Biology Commons^™

Meiothermus Ruber Mrub_0320 Gene Is An Ortholog Of The B3452 Gene, Mrub_0321 Gene Is An Ortholog Of The B3451 Gene, Mrub_0322 Gene Is An Ortholog Of The B3453 Gene, Mrub_2366 Gene Is An Ortholog Of The B3450 Gene Found In Escherichia Coli, Which Encode For Components Of An Abc Transporter Involved In Sn-Glycerol - 3-Phosphate, Jenna Hall, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes mrub_0320, mrub_0321, mrub_0322, and mrub_2366 (KEGG map number 02010). We predict these genes encode components of a sn-glycerol-3-phosphate (ABC) transporter: 1) mrub_0320 (DNA coordinates 288469..289401) encodes the permease component (aka transmembrane domain), predicted to be an ortholog; 2) mrub_0321 (DNA coordinates 289394..290218) encodes another permease domain, and also contains a transcriptional regular; ATP-binding domain (aka nucleotide binding domain); 3) mrub_0322 (DNA coordinates 290234..291541) encodes the solute binding protein; and 4) mrub_2366 (DNA coordinates 2418207..2419352 on the reverse strand) encodes for an ATP-binding domain for multiple sugar-related ABC transport systems …

Large Effect Quantitative Trait Loci For Salicinoid Phenolic Glycosides In Populus: Implications For Gene Discovery, Scott A. Woolbright, Brian J. Rehill, Richard L. Lindroth, Stephen P. Difazio, Gregory D. Martinsen, Matthew S. Zinkgraf, Gerard J. Allan, Paul Keim, Thomas G. Whitham

Faculty & Staff Scholarship

Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)—ecologically important compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We used a linkage map derived from a full-sib population of hybrid cottonwoods (Populus spp.) to search for quanti- tative trait loci (QTL) for the SPGs salicortin and HCH-salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0 P. trichocarpa genome. We discovered 21 QTL for the two traits, including a major QTL for HCH-salicortin (R2 = .52) that colocated with a …

Genetic Assessment Of Inbred Chicken Lines Indicates Genomic Signatures Of Resistance To Marek's Disease, Lingyang Xu, Yanghua He, George E. Liu, Huanmin Zhang, Hans H. Cheng, Robert L. Taylor Jr, Jiuzhou Song

Faculty & Staff Scholarship

Background: Marek’s disease (MD) is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. However, the mechanisms of genetic resistance for MD are complex and not fully understood. MD-resistant line 63 and MD-susceptible line 72 are two highly inbred progenitor lines of White Leghorn. Recombinant Congenic Strains (RCS) were developed from these two lines, which show varied susceptibility to MD.

Results: We investigated genetic structure and genomic signatures across the genome, including the line 63 and line 72, six RCSs, and two reciprocally crossed flocks between the lines 63 and 72 (F1 63 × 72 and F1 72 × …

Rest Upregulates Gremlin To Modulate Diffuse Intrinsic Pontine Glioma Vasculature, Shavali Shaik, Bridget Kennis, Shinji Maegawa, Keri Schadler, Yang Yanwen, Javad Nazarian, +Several Additional Authors

Genomics and Precision Medicine Faculty Publications

Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive glial tumor that occurs in children. The extremely poor median and 5-year survival in children afflicted with DIPG highlights the need for novel biology-driven therapeutics. Here, we have implicated the chromatin remodeler and regulator of brain development called RE1 Silencing Transcription Factor (REST), in DIPG pathology. We show that REST protein is aberrantly elevated in at least 21% of DIPG tumors compared to normal controls. Its knockdown in DIPG cell lines diminished cell growth and decreased their tumorigenicity in mouse intracranial models. DIPGs are vascularized tumors and interestingly, REST loss in …

48839 (Gmr19b04), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 48839

• Id - GMR19B04,
• Location - 2L:2432214,2435785
• Base pairs – 3571 bp

47472 (Gmr16g02), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 47472

• Id - GMR16G02
• Location 2L:2425041, 2428154
• Base pairs – 3113 bp

48770 (Gmr17e04), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 48770

• Id - GMR17E04
• Location 2L: 2428913..2432834
• Base pairs – 3921 bp

Floral Symmetry Genes Elucidate The Development And Evolution Of Oil-Bee Pollinated Flowers Of Malpighiaceae And Krameriaceae, Farahnoz N. Khojayori

