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Full-Text Articles in Microbiology

College Of Natural Sciences Newsletter, March 2021, College Of Natural Sciences Mar 2021

College Of Natural Sciences Newsletter, March 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2. Issue 3

Contents:

Page 1 Dean's Message
Page 2-3 Awards and Recognition
Page 4 Student Club Spotlight: MICROBIOLOGY CLUB
Page 5 Research Spotlight: Dr. Chakravarty
Page 6 Open PRAIRIE Data; Grants Awarded in CNS; Research Collquia
Page 7 A Busy Month in Review; Media Coverage of the College


Female Genital Tuberculosis In Pakistan - A Retrospective Review Of 10-Year Laboratory Data And Analysis Of 32 Cases, Tazeen Fatima, Rumina Hasan, Faisal Malik, Imran Ahmed, Linda Alice Bartlett, Michael G. Gravett, Sadia Shakoor Mar 2021

Female Genital Tuberculosis In Pakistan - A Retrospective Review Of 10-Year Laboratory Data And Analysis Of 32 Cases, Tazeen Fatima, Rumina Hasan, Faisal Malik, Imran Ahmed, Linda Alice Bartlett, Michael G. Gravett, Sadia Shakoor

Department of Pathology and Laboratory Medicine

Background: Female genital tuberculosis (FGTB) is an underobserved clinical entity owing to diagnostic challenges stemming from difficulty of obtaining diagnostic specimens and paucibacillary nature of the disease. Yet, FGTB is a cause of infertility, pelvic pain, or menstrual irregularities in high-burden countries. To assess laboratory and microbiology diagnostic utilization for FGTB in Pakistan, we have collected data from 2007 to 2016 to inform the need for improved laboratory diagnostics. The objectives of this study were to determine the proportion of FGTB as culture-confirmed extrapulmonary tuberculosis (EPTB) and to describe the characteristics of women with culture-confirmed FGTB in a nationwide laboratory …


Inhibition Of Zika Virus Replication By G-Quadruplex-Binding Ligands, Indian Institute Of Technology Indore, Aryamav Pattnaik, Bikash R. Sahoo, Uma Shankar, Asit K. Pattnaik, Amit Kumar, Debasis Nayak Mar 2021

Inhibition Of Zika Virus Replication By G-Quadruplex-Binding Ligands, Indian Institute Of Technology Indore, Aryamav Pattnaik, Bikash R. Sahoo, Uma Shankar, Asit K. Pattnaik, Amit Kumar, Debasis Nayak

Nebraska Center for Virology: Faculty Publications

Zika virus (ZIKV), a mosquito-transmitted Flavivirus, emerged in the last decade causing serious diseases and affecting human health globally. Currently, no licensed vaccines or antivirals are available to combat ZIKV, although several vaccine candidates are in the pipeline. In recent years, the presence of non-canonical G-quadruplex (GQ) secondary structures in viral genomes has ignited significant attention as potential targets for antiviral strategy. In this study, we identified several novel conserved potential GQ structures by analyzing published ZIKV genome sequences using an in-house algorithm. Biophysical and biochemical analysis of the RNA sequences containing these potential GQ sequences suggested the existence of …


3d Printing Of Human Microbiome Constituents To Understand Spatial Relationships And Shape Parameters In Bacteriology, Jacques Izard, Teklu Kuru Gerbaba, Shara R. P. Yumul Mar 2021

3d Printing Of Human Microbiome Constituents To Understand Spatial Relationships And Shape Parameters In Bacteriology, Jacques Izard, Teklu Kuru Gerbaba, Shara R. P. Yumul

Department of Food Science and Technology: Faculty Publications

Effective laboratory and classroom demonstration of microbiome size and shape, diversity, and ecological relationships is hampered by a lack of high-resolution, easy-to-use, readily accessible physical or digital models for use in teaching. Three-dimensional (3D) representations are, overall, more effective in communicating visuospatial information, allowing for a better understanding of concepts not directly observable with the unaided eye. Published morphology descriptions and microscopy images were used as the basis for designing 3D digital models, scaled at 20,000×, using computer-aided design software (CAD) and generating printed models of bacteria on mass-market 3D printers. Sixteen models are presented, including rod-shaped, spiral, flask-like, vibroid, …


The Response Of Marine Synechococcus To A Landscape Of Environmental Stressors: A Proteomic Exploration, Dana E. Michels Mar 2021

