Protein Degradation Regulates Phospholipid Biosynthetic Gene Expression In Saccharomyces Cerevisiae, 2019 University of Massachusetts Amherst
Protein Degradation Regulates Phospholipid Biosynthetic Gene Expression In Saccharomyces Cerevisiae, Bryan Salas-Santiago
Transcriptional regulation of most phospholipid biosynthetic genes in Saccharomyces cerevisiae is coordinated by inositol and choline. Inositol affects phosphatidic acid (PA) intracellular levels. Opi1p interacts physically with PA and is the main repressor of the phospholipid biosynthetic genes. It is localized in the endoplasmic reticulum (ER) bound to the ER membrane protein Scs2p. When PA levels drop, Opi1p is translocated into the nucleus repressing most phospholipid biosynthetic genes. The OPI1 locus was identified in a screen looking for overproduction and excretion of inositol (Opi-). Opi- mutants are generally associated with a defect in repression of the ...
Methanogens, Plausible Extraterrestrial Life Forms On Mars, And Their Tolerance To Increasing Concentrations Of Illite Clay, 2018 University of Arkansas, Fayetteville
Methanogens, Plausible Extraterrestrial Life Forms On Mars, And Their Tolerance To Increasing Concentrations Of Illite Clay, Chandler Kern
Biological Sciences Undergraduate Honors Theses
Methanogens, some of Earth’s most primitive prokaryotic organisms, are candidates for possible life forms capable of inhabiting Mars. Specifically, four different species (Methanobacterium formicicum, Methanococcus maripaludis, Methanosarcina barkeri, Methanothermobacter wolfeii) were analyzed for their tolerance to the presence of illite clay. Illite is a crystalline mineral that has been identified from regions of Mars’s surface. Results indicated that all four species grew with some success in the illite at different concentrations. This experimentation with methanogens’ abilities to survive and reproduce in the presence of illite allows for a more accurate understanding of the potential capability of microbial growth ...
Mechanism Of Incorporation And Repair Of Uracil At Highly Transcribed Genes In Saccharomyces Cerevisiae, 2018 The University of Texas M D Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Mechanism Of Incorporation And Repair Of Uracil At Highly Transcribed Genes In Saccharomyces Cerevisiae, Norah Auma Owiti
UT GSBS Dissertations and Theses (Open Access)
Recombination and mutagenesis are elevated by high levels of transcription. The correlation between transcription and genome instability is largely explained by the topological and structural changes in DNA and the associated physical obstacles generated by the transcription machinery. However, such explanation does not directly account for the unique types of mutations originating from the non-canonical residues such as uracil, which are also elevated at highly transcribed regions. Apurinic/Apyrimic or Abasic (AP) sites derived from uracil excision, accumulate at a higher rate in actively transcribed regions of the genome in S. cerevisiae and are primarily repaired by base excision repair ...
The Effects Of Inulin And Galactooligosaccharides On The Production Of Reuterin By Lactobacillus Reuteri, 2018 Olivet Nazarene University
The Effects Of Inulin And Galactooligosaccharides On The Production Of Reuterin By Lactobacillus Reuteri, Micah Forshee
Honors Program Projects
The microbiome is a dynamic community that can positively and negatively influence host health. Lactobacillus reuteri is a probiotic that has received much attention for its ability to inhibit pathogens such as Salmonella Typhimurium, Escherichia coli, and Clostridium difficile. It does so by its unique ability to metabolize glycerol into the antimicrobial compound 3-HPA, which is commonly referred to as reuterin. The ability to secrete reuterin is dependent not only on glycerol availability but also the concentration of glucose. In fact, there appears to be a “goldilocks” ratio between glucose and glycerol as either too much or too little glucose ...
