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
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.
Fecal Bacterial Communities As An Indicator Of Trophic Interactions Among Anuran Larvae, 2016 University of Southern Mississippi
Fecal Bacterial Communities As An Indicator Of Trophic Interactions Among Anuran Larvae, Steven Jacob Everman
Anurans are mass spawners, often with multiple females spawning together, resulting in thousands of tadpoles sharing a habitat. Such large numbers of tadpoles with limited dispersal can lead to intense competition for resources. Inter and intra-specific competition for food could have negative impacts on the growth and survival of smaller tadpoles. Fecal bacterial communities have the potential to be used as indicators of changes in diet making it possible to determine if tadpoles in the wild are eating the same food or not. After feeding on two prepared diets that differed in the percentage of complex carbohydrates, the fecal bacterial ...
The Elasmobranch-Microbe Relationship: Trimethylamine N-Oxide Synthesis, Urea Hydrolysis, And Microbe- Osmolyte Interactions In The Atlantic Stingray, Dasyatis Sabina, 2016 The University of Southern Mississippi
The Elasmobranch-Microbe Relationship: Trimethylamine N-Oxide Synthesis, Urea Hydrolysis, And Microbe- Osmolyte Interactions In The Atlantic Stingray, Dasyatis Sabina, Kaitlin Kelly Doucette
The elasmobranch osmoregulatory strategy is predicated on the accumulation of nitrogenous compounds, primarily urea and trimethylamine n¬-oxide (TMAO). Despite the abundance of these plasma osmolytes, it is notable that elasmobranchs appear to lack urease and TMA oxidase (Tmase), enzymes that scavenge urea-nitrogen and synthesize TMAO, respectively. However, urease and Tmase are found in many species of bacteria. Therefore, I hypothesized that intestinal bacteria are responsible for urease and Tmase activity in elasmobranchs. Absent dietary nitrogen sources, I evaluated the effects of reduced intestinal microbiota on osmoregulation in Atlantic stingray (Dasyatis sabina) in vivo. D. sabina were given daily broad-spectrum ...
Identification Of Microorganisms Isolated From Mars-Bound Spacecraft Using Maldi-Tof, 2016 Cal Poly, San Luis Obispo
Identification Of Microorganisms Isolated From Mars-Bound Spacecraft Using Maldi-Tof, Melanie K. Phillips
STAR (STEM Teacher and Researcher) Presentations
The primary goal of the Biotechnology and Planetary Protection Group (BPPG) at the Jet Propulsion Laboratory (JPL) is to prevent microbial contamination between Earth and other planetary bodies. This helps preserve the ability to study other worlds as they exist in their natural states and protects our biosphere from extraterrestrial life. The process for identifying microbes located on space-bound hardware in JPL can be more efficient and precise by using the technique called matrix-assisted laser desorption and ionization time of flight (MALDI-TOF). Once this identification technique is fully implemented, the process time will be reduced from two weeks to one ...
Relationship Between Morphogenesis And Secretion In The Filamentous Fungus Aspergillus Nidulans, 2016 University of Nebraska-Lincoln
Relationship Between Morphogenesis And Secretion In The Filamentous Fungus Aspergillus Nidulans, Lakshmi Preethi Yerra
Dissertations and Theses in Biological Sciences
Filamentous fungi have a long history in biotechnology for the production of food ingredients, pharmaceuticals and enzymes. The advancements made in recent years have earned filamentous fungi such as Aspergillus species a dominant place among microbial cell factories. Although the model fungus A. nidulans has been extensively studied, the genetic and regulatory networks that underlie morphogenesis and development have yet to be fully characterized. The Rho GTPases (Cdc42 and RacA) are one of the most important regulators of the morphogenetic processes among diverse eukaryotic organisms. Although the functions of these GTPases are relatively well-characterized, little is known about their downstream ...
