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
Measuring Bacterial Growth Using A 3d-Printable Spectrometer, 2017 The University of Akron
Measuring Bacterial Growth Using A 3d-Printable Spectrometer, Samuel R. Bunting
Honors Research Projects
Visible light spectroscopy is a commonly used technique for measuring the growth of bacterial cultures, and growth curves provide broadly important data. However, the equipment and resources required for these experiments has been restricted to higher education and industry due to high cost and sophistication. We have previously reported on an inexpensive, 3D-printable photospectrometer called the SpecPhone. This device utilizes an iPhone as the camera, along with several other, inexpensive additions to make a fully functional spectrometer. Here, the application of the SpecPhone is expanded to the quantification of actively dividing E. coli cultures. Two protocols have been developed; one ...
Proteomic Approach For Extracting Cytoplasmic Proteins From Streptococcus Sanguinis Using Mass Spectrometry, 2017 Virginia Commonwealth University
Proteomic Approach For Extracting Cytoplasmic Proteins From Streptococcus Sanguinis Using Mass Spectrometry, Fadi Elrami, Kristina Nelson, Ping Xu
Philips Institute for Oral Health Research Publications
Streptococcus sanguinis is a commensal and early colonizer of oral cavity as well as an opportunistic pathogen of infectious endocarditis. Extracting the soluble proteome of this bacterium provides deep insights about the physiological dynamic changes under different growth and stress conditions, thus defining “proteomic signatures” as targets for therapeutic intervention. In this protocol, we describe an experimentally verified approach to extract maximal cytoplasmic proteins from Streptococcus sanguinis SK36 strain. A combination of procedures was adopted that broke the thick cell wall barrier and minimized denaturation of the intracellular proteome, using optimized buffers and a sonication step. Extracted proteome was quantitated ...
Loss Of Outer Membrane Porins In Clonally Related Clinical Isolates Of Klebsiella Pneumoniae Modifies The Bacteria; Resulting In Altered Resistance To Phagocytosis By Macrophages, 2017 University of North Florida
Loss Of Outer Membrane Porins In Clonally Related Clinical Isolates Of Klebsiella Pneumoniae Modifies The Bacteria; Resulting In Altered Resistance To Phagocytosis By Macrophages, Debra Nickole Brunson
UNF Theses and Dissertations
Klebsiella pneumoniae is an opportunistic pathogen responsible for lobar pneumoniae, liver abscess, and septicemia. Clinical isolates are found to be extended spectrum beta lactamase positive with differential expression of the two classical porins, OmpK35 and OmpK36. Porin loss is associated with increased minimum inhibitory concentrations of beta lactam, cephalosporin, and carbapenem antibiotics that target the peptidoglycan. However, little is known about how porin loss affects other aspects of the cell envelope. The focus of this study was to characterize clinical isolates exhibiting differential porin expression and determine if the cumulative changes altered the resistance to phagocytosis by macrophages. The results ...
Discovery And Characterization Of Bile Acid And Steroid Metabolism Pathways In Gut-Associated Microbes, 2017 Virginia Commonwealth University
Discovery And Characterization Of Bile Acid And Steroid Metabolism Pathways In Gut-Associated Microbes, Spencer Harris
Theses and Dissertations
The human gut microbiome is a complex microbial ecosystem residing in the lumen of our gastrointestinal tract. The type and amounts of microbes present in this ecosystem varies based on numerous factors, including host genetics, diet, and environmental factors. The human gut microbiome plays an important role in normal host physiological functions, including providing energy to colonocytes in the form of short-chain fatty acids. However, gut microbial metabolites have also been associated with numerous disease states. Current tools for analyzing the gut microbiome, such as high-throughput sequencing techniques, are limited in their predictive ability. Additionally, “-omic” approaches of studying the ...