Factors Affecting The Parasitism Of Gregarine Species In Grasshoppers In Western Nebraska, 2018 University of Nebraska-Lincoln
Factors Affecting The Parasitism Of Gregarine Species In Grasshoppers In Western Nebraska, Alexandra Creigh, Kristin Mclarty, Scott Lyell Gardner
Honors Theses, University of Nebraska-Lincoln
We conducted a survey of the species of parasites found in grasshoppers around the area of Dunwoody’s Pond to investigate whether there were any species specific parasitic relationships occurring there. We collected grasshoppers from several areas around Dunwoody’s Pond totaling 15 species including Melanoplus bivittatus (Say 1825) , Melanoplus sanguinipes (Fabricius, 1798) , Melanoplus differentialis (Thomas 1865), and Melanoplus femurrubrum (De Geer 1773), along with others (Seymour et al., 2009) and compared the parasites found in them. This study is similar to one conducted in South America by Lloyd in 1951, and we hoped to find connections between species to ...
Clpxp-Regulated Proteins Suppress Requirement For Reca In Dam Mutants Of Escherichia Coli K-12, 2018 University of Massachusetts Amherst
Clpxp-Regulated Proteins Suppress Requirement For Reca In Dam Mutants Of Escherichia Coli K-12, Amie Savakis
Double strand breaks (DSB) are a common source of DNA damage in both prokaryotes and eukaryotes. If they are not repaired or are repaired incorrectly, they can lead to cell death (bacteria) or cancer (humans). In Escherichia coli, repair of DSB are typically accomplished via homologous recombination and mediated by RecA. This repair pathway, among others, is associated with activation of the SOS response. DNA adenine methyltransferase (dam) mutants have an increased number of DSB and, therefore, are notorious for being RecA-dependent for viability. Here, we show that the synthetic lethality of Δdam/ΔrecA is suppressed when clpP is removed ...
Impacts Of Genome And Nuclear Architecture On Molecular Evolution In Eukaryotes, 2018 University of Massachusetts Amherst
Impacts Of Genome And Nuclear Architecture On Molecular Evolution In Eukaryotes, Xyrus Maurer-Alcalá
The traditional view of genomes suggests that they are static entities changing slowly in sequence and structure through time (e.g. evolving over geological time-scales). This outdated view has been challenged as our understanding of the dynamic nature of genomes has increased. Changes in DNA content (i.e. polyploidy) are common to specific life-cycle stages in a variety of eukaryotes, as are changes in genome content itself. These dramatic genomic changes include chromosomal deletions (i.e. paternal chromosome deletion in insects; Goday and Esteban 2001; Ross, et al. 2010), developmentally regulated genome rearrangements (e.g. the V(D)J system ...
Evidence For The Priming Effect In Single Strain And Simplified Communities Of Estuarine Bacteria, 2017 University of Tennessee, Knoxville
Evidence For The Priming Effect In Single Strain And Simplified Communities Of Estuarine Bacteria, Abigail Amina Edwards
EURēCA: Exhibition of Undergraduate Research and Creative Achievement
Through their transformation of naturally occurring organic matter, coastal marine bacteria play an essential role in carbon cycling. A phenomenon termed the priming effect (PE) occurs when microbial communities remineralize recalcitrant organic matter faster in the presence of labile organic matter and may be prevalent in coastal systems. To understand how microbial community members interact to induce PE, it is essential to first understand the mechanisms underlying PE in single strains and simplified bacterial communities. The effect to which different concentrations and sources of labile carbon stimulated the production of bacterial biomass from riverine organic matter by two marine bacteria ...
Systematics And Biogeography Of The Cortinarius Violaceus Group And Sequestrate Evolution In Cortinarius (Agaricales), 2017 University of Tennessee, Knoxville
Systematics And Biogeography Of The Cortinarius Violaceus Group And Sequestrate Evolution In Cortinarius (Agaricales), Emma Harrower
Phylogenetics is a powerful tool used for illuminating the diversity of life on Earth, their evolution and their ecology. I created a multi-gene phylogenetic tree of Cortinarius section Cortinarius and uncovered five previously overlooked species, increasing the number of species in the section from seven to twelve. All members of the clade possess both cheilocystidia and pleurocystidia and possess a pigment known as (R)-39,49-dihydroxybphenylalanine. Ancestral state reconstruction estimated that the ancestral host was most likely an angiosperm, switching hosts when encountering novel host species in new lands, and only C. violaceus associating with the Pinaceae in North America ...
