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Full-Text Articles in Life Sciences

Combining Citizen Science And Genomics To Investigate Tick, Pathogen, And Commensal Microbiome At Single-Tick Resolution, Gaurav Chauhan, Jesse Mcclure, Jessica Hekman, Patrick W. Marsh, Jeffrey A. Bailey, Rachel F. Daniels, Diane P. Genereux, Elinor K. Karlsson Jan 2020

Combining Citizen Science And Genomics To Investigate Tick, Pathogen, And Commensal Microbiome At Single-Tick Resolution, Gaurav Chauhan, Jesse Mcclure, Jessica Hekman, Patrick W. Marsh, Jeffrey A. Bailey, Rachel F. Daniels, Diane P. Genereux, Elinor K. Karlsson

Open Access Articles

The prevalence of tickborne diseases worldwide is increasing virtually unchecked due to the lack of effective control strategies. The transmission dynamics of tickborne pathogens are influenced by the tick microbiome, tick co-infection with other pathogens, and environmental features. Understanding this complex system could lead to new strategies for pathogen control, but will require large-scale, high-resolution data. Here, we introduce Project Acari, a citizen science-based project to assay, at single-tick resolution, species, pathogen infection status, microbiome profile, and environmental conditions of tens of thousands of ticks collected from numerous sites across the United States. In the first phase of the project ...


Community-Driven Metadata Standards For Agricultural Microbiome Research, J. P. Dundore-Arias, E. A. Eloe-Fadrosh, L. M. Schriml, Gwyn A. Beattie, F. P. Brennan, P. E. Busby, R. B. Calderon, S. C. Castle, J. B. Emerson, S. E. Everhart, K. Eversole, K. E. Frost, J. R. Herr, A. I. Huerta, A. S. Iyer-Pascuzzi, A. K. Kalil, J. E. Leach, J. Leonard, J. E. Maul, B. Prithiviraj, M. Potrykus, N. R. Redekar, J. A. Rojas, K. A. T. Silverstein, D. J. Tomso, S. G. Tringe, B. A. Vinatzer, L. L. Kinkel Jan 2020

Community-Driven Metadata Standards For Agricultural Microbiome Research, J. P. Dundore-Arias, E. A. Eloe-Fadrosh, L. M. Schriml, Gwyn A. Beattie, F. P. Brennan, P. E. Busby, R. B. Calderon, S. C. Castle, J. B. Emerson, S. E. Everhart, K. Eversole, K. E. Frost, J. R. Herr, A. I. Huerta, A. S. Iyer-Pascuzzi, A. K. Kalil, J. E. Leach, J. Leonard, J. E. Maul, B. Prithiviraj, M. Potrykus, N. R. Redekar, J. A. Rojas, K. A. T. Silverstein, D. J. Tomso, S. G. Tringe, B. A. Vinatzer, L. L. Kinkel

Plant Pathology and Microbiology Publications

Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of “required” and “desirable” metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for ...


A Method For Improving The Accuracy And Efficiency Of Bacteriophage Genome Annotation, Alicia Salisbury, Philippos K. Tsourkas Jul 2019

A Method For Improving The Accuracy And Efficiency Of Bacteriophage Genome Annotation, Alicia Salisbury, Philippos K. Tsourkas

Life Sciences Faculty Publications

Bacteriophages are the most numerous entities on Earth. The number of sequenced phage genomes is approximately 8000 and increasing rapidly. Sequencing of a genome is followed by annotation, where genes, start codons, and functions are putatively identified. The mainstays of phage genome annotation are auto-annotation programs such as Glimmer and GeneMark. Due to the relatively small size of phage genomes, many groups choose to manually curate auto-annotation results to increase accuracy. An additional benefit of manual curation of auto-annotated phage genomes is that the process is amenable to be performed by students, and has been shown to improve student recruitment ...


Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig Mar 2019

Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig

Biology ETDs

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution.

In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in ...