The Response Of Marine Synechococcus To A Landscape Of Environmental Stressors: A Proteomic Exploration, Dana E. Michels

Master's Theses

In the field of marine microbial ecology, many questions remain unanswered with regards to the physiological trade-offs made by phytoplankton to maximize growth (e.g., nutrient acquisition) and minimize loss (e.g., predation defenses). These tradeoffs, which occur at the cellular level, have wide reaching impacts on food web dynamics and global biogeochemical cycles. In the first chapter, we explored the use of a non-canonical amino acid (NCAA) technique, bioorthogonal non-canonical amino-acid tagging (BONCAT), in phytoplankton model systems. This technique has potential to work well in natural systems by enabling isolation of only newly synthesized proteins during an incubation period with the …


Pirnas As Modulators Of Disease Pathogenesis, Kayla J. Rayford, Ayorinde Cooley, Jelonia T. Rumph, Ashutosh Arun, Girish Rachakonda, Fernando Villalta, Maria F. Lima, Siddharth Pratap, Smita Misra, Pius N. Nde Feb 2021

Pirnas As Modulators Of Disease Pathogenesis, Kayla J. Rayford, Ayorinde Cooley, Jelonia T. Rumph, Ashutosh Arun, Girish Rachakonda, Fernando Villalta, Maria F. Lima, Siddharth Pratap, Smita Misra, Pius N. Nde

Publications and Research

Advances in understanding disease pathogenesis correlates to modifications in gene expression within different tissues and organ systems. In depth knowledge about the dysregulation of gene expression profiles is fundamental to fully uncover mechanisms in disease development and changes in host homeostasis. The body of knowledge surrounding mammalian regulatory elements, specifically regulators of chromatin structure, transcriptional and translational activation, has considerably surged within the past decade. A set of key regulators whose function still needs to be fully elucidated are small non-coding RNAs (sncRNAs). Due to their broad range of unfolding functions in the regulation of gene expression during transcription and …


Microbial Functional Responses In Marine Biofilms Exposed To Deepwater Horizon Spill Contaminants, Rachel L. Mugge, Jennifer L. Salerno, Leila J. Hamdan Feb 2021

Microbial Functional Responses In Marine Biofilms Exposed To Deepwater Horizon Spill Contaminants, Rachel L. Mugge, Jennifer L. Salerno, Leila J. Hamdan

Faculty Publications

Marine biofilms are essential biological components that transform built structures into artificial reefs. Anthropogenic contaminants released into the marine environment, such as crude oil and chemical dispersant from an oil spill, may disrupt the diversity and function of these foundational biofilms. To investigate the response of marine biofilm microbiomes from distinct environments to contaminants and to address microbial functional response, biofilm metagenomes were analyzed from two short-term microcosms, one using surface seawater (SSW) and the other using deep seawater (DSW). Following exposure to crude oil, chemical dispersant, and dispersed oil, taxonomically distinct communities were observed between microcosms from different source …


Sensitivity Of Wild-Type And Rifampicin-Resistant O157 And Non-O157 Shiga Toxin-Producing Escherichia Coli To Elevated Hydrostatic Pressure And Lactic Acid In Ground Meat And Meat Homogenate, Abimbola Allison, Aliyar Cyrus Fouladkhah Feb 2021

Sensitivity Of Wild-Type And Rifampicin-Resistant O157 And Non-O157 Shiga Toxin-Producing Escherichia Coli To Elevated Hydrostatic Pressure And Lactic Acid In Ground Meat And Meat Homogenate, Abimbola Allison, Aliyar Cyrus Fouladkhah

Agricultural and Environmental Sciences Faculty Research

Various serogroups of Shiga toxin-producing Escherichia coli have been epidemiologically associated with foodborne disease episodes in the United States and around the globe, with E. coli O157: H7 as the dominant serogroup of public health concern. Serogroups other than O157 are currently associated with about 60% of Shiga toxin-producing E. coli related foodborne illness episodes. Current study evaluated sensitivity of the O157 and epidemiologically important non-O157 serogroups of the pathogen to elevated hydrostatic pressure and 1% lactic acid. Pressure intensity of 250 to 650 MPa were applied for 0 to 7 min for inactivation of strain mixtures of …


