Life Sciences Commons^™

Genetic Signatures For Helicobacter Pylori Strains Of West African Origin, Kennady K. Bullock, Carrie L. Shaffer, Andrew W. Brooks, Ousman Secka, Mark H. Forsyth, Mark S. Mcclain, Timothy L. Cover

Veterinary Science Faculty Publications

Helicobacter pylori is a genetically diverse bacterial species that colonizes the stomach in about half of the human population. Most persons colonized by H. pylori remain asymptomatic, but the presence of this organism is a risk factor for gastric cancer. Multiple populations and subpopulations of H. pylori with distinct geographic distributions are recognized. Genetic differences among these populations might be a factor underlying geographic variation in gastric cancer incidence. Relatively little is known about the genomic features of African H. pylori strains compared to other populations of strains. In this study, we first analyzed the genomes of …

Pore Forming Protein Assembly And The Use In Nanopore Sensing: A Study On E. Coli Proteins Clya And Ompg, Monifa Fahie

Doctoral Dissertations

Pore forming proteins are typically the proteins that form channels in membranes. They have several roles ranging from molecule transport to triggering the death of a cell. This work focuses on two E. coli pore forming proteins that have vastly differing roles in nature. Outer membrane protein G (OmpG) is an innocuous β-barrel porin while Cytolysin A (ClyA) is an α-helical pore forming toxin. For OmpG we probed its potential to be a nanopore sensor for protein detection and quantification. A small high affinity ligand, biotin, was covalently attached to loop 6 of OmpG and used to capture biotin-binding proteins. …

Defining Electron Bifurcation In The Electron-Transferring Flavoprotein Family, Amaya M. Garcia Costas, Saroj Poudel, Anne-Frances Miller, Gerrit J. Schut, Rhesa N. Ledbetter, Kathryn R. Fixen, Lance C. Seefeldt, Michael W. W. Adams, Caroline S. Harwood, Eric S. Boyd, John W. Peters

Chemistry Faculty Publications

Electron bifurcation is the coupling of exergonic and endergonic redox reactions to simultaneously generate (or utilize) low- and high-potential electrons. It is the third recognized form of energy conservation in biology and was recently described for select electron-transferring flavoproteins (Etfs). Etfs are flavin-containing heterodimers best known for donating electrons derived from fatty acid and amino acid oxidation to an electron transfer respiratory chain via Etf-quinone oxidoreductase. Canonical examples contain a flavin adenine dinucleotide (FAD) that is involved in electron transfer, as well as a non-redox-active AMP. However, Etfs demonstrated to bifurcate electrons contain a second FAD in place of the …

Comparison Of Thaumarchaeotal Populations From Four Deep Sea Basins., Stephen Techtmann, Nagissa Mahmoudi, Kendall T Whitt, Maria Fernanda Campa, Julian L Fortney, Dominique C Joyner, Terry C Hazen

Michigan Tech Publications

The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. We …

The Sponge Microbiome Project, Lucas Moitinho-Silva, Shaun Nielsen, Amnon Amir, Antonio Gonzalez, Gail Ackermann, Carlo Cerrano, Carmen Astudillo-Garcia, Cole Easson, Detmer Sipkema, Fang Liu, Georg Steinert, Giorgos Kotoulas, Grace Mccormack, Guofang Feng, James J. Bell, Jan Vicente, Johannes R. Bjork, Jose M. Montoya, Julie B. Olson, Julie Reveillaud, Laura Steindler, Mari-Carmen Pineda, Maria V. Marra, Micha Ilan, Michael W. Taylor, Paraskevi Polymenakou, Patrick M. Erwin, Peter J. Schupp, Rachel L. Simister, Rob Knight, Robert W. Thacker, Rodrigo Costa, Russell T. Hill, Susanna Lopez-Legentil, Thanos Dailianis, Timothy Ravasi, Ute Hentschel, Zhiyong Li, Nicole S. Webster, Torsten Thomas

Marine & Environmental Sciences Faculty Articles

Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other …

Mechanisms Responsible For A Φx174 Mutant's Ability To Infect Escherichia Coli By Phosphorylation, Jennifer Cox, Catherine Putonti

Catherine Putonti

The ability for a virus to expand its host range is dependent upon a successful mode of viral entry. As such, the host range of the well-studied ΦX174 bacteriophage is dictated by the presence of a particular lipopolysaccharide (LPS) on the bacterial surface. The mutant ΦX174 strain JACS-K, unlike its ancestor, is capable of infecting both its native host Escherichia coli C and E. coli K-12, which does not have the necessary LPS. The conversion of an alanine to a very reactive threonine on its virion surface was found to be responsible for the strain's expanded host range.