High-Throughput Cultivation Of Bacterioplankton From The Gulf Of Mexico And Genomics Of The First Cultured Ld12 Representative, Michael Winslow Henson Jan 2019

High-Throughput Cultivation Of Bacterioplankton From The Gulf Of Mexico And Genomics Of The First Cultured Ld12 Representative, Michael Winslow Henson

LSU Doctoral Dissertations

Cultivation of microorganisms facilitates characterization of metabolism, interspecies dependencies, virus-host interactions, and other information necessary to resolve the functions and distribution of individual taxa. However, the metabolic and physiological capacities for the majority of microbes remains unresolved because of the lack of cultivated representatives for many groups limits our ability to test cultivation-independent observations. The Northern Gulf of Mexico offers a diversity of ecosystems under the continuous threat from natural and anthropogenic disturbances, yet little is known about its native bacterioplankton community. This dissertation sought to use high-throughput cultivation over three-years at six sites to isolate important coastal bacteria to ...


Characterizing Cultivable Bacteria From Trachymyrmex Septentrionalis Fungus Gardens, Hannah Beatty May 2018

Characterizing Cultivable Bacteria From Trachymyrmex Septentrionalis Fungus Gardens, Hannah Beatty

Honors Scholar Theses

The relationship between the fungus-growing ant Trachymyrmex septentrionalis, its symbiotic cultivar fungus, and the transient and residential community of microorganisms is a diverse and complex symbiosis that has evolved over space and time. The fungus garden, comprised primarily of the cultivar fungus belonging to the family Leucocoprineae,provides an environment that hosts many bacteria, which may also play an important role in this symbiosis. Although it is known that Pseudonocardia bacteria defend the ant host against fungal pathogens, other species of bacteria that are present in these fungus gardens also likely contribute to this symbiosis. Previous studies of this system ...


Genome-Wide Screening Of Potential Rnase Y-Processed Mrnas In The M49 Serotype Streptococcus Pyogenes Nz131, Zhiyun Chen, Rahul Raghavan, Fengxia Qi, Justin Merritt, Jens Kreth Jan 2018

Genome-Wide Screening Of Potential Rnase Y-Processed Mrnas In The M49 Serotype Streptococcus Pyogenes Nz131, Zhiyun Chen, Rahul Raghavan, Fengxia Qi, Justin Merritt, Jens Kreth

Biology Faculty Publications and Presentations

RNase Y is a major endoribonuclease in Group A streptococcus (GAS) and other Gram‐positive bacteria. Our previous study showed that RNase Y was involved in mRNA degradation and processing in GAS. We hypothesized that mRNA processing regulated the expression of important GAS virulence factors via altering their mRNA stabilities and that RNase Y mediated at least some of the mRNA‐processing events. The aims of this study were to (1) identify mRNAs that were processed by RNase Y and (2) confirm the mRNA‐processing events. The transcriptomes of Streptococcus pyogenes NZ131 wild type and its RNase Y mutant (Δrny ...


A Cure For Salmonella: Engaging Students In Pathogen Microbiology And Bioinformatics, Sophie Jurgensen Jan 2018

A Cure For Salmonella: Engaging Students In Pathogen Microbiology And Bioinformatics, Sophie Jurgensen

Senior Honors Projects, 2010-2019

Advances in Next Generation Sequencing (NGS) technology have generated a vast amount of publicly available genomic data, creating a need for students with training in computational analysis. This laboratory lesson is a course-based undergraduate research experience (CURE) focusing on environmental Salmonella, a common foodborne pathogen that is of great interest to public health laboratories but is relatively less virulent than most other such pathogens. As discovery is a central tenet of CUREs, students isolate novel Salmonella enterica and related strains from stream sediment, poultry litter, or other sources in the first half of the lesson (Module 1). They also conduct ...


Detection, Diversity, And Evolution Of Fungal Nitric Oxide Reductases (P450nor), Steven Adam Higgins Aug 2017

Detection, Diversity, And Evolution Of Fungal Nitric Oxide Reductases (P450nor), Steven Adam Higgins

Doctoral Dissertations

Nitrous oxide (N2O) is a gas responsible for significant ozone layer depletion and contributes to greenhouse effects in Earth’s atmosphere. N2O is primarily generated by denitrification, whereby nitrate (NO3-) or nitrite (NO2-) is converted to gaseous N2O or N2. Teragram quantities of N2O are emitted annually from agricultural soils treated with nitrogenous fertilizers due to the activity of soil microbiota. Although bacteria and fungi harbor genes permitting denitrification, fungi lack NosZ, an enzyme responsible for reducing N2O into inert N2 gas. Historically, scientists have linked fungi to ...