When The Pandemic Opts For The Lockdown: Secretion System Evolution In The Cholera Bacterium, Francis J. Santoriello, Stefan Pukatzki Feb 2021

When The Pandemic Opts For The Lockdown: Secretion System Evolution In The Cholera Bacterium, Francis J. Santoriello, Stefan Pukatzki

Publications and Research

Vibrio cholerae, the causative agent of the diarrheal disease cholera, is a microbe capable of inhabiting two different ecosystems: chitinous surfaces in brackish, estuarine waters and the epithelial lining of the human gastrointestinal tract. V. cholerae defends against competitive microorganisms with a contact-dependent, contractile killing machine called the type VI secretion system (T6SS) in each of these niches. The T6SS resembles an inverted T4 bacteriophage tail and is used to deliver toxic effector proteins into neighboring cells. Pandemic strains of V. cholerae encode a unique set of T6SS effector proteins, which may play a role in pathogenesis or pandemic …


Characterization, Antimicrobial And Toxicity Studies Of Silver Nanoparticles Using Opuntia Ficus Indica Leaves Extracts From Effurun, Delta State, Christiana Ogwuche, Harrison Moses Feb 2021

Characterization, Antimicrobial And Toxicity Studies Of Silver Nanoparticles Using Opuntia Ficus Indica Leaves Extracts From Effurun, Delta State, Christiana Ogwuche, Harrison Moses

Tanzania Journal of Science

The silver nanoparticles were synthesized by reacting silver nitrate, a metal precursor with the extract obtained from the leaves of Opuntia ficus indica, which acts as a reducing and stabilizing agent. Formation of silver nanoparticles was indicated by colour change from light yellow to dark brown which was confirmed by ultraviolet-visible (UV-Vis) spectroscopy showing surface plasmon band at 369 nm resulting from relatively small amount of reductive biomolecules for the silver ion reduction. Scanning electron microscope (SEM) analysis gave the morphology of the nanoparticles and showed that the silver particles were of spherical shape. Fourier transform infrared (FTIR) spectrometer presented …


Potential Of Fungi Isolated From Diesel Contaminated Soil To Degrade Diesel, Oluwafemi Oyewole, Ramat Raji, Suzan Okeke, Gift Chukwuma, Japhet Yakubu Feb 2021

Potential Of Fungi Isolated From Diesel Contaminated Soil To Degrade Diesel, Oluwafemi Oyewole, Ramat Raji, Suzan Okeke, Gift Chukwuma, Japhet Yakubu

Tanzania Journal of Science

Diesel is a complex mixture and a common pollutant, consisting mainly of aliphatic hydrocarbons ranging from C9 to C23 and a number of aromatic compounds. The main purpose of this study was to isolate fungi from diesel contaminated soil for biodegradation of diesel contaminated soil. Two fungal species (Aspergillus flavus and Saccharomyces cerevisiae) were isolated from a diesel contaminated site using cultural and biochemical characterisation. The isolates were screened for their ability to utilize diesel as carbon source. The biodegradation rate of the fungi isolated was measured by determining the optical density using spectrophotometry. The fungal isolates were further tested …


Cellulase-Producing Bacteria Isolated From Mufindi Paper Mill Industrial Effluent, Iringa Tanzania, Erick Sinza, Aneth Mwakilili, Cyprian Mpinda, Sylvester Lyantagaye Feb 2021

Cellulase-Producing Bacteria Isolated From Mufindi Paper Mill Industrial Effluent, Iringa Tanzania, Erick Sinza, Aneth Mwakilili, Cyprian Mpinda, Sylvester Lyantagaye

Tanzania Journal of Science

Effluent and effluent-contaminated soil samples collected from Mufindi Paper Mill Limited, Iringa Tanzania were investigated for the presence of cellulolytic bacteria. The components of cellulase are endoglucanase, exoglucanase and β-glucosidase and these are very important for complete hydrolysis of cellulose to glucose monomers. Isolates were grown on nutrient agar and screened for cellulolytic activity on carboxymethylcellulose (CMC) agar plates using Gram’s iodine solution. Cellulases activities; endoglucanase, exoglucanase and β-glucosidase were assayed using CMC, avicel and cellobiose substrates, respectively by dinitrosalicyclic acid method. Out of 17 cellulolytic isolates obtained, crude enzyme extracts of only five isolates expressed all cellulases activities, the …