Theses and Dissertations

Specialization on insect and animal pollinators is thought to be the driving force for the evolution of floral traits. Specifically in the New World (NW), the oil-bee pollination syndrome has led to the convergence of floral characters in two distantly related families of core eudicots, Malpighiaceae and Krameriaceae. Both families display a flag-like structure that establishes a zygomorphic flower and floral oil rewards in epithelial elaiophores. These traits work concomitantly to attract and reward female oil-bees that help fertilize these flowers and in return receive oils. The underlying genetics of floral zygomorphy were studied in several clades of core eudicots, …

Analysis Of The Transcription Factors Expressed In The Mature Seed Embryos Of Moringa Oleifera Lam. Using Rna-Sequencing And De Novo Transcriptome Assembly, Vivian A. Panes, R.D Baoas

Biology Faculty Publications

Moringa oleifera Lam. is well known for its numerous documented properties, particularly its significant applications in nutrition, therapeutics, biocontrol, energy, and bioremediation. These properties are the consequences of the vibrant physiological processes of the plant in the context of the ever-changing biotic and abiotic factors, in which transcription factors play substantial roles. Transcription factors (TFs) are the regulators of gene expression. Transcription factors enable the activation or repression of transcription. Along with the advent of ultrahighthroughput sequencing technologies such as RNA sequencing (RNA-Seq), in combination with bioinformatics techniques, the investigation of the TFs of M. oleifera was made possible. This …

Interitance Pattern Of Vestigial Mutation In Drosophila Melanogaster, Tori R. Witruck, Adam Padron

A with Honors Projects

The purpose of this experiment was to determine the inheritance pattern of the vestigial mutation in Drosophila melanogaster. The experiment was to include two crosses with wild type and vestigial mutation, but the second cross experienced environmental setbacks potentially affecting the results, the experiment could lead to future testing on environmental effects on mutation.

Role Of Glycerol-3-Phosphate Permeases In Plant Defense, Juliana Moreira Soares

Theses and Dissertations--Plant Pathology

Systemic acquired resistance (SAR) is a type of plant defense mechanism that is induced after a localized infection and confers broad-spectrum immunity against related or unrelated pathogens. During SAR, a number of chemical signals and proteins generated at the site of primary infection travel to the uninfected tissues and are thought to alert the distal sites against secondary infections. Glycerol-3-phosphate (G3P) is one of the chemical signals that play an important role in SAR. G3P is synthesized in the cytosol and chloroplasts via the enzymatic activities of G3P Dehydrogenase (G3Pdh) or Glycerol Kinase (GK). Interestingly, a mutation in three of …

45833 (Gmr19d09), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45833

• Id - GMR19D09
• Location - 2L:2435128,2438996
• Base pairs – 3868 bp

48784 (Gmr17g08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 48784

• Id - GMR 17G08
• Location 2L:2450278,2451074
• Base pairs – 796 bp

45437 (Gmr18b08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45437

• Id - GMR18B08
• Location - 2L:2455899,2457734
• Base pairs – 1835 bp

Increased Fxyd1 And Pgc-1Α Mrna After Blood Flow-Restricted Running Is Related To Fibre Type-Specific Ampk Signalling And Oxidative Stress In Human Muscle, Danny Christiansen, Robyn M. Murphy, Christos G. Stathis, David Bishop

Research outputs 2014 to 2021

Aim: This study explored the effects of blood flow restriction (BFR) on mRNA responses of PGC-1α (total, 1α1, and 1α4) and Na+,K+-ATPase isoforms (NKA; α1-3, β1-3, and FXYD1) to an interval running session and determined whether these effects were related to increased oxidative stress, hypoxia, and fibre type-specific AMPK and CaMKII signalling, in human skeletal muscle. Methods: In a randomized, crossover fashion, 8 healthy men (26 ± 5 year and 57.4 ± 6.3 mL kg−1 min−1) completed 3 exercise sessions: without (CON) or with blood flow restriction (BFR), or in systemic hypoxia (HYP, ~3250 m). A muscle sample was collected …