Assessment Of A Metaviromic Dataset Generated From Nearshore Lake Michigan, Siobhan C. Watkins, Neil Kuehnle, C Anthony Ruggeri, Kema Malki, Katherine Bruder, Jinan Elayyan, Kristina Damisch, Naushin Vahora, Paul O'Malley, Brianne Ruggles-Sage, Zachary Romer, Catherine Putonti

Catherine Putonti

Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, and affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have been less studied in freshwaters, despite representing a potentially more diverse environment. Lake Michigan is one of the largest bodies of freshwater on the planet, yet to date the diversity of its phages has yet to be examined. Here, we present a composite survey of viral ecology in the nearshore waters of Lake Michigan. Sequence analysis was performed using a web server previously used to analyse …

Bacterial Motility And Its Role In Biofilm Formation, Clayton J. Culp, Arezoo M. Ardekani, Adib Ahmadzadegan

The Summer Undergraduate Research Fellowship (SURF) Symposium

Bacterial biofilms are known to cause millions of dollars in damage in the medical industry per year via infection of central venous catheters, urinary catheters, and mechanical heart valves. Unfortunately, there are some characteristics of biofilm formation that are yet to be fully understood. Recently much work has been done to investigate the motility characteristics of bacteria with hopes of better understanding the phenomena of biofilm formation. Still, one of the least understood stages is bacterial attachment or adhesion, a process designed to anchor bacteria in an advantageous environment. Providing a better understanding of bacterial motility near solid interfaces will …

Dna Analysis Of Surfactant-Associated Bacteria In A Natural Sea Slick In The Gulf Of Mexico Observed By Terrasar-X, Kathryn Howe

HCNSO Student Theses and Dissertations

Under low wind speed conditions, surfactants accumulate at the air-sea interface, dampen short-gravity capillary (Bragg) waves, and form natural sea slicks that are detectable visually and in synthetic aperture radar (SAR) imagery. Marine organisms, such as phytoplankton, zooplankton, seaweed, and bacteria, produce and degrade surfactants during various life processes. This study coordinates in situ sampling with TerraSAR-X satellite overpasses in order to help guide microbiological analysis of the sea surface microlayer (SML) and associated subsurface water (SSW). Samples were collected in the Gulf of Mexico during a research cruise (LASER) in February 2016 to determine abundance of surfactant associated bacteria …

Enumeration And Identification Of Selected Bacteria In Water Samples From The Alapahoochee River System, Jenifer Turco Ph.D., James A. Nienow

Georgia Journal of Science

Escherichia coli and enterococci were enumerated in water collected biweekly for one year at ten stations in the Alapahoochee River system. The concentrations of E.coli were usually below a standard of 576 colony forming units (cfu) per 100 ml, except after heavy rain. At five stations the concentrations of enterococci were gener­ally above a standard of 151 cfu/100 ml. Concentrations of both groups showed a direct but weak correlation with pH. For quality control, 772 colonies typical of E. coli and 773 colonies typical of enterococcus were tested by the appropriate verification procedures. Sixty-six (8.5%) of the former, and 57 …

The Effect Of Management Practices On Bacterial, Fungal, And Nematode Communities On Cool Season Turfgrass, Elisha Allan-Perkins

Doctoral Dissertations

Golf courses comprise 50 million acres in the United States of highly managed turf susceptible to abiotic and biotic stressors. A growing area of interest is utilizing microbes to improve plant growth, increase disease and stress tolerance, and reduce pathogens. In order to develop these new practices, we must gain an understanding of turfgrass microbial communities and how they are affected by management practices. We characterized bacteria, fungi, and nematodes on three golf courses: one organic, one with reduced inputs, and one conventional. We took samples from three management areas on each course representing different management intensities (roughs, fairways, and …

Summary Report Of Enhanced Monitoring And Pollution Source Tracking Efforts In The Willard Beach Watershed, Maine, 2012-2016, M. Sims, K. Kaczor

Maine Sea Grant Publications

Willard Beach is a popular recreation area located in South Portland used primarily by families with young children. Routine monitoring at the beach revealed elevated bacteria levels, prompting the need for enhanced monitoring within the watershed to determine the nature and extent of potential bacteria inputs. Although the waste of domestic and wild animals can contribute to impaired water quality and pose a public health risk, efforts have focused primarily on identifying and removing human sources (e.g. malfunctioning septic systems, faulty sewer lines) of fecal pollution.