Effects Of Time On Ph, Total Bacteria Counts, And Total Hydrocarbon Contents In The Bioremediation Of Crude Oil Contaminated Soil Using Indigenous Bio-Stimulants, Ita Uwidia, Osalodion Uwidia Feb 2021

Effects Of Time On Ph, Total Bacteria Counts, And Total Hydrocarbon Contents In The Bioremediation Of Crude Oil Contaminated Soil Using Indigenous Bio-Stimulants, Ita Uwidia, Osalodion Uwidia

Tanzania Journal of Science

This study was conducted to investigate the effect of time on pH, total bacteria counts, and total hydrocarbon contents in the bioremediation of crude oil contaminated soil using pig waste and sawdust as bio-stimulants. Dried soil samples (500 g each) were weighed each into seven different plastic bowls, and each bowl was contaminated with 10 g of crude oil. Six of the contaminated soil samples in six of the plastic bowls were amended with a combination of pig waste and sawdust as bio-stimulants in the ratio of 1:1 in amounts of 150 g, 125 g, 100 g, 75 g, 50 …


Rasagiline Effects On Glucose Metabolism, Cognition, And Tau In Alzheimer’S Dementia, Dawn C. Matthews, Aaron Ritter, Ronald G. Thomas, Randolph D. Andrews, Ana S. Lukic, Carolyn Revta, Jefferson W. Kinney, Babak Tousi, James B. Leverenz, Howard Fillit, Kate Zhong, Howard H. Feldman, Jeffrey Cummings Feb 2021

Rasagiline Effects On Glucose Metabolism, Cognition, And Tau In Alzheimer’S Dementia, Dawn C. Matthews, Aaron Ritter, Ronald G. Thomas, Randolph D. Andrews, Ana S. Lukic, Carolyn Revta, Jefferson W. Kinney, Babak Tousi, James B. Leverenz, Howard Fillit, Kate Zhong, Howard H. Feldman, Jeffrey Cummings

Integrated Health Sciences Faculty Research

Background: A Phase II proof of concept (POC) randomized clinical trial was conducted to evaluate the effects of rasagiline, a monoamine oxidase B (MAO-B) inhibitor approved for Parkinson disease, in mild to moderate Alzheimer's disease (AD). The primary objective was to determine if 1 mg of rasagiline daily for 24 weeks is associated with improved regional brain metabolism (fluorodeoxyglucose–positron emission tomography [FDG-PET]) compared to placebo. Secondary objectives included measurement of effects on tau PET and evaluation of directional consistency of clinical end points. Methods: This was a double-blind, parallel group, placebo-controlled, community-based, three-site trial of 50 participants randomized 1:1 to …


Cryo-Electron Tomography Of Candida Glabrata Plasma Membrane Proteins, Cristina Jiménez-Ortigosa, Jennifer Jiang, Muyuan Chen, Xuyuan Kuang, Kelley R Healey, Paul Castellano, Nikpreet Boparai, Steven J Ludtke, David S Perlin, Wei Dai Feb 2021

Cryo-Electron Tomography Of Candida Glabrata Plasma Membrane Proteins, Cristina Jiménez-Ortigosa, Jennifer Jiang, Muyuan Chen, Xuyuan Kuang, Kelley R Healey, Paul Castellano, Nikpreet Boparai, Steven J Ludtke, David S Perlin, Wei Dai

Faculty, Staff and Students Publications

Fungal plasma membrane proteins have long been recognized as targets for the development of antifungal agents. Despite recent progress in experimental approaches and computational structural predictions, our knowledge of the structural dynamics and spatial distribution of these membrane proteins in the context of their native lipid environment remains limited. By applying cryo-electron tomography (cryoET) and subtomogram analysis, we aim to characterize the structural characteristics and spatial distribution of membrane proteins present in Candida glabrata plasma membranes. This study has resulted in the identification of the membrane-embedded structure of the fungal H+-ATPase, Pma1. Tomograms of the plasma membrane revealed that Pma1 …


Japanese Quail (Coturnix Japonica) As A Novel Model To Study The Relationship Between The Avian Microbiome And Microbial Endocrinology-Based Host-Microbe Interactions, James Keane, Joshua M. Lyte, Julia Eckenberger, Nicholas Anthony, Sandip Shrestha, Daya Marasini, Karrie M. Daniels, Valentina Caputi, Annie M. Donoghue, Mark Lyte Feb 2021