Accumulation And Expression Of Multiple Antibiotic Resistance Genes In Arcobacter Cryaerophilus That Thrives In Sewage, Jess A. Millar, Rahul Raghavan Apr 2017

Accumulation And Expression Of Multiple Antibiotic Resistance Genes In Arcobacter Cryaerophilus That Thrives In Sewage, Jess A. Millar, Rahul Raghavan

Biology Faculty Publications and Presentations

We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also ...


Genomic Analysis Of Factors Associated With Low Prevalence Of Antibiotic Resistance In Extraintestinal Pathogenic Escherichia Coli Sequence Type 95 Strains, Craig M. Stephens, Sheila Adams-Sapper, Manraj Sekhon, James R. Johnson, Lee W. Riley Apr 2017

Genomic Analysis Of Factors Associated With Low Prevalence Of Antibiotic Resistance In Extraintestinal Pathogenic Escherichia Coli Sequence Type 95 Strains, Craig M. Stephens, Sheila Adams-Sapper, Manraj Sekhon, James R. Johnson, Lee W. Riley

Biology

Extraintestinal pathogenic Escherichia coli (ExPEC) strains belonging to multilocus sequence type 95 (ST95) are globally distributed and a common cause of infections in humans and domestic fowl. ST95 isolates generally show a lower prevalence of acquired antimicrobial resistance than other pandemic ExPEC lineages. We took a genomic approach to identify factors that may underlie reduced resistance. We fully assembled genomes for four ST95 isolates representing the four major fimH-based lineages within ST95 and also analyzed draft-level genomes from another 82 ST95 isolates, largely from the western United States. The fully assembled genomes of antibiotic-resistant isolates carried resistance genes exclusively on ...


Genomic Characterization Of Dairy Associated Leuconostoc Species And Diversity Of Leuconostocs In Undefined Mixed Mesophilic Starter Cultures, Cyril A. Frantzen, Witold Kot, Thomas B. Pederson, Ylva M. Ardo, Jeff R. Broadbent, Horst Neve, Lars H. Hansen, Fabio Dal Bello, Hilde M. Østlie, Hans P. Kleppen, Finn K. Vogensen, Helge Holo Feb 2017

Genomic Characterization Of Dairy Associated Leuconostoc Species And Diversity Of Leuconostocs In Undefined Mixed Mesophilic Starter Cultures, Cyril A. Frantzen, Witold Kot, Thomas B. Pederson, Ylva M. Ardo, Jeff R. Broadbent, Horst Neve, Lars H. Hansen, Fabio Dal Bello, Hilde M. Østlie, Hans P. Kleppen, Finn K. Vogensen, Helge Holo

Nutrition, Dietetics, and Food Sciences Faculty Publications

Undefined mesophilic mixed (DL-type) starter cultures are composed of predominantly Lactococcus lactis subspecies and 1–10% Leuconostoc spp. The composition of the Leuconostoc population in the starter culture ultimately affects the characteristics and the quality of the final product. The scientific basis for the taxonomy of dairy relevant leuconostocs can be traced back 50 years, and no documentation on the genomic diversity of leuconostocs in starter cultures exists. We present data on the Leuconostoc population in five DL-type starter cultures commonly used by the dairy industry. The analyses were performed using traditional cultivation methods, and further augmented by next-generation DNA ...