Engineering A Mutation In The Heparin Binding Pocket Of The Human Fibroblast Growth Factor, 2016 University of Arkansas, Fayetteville
Engineering A Mutation In The Heparin Binding Pocket Of The Human Fibroblast Growth Factor, Roshni Patel
Chemistry & Biochemistry Undergraduate Honors Theses
Fibroblast growth factors (FGFs) are family of proteins that belong to a group of growth factors that are found in mammals and play an important role in angiogenesis, differentiation, organogenesis, and tissue repair. In summary, their main functionality is involved in cell division and proliferation. Because FGFs plays such a vital role in cell proliferation, they are mainly involved in the process of wound healing and injuries. FGF binds to its ligand, heparin—a heavily sulfated glycosaminoglycan. The binding of heparin to FGF occurs through electrostatic interactions, specifically between the negatively charged sulfate groups on heparin and positively charged residues ...
Oxidative Stress Response In Archaea: Elucidation Of Oxidant Sensing And Tolerance Mechanisms In Methanosarcina Acetivorans, 2016 University of Arkansas, Fayetteville
Oxidative Stress Response In Archaea: Elucidation Of Oxidant Sensing And Tolerance Mechanisms In Methanosarcina Acetivorans, Matthew Edward Jennings
Theses and Dissertations
Methanogens are archaea possessing a conserved metabolic pathway which produces methane. Many of the enzymes in the methanogenesis pathway are Fe-S proteins, meaning methanogens are sensitive to conditions which disrupt Fe-S clusters. Molecular oxygen is capable of disrupting Fe-S clusters through oxidation of the iron atoms. Furthermore, reduced iron can facilitate the production of reactive oxygen species (ROS), meaning methanogens must possess antioxidant mechanisms. Detection and eradication of ROS is important for all cells, due to the potentially fatal consequences of unchecked oxidation. This dissertation presents two separate projects investigating mechanisms the model methanogen Methanosarcina acetivorans possess for dealing with ...
Genomic Diversity Of Pseudoalteromonas Atlantica From Geographically Distant Deep Marine Basins, 2016 The University of Tennessee Knoxville
Genomic Diversity Of Pseudoalteromonas Atlantica From Geographically Distant Deep Marine Basins, Erika N. Youngquist
University of Tennessee Honors Thesis Projects
No abstract provided.
The Prevalence Of Escherichia Coli And Fecal Coliforms On Backpacks Of College Students In Central Kentucky, Samantha Mcmichael
Butler Journal of Undergraduate Research
Escherichia coli (E. coli) is a gram negative, rod-shaped, facultative anaerobic bacterium, it is normally found in the lower intestines of warm-blooded animals and humans. E. coli and/or fecal coliforms have been used as fecal indicators in water, food, and contact surfaces. The purpose of this experiment is to identify the prevalence of E. coli and fecal coliforms on the bottom of backpacks belonging to college students in central Kentucky. Forty samples were taken from bottoms of college students’ backpacks in central Kentucky. Sterile swabs were used to collect the samples from the backpacks. The swabs were placed ...
No Nonsense: The Protection Of Wild-Type Mrnas From Nonsense-Mediated Mrna Decay In Saccharomyces Cerevisiae, 2016 University of Nebraska-Lincoln
No Nonsense: The Protection Of Wild-Type Mrnas From Nonsense-Mediated Mrna Decay In Saccharomyces Cerevisiae, Krista Patefield
Dissertations and Theses in Biological Sciences
Gene regulation in eukaryotes is tightly controlled at multiple levels to ensure proper expression and cellular homeostasis. Misregulation of gene expression is a common source of genetic disease. One mechanism by which cells are able to control gene expression is through the synthesis and degradation of the mRNA molecules encoding the genes. The transcription and degradation of mRNA molecules controls the pool mRNAs that are available to the translational machinery. One of the well-studied mRNA decay pathways is the Nonsense-Mediated mRNA Decay pathway (NMD). Originally, NMD was discovered as a posttranscriptional mRNA surveillance mechanism responsible for the deadenylation-independent decapping and ...
Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions, 2016 Virginia Commonwealth University
Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions, J. Harry Caufield
Theses and Dissertations
The emergence of genomics as a discrete field of biology has changed humanity’s understanding of our relationship with bacteria. Sequencing the genome of each newly-discovered bacterial species can reveal novel gene sequences, though the genome may contain genes coding for hundreds or thousands of proteins of unknown function (PUFs). In some cases, these coding sequences appear to be conserved across nearly all bacteria. Exploring the functional roles of these cases ideally requires an integrative, cross-species approach involving not only gene sequences but knowledge of interactions among their products. Protein interactions, studied at genome scale, extend genomics into the field ...
The Characterization Of Monoclonal Antibodies Specific To Hpv45 L1 Protein, 2016 University of Colorado, Boulder
The Characterization Of Monoclonal Antibodies Specific To Hpv45 L1 Protein, Allie Morgan
Undergraduate Honors Theses
Cervical cancer is one of the leading causes of death from cancer around the world, resulting in nearly 300,000 deaths each year (Torre et al., 2012). Infection with high risk types of Human Papillomavirus is the primary etiologic event associated with the development of cervical cancer (Wallboomers, 1999). Since 2006, HPV vaccines have dramatically decreased cases of cervical cancer in developed countries. However, because these vaccines are expensive and require cold chain storage, their use in developing countries, where 85% of deaths from cervical cancer occur, has been limited (Torre et al., 2012; Kane, 2006). Development of second generation ...
Expansion Of And Reclassification Within The Family Lachnospiraceae, 2016 University of Massachusetts - Amherst
Expansion Of And Reclassification Within The Family Lachnospiraceae, Kelly N. Haas
Doctoral Dissertations May 2014 - current
Many of the taxa in the family Lachnospiraceae are currently misclassified as Clostridium spp. Here attempt to rectify many of these issues, beginning with an in-depth genomic and physiologic analysis of Clostridium methoxybenzovorans, culminating in the assertion that is a heterotype of Clostridium indolis, followed by reclassification of the broader group in which this organism resides. We propose two novel genera, Lacriformis and Enterocloster, to reclassify this clade, this includes reclassification of Clostridium sphenoides, Clostridium indolis, Clostridium saccharolyticum, Clostridium celerecrescens, Clostridium xylanolyticum, Clostridium algidixylanolyticum, Clostridium aerotolerans, Clostridium amygdalinum, and Desulfotomaculum guttoideum as Lacriformis sphenoides, comb. nov., Lacriformis indolis, comb. nov ...
Aeromonas Hydrophila In Amphibians: Harmless Bystander Or Opportunistic Pathogen, 2016 University of Central Florida
Aeromonas Hydrophila In Amphibians: Harmless Bystander Or Opportunistic Pathogen, Zachary P. Rivas
Honors in the Major Theses
For several decades amphibian populations have been declining. Historically, the bacterium A. hydrophila (Ah) was hypothesized to be the causal factor in amphibian disease and population declines. However, with the discovery of a chytrid fungus, Batrachochytrium dendrobatidis (Bd) in 1998, which was identified on the skin of amphibians during documented mortality events, Ah research became of minor interest as focus shifted to Bd. Recent studies into the immunocompromising abilities of Bd, however, have opened new questions about its relationship with Ah and their combined effects on a host.
In this study, I explore the relationship between infection with these two ...
Influence Of Lactobacillus Rhamnosus Isolated From “Amabere Amaruranu” Cultured Milk On Adipogenesis, 2015 East Tennessee State University
Influence Of Lactobacillus Rhamnosus Isolated From “Amabere Amaruranu” Cultured Milk On Adipogenesis, Justin E. Kotala
Electronic Theses and Dissertations
This study was performed to test the in vitro effects of a Lactobacillus rhamnosus isolate from “amabere amaruranu”, a traditional Kenyan cultured milk, on 3T3-L1 and Caco-2 cell lines. Cultures of fully mature 3T3-L1 adipocytes were treated with bacterial isolate cell extract (CE), filtered spent broth (FSB) from overnight bacterial culture, or with a PBS control. Expression levels of PPAR³1 and 2, C/EBP±, and ATGL proteins in 3T3-L1 cells were upregulated by FSB treatment. CE treatment did not affect protein expression levels. Expression of MTTP and SREBP-1c proteins in Caco-2 cells showed no change with either treatment. Optical density ...