Jmh Dissertation 2016.Pdf, 2016 University of Massachusetts - Amherst
Jmh Dissertation 2016.Pdf, Jennifer Hayashi
The Roles Of Biotin In Candida Albicans Physiology, 2016 University of Nebraska-Lincoln
The Roles Of Biotin In Candida Albicans Physiology, Nur Ras Aini Ahmad Hussin
Dissertations and Theses in Biological Sciences
Due to the increased number of immunocompromised patients, infections by Candida albicans have significantly increased in recent years. C. albicans transition from yeast to germ tubes is an essential factor for virulence. In this study we noted that Lee's medium, commonly used to induce filamentation, contained 500-fold more biotin than needed for growth. Thus, we investigated the effects of excess biotin on growth rate and filamentation by C. albicans in different media. At 37 °C, excess biotin (4 µM) enhanced germ tube formation (GTF) ca. 10-fold in both Lee's medium and a defined glucose proline medium, and ca ...
Characterization Of Antimicrobial Activity Of Culturable Bacteria Isolated From Krubera-Voronja Cave, 2016 Vilnius University
Characterization Of Antimicrobial Activity Of Culturable Bacteria Isolated From Krubera-Voronja Cave, Aiste Klusaite, Vida Vickackaite, Birute Vaitkeviciene, Rasa Karnickaite, Dominykas Bukelskis, Ieva Kieraite-Aleksandrova, Nomeda Kuisiene
International Journal of Speleology
In the present study we aimed to perform the first analysis of antimicrobial activity of bacteria isolated from Krubera-Voronja Cave, with the main focus on their activity against Grampositive bacteria, including Gram-positive pathogens. Using five different media, in total 874 heterotrophic cultures were isolated from water and sediment samples collected in Krubera-Voronja Cave at a depth from 220 m to 1640 m. 14.0% of all isolates demonstrated antibacterial activity against Gram-positive and Gram-negative test microorganisms. Our results show that this percentage was not uniform; it increased with the sampling depth and was the highest in the lower part of ...
The Effects Of Exogenous Fatty Acids On Enterococcus Faecalis Og1rf, 2016 University of Tennessee, Knoxville
The Effects Of Exogenous Fatty Acids On Enterococcus Faecalis Og1rf, Holly Elizabeth Johnson Saito
Enterococcus faecalis is a commensal of the mammalian intestine and an opportunistic pathogen that infects various locations in the human host. Specifically, the organism can infect surgical wounds, the urinary tract, and is an agent of endocarditis. Regardless of niche, this organism has access to fatty acid sources in the host, which may influence its ability to survive and cause infection; yet, the effects of exogenous fatty acids were unknown in E. faecalis. We have shown that complex sources of fatty acids such as bile or serum can significantly alter the membrane content and protect E. faecalis from acute membrane ...
Biosynthesis And Roles Of Virulence Conferring Cell Wall Associated Dimycocerosate Esters In Mycobacterium Marinum, 2016 Graduate Center, City University of New York
Biosynthesis And Roles Of Virulence Conferring Cell Wall Associated Dimycocerosate Esters In Mycobacterium Marinum, Poornima Mohandas
All Graduate Works by Year: Dissertations, Theses, and Capstone Projects
Mycobacterial species include a variety of obligate and opportunistic pathogens that cause several important diseases affecting mankind such as tuberculosis and leprosy. The most unique feature of these bacteria is their intricate cell wall that poses a permeability barrier to antibiotics and contributes to their pathogenicity and persistence within the host. The cell wall hosts several complex lipids such as dimycocerosate esters (DIMs), which are found in many clinically relevant pathogenic species of mycobacteria. DIMs have been implicated in the virulence of mycobacteria and play a major role in helping the bacteria evade host immune responses. It is therefore crucial ...
