Life Sciences Commons^™

Comparative Analysis Of Small Non-Coding Rna And Messenger Rna Expression In Somatic Cell Nuclear Transfer And In Vitro-Fertilized Bovine Embryos During Early Development Through The Maternal-To-Embryonic Transition, Jocelyn Marie Cuthbert

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Cloning animals using somatic cell nuclear transfer (scNT) was first successfully demonstrated with the birth of Dolly the sheep, but the process of cloning remains highly inefficient. By improving our understanding of the errors that may occur during cloned cattle embryo development, we could obtain a greater understanding of how specific molecular events contribute to successful development. The central dogma of biology refers to the process of DNA being transcribed into messenger RNA (mRNA) and the translation of mRNA into proteins, which ultimately carry out the functions encoded by genes. The epigenetic code is defined as the array of chemical …

Mapping Transcriptional Changes Associated With The Maternal-To-Embryonic Transition In Bovine Embryos To Small Non-Coding Rna Profiles In Both In Vitro-Fertilized And Scnt Cattle Embryos, Abby D. Benninghoff, Jocelyn Cuthbert

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Supplementary File 1. Normalized reads for annotated mRNA transcripts. Microsoft Excel document providing normalized sequencing reads per sample.

Supplementary File 2. Results of DESeq2 analyses for annotated mRNAs. Microsoft Excel document with results of DESeq2 differential expression analysis comparing scNT vs IVF embryos at each developmental stage and sequential comparisons of developmental stage for both IVF and scNT embryos.

Supplementary File 3. Results of Metascape ontology analyses for differentially expressed mRNAs. Microsoft Excel document with results of Metascape ontology analyses for biological processes associated with predicted mRNA targets of differentially expressed miRNAs.

Supplementary File 4. Cytoscape networks for differentially expressed …

Profiling Of Small Non-Coding Rna In Bovine Somatic Cell Nuclear Transfer Embryos During Early Development Through The Maternal-To-Embryonic Transition, Abby D. Benninghoff, Jocelyn Cuthbert

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Supplementary File 1. Read lengths and annotation summaries of sncRNA: Microsoft Excel document with information from small RNA sequencing on the aligned, annotated reads.

Supplementary File 2. Normalized and variance-stabilized values for annotated sncRNAs: Microsoft Excel document with normalized and variance-stabilized reads generated by RNA sequencing of small non-coding RNA from cattle embryos.

Supplementary File 3. Results of DESeq2 analyses for miRNAs, tRNA fragments and piRNAs: Microsoft Excel document with results of DESeq2 differential expression analysis comparing scNT vs IVF embryos at each developmental stage and sequential comparisons of developmental stage for both IVF and scNT embryos.

Supplementary File 4. …

Evaluating The Potential Of Repurposing Commercially Available Drugs For The Treatment Of Viral Infections, Brennan Connor Mcewan

Undergraduate Honors Capstone Projects

Viral infections that are often overlooked as common seasonal illnesses such as influenza can rapidly become a public threat. They threaten society as new, more dangerous strains of these common viruses emerge and as strains develop resistance to current vaccines and antiviral treatments (Kochanek, Murphy, Xu, & Tejada-Vera, 2014). To combat this, the development of antiviral treatments with novel mechanisms of action is essential. Repurposing drugs instead of developing new drugs can save years of development time and hundreds of millions of dollars (DiMasi, Hansen, & Grabowski, 2003). To support the effort to discover drugs with unique mechanisms of action, …

Mobile Elements Shape Plastome Evolution In Ferns, Tanner A. Robison, Amanda L. Grusz, Paul G. Wolf, Jeffrey P. Mower, Blake D. Fauskee, Karla Sosa, Eric Schuettpelz

Biology Faculty Publications

Plastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even …

Lanthanide-Doped Ceria Nanoparticles As Backside Coaters To Improve Silicon Solar Cell Efficiency, Ali Hajjiah, Effat Samir, Nader Shehata, Mohamed Salah