Review Of The Algal Biology Program Within The National Alliance For Advanced Biofuels And Bioproducts, Clifford J. Unkefer, Richard T. Sayre, Jon K. Magnuson, Daniel B. Anderson, Ivan Baxter, Ian K. Balby, Judith K. Brown, Michael Carleton, Rose Ann Cattolico, Taraka Dale, Timothy P. Devarenne, C. Meghan Downes, Susan K. Dutcher, David T. Fox, Ursula Goodenough, Jan Jaworski, Jonathan E. Holladay, David M. Kramer, Andrew T. Koppisch, Mary S. Lipton, Babetta L. Marrone, Margaret Mccormick, István Molnár, John B. Mott, Kimberly L. Ogden, Ellen A. Panisko, Matteo Pellegrini, Juergen Polle, James W. Richardson, Martin Sabarsky, Shawn R. Starkenburg, Gary D. Stormo, Munehiro Teshima, Scott N. Twary, Pat J. Unkefer, Joshua S. Yuan, José A. Olivares Jan 2017

Review Of The Algal Biology Program Within The National Alliance For Advanced Biofuels And Bioproducts, Clifford J. Unkefer, Richard T. Sayre, Jon K. Magnuson, Daniel B. Anderson, Ivan Baxter, Ian K. Balby, Judith K. Brown, Michael Carleton, Rose Ann Cattolico, Taraka Dale, Timothy P. Devarenne, C. Meghan Downes, Susan K. Dutcher, David T. Fox, Ursula Goodenough, Jan Jaworski, Jonathan E. Holladay, David M. Kramer, Andrew T. Koppisch, Mary S. Lipton, Babetta L. Marrone, Margaret Mccormick, István Molnár, John B. Mott, Kimberly L. Ogden, Ellen A. Panisko, Matteo Pellegrini, Juergen Polle, James W. Richardson, Martin Sabarsky, Shawn R. Starkenburg, Gary D. Stormo, Munehiro Teshima, Scott N. Twary, Pat J. Unkefer, Joshua S. Yuan, José A. Olivares

Publications and Research

In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortiumbegan, littlewas known about themolecular basis of algal biomass or oil production. Very fewalgal genome sequenceswere available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played bymetabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in ...


Whole Genome Sequencing As A Tool For Identifying Phenotypic Properties And Underlying Genetic Mechanisms In Staphylococcus Pseudintermedius, Matthew C. Riley Dec 2016

Whole Genome Sequencing As A Tool For Identifying Phenotypic Properties And Underlying Genetic Mechanisms In Staphylococcus Pseudintermedius, Matthew C. Riley

Doctoral Dissertations

Staphylococcus pseudintermedius is a Gram-positive bacterial opportunistic pathogen commonly associated with dermal infections in canines, but capable of causing serious disease in other species. Reports of human infections caused by S. pseudintermedius along with an increase in resistance to multiple antibiotics highlights the importance of this organism. Whole genome sequencing can allow large scale investigation of genetic mechanisms underlying phenotypic properties that contribute to the expansion of successful S. pseudintermedius clonal lineages.

The increase in multidrug and methicillin-resistant S. pseudintermedius (MRSP) may result from horizontal transfer of genetic material between bacterial isolates, yet is thought to be rare in Staphylococci ...


Characterization Of The Marine Sponge Amphimedon Compressa Microbiome Across A Spatial Gradient, Renee Michelle Potens May 2016

Characterization Of The Marine Sponge Amphimedon Compressa Microbiome Across A Spatial Gradient, Renee Michelle Potens

HCNSO Student Theses and Dissertations

Diverse and ecologically important microbial communities (microbiomes) are symbiotic within marine sponges. In this study, the microbiome of Amphimedon compressa from three sample locations (Broward and Dade Counties, Southeast Florida, USA and the Southern Caribbean, Bocas del Toro, Panama) is characterized using 16S rRNA Illumina sequencing. The predominant taxa are Proteobacteria and Cyanobacteria, as expected for Low Microbial Abundance sponges, accounting for over 53% of the total microbiome community. The numbers of Operational Taxonomic Units (OTUs) decrease from Broward County (2,900) to Dade County (2,300) and then Bocas del Toro (1,200). The correlates to a decreasing north-south ...