The Effects Of Quorum Sensing And Temperature On The Soluble Proteome Of Vibrio Salmonicida, 2016 California Polytechnic State University, San Luis Obispo
The Effects Of Quorum Sensing And Temperature On The Soluble Proteome Of Vibrio Salmonicida, Christopher L. Massey
Master's Theses and Project Reports
Vibrio salmonicida causes cold-water vibriosis in salmon populations around the world and causes financial damage to fisheries designed to farm these salmon. Very little is known about the physiology of how V. salmonicida causes disease and measures to contain vibriosis are restricted to either vaccinating individual fish against disease or administering antibiotics when an outbreak is detected. These procedures are costly and increase the risk for selection of antibiotic-resistant V. salmonicida strains. A recent reoccurrence of outbreaks in Norwegian fisheries provided incentive to better understand the virulence mechanisms of V. salmonicida. In this thesis, a proteomic approach was used to ...
Handwashing: A Study Of The History, Methods, And Psychology Surrounding Hand Hygiene, 2016 Liberty University
Handwashing: A Study Of The History, Methods, And Psychology Surrounding Hand Hygiene, Daniel J. Remillard
Senior Honors Theses
This paper covers three different areas concerning handwashing. First a review of the history of handwashing is done, going from ancient times to its introduction into modern medicine via Dr. Ignaz Semmelweis. This section gives a sobering reminder not to instantly reject data that comes in conflict with prevalent thought.
Then current medical knowledge about handwashing is examined, and the conclusion reached states that handwashing is best done with non-antibacterial soap.
Finally, a review of the psychology of handwashing shows that medical professionals often tend toward neglect if unwatched and unmotivated by an outside source. However, those suffering from obsessive ...
Environmentally Driven Orchestration Of Metabolisms By Prochlorococcus Spp., 2016 University of Tennessee - Knoxville
Environmentally Driven Orchestration Of Metabolisms By Prochlorococcus Spp., Martin James Szul
In the oligotrophic waters of the world’s open oceans physical factors such as pH, salinity, and temperature are generally stable. The nutrient limited conditions as well as the low environmental variability endemic to these ecosystems select for specialists that gain fitness advantages through minimalism, efficiency, and thrift. These physical characteristics are thought to reduce nutrient demand while allowing for constant metabolic activity and growth, but the mechanisms that promote these fitness advantages are currently unknown. To better understand how these physiologies improve selective fitness for the dominant phytoplankton, we observed metabolic parameters under environmental conditions typical to these waters ...
Biophysical Studies Of Cell Division Protein Localization Mechanisms In Escherichia Coli, 2016 University of Tennessee - Knoxville
Biophysical Studies Of Cell Division Protein Localization Mechanisms In Escherichia Coli, Matthew Wayne Bailey
How nanometer-scale proteins position accurately within micron-scale bacteria has intrigued both biologists and physicists alike. A critical process requiring precise protein localization is cell division. In most bacteria, cell division starts with the self-assembly of the FtsZ proteins into filaments that form a ring-like structure encircling the cell at its middle, the Z-ring. The Z-ring is a scaffold for additional proteins that synthesize the lateral cell wall which separates the two daughter cells. If division planes are misplaced relative to bacterial chromosomes, also called nucleoids, daughter cells with incomplete genetic material can be produced. In Escherichia coli, research carried out ...
Xct Increases Tuberculosis Susceptibility By Regulating Antimicrobial Function And Inflammation, 2016 Guangdong Medical College
Xct Increases Tuberculosis Susceptibility By Regulating Antimicrobial Function And Inflammation, Yi Cai, Subhalaxmi Nambi, Christopher M. Sassetti, Fudi Wang, Xinchun Chen
Open Access Articles
The physiological functions of macrophage, which plays a central role in the pathogenesis of tuberculosis, depend on its redox state. System xc-, a cystine-glutamate transporter, which consists of xCT and CD98, influences many ROS-dependent pathways by regulating the production of the antioxidant glutathione. xCT's ability to alter this critical host redox balance by increasing the glutathione synthesis aspect of phagocyte physiology suggested that it might influence tuberculosis pathogenesis. In this study, we found that the xCT expression was increased in peripheral blood monocyte of active tuberculosis. xCT expression in macrophage was induced by Mycobacterium tuberculosis (Mtb) through TLR2/Akt- ...