Biology Faculty Publications

This paper introduces lanthanide-doped ceria nanoparticles as silicon solar cell back-side coaters, showing their influence on the solar cell efficiency. Ceria nanoparticles can be synthesized to have formed oxygen vacancies (O-vacancies), which are associated with converting cerium ions from the Ce⁴⁺ state ions to the Ce³⁺ ones. These O-vacancies follow the rule of improving silicon solar cell conductivity through a hopping mechanism. Besides, under near-ultra violet (near-UV) excitation, the reduced trivalent cerium Ce³⁺ ions are directly responsible for down converting the un-absorbed UV wavelengths to a resultant green photo-luminescence emission at ~520 nm, which is absorbed through …

Expression Of Wnt-Signaling Pathway Genes And Their Associations With Mirnas In Colorectal Cancer, Martha L. Slattery, Lila E. Mullany, Lori C. Sakoda, Wade S. Samowitz, Roger K. Wolff, John R. Stevens, Jennifer S. Herrick

Mathematics and Statistics Faculty Publications

The Wnt-signaling pathway functions in regulating cell growth and thus is involved in the carcinogenic process of several cancers, including colorectal cancer. We tested the hypothesis that multiple genes in this signaling pathway are dysregulated and that miRNAs are associated with these dysregulated genes. We used data from 217 colorectal cancer (CRC) cases to evaluate differences in Wnt-signaling pathway gene expression between paired CRC and normal mucosa and identify miRNAs that are associated with these genes. Gene expression data from RNA-Seq and miRNA expression data from Agilent Human miRNA Microarray V19.0 were analyzed. We focused on genes most strongly associated …

Rotating Algal Biofilm Reactors: Mathematical Modeling And Lipid Production, Paul A. Woolsey

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Harvesting of algal biomass presents a large barrier to the success of biofuels made from algae feedstock. Small cell sizes coupled with dilute concentrations of biomass in lagoon systems make separation an expensive and energy intense-process. The rotating algal biofilm reactor (RABR) has been developed at USU to provide a sustainable technology solution to this issue. Algae cells grown as a biofilm are concentrated in one location for ease of harvesting of high density biomass. A mathematical model of this biofilm system was developed based on data generated from three pilot scale reactors at the City of Logan, Utah wastewater …

The Role Of Phosphoinositide Signaling In Breast Cancer Metastasis Suppressor 1-Mediated Metastasis Suppression Of Human Breast Carcinoma Cells, Sitaram Harihar

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Breast cancer is the most common non-skin cancer in women and the second most common cause of cancer-related death in U.S. women. Despite numerous advances in treatment strategies against breast cancer, the presence of undetected distant metastasis of the primary tumor remains the main cause of mortality. Current screening and detection methods such as mammograms are simply not sensitive enough to detect formation of metastasis. Further, currently available therapies against metastatic breast cancer do not provide a complete cure for the disease. Thus, understanding the biology and molecular factors involved in cancer metastasis will help aid in preventing the onset …

Genetic And Biochemical Studies Of Plasmid Pir52-1 In Lactobacillus Helveticus, Cody Alexander Tramp

Undergraduate Honors Capstone Projects

Lactobacillus helveticus is a species of lactic acid bacteria. These bacteria, which produce lactic acid as a major product of carbohydrate metabolism, are used industrially to produce cheese and other fermented dairy products (Ebringer et al., 2008). Many species of lactic acid bacteria also possess probiotic characteristics and when ingested potentially confer increased immune function, regulate gut microbiota, and improve digestion in the host (Reid, 2008). Genetic studies of these probiotic effects and other characteristics of L. helveticus and related species have been hindered by the lack of stably replicating plasmid vectors. Plasmid vectors for several Lactobacillus species have been …

An Entrepreneurial Approach To Librarianship, Flora G. Shrode, Jennifer R. Duncan, Wendy Holliday