A Genetic And Biochemical Analysis Of Sulfolobus Spindle-Shaped Virus 1, Eric Alexander Iverson Dec 2015

A Genetic And Biochemical Analysis Of Sulfolobus Spindle-Shaped Virus 1, Eric Alexander Iverson

Dissertations and Theses

Viruses infecting the Archaea exhibit a tremendous amount of morphological and genetic diversity. This is especially true for crenarchaeal viruses from the family Fuselloviridae, which possess spindle-shaped capsids and genomes that harbor a great number of uncharacterized genes. The functions of these unidentified gene products are of interest as they have the potential to provide valuable insights into the fusellovirus infection cycle and archaeal viruses in general. In an effort to better characterize the genetic requirements of the Fuselloviridae, we have performed genetic and biochemical experiments using the best studied fusellovirus, Sulfolobus spindle-shaped virus 1 (SSV1).

A comprehensive genetic analysis ...


Advancing Phage Genomics And Honeybee Health Through Discovery And Characterization Of Paenibacillaceae Bacteriophages, Bryan Douglas Merrill Jun 2015

Advancing Phage Genomics And Honeybee Health Through Discovery And Characterization Of Paenibacillaceae Bacteriophages, Bryan Douglas Merrill

Theses and Dissertations

The Paenibacillaceae family of bacteria includes two species known to infect the hives of honeybees, Paenibacillus larvae and Brevibacillus laterosporus. P. larvae, the causative agent of American Foulbrood (AFB) causes a lethal infection of honeybee larvae, while B. laterosporus is a secondary invader following European Foulbrood (EFB) infection. Increasing antibiotic resistance of P. larvae bacteria has prompted a search for alternative treatment methods for this disease. Bacteriophages are the most diverse life forms on earth and can provide important insights about the bacterial hosts they infect. However, few Paenibacillaceae phages have been isolated or characterized. In this study, the first ...


Genomic Analyses Of Paenibacillus Polymyxa Cr1, A Bacterium With Potential Applications In Biomass Degradation And Biofuel Production, Alexander W. Eastman May 2015

Genomic Analyses Of Paenibacillus Polymyxa Cr1, A Bacterium With Potential Applications In Biomass Degradation And Biofuel Production, Alexander W. Eastman

Electronic Thesis and Dissertation Repository

Lignin is a polyphenolic heteropolymer constituting between 18 to 35% of lignocellulose and is recognized as preventative of cellulosic biofuel commercialization. Paenibacillus polymyxa CR1 was isolated from naturally degrading corn stover and shown to produce alcohols using lignin as a sole carbon source. Genome sequencing and comparative genomics of P. polymyxa CR1 identified two homologs, a Dyp-type peroxidase and a laccase, which have previously been implicated in lignin metabolism in other bacteria. Knockout mutants of the identified genes displayed no growth deficiency and P. polymyxa CR1 is incapable of metabolizing common aromatic intermediates of lignin, suggesting the bacterium employs a ...


Structural Insights Into The Architecture Of The Hyperthermophilic Fusellovirus Ssv1, Kenneth M. Stedman, Melissa Deyoung, Mitul Saha, Michael B. Sherman, Marc C. Morais Nov 2014

Structural Insights Into The Architecture Of The Hyperthermophilic Fusellovirus Ssv1, Kenneth M. Stedman, Melissa Deyoung, Mitul Saha, Michael B. Sherman, Marc C. Morais

Biology Faculty Publications and Presentations

The structure and assembly of many icosahedral and helical viruses are well-characterized. However, the molecular basis for the unique spindle-shaped morphology of many viruses that infect Archaea remains unknown. To understand the architecture and assembly of these viruses, the spindle-shaped virus SSV1 was examined using cryo-EM, providing the first 3D-structure of a spindle-shaped virus as well as insight into SSV1 biology, assembly and evolution. Furthermore, a geometric framework underlying the distinct spindle-shaped structure is proposed.