Maine Healthy Beaches Program 2016 Annual Report To U.S. Epa, K. Kaczor, M. Sims

Maine Sea Grant Publications

Maine Healthy Beaches (MHB) is managed by the Maine Department of Environmental Protection (ME DEP) and coordinated by the University of Maine Cooperative Extension (UMaine Extension). In 2016, this team worked with 28 local management entities to conduct routine monitoring, assessment, and public notification of water quality conditions for 60 beach management areas spanning Kittery to Mount Desert Island. MHB staff continued to build local capacity for well-informed beach management and to address pollution issues when they arose during the beach season.

Summary Report Of Enhanced Monitoring And Pollution Source Tracking Efforts In Goosefare Brook, Maine, 2012-2016, M. Sims, K. Kaczor

Maine Sea Grant Publications

The Goosefare Brook (GFB) forms the border between the City of Saco to the south and Town of Old Orchard Beach (OOB) to the north. In response to concerns over water quality in the mouth and adjacent beach water, the Maine Healthy Beaches (MHB) program has supported multi-year enhanced monitoring and pollution source tracking efforts, held Stakeholder Workshops, and more to address impaired water quality throughout the watershed. Over the past five years, the MHB program has focused primarily on paired enterococci and optical brightener samples in OOB’s New Salt Rd. Tributary (NSRT). This work identified widespread bacterial contamination throughout …

From Bacteria To Fish: Ecological Consequences Of Seasonal Hypoxia In A Great Lakes Estuary, Anthony Weinke, Bopaiah Biddanda

Funded Articles

The occurrence of bottom-water hypoxia is increasing in bodies of water around the world. Hypoxia is of concern due to the way it negatively impacts lakes and estuaries at the whole ecosystem level. During 2015, we examined the influence of hypoxia on the Muskegon Lake ecosystem by collecting surface- and bottom-water nutrient samples, bacterial abundance counts, benthic fish community information, and performing profiles of chlorophyll and phycocyanin as proxies for phytoplankton and cyanobacterial growth, respectively. Several significant changes occurred in the bottom waters of the Muskegon Lake ecosystem as a result of hypoxia. Lake-wide concentrations of soluble reactive phosphorus (SRP) …

Microbial Extracellular Polymeric Substances (Epss) In Ocean Systems, Alan W. Decho, Tony Gutierrez

Faculty Publications

Microbial cells (i.e., bacteria, archaea, microeukaryotes) in oceans secrete a diverse array of large molecules, collectively called extracellular polymeric substances (EPSs) or simply exopolymers. These secretions facilitate attachment to surfaces that lead to the formation of structured ‘biofilm’ communities. In open-water environments, they also lead to formation of organic colloids, and larger aggregations of cells, called ‘marine snow.’ Secretion of EPS is now recognized as a fundamental microbial adaptation, occurring under many environmental conditions, and one that influences many ocean processes. This relatively recent realization has revolutionized our understanding of microbial impacts on ocean systems. EPS occur in a range …

Survey Of Microbial Urea Degrader Diversity In Two Freshwater Ecosystems: Lake Shenandoah And The Shenandoah River, Naomi E. Gilbert

Senior Honors Projects, 2010-2019

One of the primary drivers of cyanobacterial harmful algal blooms (cHABs) in freshwater systems is nutrient loading, particularly of nitrogen and phosphorus. There has been an increased focus on assessing the role of nitrogen (N) in freshwater lakes and rivers that suffer cHABs. Urea, a widely-used, N-rich fertilizer, is a source of interest due to its abundance in freshwater ecosystems, primarily caused by anthropogenic nutrient loading. While recent work has shown that cHAB population succession may favor the toxic cyanobacterium Microcystis in urea-rich waters, the diversity of the associated bacterial community capable of degrading urea has yet to be determined. …

The Effect Of Staphylococcus Aureus On Stiffness Of Cortical Bone, Ariel N. Kunde