Defining Environmental Stresses That Activate The Rna Repair Operon In Salmonella Typhimurium, 2016 Olivet Nazarene University
Defining Environmental Stresses That Activate The Rna Repair Operon In Salmonella Typhimurium, Caleb M. Gulledge
Honors Program Projects
RNA polymerase holoenzyme (Eσ) mediates transcription in eubacteria, and is composed of five constant subunits (α2ββ’ω) and a variable sigma (σ) subunit that is responsible for promoter recognition and initiation of transcription. An alternative sigma factor in Salmonella Typhimurium, σ54 (also called RpoN), is mechanistically different than classical σ70-type sigmas, requiring a different promoter consensus sequence, an activator, and ATP hydrolysis. The Rtc RNA repair operon lies within the regulon of RpoN in S. Typhimurium, but has no known physiological function. Previous work characterized similar systems in archaea and humans, which were determined ...
Antibiotic Efficacy And Interaction In Escherichia Coli During Varying Nutrient Conditions, Kristina K. Millar
Scripps Senior Theses
Due to the recent rise in antibiotic resistant pathogens, and the difficulties surrounding the quest for new antibiotics, many researchers have started revisiting antibiotic interactions in hopes of finding new treatment options. The primary outcome of this project was to examine the efficacy of concomitant antibiotic use under varying nutrient conditions, to identify variations in antibiotic interactions. Antibiotic interactions were studied, utilizing E. coli as a model bacterial system, grown in four different media types. E. coli cultures were treated with streptomycin, tobramycin, erythromycin, and amikacin individually and in a pairwise fashion at varying doses. We found that at least ...
Microbial Community And Chemical Characteristics Of Swine Manure During Maturation, 2016 United States Department of Agriculture
Microbial Community And Chemical Characteristics Of Swine Manure During Maturation, Steven L. Trabue, Brian J. Kerr, Bradley L. Bearson, Manhoi Hur, Timothy Parkin, Eve S. Wurtele, Cherrie J. Ziemer
Genetics, Development and Cell Biology Publications
Swine diet formulations have the potential to lower animal emissions, including odor and ammonia (NH3). The purpose of this study was to determine the impact of manure storage duration on manure chemical and microbial properties in swine feeding trials. Three groups of 12 pigs were fed a standard corn–soybean meal diet over a 13-wk period. Urine and feces were collected at each feeding and transferred to 12 manure storage tanks. Manure chemical characteristics and headspace gas concentrations were monitored for NH3, hydrogen sulfide (H2S), volatile fatty acids, phenols, and indoles. Microbial analysis of the stored ...
Toxicity Of Engineered Nanomaterials To Plant Growth Promoting Rhizobacteria, 2016 University of Kentucky
Toxicity Of Engineered Nanomaterials To Plant Growth Promoting Rhizobacteria, Ricky W. Lewis
Theses and Dissertations--Plant and Soil Sciences
Engineered nanomaterials (ENMs) have become ubiquitous in consumer products and industrial applications, and consequently the environment. Much of the environmentally released ENMs are expected to enter terrestrial ecosystems via land application of nano-enriched biosolids to agricultural fields. Among the organisms most likely to encounter nano-enriched biosolids are the key soil bacteria known as plant growth promoting rhizobacteria (PGPR). I reviewed what is known concerning the toxicological effects of ENMs to PGPR and observed the need for high-throughput methods to evaluate lethal and sublethal toxic responses of aerobic microbes. I addressed this issue by developing high-throughput microplate assays which allowed me ...
Expansion Of And Reclassification Within The Family Lachnospiraceae, 2016 University of Massachusetts - Amherst
Expansion Of And Reclassification Within The Family Lachnospiraceae, Kelly N. Haas
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 ...