Biology Commons^™

Identification Of The Potentiating Mutations And Synergistic Epistasis That Enabled The Evolution Of Inter-Species Cooperation, Sarah Douglas, Lon Chubiz, William Harcombe, Christopher Marx

Biology Department Faculty Works

Microbes often engage in cooperation through releasing biosynthetic compounds required by other species to grow. Given that production of costly biosynthetic metabolites is generally subjected to multiple layers of negative feedback, single mutations may frequently be insufficient to generate cooperative phenotypes. Synergistic epistatic interactions between multiple coordinated changes may thus often underlie the evolution of cooperation through overproduction of metabolites. To test the importance of synergistic mutations in cooperation we used an engineered bacterial consortium of an Escherichia coli methionine auxotroph and Salmonella enterica. S. enterica relies on carbon by-products from E. coli if lactose is the only carbon source. …

Dna Sequences Of The Mitochondrial Cytochrome C Oxidase I (Coi) Genes From Deep Sea Fishes. Cruises Dp01 And Dp02 From May 2015 - August 2015, Andrea Bernard, Max Weber, Kimberly A. Finnegan, Mahmood S. Shivji, Ron Eytan

DEEPEND Datasets

The deep sea ecosystem is believed to contain the highest biomass of fish in the oceans. However, the taxonomic diversity in this ecosystem is incompletely described and likely to be vastly underestimated. DNA sequence data (barcodes) have become a key tool to discover hidden biodiversity. We generated mitochondrial DNA barcode datasets based on the Cytochrome c oxidase I (COI) gene from deep sea fishes. These data were analyzed using phylogenetic and statistical methods to reveal cryptic species and make taxonomic linkages between adult fishes and their early life stages. These datasets were generated from fishes collected in the Northern Gulf …

Gene Expression Profiling In The Larval Fat Body Of Desiccation Selected Drosophila Melanogaster, Adriana Michelle Charles

UNLV Theses, Dissertations, Professional Papers, and Capstones

Drosophila melanogaster selected for resistance to desiccation (no food or water) display slower development and a higher body mass compared to fed controls due to an extended third larval instar. I hypothesize that desiccation selected D. melanogaster larvae will have a different gene expression profile compared to fed controls. Separate populations of D. melanogaster were subjected to desiccation (no food or water), starvation (no food) until 80-85% mortality, for 75 generations. mRNA from the larval fat body was collected at 88 hours, 96 hours, 112 hours and 120 hours post-hatching. Four replicate samples were used for each condition and time …

Demethylated Hsatii Dna And Hsatii Rna Foci Sequester Prc1 And Mecp2 Into Cancer-Specific Nuclear Bodies, L. L. Hall, M. Byron, Dawn M. Carone, T. W. Whitfield, G. P. Pouliot, A. Fischer, P. Jones, J. B. Lawrence

Biology Faculty Works

This study reveals that high-copy satellite II (HSATII) sequences in the human genome can bind and impact distribution of chromatin regulatory proteins and that this goes awry in cancer. In many cancers, master regulatory proteins form two types of cancer-specific nuclear bodies, caused by locus-specific deregulation of HSATII. DNA demethylation at the 1q12 mega-satellite, common in cancer, causes PRC1 aggregation into prominent Cancer-Associated Polycomb (CAP) bodies. These loci remain silent, whereas HSATII loci with reduced PRC1 become derepressed, reflecting imbalanced distribution of UbH2A on these and other PcG-regulated loci. Large nuclear foci of HSATII RNA form and sequester copious MeCP2 …

Rapid Increase In Genetic Diversity In An Endemic Patagonian Tuco-Tuco Following A Recent Volcanic Eruption, Jeremy L. Hsu, Sharon Kam, Mauro N. Tammone, Eileen A. Lacey, Elizabeth A. Hadly

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Catastrophic natural events can have profound impacts on patterns of genetic diversity. Due to the typically unpredictable nature of such phenomena, however, few studies have been able to directly compare patterns of diversity before and after natural catastrophic events. Here, we examine the impacts of a recent volcanic eruption in southern Chile on genetic variation in the colonial tuco-tuco (Ctenomys sociabilis), a subterranean species of rodent endemic to the area most affected by the June 2011 eruption of the Puyehue-Cordón Caulle volcanic complex. To provide a comparative context for interpreting changes in genetic variation in this species, we …