Japanese Quail (Coturnix Japonica) As A Novel Model To Study The Relationship Between The Avian Microbiome And Microbial Endocrinology-Based Host-Microbe Interactions, James Keane, Joshua M. Lyte, Julia Eckenberger, Nicholas Anthony, Sandip Shrestha, Daya Marasini, Karrie M. Daniels, Valentina Caputi, Annie M. Donoghue, Mark Lyte

Articles

Background

Microbial endocrinology, which is the study of neuroendocrine-based interkingdom signaling, provides a causal mechanistic framework for understanding the bi-directional crosstalk between the host and microbiome, especially as regards the effect of stress on health and disease. The importance of the cecal microbiome in avian health is well-recognized, yet little is understood regarding the mechanisms underpinning the avian host-microbiome relationship. Neuroendocrine plasticity of avian tissues that are focal points of host-microbiome interaction, such as the gut and lung, has likewise received limited attention. Avian in vivo models that enable the study of the neuroendocrine dynamic between host and microbiome are …


The C. Neoformans Cell Wall: A Scaffold For Virulence, Christine Chrissian Feb 2021

The C. Neoformans Cell Wall: A Scaffold For Virulence, Christine Chrissian

Dissertations, Theses, and Capstone Projects

Cryptococcus neoformans is a globally distributed opportunistic fungal pathogen and the causative agent of life threatening cryptococcal meningoencephalitis in immunocompromised individuals, resulting in ~180,000 deaths each year worldwide. A primary virulence-associated trait of this organism is the production of melanin. Melanins are a class of diverse pigments produced via the oxidation and polymerization of aromatic ring compounds that have a characteristically complex, heterogenous, and amorphous structure. They are synthesized by representatives of all biological kingdoms and share a multitude of remarkable properties such as the ability to absorb ultraviolet (UV) light and protect against ionizing radiation. Melanin production in fungi …


Mining Selected Metagenomes/Metatranscriptomes For Biosynthetic Gene Clusters And Antimicrobial Resistance Genes, Ahmed Yamany Jan 2021

Mining Selected Metagenomes/Metatranscriptomes For Biosynthetic Gene Clusters And Antimicrobial Resistance Genes, Ahmed Yamany

Theses and Dissertations

Antimicrobial resistance is one of the serious global challenges in the current century. The fact that resistance genes transfer between bacteria, coupled with the fact that the world is connected through complex dynamics. Studying microbial behavior and understanding the different factors coffering microbial resistance to a broad spectrum of the available drug classes, parallel with a comprehensive analysis of the natural microbial products as the primary source of the novel antibiotics, might shed some light on solutions for this problem. Microbial environments harbor a wide range of secondary metabolites (SM) with different functional groups. SMs are not directly involved in …


Transcriptional Coupling And Repair Of 8-Oxog Activate A Reca-Dependent Checkpoint That Controls The Onset Of Sporulation In Bacillus Subtilis, Valeria P. Suárez, Lissett E. Martínez, Hilda C. Leyva-Sánchez, Luz I. Valenzuela-García, Reyna Lara-Martínez, Luis F. Jiménez-García, Norma Ramírez-Ramírez, Armando Obregon-Herrera, Mayra Cuéllar-Cruz, Eduardo A. Robleto, Mario Pedraza-Reyes Jan 2021

Transcriptional Coupling And Repair Of 8-Oxog Activate A Reca-Dependent Checkpoint That Controls The Onset Of Sporulation In Bacillus Subtilis, Valeria P. Suárez, Lissett E. Martínez, Hilda C. Leyva-Sánchez, Luz I. Valenzuela-García, Reyna Lara-Martínez, Luis F. Jiménez-García, Norma Ramírez-Ramírez, Armando Obregon-Herrera, Mayra Cuéllar-Cruz, Eduardo A. Robleto, Mario Pedraza-Reyes

Life Sciences Faculty Research

© 2021, The Author(s). During sporulation Bacillus subtilis Mfd couples transcription to nucleotide excision repair (NER) to eliminate DNA distorting lesions. Here, we report a significant decline in sporulation following Mfd disruption, which was manifested in the absence of external DNA-damage suggesting that spontaneous lesions activate the function of Mfd for an efficient sporogenesis. Accordingly, a dramatic decline in sporulation efficiency took place in a B. subtilis strain lacking Mfd and the repair/prevention guanine oxidized (GO) system (hereafter, the ∆GO system), composed by YtkD, MutM and MutY. Furthermore, the simultaneous absence of Mfd and the GO system, (i) sensitized sporulating …


