Microbiology Commons^™

Local Corticotropin Releasing Hormone (Crh) Signals To Its Receptor Crhr1 During Postnatal Development Of The Mouse Olfactory Bulb, Isabella Garcia, Paramjit K Bhullar, Burak Tepe, Joshua Ortiz-Guzman, Longwen Huang, Alexander M Herman, Lesley Chaboub, Benjamin Deneen, Nicholas J Justice, Benjamin R Arenkiel

Faculty, Staff and Students Publications

Neuropeptides play important physiological functions during distinct behaviors such as arousal, learning, memory, and reproduction. However, the role of local, extrahypothalamic neuropeptide signaling in shaping synapse formation and neuronal plasticity in the brain is not well understood. Here, we characterize the spatiotemporal expression profile of the neuropeptide corticotropin-releasing hormone (CRH) and its receptor CRHR1 in the mouse OB throughout development. We found that CRH-expressing interneurons are present in the external plexiform layer, that its cognate receptor is expressed by granule cells, and show that both CRH and CRHR1 expression enriches in the postnatal period when olfaction becomes important towards olfactory-related …

Effect Of Two-Year Caloric Restriction On Bone Metabolism And Bone Mineral Density In Non-Obese Younger Adults: A Randomized Clinical Trial, Dt Villareal, L Fontana, Sk Das, Et Al.

Faculty, Staff and Students Publications

Although caloric restriction (CR) could delay biologic aging in humans, it is unclear if this would occur at the cost of significant bone loss. We evaluated the effect of prolonged CR on bone metabolism and bone mineral density (BMD) in healthy younger adults. Two-hundred eighteen non-obese (body mass index [BMI] 25.1?±?1.7?kg/m(2) ), younger (age 37.9?±?7.2 years) adults were randomly assigned to 25% CR (CR group, n?=?143) or ad libitum (AL group, n?=?75) for 2 years. Main outcomes were BMD and markers of bone turnover. Other outcomes included body composition, bone-active hormones, nutrient intake, and physical activity. Body weight (-7.5?±?0.4 versus …

Toxicity Of Engineered Nanomaterials To Plant Growth Promoting Rhizobacteria, Ricky W. Lewis

Theses and Dissertations--Plant and Soil Sciences

Engineered nanomaterials (ENMs) have become ubiquitous in consumer products and industrial applications, and consequently the environment. Much of the environmentally released ENMs are expected to enter terrestrial ecosystems via land application of nano-enriched biosolids to agricultural fields. Among the organisms most likely to encounter nano-enriched biosolids are the key soil bacteria known as plant growth promoting rhizobacteria (PGPR). I reviewed what is known concerning the toxicological effects of ENMs to PGPR and observed the need for high-throughput methods to evaluate lethal and sublethal toxic responses of aerobic microbes. I addressed this issue by developing high-throughput microplate assays which allowed me …

Tillage And Fertilization Influences On Autotrophic Nitrifiers In Agricultural Soil, Shuang Liu

Theses and Dissertations--Plant and Soil Sciences

Nitrification is a biological oxidation of NH₃ to NO₂^- and then to NO₃^-. Understanding how the nitrifier community responds to agricultural management is essential because the community composition is complex and functional distinction of subgroups occurs. Better managing nitrifiers could benefit the environment by increasing nitrogen (N) fertilizer use efficiency, decreasing NO₃^- leaching, and reducing NO and N₂O emissions. This study examined how long-term N fertilization and tillage influenced nitrifier density, ratios, nitrification rates, and the community structure of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and nitrite-oxidizing bacteria (NOB). The …

Studies On Regulation Of Pqq-Dependent Phosphate Solubilization Among Rhizosphere Dwelling Bacteria, Ran An

Theses and Dissertations--Plant and Soil Sciences

Plant growth promotion can be enhanced by soil- and rhizosphere-dwelling bacteria by a several different methods. One method is by promoting nutrient acquisition from soil. Phosphorus is an essential nutrient that plants obtain from soil, but in many cases it is immobilized in forms that are not available for plant uptake. Bacteria can solubilize insoluble soil phosphates by secreting gluconic acid. This chemical is produced from glucose by the activity of the bacterial enzyme glucose dehydrogenase, which requires a coenzyme called PQQ. In this dissertation, I studied the regulation of the glucose dehydrogenase enzyme and the PQQ coenzyme in the …

Diversity Of Free-Living Nitrogen Fixing Bacteria In The Badlands Of South Dakota, Bibha Dahal

Electronic Theses and Dissertations

Biological Nitrogen Fixation is carried out by a highly diverse group of members of the domains Bacteria and Archaea which express a nitrogenase enzyme complex and are termed diazotrophs. The best known diazotrophs form symbiotic associations with plants, but free-living nitrogen fixing bacteria also contribute a substantial amount of nitrogen to ecosystems, including arid lands. The aim of this study was to isolate free-living diazotrophs from the soil crusts of sod tables of South Dakota Badlands. Samples were obtained from sod tables and the surrounding base (matrix) in spring and fall of 2014. A culture dependent approach was used to …