Flora Shrode

Librarians from Utah State University explain recent efforts to encourage subject librarians to take a more holistic view of their roles. We are shifting from a traditional emphasis primarily on collection development and refocusing on natural connections between collections, instruction, liaison, and reference service. The poster provides background about Utah State University’s situation and explains our approach to analyzing local needs and culture to inform development of a new organizational structure. We describe our vision of subject librarianship, the process by which we assessed librarians’ ideas and goals for performing as subject librarians, and the actions we are taking to …

An Entrepreneurial Approach To Librarianship, Flora Shrode, Jennifer Duncan, Wendy Holliday

Library Faculty & Staff Publications

Librarians from Utah State University explain recent efforts to encourage subject librarians to take a more holistic view of their roles. We are shifting from a traditional emphasis primarily on collection development and refocusing on natural connections between collections, instruction, liaison, and reference service. The poster provides background about Utah State University’s situation and explains our approach to analyzing local needs and culture to inform development of a new organizational structure. We describe our vision of subject librarianship, the process by which we assessed librarians’ ideas and goals for performing as subject librarians, and the actions we are taking to …

Expression Analysis Of Plant Defense Responses During The Establishment Of Biotrophy And Role Of Abiotic Stress In The Infection Of Dyer’S Woad (Isatis Tinctoria) By Puccinia Thlaspeos, Elizabeth Thomas

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The kinetics and amplitude of the salicylic acid-responsive pathogenesis-related (PR) genes and the cytochrome P450 gene ItCYP79B2 in the compatible interaction between Puccinia thlaspeos and dyer’s woad (Isatis tinctoria) during the first 72 hours of inoculation were examined. Immediately following penetration of the host by the rust pathogen, there was a modest up-regulation of PR genes but a significant down-regulation of ItCYP79B2 expression. During haustoria formation, a significant pathogen-mediated suppression of PR genes was observed with a corresponding up-regulation of ItCYP79B2. This potentially facilitates haustoria formation by P. thlaspeos. After haustoria formation, a more …

Phenotypic And Genotypic Analysis Of Amino Acid Metabolism In Lactobacillus Helveticus Cnrz 32, Jason K. Christiansen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This study investigated genetic predictions for amino acid biosynthesis and catabolism by Lactobacillus helveticus CNRZ 32, a commercial cheese flavor adjunct that reduces bitterness and intensifies flavor notes. Conversion of amino acids into volatile and nonvolatile flavor compounds by L. helveticus and other lactic acid bacteria in cheese is thought to represent the rate-limiting step in the development of mature cheese flavor and aroma. One of the primary mechanisms for amino acid breakdown by these microbes involves the reversible action of enzymes involved in biosynthetic pathways, so our group investigated the genetics of amino acid biosynthesis in L. helveticus CNRZ …

Catalase Activity Mediates The Inhibitory Actions Of 24,25 Dihydroxyvitamin D3, Sven L. Peery

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The steroid hormone 1,25-dihydroxyvitamin D₃ [1,25(OH)₂D₃] rapidly stimulates the uptake of phosphate in isolated chick intestinal cells, while the steroid 24,25-dihydroxyvitamin D₃ [24,25(OH)₂D₃] inhibits the rapid stimulation by 1,25(OH)₂D₃. Earlier work in this laboratory has indicated that a cellular binding protein for the 24,25(OH)₂D₃ is the enzyme catalase. Since binding resulted in decreased catalase activity and increased H₂O₂ production, studies were undertaken to determine if pro-oxidant conditions mimicked the inhibitory actions of 24,25(OH)₂D₃, and anti-oxidant conditions …

Development And Characterization Of Eukaryotic Biomimetic Liposomes, Bradley Jay Taylor