About Logan Weihe And Beloved Microcosm, 2017 University of Illinois at Chicago
About Logan Weihe And Beloved Microcosm, Logan M. Weihe
Steeplechase: An ORCA Student Journal
No abstract provided.
Anti-Staphylococcal Activity Of Variovorax Paradoxus Eps, 2017 California State University, San Bernardino
Anti-Staphylococcal Activity Of Variovorax Paradoxus Eps, Patricia Holt-Torres
Electronic Theses, Projects, and Dissertations
Variovorax paradoxus EPS is a gram-negative rod isolated from the sunflower rhizosphere at CSUSB. Preliminary research has shown that Variovorax paradoxus EPS has anti-staphylococcal activity in liquid and solid co-culture. Anti-staphylococcal activity of Wild type and V. paradoxus EPS 𝚫4519 on 0.5% YE agar with embedded S. aureus AH1710 supports the idea that a soluble molecule is responsible for this activity, as the agar acted as a physical barrier between V. paradoxus EPS and S. aureus colonies. Preliminary genetic analysis of V. paradoxus EPS identified three loci that suitable candidates for the synthesis of a potential anti-staphylococcal small ...
Functional Consequences Of Rna Exosome Complex Alteration By Conformational Changes And Cofactor Binding, 2017 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Functional Consequences Of Rna Exosome Complex Alteration By Conformational Changes And Cofactor Binding, Jaeil Han
UT GSBS Dissertations and Theses (Open Access)
The RNA exosome is an essential 3’-5 ribonuclease that processes or degrades a variety of RNA species in eukaryotes. It is composed of nine structural cores and one catalytic subunit, Rrp44. Structural studies captured two different conformations of Rrp44, Rrp44ch (channel) and Rrp44da (direct-access). The Rrp44ch appears to recruit RNA substrates from the central channel formed by the core subunits, while the substrate is directly recruited to Rrp44da bypassing the central channel. Although in vivo function of the Rrp44ch-exosome is extensively studied, the function or even the presence of the Rrp44da-exosome ...
An Integrated Bioinformatic/Experimental Approach For Discovering Novel Type Ii Polyketides Encoded In Actinobacterial Genomes, Wubin Gao
Discovery of new natural products (NPs) is critical both for diseases treatment and crops protection. Numerous NP biosynthetic gene clusters (BGCs) in sequenced microbial genomes allow identification of new NPs through genome mining. Developing an integrated bioinformatic/experimental approach for discovering novel type II polyketides (PK-IIs) facilitates investigation of this family of NPs in an efficient, systematic way. Here, we developed an approach to analyze ketosynthase α/β (KSα/β) gene sequences to predict PK-II core structures, allowing us to target novel PK-II BGCs either from isolated genomic DNA or genomes from the NCBI databank, and to isolate novel PK-IIs ...
Candida And Pseudomonas Interact To Enhance Mucosal Infection In Transparent Zebrafish, 2017 The University of Maine
Candida And Pseudomonas Interact To Enhance Mucosal Infection In Transparent Zebrafish, Audrey C. Bergeron
Electronic Theses and Dissertations
Polymicrobial communities exist throughout the human body and include both fungi and bacteria. During disease, cross-kingdom interactions among bacteria, fungi, and/or the immune system can alter virulence and lead to complex polymicrobial infections. The fungus C. albicans is among the most commonly isolated fungi in the context of fungal-bacterial co-infections and is often accompanied by the bacterium P. aeruginosa at a variety of sites throughout the body including mucosal tissues such as the lung. In vitro, C. albicans and P. aeruginosa have a cyclic, bi-directional, and largely antagonistic relationship, but these interactions do not account for the role of ...
The Fitness Effects Of Biofilm Formation And Toxin Production In Natural Yeast Isolates, 2017 College of William and Mary
The Fitness Effects Of Biofilm Formation And Toxin Production In Natural Yeast Isolates, Bernadette M. Deschaine
Undergraduate Honors Theses
Biofilms are complex, cooperative microbial communities encased in an extracellular matrix and attached to a surface. Biofilms are ubiquitous in virtually all environments and perform many important ecological functions. They can also cause dangerous, drug-resistant infections. There is thus great interest in studying biofilms and how to combat them.