Genotypic And Phenotypic Comparison Of Bacteroides Ovatus, B. Thetaiotaomicron, And B. Xylanisolvens Isolates Obtained From Cow, Goat, Human, And Pig Feces, Todd Atherly Jan 2014

Genotypic And Phenotypic Comparison Of Bacteroides Ovatus, B. Thetaiotaomicron, And B. Xylanisolvens Isolates Obtained From Cow, Goat, Human, And Pig Feces, Todd Atherly

Graduate Theses and Dissertations

ABSTRACT

Gastrointestinal Bacteroides play an important role in the health of their hosts. Do these Bacteroides perform the same functions in hosts that have different diets or gastrointestinal physiology? Do they show any co-evolution with the host environment? Within this study103 isolates of B. ovatus, B. thetaiotaomicron, and B. xylanisolvens were recovered from cow, goat, human and pig fecal enrichments with cellulose or xylan/pectin. Isolates were compared using 16S rRNA gene sequencing, repetitive sequence based-PCR (rep-PCR), and phenotypic microarrays. Analysis of 16S rRNA gene sequences revealed high percent sequence identity in these Bacteroides; with distinct phylogenetic groupings by bacterial ...


Characterization Of Uncultured, Human Oral Microbiota Using A Targeted, Single-Cell Genomics Approach, Alisha Gail Campbell May 2013

Characterization Of Uncultured, Human Oral Microbiota Using A Targeted, Single-Cell Genomics Approach, Alisha Gail Campbell

Doctoral Dissertations

Microbial communities associated with the human oral cavity are complex, and many oral microbes have yet to be cultured. These uncultured community members are of interest ecologically and phylogenetically, and a number of uncultured species have been positively correlated with oral diseases such as periodontitis. Thus, an approach was adapted to selectively separate single cells from mixed populations of oral bacteria and obtain genomic information for uncultured community members. A combination of fluorescent labeling, cell sorting with flow cytometry and multiple displacement amplification was used to obtain sufficient genomic material for whole-genome pyrosequencing.

The first targets were from uncultured oral ...


Detection Of Bacterial Retroelements Using Genomics, Sen Mu May 2013

Detection Of Bacterial Retroelements Using Genomics, Sen Mu

Electronic Theses and Dissertations

The reverse flow of genetic information can occur when a special DNA polymerase called Reverse Transcriptase (RT) copies the genetic information in an RNA molecule back into a complementary DNA. One type of RT encoding gene found in bacteria is called a retron element. Recent bacterial genome sequencing projects have revealed many examples of retron RT genes. This gene assignment is based on comparison with a few known retron RT proteins. However, RT proteins are highly diverse in their amino acid sequences, and thus the assigned identity of these RT proteins as retrons in genome databases is questionable. One way ...


The Evolution Of Host Specificity In The Vertebrate Gut Symbiont Lactobacillus Reuteri, Steven Frese Nov 2012

The Evolution Of Host Specificity In The Vertebrate Gut Symbiont Lactobacillus Reuteri, Steven Frese

Dissertations, Theses, & Student Research in Food Science and Technology

The vertebrate gut is home to one of the densest populations of life on Earth. This microbial community has a profound effect on host health, nutrition, development, behavior, and evolution. However, very little is known about how these microbes have evolved with their vertebrate hosts, how and whether they select hosts or how they remain associated with their hosts. Recent work identified Lactobacillus reuteri as an organism that is composed of host-specific sub-populations, each population associated with a different host animal. Representatives from each host-associated population were tested for their ability to colonize gnotobiotic mice, which only rodent strains could ...


Using Comparative Genomics For Inquiry-Based Learning To Dissect Virulence Of Escherichia Coli O157:H7 And Yersinia Pestis, David J. Baumler, Lois M. Banta, Kai F. Hung, Jodi A. Schwarz, Eric L. Cabot, Jeremy D. Glasner, Nicole T. Perna Apr 2012

Using Comparative Genomics For Inquiry-Based Learning To Dissect Virulence Of Escherichia Coli O157:H7 And Yersinia Pestis, David J. Baumler, Lois M. Banta, Kai F. Hung, Jodi A. Schwarz, Eric L. Cabot, Jeremy D. Glasner, Nicole T. Perna

Faculty Research & Creative Activity

Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis ...