Mfd Affects Global Transcription And The Physiology Of Stressed Bacillus Subtilis Cells, Holly Anne Martin, Anitha Sundararajan, Tatiana S. Ermi, Robert Heron, Jason Gonzales, Kaiden Lee, Diana Anguiano-Mendez, Faye Schilkey, Mario Pedraza-Reyes, Eduardo A. Robleto Jan 2021

Mfd Affects Global Transcription And The Physiology Of Stressed Bacillus Subtilis Cells, Holly Anne Martin, Anitha Sundararajan, Tatiana S. Ermi, Robert Heron, Jason Gonzales, Kaiden Lee, Diana Anguiano-Mendez, Faye Schilkey, Mario Pedraza-Reyes, Eduardo A. Robleto

Life Sciences Faculty Research

© Copyright © 2021 Martin, Sundararajan, Ermi, Heron, Gonzales, Lee, Anguiano-Mendez, Schilkey, Pedraza-Reyes and Robleto. For several decades, Mfd has been studied as the bacterial transcription-coupled repair factor. However, recent observations indicate that this factor influences cell functions beyond DNA repair. Our lab recently described a role for Mfd in disulfide stress that was independent of its function in nucleotide excision repair and base excision repair. Because reports showed that Mfd influenced transcription of single genes, we investigated the global differences in transcription in wild-type and mfd mutant growth-limited cells in the presence and absence of diamide. Surprisingly, we found …


Sustainable Bioproduction By Rhodopseudomonas Palustris Tie-1 Through Metabolic Engineering¬¬¬, Wei Bai Jan 2021

Sustainable Bioproduction By Rhodopseudomonas Palustris Tie-1 Through Metabolic Engineering¬¬¬, Wei Bai

McKelvey School of Engineering Graduate Student Theses & Dissertations

The heavy reliance of the petroleum industry for raw material and the rising atmospheric CO2 caused by this reliance have driven the research and development of sustainable alternatives. Microbial production of chemicals, such as fuel and plastic, has been viewed as a feasible method. The wide selection of substrates by microbes enables them to produce chemicals using naturally abundant material or industrial waste, such as CO2, making the production sustainable. Compared to the model organisms such as Escherichia coli, Saccharomyces cerevisiae, many non-model organisms have a broader selection for carbon, electron, and nitrogen sources, making them great candidates for sustainable …


Inhibition Of Biofilm Formation By The Synergistic Action Of Egcg-S And Antibiotics, Shrameeta Shinde, Lee Lee, Tinchun Chu Jan 2021

Inhibition Of Biofilm Formation By The Synergistic Action Of Egcg-S And Antibiotics, Shrameeta Shinde, Lee Lee, Tinchun Chu

Department of Biology Faculty Scholarship and Creative Works

Biofilm, a stress-induced physiological state, is an established means of antimicrobial tolerance. A perpetual increase in multidrug resistant (MDR) infections associated with high mortality and morbidity have been observed in healthcare settings. Multiple studies have indicated that the use of natural products can prevent bacterial growth. Recent studies in the field have identified that epigallocatechin gallate (EGCG), a green tea polyphenol, could disrupt bacterial biofilms. A modified lipid-soluble EGCG, epigallocatechin-3-gallate-stearate (EGCG-S), has enhanced the beneficial properties of green tea. This study focuses on utilizing EGCG-S as a novel synergistic agent with antibiotics to prevent or control biofilm. Different formulations of …


A Peek Inside The Machines Of Bacterial Nucleotide Excision Repair, Thanyalak Kraithong, Silas Hartley, David Jeruzalmi, Danaya Pakotiprapha Jan 2021

A Peek Inside The Machines Of Bacterial Nucleotide Excision Repair, Thanyalak Kraithong, Silas Hartley, David Jeruzalmi, Danaya Pakotiprapha

Publications and Research

Double stranded DNA (dsDNA), the repository of genetic information in bacteria, archaea and eukaryotes, exhibits a surprising instability in the intracellular environment; this fragility is exacerbated by exogenous agents, such as ultraviolet radiation. To protect themselves against the severe consequences of DNA damage, cells have evolved at least six distinct DNA repair pathways. Here, we review recent key findings of studies aimed at understanding one of these pathways: bacterial nucleotide excision repair (NER). This pathway operates in two modes: a global genome repair (GGR) pathway and a pathway that closely interfaces with transcription by RNA polymerase called transcription-coupled repair (TCR). …