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This study developed and characterized phospholipid vesicles, or liposomes, that mimic cell surfaces. Microemulsified liposomes contained biotinylated phosphatidylethanolamine, allowing them to be immobilized to avidin-coated glass. Laminin (LN), glycosphingolipids (GMl and GM3), and Escherichia coli's mechanosensitive channel of large conductance (EcoMscL) were embedded into liposome membranes. It was determined whether these embedded molecules exhibited their physiological roles of adhesion, cell recognition, and mechanosensation, respectively. Confocal laser scanning microscopy (CLSM) was employed to examine the interaction of fluorescently probed proteins, toxins, and bacteria with the immobilized microemulsified liposomes. Capture of individual and simultaneous multiple species of bacteria by GMl, GM3, …

The Role Of The Arabidopsis Phosphatidylinositol 3-Kinase In Vacuolar Protein Transport, Christopher A. Jones

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In all eukaryotic organisms vesicle-mediated protein transport is crucial for maintaining cellular homeostasis. Over the past decade significant strides have been made in elucidating the molecular mechanisms governing this complex process. Both genetic and biochemical studies have demonstrated the unequivocal involvement of class III phospatidylinositol 3-kinases (PtdIns 3-kinases) in regulating vesicle transport. While PtdIns 3-kinases have been well studied in both yeast and mammalian systems, the role of these enzymes in plants is poorly understood. In the present study, we demonstrate that the Arabidopsis Ptdlns 3-kinase is localized to the cytoplasm, and perhaps the Golgi apparatus. Moreover, we show that …

Altered T Cell-Mediated Immunity And Infectious Factors In Autism, Yong Hu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Three major questions were addressed in this dissertation: 1) Do immune abnormalities associated with autism primarily alter CD4+ T cell-mediated or humoral immune responses? 2) Are specific T cell clones expanded in autism? 3) Which, if any, infectious agents play a role in autism?

CD4+ T cell-mediated (Th1) or humoral (Th2) immune responses can be distinguished on the basis of the cytokines expressed. CD4+ T-cells secrete interleukin type 2 (IL-2) and interferon-γ, whereas a Th2 response is associated with secretion of interleukin type 4(IL-4). mRNA extracted from peripheral blood mononuclear nuclear cells (PBMC) showed significantly increased levels of IL-2 and …

A New Model Species For Cultured Teleost Retinal Cell Studies: Light And Scanning Electron Microscopy, Lori Ann Steinfeldt

Undergraduate Honors Capstone Projects

Purpose: To examine retinal horizontal and bipolar cells cultured from goldfish (Carassius auratus), black crappie (Pomoxis nigromaculatus) and bluegill (Lepomis macrochirus) on the light and electron microscope levels; and to compare them with cells from a more established model, the wild white bass (Roccus chrysops). Methods: Retinas from all species were dissociated by methods developed with wild white bass (Dowling et al., 1985). Cell type was identified within the first 3 hr and cells were cultured for up to 2 wk in L-15 medium. At various intervals, cells were fixed in glutaraldehyde, …

Chlorophyll Fluorescence Probe Of Ultraviolet-B Photoinhibition Of Primary Photoreactions In Intact Leaves, Robert S. Nowak

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Damage to primary photosynthetic reactions caused by environmental stress can be assessed by measurement of chlorophyll fluorescence induction in intact leaves. This approach was applied in studies of ultraviolet-B photoinhibition of photosynthesis in Pisum sativum L. and Rumex patientia L. leaves. At ultraviolet-B dose rates insufficient to cause inhibition of net photosynthesis, changes in the magnitude of fluorescence transients did occur, which suggested direct effects on chloroplast pigments in Pisum and inhibition of photosynthetic electron transport between the photosystems in both species. Leaves of these two species subjected to a much higher dose rate had a significant reduction of net …

Leaf Development Of Rumex Patientia L. Exposed To Uv Irradiation (280-320 Nm), Judith G. Dickson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Two factors which affect leaf ontogeny and ultimate leaf size: (1) the rate and duration of cell expansion, and (2) the rate and duration of cell division, were examined for their role in the slowed early growth rate and smaller ultimate leaf size when plants are exposed to ultraviolet-B (UV-B) radiation. Rumex patientia L. was grown in controlled environment chambers under enhanced UV-B radiation (equivalent to daily solar UV-B irradiation at 40°N latitude in mid-May with an atmospheric ozone concentration of 0.20 atm-cm) and control treatments. The pattern of growth as expressed in changes of mean cell size of two …