Method Assessment For Microalgae Quantification In Wastewater Treatment And Biofuel Production, 2015 University of Arkansas at Fayetteville
Method Assessment For Microalgae Quantification In Wastewater Treatment And Biofuel Production, Kristen S. Harrison
Crop, Soil and Environmental Sciences Undergraduate Honors Theses
There is growing interest in the use of microalgae for wastewater treatment and biofuel production. However, there is not yet a reliable, user-friendly method of quantifying the biomass and lipid production of a large sample of algae. This study aims to establish and validate new methods for green microalgae quantification using the Microplate reader and the Coulter Counter. Chlorella vulgaris was chosen as the ‘ideal’ algal species for wastewater treatment and biofuel production due to its structure, lipid production, and pollution removal ability. Three traditional quantification methods -- microscope cell count, lipid separation, and chlorophyll extraction -- were compared to the Microplate ...
Epidemiology Of Select Species Of Filarial Nematodes In Free-Ranging Moose (Alces Alces) Of North America, 2015 University of Tennessee - Knoxville
Epidemiology Of Select Species Of Filarial Nematodes In Free-Ranging Moose (Alces Alces) Of North America, Caroline Mae Grunenwald
North American moose (Alces alces) are a culturally and economically valued species. Recent population declines raise concern for the survivability of this natural resource. The Minnesota population has experienced the most dramatic decline, with a 60% loss in total numbers since 2006. Nematode parasites, particularly some species of filarids, are important pathogens of moose and could be contributing to morbidity and mortality. This study investigates the eco-epidemiology of two filarial parasites of moose: Rumenfilaria andersoni and Elaeophora schneideri. By surveying cervid species from six U.S. states, we discovered R. andersoni was present in moose from all sample locations with ...
Production And Harvest Of Microalgae In Wastewater Raceways With Resource Recycling, 2015 California Polytechnic State University, San Luis Obispo
Production And Harvest Of Microalgae In Wastewater Raceways With Resource Recycling, Alexander Colin Roberts
Master's Theses and Project Reports
Microalgae can be grown on municipal wastewater media to both treat the wastewater and produce feedstock for algae biofuel production. However the reliability of treatment must be demonstrated, as well as high areal algae productivity on recycled wastewater media and efficient sedimentation harvesting. This processes was studied at pilot scale in the present research.
A pilot facility was operated with nine CO2-supplemented raceway ponds, each with a 33-m2 surface area and a 0.3-m depth, continuously from March 6, 2013 through September 24, 2014. The ponds were operated as three sets of triplicates with two sets continuously ...
Variation In Microbiome Composition And Stability For A Vancomycin Treated Primary Sclerosing Cholangitis Patient With Ulcerative Colitis Compared With Controls, 2015 California Polytechnic University, San Luis Obispo
Variation In Microbiome Composition And Stability For A Vancomycin Treated Primary Sclerosing Cholangitis Patient With Ulcerative Colitis Compared With Controls, Alanna Dubrovsky
The bacterial composition of the human intestines contributes to much more than just digestion. In the inflammatory, autoimmune conditions primary sclerosing cholangitis (PSC) and ulcerative colitis (UC), the microbiome may be, in some cases, a factor. To gain a better understanding of the composition and stability of the microbiome in a patient treated with vancomycin for PSC, terminal restriction fragment (TRF) analysis was performed on 13 controls and 1 patient, and 16s rRNA microbiome composition analysis was performed on 1 patient and 3 controls. Results showed similar levels of stability, with surprising differences in composition.