Sustainable Bioproduction By Rhodopseudomonas Palustris Tie-1 Through Metabolic Engineering, Wei Bai Jan 2021

Sustainable Bioproduction By Rhodopseudomonas Palustris Tie-1 Through Metabolic Engineering, Wei Bai

McKelvey School of Engineering Graduate Student Theses & Dissertations

The heavy reliance of the petroleum industry for raw material and the rising atmospheric CO2 caused by this reliance have driven the research and development of sustainable alternatives. Microbial production of chemicals, such as fuel and plastic, has been viewed as a feasible method. The wide selection of substrates by microbes enables them to produce chemicals using naturally abundant material or industrial waste, such as CO2, making the production sustainable. Compared to the model organisms such as Escherichia coli, Saccharomyces cerevisiae, many non-model organisms have a broader selection for carbon, electron, and nitrogen sources, making them great candidates for sustainable …


Metabolomics-Based Analysis Of Miniature Flask Contents Identifies Tobacco Mixture Use Among The Ancient Maya, Mario Zimmermann, Korey J. Brownstein, Luis Pantoja Díaz, Iliana Ancona Aragón, Scott R. Hutson, Barry Kidder, Shannon Tushingham, David R. Gang Jan 2021

Metabolomics-Based Analysis Of Miniature Flask Contents Identifies Tobacco Mixture Use Among The Ancient Maya, Mario Zimmermann, Korey J. Brownstein, Luis Pantoja Díaz, Iliana Ancona Aragón, Scott R. Hutson, Barry Kidder, Shannon Tushingham, David R. Gang

Anthropology Faculty Publications

A particular type of miniature ceramic vessel locally known as “veneneras” is occasionally found during archaeological excavations in the Maya Area. To date, only one study of a collection of such containers successfully identified organic residues through coupled chromatography–mass spectrometry methods. That study identified traces of nicotine likely associated with tobacco. Here we present a more complete picture by analyzing a suite of possible complementary ingredients in tobacco mixtures across a collection of 14 miniature vessels. The collection includes four different vessel forms and allows for the comparison of specimens which had previously formed part of museum exhibitions with recently …


Oligodendroglial Epigenetics, From Lineage Specification To Activity-Dependent Myelination, Mathilde Mathilde Pruvost, Sarah Moyon Jan 2021

Oligodendroglial Epigenetics, From Lineage Specification To Activity-Dependent Myelination, Mathilde Mathilde Pruvost, Sarah Moyon

Advanced Science Research Center

Oligodendroglial cells are the myelinating cells of the central nervous system. While myelination is crucial to axonal activity and conduction, oligodendrocyte progenitor cells and oligodendrocytes have also been shown to be essential for neuronal support and metabolism. Thus, a tight regulation of oligodendroglial cell specification, proliferation, and myelination is required for correct neuronal connectivity and function. Here, we review the role of epigenetic modifications in oligodendroglial lineage cells. First, we briefly describe the epigenetic modalities of gene regulation, which are known to have a role in oligodendroglial cells. We then address how epigenetic enzymes and/or marks have been associated with …


Pressure Effects On Sulfur‐Oxidizing Activity Of Thiobacillus Thioparus, Jorge R. Osman, Hervé Cardon, Gilles Montagnac, Aude Picard, Isabelle Daniel Jan 2021

Pressure Effects On Sulfur‐Oxidizing Activity Of Thiobacillus Thioparus, Jorge R. Osman, Hervé Cardon, Gilles Montagnac, Aude Picard, Isabelle Daniel

Life Sciences Faculty Research

Carbon capture and storage technologies are crucial for reducing carbon emission from power plants as a response to global climate change. The CarbFix project (Iceland) aims at examining the geochemical response of injected CO2 into subsurface reservoirs. The potential role of the subsurface biosphere has been little investigated up to now. Here, we used Thiobacillus thioparus that became abundant at the CarbFix1 pilot site after injection of CO2 and purified geothermal gases in basaltic aquifer at 400–800 m depth (4–8 MPa). The capacity of T. thioparus to produce sulfate, through oxidation of thiosulfate, was measured by Raman spectroscopy as a …