Uvb Induced Mutation Of P53 In Non Melanoma Skin Cancer, Raizy Berger

The Science Journal of the Lander College of Arts and Sciences

There is a clear correlation between excessive sun exposure and the development of skin cancer. UVB radiation from the sun is potent, and as the ozone layer gets depleted, more UVB can reach Earth and cause cell damage. UV radiation causes DNA lesions, such as 6-4 photoproducts and cyclobutane pyrimidine dimers. Cyclobutane pyrimidine dimers are more abundant and take longer to be repaired and therefore are responsible for most of the mutation and DNA damage. These DNA lesions lead to mutation of the p53 gene. The signature mutation on p53 from UV radiation is a CC to TT mutation, which …

45442 (Gmr18d08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45442

• Id - GMR 18D08
• Location - 2L:2446783,2449086
• Base pairs – 2303 bp

49283 (Gmr19c03), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 49283

• Id - GMR19C03
• Location - 2L:2440970,2444735
• Base pairs – 3765 bp

An Assessment Of Inheritance Patterns In Two Mutant Eye-Color Traits Of Drosophila Melanogaster, Jedidiah Heiser, Seth B. Yates

A with Honors Projects

This experiment was a two generation test cross (from F0 to F1 and F1 to F2) to check the patterns of inheritance and their chi-square significance. Wild-type males and females were paired with the opposite sex of the two mutant groups -- Sepia eyes and White eyes. The pairing thus resulted in 4 tube conditions. Generations were counted and identified by sex and phenotype -- Wild-type or Mutant. The next generation was seeded with approximately 6 - 8 individuals from each sex and released once the next generation reached their pupal phase. Fresh tubes were seeded between F1 and F2. …

Building Capacity For A Global Genome Editing Observatory: Conceptual Challenges, J. Benjamin Hurlbut, Sheila Jasanoff, Krishanu Saha, Aziza Ahmed, Anthony Appiah, Elizabeth Bartholet, Francoise Baylis, Gaymon Bennett, George Church, I. Glenn Cohen, George Daley, Kevin Finneran, William Hurlbut, Rudolf Jaenisch, Laurence Lwoff, John Paul Kimes, Peter Mills, Jacob Moses, Buhm Soon Park, Erik Parens, Rachel Salzman, Abha Saxena, Hilton Simmet, Tania Simoncelli, O. Carter Snead, Kaushik Sunder Rajan, Robert D. Truog, Patricia Williams, Christiane Woopen

Journal Articles

A new infrastructure is urgently needed at the global level to facilitate exchange on key issues concerning genome editing. We advocate the establishment of a global observatory to serve as a center for international, interdisciplinary, and cosmopolitan reflection.

Dna Extraction And Microsatellite Amplification Of Daphnia Pulicaria Resting Eggs: Analysis Of Allele Frequencies Through Time, Anna Ries

Departmental Honors Projects

A paleoecological approach allows for the study of genetic change in populations over longer periods of time than would be possible if one were sampling populations from year to year. Daphnia and other cladoceran zooplankton are amenable to this type of study because they produce diapausing embryos (ephippial eggs) when they sexually reproduce, and these resting eggs can remain viable for decades to centuries in lake sediments. This study uses paleoecological methods as well as a new methodology for ephippial DNA extraction and amplification to assay for genetic variation in ephippial eggs obtained from sediments of varying ages from Square …

Draft Genome Sequence Of Streptomyces Sp. Strain Jv178, A Producer Of Clifednamide-Type Polycyclic Tetramate Macrolactams, Yunci Qi, John M. D’Alessandro, Joshua A.V Blodgett

Biology Faculty Research

Here, we report the draft genome sequence of Streptomyces sp. JV178, a strain originating from Connecticut (USA) garden soil. This strain produces the polycyclic tetramate macrolactam compounds clifednamides A and B. The draft genome contains 10.65 Mb, 9,045 predicted protein coding sequences, and several natural product biosynthetic loci.

Building Capacity For A Global Genome Editing Observatory: Institutional Design, Krishanu Saha, J. Benjamin Hurlbut, Sheila Jasanoff, Aziza Ahmed, Anthony Appiah, Elizabeth Bartholet, Francoise Baylis, Gaymon Bennett, George Church, I. Glenn Cohen, George Daley, Kevin Finneran, William Hurlbut, Rudolf Jaenisch, Laurence Lwoff, John Paul Kimes, Peter Mills, Jacob Moses, Buhm Soon Park, Erik Parens, Rachel Salzman, Abha Saxena, Hilton Simmet, Tania Simoncelli, O. Carter Snead, Kaushik Sunder Rajan, Robert D. Truog, Patricia Williams, Christiane Woopen

Journal Articles

A new infrastructure is urgently needed at the global level to facilitate exchange on key issues concerning genome editing. We advocate the establishment of a global observatory to serve as a center for international, interdisciplinary, and cosmopolitan reflection.

