing its expression …

Decrypting Female Attractivity In Garter Snakes, Holly Rucker

Senior Honors Projects, 2010-2019

Pheromones are utilized by many species as sexual signals driving mate choice, and pheromone production in vertebrates hinges on sex hormone action. Female red-sided garter snakes (Thamnophis sirtalis parietalis) produce a skin-based sex pheromone used by males for mate detection and selection. Estradiol is necessary for pheromone production, yet the specific mechanisms within the skin are unknown. Central to this is the metabolism of testosterone to estradiol via the enzyme aromatase. It is hypothesized that female garter snakes synthesize estradiol locally in the skin and maintain pheromone production via tissue-specific regulation of aromatase. Further, I hypothesize that female …

Gene Expression In The Right Ventricle During Development Of Pulmonary Hypertension, Jennifer Drake

Jennifer Drake

Pulmonary arterial hypertension (PAH) is a disease of the lung vessels that causes severe effects on the right ventricle of the heart; ultimately, most patients with severe PAH die as a result of right heart failure. However, little is known about the causes of right heart failure. Here, we describe a pattern of gene expression that differs between the normal rat left ventricle (LV) and right ventricle (RV). These genes are known to be involved in the development of the heart as well as adaptations to the heart during stress. This gene expression pattern is used as a baseline to …

Transcriptional Regulation Factors Of The Human Mitochondrial Aspartate/Glutamate Carrier Gene, Isoform 2 (Slc25a13): Usf1 As Basal Factor And Foxa2 As Activator In Liver Cells, Paolo Convertini, Simona Todisco, Francesco De Santis, Ilaria Pappalardo, Dominga Iacobazzi, Maria Antonietta Castiglione Morelli, Yvonne N. Fondufe-Mittendorf, Giuseppe Martelli, Ferdinando Palmieri, Vittoria Infantino

Molecular and Cellular Biochemistry Faculty Publications

Mitochondrial carriers catalyse the translocation of numerous metabolites across the inner mitochondrial membrane, playing a key role in different cell functions. For this reason, mitochondrial carrier gene expression needs tight regulation. The human SLC25A13 gene, encoding for the mitochondrial aspartate/glutamate carrier isoform 2 (AGC2), catalyses the electrogenic exchange of aspartate for glutamate plus a proton, thus taking part in many metabolic processes including the malate-aspartate shuttle. By the luciferase (LUC) activity of promoter deletion constructs we identified the putative promoter region, comprising the proximal promoter (−442 bp/−19 bp), as well as an enhancer region (−968 bp/−768 bp). Furthermore, with different …

Rna Interference And Validation Of Reference Genes For Gene Expression Analyses Using Qpcr In Southern Pine Beetle, Dendroctonus Frontalis, Bethany R. Kyre, Thais B. Rodrigues, Lynne K. Rieske

Entomology Faculty Publications

RNA interference (RNAi) is a highly specific gene-silencing mechanism that can cause rapid insect mortality when essential genes are targeted. RNAi is being developed as a tool for integrated pest management of some crop pests. Here we focus on an aggressive forest pest that kills extensive tracts of pine forests, the southern pine beetle (SPB), Dendroctonus frontalis. We sought to identify reference genes for quantitative real-time PCR (qPCR) and validate RNAi responses in SPB by mortality and gene silencing analysis. Using an adult beetle feeding bioassay for oral ingestion of dsRNA, we measured the expression and demonstrated knockdown of …

Feature Selection For Longitudinal Data By Using Sign Averages To Summarize Gene Expression Values Over Time, Suyan Tian, Chi Wang

Biostatistics Faculty Publications

With the rapid evolution of high-throughput technologies, time series/longitudinal high-throughput experiments have become possible and affordable. However, the development of statistical methods dealing with gene expression profiles across time points has not kept up with the explosion of such data. The feature selection process is of critical importance for longitudinal microarray data. In this study, we proposed aggregating a gene’s expression values across time into a single value using the sign average method, thereby degrading a longitudinal feature selection process into a classic one. Regularized logistic regression models with pseudogenes (i.e., the sign average of genes across time as predictors) …

Hawaiian Picture‐Winged Drosophila Exhibit Adaptive Population Divergence Along A Narrow Climatic Gradient On Hawaii Island, Jon Eldon, M. Renee Bellinger, Donald K. Price

Life Sciences Faculty Research

1. Anthropogenic influences on global processes and climatic conditions are increasingly affecting ecosystems throughout the world. 2. Hawaii Island’s native ecosystems are well studied and local long‐term climatic trends well documented, making these ecosystems ideal for evaluating how native taxa may respond to a warming environment. 3.This study documents adaptive divergence of populations of a Hawaiian picture‐winged Drosophila, D. sproati, that are separated by only 7 km and 365 m in elevation. 4.Representative laboratory populations show divergent behavioral and physiological responses to an experimental low‐intensity increase in ambient temperature during maturation. The significant interaction of source population by temperature treatment …

Association Of Age, Sex, And Pyrethroid Resistance Status On Survival And Cytochrome P450 Gene Expression In Aedes Aegypti (L.), Leslie C. Rault, Scott T. O'Neal, Ellis J. Johnson, Troy D. Anderson

Department of Entomology: Faculty Publications

Aedes aegypti is a vector of viruses that negatively impact human health. Insecticide resistance complicates mosquito control efforts, but understanding the mechanisms of resistance can help to improve management practices. This study examined different factors that could influence the interpretation of toxicity bioassays and gene expression studies in A. aegypti, including sex and age, in the context of resistance to pyrethroids. Bioassays using a pyrethroid-resistant strain, Puerto Rico (PR), and a pyrethroid-susceptible strain, Rockefeller (Rock), of A. aegypti were conducted with females and males of three age groups to determine differences in mortality induced by deltamethrin. Overall, strain was …

Adipose-Derived Autotaxin Regulates Inflammation And Steatosis Associated With Diet-Induced Obesity, J. Anthony Brandon, Maria Kraemer, Julia Vandra, Suchismita Halder, Margo F. Ubele, Andrew J. Morris, Susan S. Smyth

Gill Heart & Vascular Institute Faculty Publications

Autotaxin (ATX) is a secreted enzyme that generates the bioactive lipid lysophosphatidic acid (LPA). We generated mice with global inducible post-natal inactivation or adipose-specific loss of the Enpp2 gene encoding ATX. The animals are phenotypically unremarkable and exhibit differences in adipocyte size and adipose tissue expression of inflammatory genes after high fat feeding without gross differences in fat distribution or body mass. Surprisingly, both models of Enpp2- deficiency exhibited marked protection from high fat diet-induced hepatic steatosis. This phenotype was not associated with differences in dietary fat absorption but may be accounted for by differences in hepatic expression of …

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 …

Proximate And Ultimate Consequences Of Stressed-Induced Maternal, Paternal, And Joint Parental Effects In A Changing World, Whitley Rayen Lehto

Electronic Theses and Dissertations

Parental experience can alter the developmental and rearing environments of offspring, resulting in parental effects on offspring traits. I addressed the consequences of stress-induced maternal, paternal, and joint parental effects from both ultimate (ecological/evolutionary) and proximate (physiological/epigenetic) perspectives. I used a full-factorial design in which threespine stickleback (Gasterosteus aculeatus) mothers, fathers, both, or neither were exposed to a model predator at developmentally appropriate times to test for predator-induced maternal, paternal, and joint parental effects on daughters’ mating behavior and egg glucocorticoids (stress hormones) and on offspring gene expression. Maternal and paternal predator exposure independently yielded daughters who preferred …