Complete Genome Sequence Of Strain Ss-5, A Magnetotactic Gammaproteobacterium Isolated From The Salton Sea, A Shallow, Saline, Endorheic Rift Lake Located On The San Andreas Fault In California, Denis Trubitsyn, Caroline L. Monteil, Corey Geurink, Viviana Morillo Lopez, Luiz Gonzaga Paula De Almeida, Ana Tereza Ribeiro De Vasconcelos, Fernanda Abreu, Dennis A. Bazylinski, Christopher T. Lefevre Jan 2021

Complete Genome Sequence Of Strain Ss-5, A Magnetotactic Gammaproteobacterium Isolated From The Salton Sea, A Shallow, Saline, Endorheic Rift Lake Located On The San Andreas Fault In California, Denis Trubitsyn, Caroline L. Monteil, Corey Geurink, Viviana Morillo Lopez, Luiz Gonzaga Paula De Almeida, Ana Tereza Ribeiro De Vasconcelos, Fernanda Abreu, Dennis A. Bazylinski, Christopher T. Lefevre

Life Sciences Faculty Research

© 2021 American Society for Microbiology. All rights reserved. We report the 3.7-Mb genome sequence of strain SS-5, a magnetotactic, sulfur-oxidizing rod and member of the family Chromatiaceae of the class Gammaproteobacteria, which biomineralizes membrane-bound, elongated, prismatic octahedral, magnetite nanocrystals. This genome sequence brings further diversity for understanding the origin and evolution of magnetotaxis and magnetosome biomineralization.


The Association Of Chest Radiographic Findings And Severity Scoring With Clinical Outcomes In Patients With Covid-19 Presenting To The Emergency Department Of A Tertiary Care Hospital In Pakistan, Raima Kaleemi, Kiran Hilal, Ainan Arshad, Russell S. Martins, Avinash Nankani, Tanveer Ul Haq, Sundas Basharat, Zeeshan Ansar Jan 2021

The Association Of Chest Radiographic Findings And Severity Scoring With Clinical Outcomes In Patients With Covid-19 Presenting To The Emergency Department Of A Tertiary Care Hospital In Pakistan, Raima Kaleemi, Kiran Hilal, Ainan Arshad, Russell S. Martins, Avinash Nankani, Tanveer Ul Haq, Sundas Basharat, Zeeshan Ansar

Department of Radiology

Introduction: While chest x-rays (CXRs) represent a cost-effective imaging modality for developing countries like Pakistan, their utility for the prognostication of COVID-19 has been minimally explored. Thus, we describe the frequency and distribution of CXR findings, and their association with clinical outcomes of patients with COVID-19.
Methods: All adult (≥ 18 years) patients presenting between 28th February-31st May to the emergency department of a tertiary care hospital in Pakistan, who were COVID-19 positive on RT-PCR with CXR done on presentation, were included. A CXR Severity Score (CXR-SS) of 0-8 was used to quantify the extent of pulmonary infection on CXR, …


Single-Cell Fluidic Force Microscopy Reveals Stress- Dependent Molecular Interactions In Yeast Mating, Marion Mathelié-Guinlet, Felipe Viela, JéRôMe Dehullu, Sviatlana Filimonava, Jason M. Rauceo, Peter N. Lipke, Yves F. DufrêNe Jan 2021

Single-Cell Fluidic Force Microscopy Reveals Stress- Dependent Molecular Interactions In Yeast Mating, Marion Mathelié-Guinlet, Felipe Viela, JéRôMe Dehullu, Sviatlana Filimonava, Jason M. Rauceo, Peter N. Lipke, Yves F. DufrêNe

Publications and Research

Sexual agglutinins of the budding yeast Saccharomyces cerevisiae are proteins mediating cell aggregation during mating. Complementary agglutinins expressed by cells of opposite mating types “a” and “α” bind together to promote agglutination and facilitate fusion of haploid cells. By means of an innovative single-cell manipulation assay combining fluidic force microscopy with force spectroscopy, we unravel the strength of single specific bonds between a- and α-agglutinins (~100 pN) which require pheromone induction. Prolonged cell–cell contact strongly increases adhesion between mating cells, likely resulting from an increased expression of agglutinins. In addition, we highlight the critical role of disulfide bonds of the …