Using Comparative Genomics For Inquiry-Based Learning To Dissect Virulence Of Escherichia Coli O157:H7 And Yersinia Pestis, David J. Baumler, Lois M. Banta, Kai F. Hung, Jodi A. Schwarz, Eric L. Cabot, Jeremy D. Glasner, Nicole T. Perna Jan 2012

Using Comparative Genomics For Inquiry-Based Learning To Dissect Virulence Of Escherichia Coli O157:H7 And Yersinia Pestis, David J. Baumler, Lois M. Banta, Kai F. Hung, Jodi A. Schwarz, Eric L. Cabot, Jeremy D. Glasner, Nicole T. Perna

Kai F. Hung

Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis ...


Using Comparative Genomics For Inquiry-Based Learning To Dissect Virulence Of Escherichia Coli O157:H7 And Yersinia Pestis, David Baumler, Lois Banta, Kai Hung, Jodi Schwarz, Eric Cabot, Jeremy Glasner, Nicole Perna Jan 2012

Using Comparative Genomics For Inquiry-Based Learning To Dissect Virulence Of Escherichia Coli O157:H7 And Yersinia Pestis, David Baumler, Lois Banta, Kai Hung, Jodi Schwarz, Eric Cabot, Jeremy Glasner, Nicole Perna

Faculty Research & Creative Activity

Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis ...


Niche Of Harmful Alga Aureococcus Anophagefferens Revealed Through Ecogenomics, Christopher Gobler, Dianna Berry, Sonya Dyhrman, Steven Wilhelm Jan 2011

Niche Of Harmful Alga Aureococcus Anophagefferens Revealed Through Ecogenomics, Christopher Gobler, Dianna Berry, Sonya Dyhrman, Steven Wilhelm

Steven Wilhelm

Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics ...


Niche Of Harmful Alga Aureococcus Anophagefferens Revealed Through Ecogenomics, Christopher Gobler, Dianna Berry, Sonya Dyhrman, Steven Wilhelm Jan 2011

Niche Of Harmful Alga Aureococcus Anophagefferens Revealed Through Ecogenomics, Christopher Gobler, Dianna Berry, Sonya Dyhrman, Steven Wilhelm

Microbiology Publications and Other Works

Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics ...


Microbial Nad Metabolism: Lessons From Comparative Genomics, Francesca Gazzaniga, Rebecca Stebbins, Sheila Z. Chang, Mark A. Mcpeek, Charles Brenner Sep 2009

Microbial Nad Metabolism: Lessons From Comparative Genomics, Francesca Gazzaniga, Rebecca Stebbins, Sheila Z. Chang, Mark A. Mcpeek, Charles Brenner

Open Dartmouth: Peer-reviewed articles by Dartmouth faculty

NAD is a coenzyme for redox reactions and a substrate of NAD-consuming enzymes, including ADP-ribose transferases, Sir2-related protein lysine deacetylases, and bacterial DNA ligases. Microorganisms that synthesize NAD from as few as one to as many as five of the six identified biosynthetic precursors have been identified. De novo NAD synthesis from aspartate or tryptophan is neither universal nor strictly aerobic. Salvage NAD synthesis from nicotinamide, nicotinic acid, nicotinamide riboside, and nicotinic acid riboside occurs via modules of different genes. Nicotinamide salvage genes nadV and pncA, found in distinct bacteria, appear to have spread throughout the tree of life via ...


Cis-Regulatory Sequence And Co-Regulatory Transcription Factor Functions In Erα-Mediated Transcriptional Repression, Richard Leroy Smith Jul 2009

Cis-Regulatory Sequence And Co-Regulatory Transcription Factor Functions In Erα-Mediated Transcriptional Repression, Richard Leroy Smith

Theses and Dissertations

Estrogens exert numerous actions throughout the human body, targeting healthy tissue while also enhancing the proliferative capacity of breast cancers. Estrogen signaling is mediated by the estrogen receptor (ER), which binds DNA and ultimately affects the expression of adjacent genes. Current understanding of ER-mediated transcriptional regulation is mostly limited to genes whose transcript levels increase following estrogen exposure, though recent studies demonstrate that direct down-regulation of estrogen-responsive genes is also a significant feature of ER action. We hypothesized that differences in cis-regulatory DNA was a factor in determining target gene expression and performed computational and experimental studies to test this ...