Respiratory Metabolism And Energy Requirements Of Embryo, Larval And Juvenile Mountain Whitefish, Prosopium Williamsoni, Pokkavil Karunakara Rajagopal

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The upper optimum temperature for embryonic development of mountain whitefish is 6 C, and for the post yolk sac stage is 9 to 12 C. The need to know effects on all stages in the life cycle in cases of thermal pollution is demonstrated. Abnormalities caused by thermal pollution in hatched larvae were agape jaws, coloboma or fissure of the eye, monophthalmia or the presence of only one eye, monomicrophthalmia or the presence of one small eye and one case of twinning. High mortalities of eggs occurred at 9 C and higher.

Study of the energy expenditure, by the dry …

A Fine-Structural Study Of Aberrant Meiotic Cytokinesis In An Autosomal Male Sterile Mutant (Ms(2)3r) Of Drosophila Melonogaster, Laura J. Laughran

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The ultrastructure of abnormal meiotic cytokinesis in an autosomal male sterile mutant of Drosophila melanogaster is described. In the mutant ms(2)3R mitotic cytokinesis proceeds normally, but abnormal meiotic divisions give rise to four spermatids developing in one cytoplasmic mass. The contractile ring which is responsible for cell constriction during cytokinesis appears to form and function normally during meiosis. Ring canals which form intercellular bridges between synchronously developing spermatids are also apparently normal. However, there is an apparent adhesion and subsequent disintegration of the furrow membranes after division is completed. In addition to double membrane fragments in areas of open …

Modification Of Ontogenic Expression Due To Relocation Of The Ry+ Gene In Drosophila Melanogaster, Allen A. Badgett Jr.

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The ry⁺ gene of Drosophila melanogaster and its associated enzyme, xanthine dehydrogenase, were employed in an analysis of the relationship between regulation and the location of a gene in the genome. Enzyme assays as an indication of gene activity were performed on genotypes containing zero, one and two doses of ry⁺ genes. Xanthine dehydrogenase activity of rosy genes in normal and relocated positions was determined during development.

The results indicate: 1) the gene ry⁺ is differentially active during ontogeny; 2) the activity during ontogeny is proportional to the number of ry⁺ genes present in the genome; …

Spermiogenesis In Two Male-Sterile Third-Chromosome Mutants Of Drosophila Melanogaster, Richard F. Wilkinson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

An ultrastructural study of sperm differentiation was made on two male-sterile mutants of Drosophila melanogaster. The mutations were induced on the third chromosome with the monoalkylating agent ethyl methanesulfonate and were maintained in stock cultures over a balancer chromosome using a system of multiple inversions. The stages of sperm differentiation, a most dramatic form of cellular differentiation, were then studied at the electron microscope level to determine the effect of the mutations on sperm structure and to correlate those changes with normal sperm development.

Studies of the genetic control of cellular differentiation have been hampered by difficulties in devising …

Induction And Initial Characterization Of Male-Sterile Mutants On The Second Chromosome Of Drosophila Melanogaster, Susan M. Graves

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Fourteen recessive, male-sterile, autosomal mutants of Drosophila melanogaster were induced using ethyl methanesulfonate. The techniques employed restricted the recovery of mutants to those located on the second chromosome. Eleven of the mutants were male-sterile at 23°C, and the remaining three, though fertile at 23°C, were male-sterile at 28°C. Complementation tests involving all possible pairs of mutations showed each to be located in a unique cistron.

Spermiogenesis in each mutant was studied by light microscopy to determine the stage at which cellular differentiation deviates from normal and to characterize the associated gross abnormalities. Phase contrast microscopy showed that each mutant sterile …