Post-Transcriptional Regulation Of The Drosophila Anterior Determinant, Bicoid, John Mclaughlin

Dissertations, Theses, and Capstone Projects

In a wide variety of biological contexts, messenger RNA (mRNA) is known to have a complex and dynamic life cycle. In particular, the localization and translational control of mRNA are essential for proper development in eukaryotes. The fly Drosophila melanogaster is an excellent model for studying these processes. During D. melanogaster oogenesis, several mRNAs are trafficked and localized within the developing egg chamber, and regulated at the translational level to enable embryo patterning. One such mRNA, bicoid, is localized at the anterior of the oocyte and translated in the early embryo, where its encoded protein directs formation of the fly's …

Mrub_2294, Mrub_2293, And Mrub_1942 Genes Are Orthologs Of E. Coli B2476, B1131, And B4006 Genes, Respectively, Lindsay Popp, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

No abstract provided.

Mrub_1304, Mrub_2007 And Mrub_2006 Are Orthologs Of E. Coli B_3189, B_3972, And B_0091, Respectively Within The Peptidoglycan Biosynthesis Pathway, Mylaun E. Griffith, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

No abstract provided.

Mrub_0860, Mrub_0701 And Mrub_2285 Are Orthologous To E. Coli B2892, B2562 And B3863 Within The Recfor Pathway For Homologous Recombination, Bailey Englund, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tool associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict the gene function. We investigated the biological function of the genes Mrub_0860, Mrub_0701,and Mrub_2285. We predicted that Mrub_0860 (DNA coordinates 842934..844868 on the forward strand) encodes for the enzyme single-stranded DNA-specific exonuclease, which is in the first step of homologous recombination via the RecFOR pathway (KEGG map number 03440). The E. coli K12 MG1655 ortholog is predicted to be b2892, which has the gene identifier …

The Hetz Gene Regulates Heterocyst Formation In Anabaena Sp. Strain Pcc 7120, Patrick Videau, Vaille Swenson, Michael Gaylor, S M. O'Hanlon, L M. Cozy

Research & Publications

To form a complex multicellular organism, stem cells must differentiate into each cell/tissue type along proper spatiotemporal scales. The study of differentiation and organismal development has historically been conducted in prokaryotes due to their genetic and morphological simplicity. Anabaena sp. strain PCC 7120 is a multicellular filamentous cyanobacterium that differentiates a morphologically distinct secondary cell type, the heterocyst, in response to a lack of combined environmental nitrogen. Heterocysts are regularly spaced along filaments and fix atmospheric dinitrogen to maintain organismal viability in its absence. Previous work suggested that the hetZ gene is involved in heterocyst differentiation, but the insertional mutants …

Fisheries Management Paper No.283 - Abalone Resource Of Western Australia Harvest Strategy 2106 - 2021, Department Of Fisheries Western Australia

Fisheries Management Papers

Harvest strategies for aquatic resources managed by the Western Australian Department of Fisheries (the Department) are formal documents prepared to support the decision-making processes required to ensure the management of these resources are consistent with the principles of Ecologically Sustainable Development (ESD). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA) and Section 9 of the Aquatic Resources Management Act, which will replace the FRMA once proclaimed.

The publication of these strategies is intended to make the decision-making considerations and processes for the management of specified aquatic resources publicly transparent and provide …

Analysis Of The Oil Biosynthesis Transcripts Of The Moringa Oleifera Lam. Mature Seed Embryos Using Rna Sequencing, Vivian A. Panes, A Kitazumi, M Butler, R.D Baoas, B.G De Los Reyes

Biology Faculty Publications

Moringa oleifera seeds are capable of producing 40% edible oils that are gaining significance due to its nutritional advantages. Several studies have examined M. oleifera seed oil, nevertheless, these studies focused on the extraction of oil and methods of biodiesel production. There is a paucity of information on transcriptome level studies to determine the unigenes involved in oil biosynthesis metabolic pathways. The main objective of this study is to explore the transcriptome of the mature embryo of M. oleifera Lam. particularly the key genes related to oil biosynthesis. The transcriptome reflects the set of genes that are actively expressed at …

Genetic Analysis Of Serf Gene Function In Drosophila Melanogaster And Its Contribution To A Fly Model Of Spinal Muscular Atrophy, Swagata Ghosh