Graduate Theses

Osteomyelitis, a term for bone infection, is a common cause of hospitalization in the United States. Infection leading to osteomyelitis is almost always a product of bacterial origin. Although polymicrobial presence is seen at infection sites of osteomyelitis, Staphylococcus aureus is most commonly isolated and found to be the cause of more than 95% of bone infection in adults. This organism is a common commensal of humans that is carried by an estimated 60% of the US population. S. aureus is transferred by infected asymptomatic individuals, and its ability to proliferate under a variety of environmental conditions contributes to the …

The Antimicrobial And Biofilm Disruption Activity Of Novel Amphiphiles, Elizabeth A. Rogers

Masters Theses, 2010-2019

Antibiotic resistant infections are responsible for approximately 23,000 deaths every year in the United States alone. The formation of bacterial biofilms makes resistant bacteria difficult to eliminate completely using chemical treatment. Therefore, novel antimicrobial compounds such as amphiphiles are essential to slow or stop the spread of resistant bacteria. Several novel series of amphiphiles were synthesized, and discrete aspects of their chemical structure were altered to investigate the relationship between structure and antibacterial activity. Minimum inhibitory concentration (MIC) assays were used to measure antibacterial activity against two Gram-negative and five Gram-positive bacteria, and the most effective compounds were tested for …

Maine Healthy Beaches Program Excerpts From Data Analysis, 2006-2015, K. Kaczor, M. Sims

Maine Sea Grant Publications

No abstract provided.

Preliminary Analyses Of The Diversity Of Soil Microbes On The Campus Of The University Of The Incarnate Word, Viridiana Wheeler

Theses & Dissertations

Soil samples were examined outside Bonilla Science Hall on the campus of the University of the Incarnate Word in San Antonio, Texas, at three time points between the calendar years 2016 and 2017. These time points correspond to Fall, Winter, and Spring. Samples were taken at two topsoil depths, 1 cm and 4 cm, to determine if there is a difference in bacterial load or distribution across the time frame examined.

Soil samples were diluted and plated on nutrient agar plates in order to identify unique colony morphologies. A total of 132 distinct morphological isolates were identified and sequenced. Of …

Environmental Factors, Not Plants, Contribute To Functional Diversity Of Soil Bacteria In The Dunes Of Lake Michigan., Andrea Stark Howes

Electronic Theses and Dissertations

Soil bacteria play important roles in nutrient cycling and other ecosystem functions, and many biotic and abiotic factors can influence bacterial functional diversity. The goal of this field study was to examine differences among bacterial communities in sand dunes of Lake Michigan. I used Biolog Ecoplates™ to compare bacteria functional diversity associated with four different plant species: the native dune-building grass Ammophila breviligulata, invasive species Leymus arenarius and Gypsophila paniculata, and native legume Lathyrus japonicus across 13 sites in Michigan, representing a gradient in abiotic factors such as precipitation and temperature. I found no differences in bacterial function associated with …

The Use Of Probiotics To Control The Microbial Load Present In Commercial Broiler Chicken Hatch Cabinets As An Alternative To Formaldehyde Fumigation, Lucas Elzie Graham

Graduate Theses and Dissertations

Formaldehyde has been used for decades as a disinfectant in the poultry hatchery. Hatch cabinets are treated with formaldehyde to control the microbial bloom that occurs inside of the hatch cabinet as the hatch progresses. Even with formaldehyde being a known human carcinogen and the detriment that it has on living creatures millions of chicks are exposed to formaldehyde in the hatch cabinet. In these experiments we tested a lyophilized probiotic spray inside of the hatch cabinets from day nineteen to day twenty one to control the microbial bloom that occurs. Hatch cabinet environments were sampled in six experiments. Media …

Enhancement Of Reactive Oxygen Species Production And Chlamydial Infection By The Mitochondrial Nod-Like Family Member Nlrx1, Ali A. Abdul-Sater, Najwene Saïd-Sadier, Verissa M. Lam, Bhavni Singh, Matthew A. Pettengill, Fraser Soares, Ivan Tattoli, Simone Lipinski, Stephen E. Girardin, Philip Rosenstiel, David M. Ojcius

David M. Ojcius

Chlamydia trachomatis infections cause severe and irreversible damage that can lead to infertility and blindness in both males and females. Following infection of epithelial cells, Chlamydia induces production of reactive oxygen species (ROS). Unconventionally, Chlamydiae use ROS to their advantage by activating caspase-1, which contributes to chlamydial growth. NLRX1, a member of the Nod-like receptor family that translocates to the mitochondria, can augment ROS production from the mitochondria following Shigella flexneri infections. However, in general, ROS can also be produced by membrane-bound NADPH oxidases. Given the importance of ROS-induced caspase-1 activation in growth of the chlamydial vacuole, we investigated the …

Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver

Chemistry Honors Papers

The carbon monoxide (CO) sensing heme protein, CooA, is a transcription factor which exists in several bacteria that utilize CO as an energy source. CooA positively regulates the expression of coo genes in the presence of CO such that the corresponding proteins may metabolize CO. The present studies have yielded the unexpected result that Fe(III) CooA binds DNA tightly at pH < 7, deviating from all previously reported work which indicate that CooA DNA binding is initiated only when the exogenous CO effector reacts with the Fe(II) CooA heme. This observation suggests that the disruption of one or more salt bridges upon effector binding may be a critical feature of the normal CooA activation mechanism. To test this possibility, several protein variants that eliminated a selected salt bridge for the CooA homolog from Rhodospirillum rubrum were prepared via site-directed mutagenesis. Samples of these variant proteins, which were overexpressed in Escherichia coli, were then characterized by spectroscopic methods and functional assays to investigate the impact these mutations had on CooA heme coordination …

Dual-Functional-Tag-Facilitated Protein Labeling And Immobilization, Xinyi Zhang, Wei Lu, Kevin Kwan, Dibakar Bhattacharyya, Yinan Wei

Chemistry Faculty Publications

An important strategy in the construction of biomimetic membranes and devices is to use natural proteins as the functional components for incorporation in a polymeric or nanocomposite matrix. Toward this goal, an important step is to immobilize proteins with high efficiency and precision without disrupting the protein function. Here, we developed a dual-functional tag containing histidine and the non-natural amino acid azidohomoalanine (AHA). AHA is metabolically incorporated into the protein, taking advantage of the Met-tRNA and Met-tRNA synthetase. Histidine in the tag can facilitate metal-affinity purification, whereas AHA can react with an alkyne-functionalized probe or surface via well-established click chemistry. …

Role Of The Interleukin-22 And Stat3 Signaling Pathway In Gut Barrier Maintenance Following Intoxication And Burn Injury, Adam M. Hammer

Dissertations

More than half of patients admitted to burn centers for treatment have measurable alcohol levels in their blood. Intoxication that precedes a traumatic burn injury leads to worsened patient outcomes, including higher rates of infection and sepsis. The intestines harbor the largest concentration of bacteria in the human host. Any disruption of the intestinal barrier as a result of intoxication and burn injury could contribute to infection and/or sepsis from gut-derived microbes. Previous work has demonstrated that the intestinal barrier becomes leaky, and that administration of interleukin-22 (IL-22) significantly reduces gut barrier leakiness following alcohol and burn injury. However, the …

Microbial Communities Associated With Stable Fly (Diptera: Muscidae) Larvae And Their Developmental Substrates, Erin Scully, Kristina Friesen, Brian Wienhold, Lisa M. Durso

Department of Entomology: Faculty Publications

Bacteria are essential for stable fly (Stomoxys calcitrans (L.)) larval survival and development, but little is known about the innate microbial communities of stable flies, and it is not known if their varied dietary substrates influence their gut microbial communities. This investigation utilized 454 sequencing of 16S and 18S amplicons to characterize and compare the bacterial and eukaryotic microbial communities in stable fly larvae and their developmental substrates. The microbial community of the third-instar stable fly larvae is unambiguously distinct from the microbial community of the supporting substrate, with bacterial communities from larvae reared on different substrates more similar …

Best Practices For Healthy Beaches And Watersheds In Maine: Potential Bioremediation Strategies For Improving Water Quality, Elyse Defranco

Maine Sea Grant Publications

Maine’s watersheds face many challenges from human inputs, with pollution threatening the health of our beaches, rivers, and aquaculture operations. Maine’s rural communities often lack the resources to update aging sewer infrastructure or to adequately maintain septic systems, and these sources of pollution impact watershed health. In addition to addressing sources of pollution, which can be difficult to ascertain and challenging to address when located, bioremediation practices have the potential to aid in clean-up efforts. New technological advances and research discoveries in creative forms of bioremediation are being developed and are producing promising case studies around the world. These new …

2016 Goosefare Brook Mst Summary And Next Steps, M. Sims, K. Kaczor

Maine Sea Grant Publications

No abstract provided.