Environmental Dna Analysis Of An Obligate Subterranean Shrimp, Jennifer S. Nix

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Tetratricopeptide 39c (Ttc39c) Is Upregulated During Skeletal Muscle Atrophy And Is Necessary For Muscle Cell Differentiation, Caleb Hayes

UNF Graduate Theses and Dissertations

Ttc39c has been identified as a novel gene in skeletal muscle that is upregulated in response to neurogenic atrophy in mice. Quantitative PCR and Western blot analysis confirmed that Ttc39c is expressed in both proliferating and differentiated muscle cells. Furthermore, comparison of Ttc39c expression in undifferentiated and differentiated C₂C₁₂ cells demonstrated that Ttc39c levels peak in early differentiation, but decreases as cells become fully differentiated myotubes. The transcriptional regulation of Ttc39c was examined by cloning promoter fragments of the gene and fusing it with the SEAP reporter gene. The Ttc39c reporter gene constructs were transfected into muscle …

Natural And Anthropogenic Drivers Of Tree Evolutionary Dynamics, Brandon M. Lind

Theses and Dissertations

Species of trees inhabit diverse and heterogeneous environments, and often play important ecological roles in such communities. As a result of their vast ecological breadth, trees have become adapted to various environmental pressures. In this dissertation I examine various environmental factors that drive evolutionary dynamics in threePinusspecies in California and Nevada, USA. In chapter two, I assess the role of management influence of thinning, fire, and their interaction on fine-scale gene flow within fire-suppressed populations of Pinus lambertiana, a historically dominant and ecologically important member of mixed-conifer forests of the Sierra Nevada, California. Here, I find evidence …

Identification Of Novel Mites (Miniature Inverted-Repeat Transposable Elements) In Coxiella Burnetii: Implications For Protein And Small Rna Evolution, Shaun Wachter, Rahul Raghavan, Jenny Wachter, Michael F. Minnick

Biology Faculty Publications and Presentations

Background: Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii’s genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature invertedrepeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities. However, information regarding bacterial MITEs is limited. Results: We describe two MITE families discovered during research on small non-coding …

The Genome Of Austrofundulus Limnaeus Offers Insights Into Extreme Vertebrate Stress Tolerance And Embryonic Development, Josiah Tad Wagner, Param Priya Singh, Amie L. Romney, Claire L. Riggs, Patrick Minx, Steven Cody Woll, Jake Roush, Wesley C. Warren, Anne Brunet, Jason E. Podrabsky

Center for Life in Extreme Environments Publications

Background: The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system.

Results: We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy …

Crispr Genetic Editing: Paths For Christian Acceptance And Analysis Of In Vivo And In Vitro Efficiency, Mandeep Sandhu

Scripps Senior Theses

With advancements in CRISPR-cas9 broadening the potential paths for clinical usage of genetic editing, conversations about genetic editing have grown to outside simply scientific communities and into mainstream conversations. This study focuses specifically on Christian discourse of genetic editing and locates four major tensions for many Christians when they think about genetic editing: beginning of life, Creator-human relationship, imago Dei, and stewardship. With these major concerns in mind, I identify epigenetics, somatic cell genetic editing, and in vivo genetic editing research as important research paths to pursue as they can potentially produce techniques that more Christian individuals would feel comfortable …

Effects Of Gli-Similar 3 Knockout Mutations On The Expression Of Insulin Transcription And Pancreatic Islet Development In Zebrafish, Dylan James Hammrich

Murray State Theses and Dissertations

Blood glucose homeostasis is a critical component in the physiological health of vertebrates. Regulation of blood glucose levels is the responsibility of the endocrine pancreas, which excretes hormones to the bloodstream in response to changes in glucose concentrations. The hormones excreted from the pancreas include insulin, which is secreted form the β cells of the pancreas and signals uptake of excess glucose by the peripheral tissues, and glucagon, which is secreted from the α cells and signals release of glucose to the bloodstream through gluconeogenesis in the liver. The Krüppel-like zinc finger protein Gli-Similar 3 (Glis3) is a transcription factor …