Theses and Dissertations--Biology

The Serf gene is evolutionarily highly conserved but its biological function is not known in any organism. In human, SERF1/H4F5 was first identified as a modifier of the disease Spinal Muscular Atrophy (SMA). SMA is caused by mutations in the Survival Motor Neuron 1(SMN1) gene leading to diminished levels of the Smn protein. More than 90% of patients with the most severe form of SMA have deletions that remove SERF1 as well as mutaions within SMN1. Hence, loss of Serf activity is hypothesized to exacerbate SMA disease progression. The primary motivation of this thesis was to test …

Uncovering Candidate Cold Tolerance Genes In Maize (Zea Mays), Raeann N. Goering

Departmental Honors Projects

With booming populations soon to overwhelm the world's food production capabilities, studying what makes crop organisms, like maize, efficient is crucial to ensure that the demand for food is met. Planting earlier in the spring would lengthen the crop season and produce larger yields provided the crop is tolerant to early spring’s low temperatures. Plants can adjust to abiotic stresses through biochemical changes controlled by transcription of genes. Trained plants can be produced by pre-exposing them to a lesser stress, allowing them to recover, then exposing them to a greater, longer stress. It is hypothesized that trained plants will tolerate …

An Undergraduate Cell Biology Lab: Western Blotting To Detect Proteins From Drosophila Eye, Neha Gogia, Ankita Sarkar, Amit Singh

Biology Faculty Publications

We have developed an undergraduate laboratory to allow detection and localization of proteins in the compound eye of Drosophila melanogaster, a.k.a fruit fly. This lab was a part of the undergraduate curriculum of the cell biology laboratory course aimed to demonstrate the use of Western Blotting technique to study protein localization in the adult eye of Drosophila. Western blotting, a two-day laboratory exercise, can be used to detect the presence of proteins of interests from total protein isolated from a tissue. The first day involves isolation of proteins from the tissue and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide) gel …

Real-Time Quantitative Pcr To Demonstrate Gene Expression In An Undergraduate Lab, Abijeet Singh Mehta, Amit Singh

Biology Faculty Publications

The objective of this teaching note is to develop a laboratory exercise, which allows students to get a hands-on experience of a molecular biology technique to analyze gene expression. The short duration of the biology laboratory for an undergraduate curriculum is the biggest challenge with the development of new labs. An important part of cell biology or molecular biology undergraduate curriculum is to study gene expression. There are many labs to study gene expression in qualitative manner. The commonly used reporter gene expression studies are primarily qualitative. However, there is no hands-on experience exercise to quantitatively determine gene expression. Therefore, …

Evolution Of Antagonistic Relationships In Proteins: A Case Study Of Radialis- And Diviricata-Like Genes, Ao Gao

Theses and Dissertations

The antagonistic relationship of proteins describes the opponent interactions that result in one protein suppressing the function of another. Developmental genetic studies of Antirrhinum majus demonstrated that two transcription factors from the MYB gene family, RAD and DIV, interact through antagonism to regulate floral dorsoventral asymmetry. Interestingly, similar antagonistic interactions were found among proteins of FSM1 (RAD-like), MYBI (DIV-like), and DRIF in Solanum lycopersicum, which is involved in fruit development. Here, we report on the homology of these antagonistic MYB proteins based on reconstruction of the phylogeny of I-box-like and R-R-type clades, where RAD- and DIV-like belong, …

Cullin-4 Regulates Wingless And Jnk Signaling-Mediated Cell Death In The Drosophila Eye., Meghana Tare, Ankita Sarkar, Shimpi Bedi, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

In all multicellular organisms, the fundamental processes of cell proliferation and cell death are crucial for growth regulation during organogenesis. Strict regulation of cell death is important to maintain tissue homeostasis by affecting processes like regulation of cell number, and elimination of unwanted/unfit cells. The developing Drosophila eye is a versatile model to study patterning and growth, where complex signaling pathways regulate growth and cell survival. However, the molecular mechanisms underlying regulation of these processes is not fully understood. In a gain-of-function screen, we found that misexpression of cullin-4 (cul-4), an ubiquitin ligase, can rescue reduced eye mutant phenotypes. Previously, …

Examination Of The Relevance Of Pi3k And Pten Pathway In Ustilago Maydis., Nathaniel Edward Dalton