The research presented here uses natural isolates of the budding yeast, Saccharomyces cerevisiae, to explore the fitness effects of biofilm formation. Biofilm-forming and non-biofilm-forming strains were grown alone and in mixed colonies with and without inducing biofilm formation, and the change in biofilm-strain frequency used to determine what conditions favor biofilm-forming ...
Bioethics In The Work Of Ernest Everett Just: + Missing - Some 400 Pages, 2017 Southern Methodist University
Bioethics In The Work Of Ernest Everett Just: + Missing - Some 400 Pages, Theodore Walker
Perkins Faculty Research and Special Events
Biology + ethics = bioethics. Here we see that Howard University biologist Ernest Everett Just (born 1883, died 1941) connected biology to ethics.
According to Just, various forms of specific biology (including especially cell biology) plus “general biology” are necessary for explaining adequately the origin of ethical behaviors. Social ethical behaviors, especially mutual aid and cooperative interactions with others and the environment, are essential to evolutionary advances among living creatures, ranging from humans to cells. Accordingly, theory of ethics (moral theory) should have roots in biology.
Also, Just wrote an unpublished book-length manuscript—“some 400 typed pages” (Just 1940)—on seeking the ...
Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, 2017 SUNY Stony Brook
Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest
Interdisciplinary Research Data
To develop broadly useful methods for the genetic manipulation of Labyrinthulomycetes (a diverse group of ubiquitous osmoheterotrophic marine protists), it is essential to understand the similarities and differences in regulation of gene expression among them. Toward this end we have used FIMO from the MEME suite (http://meme-suite.org/doc/fimo.html) to identify potential transcription factor binding sites in each of the three available genome sequences: Aplanochytrium kerguelense PBS07, Schizochytrium aggregatum ATCC 28209, and Aurantiochytrium limacinum ATCC MYA-1381
Letter From The Dean, 2017 University of Arkansas, Fayetteville
Letter From The Dean, Lona Robertson
Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences
No abstract provided.
Investigation Of Media Effects On Sinorhizobium Meliloti Glucose Minus, 2017 University of Redlands
Investigation Of Media Effects On Sinorhizobium Meliloti Glucose Minus, Roxana Apostol
Undergraduate Honors Theses
Although nitrogen fertilizers have certain benefits, the over application of such compounds often results in damages to the ecosystem. In this project, we focus our study on Sinorhizobiom meliloti, a species that lives in symbiosis with alfalfa plants, and through its nitrogen fixation capabilities, restores nitrogen levels in the soil. In our study we aim to gain a better understanding of the carbon metabolism in S. meliloti, mainly by looking at growth patterns in the presence of different carbon sources. Our research picked up on Erik Arvey’s discoveries which pointed out that sucrose inhibits growth of certain glucose minus ...
Toward The History Of Study Of Symbiogenesis: On The English Translation Of B. M. Kozo-Polyansky’S A New Principle Of Biology (1924), Victor Fet
We reproduce the text by Victor Fet, which was read on 6 October 2011 at the Moscow Society of Naturalists during the presentation of new book translation (B.M. Kozo- Polyansky. Symbiogenesis: A New Principle of Evolution / transl. by Victor Fet; ed. by Victor Fet & Lynn Margulis. Cambridge, Mass.: Harvard University Press, 2010. 138 p.) This half- forgotten book by Boris M. Kozo-Polyansky was known only by name to Western biologists. Victor Fet gives a brief history of this new translation, enthusiastically initiated and supported by Lynn Margulis (1938–2011), a famous naturalist who was always eager to gave credit where credit was due. Kozo- Polyansky, along with Merezhkovsky, Portier, and Wallin, pioneered symbiogenetic ideas that were brilliantly developed and vindicated starting from 1960–1970s. It was Lynn Margulis who noticed also that Kozo- Polyansky preceded E. Chatton in recognizing the profound diff erence between prokaryotes and eukaryotes; in fact, he maintained that this difference was due to symbiogenetic, complex nature of the eukaryotic cell! Two “scientistic” poems (in Russian) by Victor Fet are included, dedicated to all the prophets and martyrs of science.