Electronic Theses and Dissertations

Ustilago maydis is a fungal pathogen that is an obligate parasite on Zea mays (Corn) in order to undergo and complete its sexual life cycle. The cells grow as a haploid form until they meet a compatible partner and undergo a dimorphic switch from a budding yeast-like cell type to a filamentous dikaryon. Infection of the host plant is characterized by leaf chlorosis, anthocyanin content, and formation of large galls that develop on the stem, leaves, cobs, and flowers. Many signaling cascades such as MAPK and PKA are involved in the regulation of the infection lifecycle. The Phosphatidylinosotiol 3 Kinase/ …

Weighted-Samgsr: Combining Significance Analysis Of Microarray-Gene Set Reduction Algorithm With Pathway Topology-Based Weights To Select Relevant Genes, Suyan Tian, Howard H. Chang, Chi Wang

Biostatistics Faculty Publications

Background: It has been demonstrated that a pathway-based feature selection method that incorporates biological information within pathways during the process of feature selection usually outperforms a gene-based feature selection algorithm in terms of predictive accuracy and stability. Significance analysis of microarray-gene set reduction algorithm (SAMGSR), an extension to a gene set analysis method with further reduction of the selected pathways to their respective core subsets, can be regarded as a pathway-based feature selection method.

Methods: In SAMGSR, whether a gene is selected is mainly determined by its expression difference between the phenotypes, and partially by the number of pathways to …

Parallel Mutations Result In A Wide Range Of Cooperation And Community Consequences In A Two-Species Bacterial Consortium, Sarah Douglas, Lon Chubiz, William Harcombe, F. Ytreberg, Christopher Marx

Biology Department Faculty Works

Multi-species microbial communities play a critical role in human health, industry, and waste remediation. Recently, the evolution of synthetic consortia in the laboratory has enabled adaptation to be addressed in the context of interacting species. Using an engineered bacterial consortium, we repeatedly evolved cooperative genotypes and examined both the predictability of evolution and the phenotypes that determine community dynamics. Eight Salmonella enterica serovar Typhimurium strains evolved methionine excretion sufficient to support growth of an Escherichia coli methionine auxotroph, from whom they required excreted growth substrates. Non-synonymous mutations in metA, encoding homoserine trans-succinylase (HTS), were detected in each evolved S. enterica …

Review Of "A Primer Of Human Genetics" By G. Gibson, John B. Jenkins

Biology Faculty Works

No abstract provided.

Population Dynamics And Genetic Differentiation Of The Threatened Freshwater Mussel Species Fusconaia Askewi, Fusconaia Lananensis, And Pleurobema Riddellii, Edith D. Plants-Paris

Biology Theses

North America has the most diverse freshwater mussel fauna in the world with approximately 300 species; unfortunately, extinction rates for freshwater mussels rivals the rates of many other groups of organisms. Population-level natural life history data is essential in the management of species of conservation concern, yet basic information about freshwater mussel life-history and demographic traits are unknown for many species. To further complicate matters, taxonomic uncertainty exists among some members of the group. The work detailed herein had two goals: to gain further understanding of the taxonomic relationship between Fusconaia lananensis and F. askewi by sequencing genes that had …

Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots

STAR Program Research Presentations

The CRISPR-Cas system is an adaptive immune system found in bacteria which helps protect against the invasion of other microorganisms. This system induces double stranded breaks at precise genomic loci (1) in which repairs are initiated and insertions of a target are completed in the process. This mechanism can be used in eukaryotic cells in combination with sgRNAs (1) as a tool for genome editing. By using this CRISPR-Cas system, in addition to the “safe harbor locus,” ROSAβ26, the incorporation of a target gene into a site that is not susceptible to gene silencing effects can be achieved through few …

The Role Of Mfd In Stationary-Phase Oxidative Damage Repair In Bacillus Subtilis, Katelyn E. Porter

UNLV Theses, Dissertations, Professional Papers, and Capstones

Since the 1950’s it has been shown that bacterial cells accumulate mutations even in non- dividing conditions, but how this type of mutation occurs is still highly debated. In Bacillus subtilis, Mfd, a precursor of the nucleotide excision repair (NER) system, mediates the formation of mutations in stationary-phase or non-replicating cells. In growing cells, Mfd recruits repair when RNA polymerase is stalled during transcription; it then recruits proteins from NER to repair damage. Here, we examine the hypothesis that Mfd mediates the formation of mutations by interacting with cellular components that repair reactive oxygen species (ROS), a natural byproduct of …

Sex Chromosome-Wide Transcriptional Suppression And Compensatory Cis-Regulatory Evolution Mediate Gene Expression In The Drosophila Male Germline, Emily L. Landeen, Christina A. Muirhead, Lori Wright, Colin D. Meiklejohn, Daven C. Presgraves

School of Biological Sciences: Faculty Publications

The evolution of heteromorphic sex chromosomes has repeatedly resulted in the evolution of sex chromosome-specific forms of regulation, including sex chromosome dosage compensation in the soma and meiotic sex chromosome inactivation in the germline. In the male germline of Drosophila melanogaster, a novel but poorly understood form of sex chromosome-specific transcriptional regulation occurs that is distinct from canonical sex chromosome dosage compensation or meiotic inactivation. Previous work shows that expression of reporter genes driven by testis-specific promoters is considerably lower—approximately 3-fold or more—for transgenes inserted into X chromosome versus autosome locations. Here we characterize this transcriptional suppression of X-linked …

Cloning, Characteristics, And Functional Analysis Of Rabbit Nadph Oxidase 5, Feng Chen, Caiyong Yin, Christiana Dimitropoulou, David J.R. Fulton

Bioelectrics Publications

Background: Nox5 was the last member of the Nox enzyme family to be identified. Functionally distinct from the other Nox isoforms, our understanding of its physiological significance has been hampered by the absence of Nox5 in mouse and rat genomes. Nox5 is present in the genomes of other species such as the rabbit that have broad utility as models of cardiovascular disease. However, the mRNA sequence, characteristics, and functional analysis of rabbit Nox5 has not been fully defined and were the goals of the current study.

Methods: Rabbit Nox5 was amplified from rabbit tissue, cloned, and sequenced. COS-7 cells were …

The Maintenance Of Phenotypic Divergence Through Sexual Selection: An Experimental Study In Barn Swallows Hirundo Rustica, Rebecca Safran, Yoni Vortman, Brittany R. Jenkins, Joanna K. Hubbard, Matt Wilkins, Rachel J. Bradley, Arnon Lotem

School of Biological Sciences: Faculty Publications

Previous studies have shown that sexual signals can rapidly diverge among closely related species. However, we lack experimental studies to demonstrate that differences in trait-associated reproductive performance maintain sexual trait differences between closely related populations, in support for a role of sexual selection in speciation. Populations of Northern Hemisphere distributed barn swallows Hirundo rustica are closely related, yet differ in two plumage-based traits: ventral color and length of the outermost tail feathers (streamers). Here we provide experimental evidence that manipulations of these traits result in different reproductive consequences in two subspecies of barn swallow: (H. r. erythrogaster in North …

Loss Of Cell Adhesion Increases Tumorigenic Potential Of Polarity Deficient Scribble Mutant Cells, Indrayani Waghmare, Madhuri Kango-Singh

Biology Faculty Publications

Epithelial polarity genes are important for maintaining tissue architecture, and regulating growth. The Drosophila neoplastic tumor suppressor gene scribble (scrib) belongs to the basolateral polarity complex. Loss of scrib results in disruption of its growth regulatory functions, and downregulation or mislocalization of Scrib is correlated to tumor growth. Somatic scribble mutant cells (scrib-) surrounded by wild-type cells undergo apoptosis, which can be prevented by introduction of secondary mutations that provide a growth advantage. Using genetic tools in Drosophila, we analyzed the phenotypic effects of loss of scrib in different growth promoting backgrounds. We investigated if a central …

The Role Of Daf-19 In Non-Ciliated Neurons: How Is Neural Development Regulated By Different Daf-19 Isoforms?, Zabdiel Ek Vazquez

Lawrence University Honors Projects

A degenerative disease-like phenotype, specifically reduction in synaptic protein levels in adult worms, is correlated with loss-of-function of the only RFX transcription factor gene, daf-19, in C. elegans. This gene encodes four known transcription factor isoforms, two of which are correlated with particular functions. The DAF-19C isoform activates genes responsible for cilia development, while DAF-19M is needed for cilia specification in males. A comparison of the transcriptome of daf-19 null and isogenic wild type adult worms suggests both positive and negative regulation of gene expression is correlated with the presence of DAF-19 proteins. We have assessed DAF-19 regulation …