The Search For Modifiers Of The Maze Gametophyte Factor Ga1-S And Quantitative Trait Polymorphisms Emerging From Doubled-Haploid Maize Lines, Vivek Shrestha

Electronic Theses and Dissertations

The project was designed to conduct two independent projects. The first project was to identify the genomic localization of the modifiers of the maize gametophyte factor (Ga1-s) and the second project was to establish and identify heritable polymorphic lines that have descended from a single doubled-haploid B73 plant. The objectives were (1) to search for modifier genes and loci on the maize chromosomes for the trait and determine genetic effects of them using QTL mapping; (2) to demonstrate the heritable polymorphism of the quantitative traits emerged from the descendants of a single doubled-haploid maize plant. Regarding the QTL …

Development And Characterization Of A Recombinant Orf Virus Vector Expressing The Spike Protein Of Porcine Epidemic Diarrhea Virus, Kyle Hain

Electronic Theses and Dissertations

Orf virus (ORFV), the type member of the genus Parapoxvirus of the family Poxviridae, causes orf or cutaneous pustular dermatitis in sheep and goats. ORFV is a ubiquitous virus capable of re-infecting its hosts multiple times over time. ORFV causes a non-systemic, self-limiting disease which is usually restricted to the skin surrounding the virus entry sites. ORFV has evolved several immunomodulatory proteins (IMPs) that evade and/or modulate host immune responses to infection and contribute to virus virulence and disease pathogenesis. Given biological properties and unique immunomodula tor y properties, ORFV has gained significant attention in recent years for its …

The Loss Of Methanol Utilization In Methylobacteria, Justin T. Skariah

Theses and Dissertations

Methylobacteria primary uses Cl substrates as a carbon and energy source. This experiment was performed to see if Methylobacteria would lose the ability to use Cl compound methanol after prolonged exposure to multi-carbon substrates. To determine this, the bacteria was grown on MR2A3 (multi-carbon substrates) and MOM (single-carbon substrates) for multiple generations and tested for loss of function on a series of generations. These tests include streaking plates of MOM and R2A with bacteria from MR2A3 then getting a bacterial colony count and also toothpick transfers of the colonies to verify findings. After 20 generations there were no significant decrease …

The Contribution Of Marine Aggregate-Associated Bacteria To The Accumulation Of Pathogenic Bacteria In Oysters: An Agent-Based Model, Andrew M. Kramer, J. Evan Ward, Fred C. Dobbs, Melissa L. Pierce

OES Faculty Publications

Bivalves process large volumes of water, leading to their accumulation of bacteria, including potential human pathogens (e.g., vibrios). These bacteria are captured at low efficiencies when freely suspended in the water column, but they also attach to marine aggregates, which are captured with near 100% efficiency. For this reason, and because they are often enriched with heterotrophic bacteria, marine aggregates have been hypothesized to function as important transporters of bacteria into bivalves. The relative contribution of aggregates and unattached bacteria to the accumulation of these cells, however, is unknown. We developed an agent-based model to simulate accumulation of vibrio-type bacteria …

Diversity Of The Beneficial Bacterium Oxalobacter Formigenes Isolated From The Human Gut, Karen Shaw

Masters Theses

Oxalobacter formigenes is an anaerobic, oxalate degrading organism that colonizes in the mammalian intestinal tract. Currently, O. formigenes is divided into two groups via PCR of the oxc gene. Pulsed field gel electrophoresis (PFGE) is a technique used to resolve large pieces of DNA. Typically, PFGE is used to identify differences between strains for pathogenic bacteria, but this study sought to use it to further understand the diversity of a probiotic organism. This study aimed to develop a methodology for utilizing PFGE to examine O. formigenes. The methodology involved lysing O. formigenes cells in plugs, first in proteinase K, …

Inhibition Of Bacterial Growth And Prevention Of Bacterial Adhesion With Localized Nitric Oxide Delivery, Julia Osborne

Dissertations, Master's Theses and Master's Reports

Bacterial infections continue to be a problem at the site of an indwelling medical device, and over the years, various bacterial strains have become more resistant to current antibiotic treatments. Bacterial infection at an indwelling medical device can be dangerous and affect the performance of the medical device which can ultimately lead to the failure of the device due to bacterial resistance to treatment.

Nitric Oxide (NO) has been shown to possess antibacterial properties to prevent and inhibit bacterial growth. NO releasing coatings on indwelling medical devices could provide a reduction in bacterial infections that occur at the device site …

Adenovirus Evasion Of Cell-Intrinsic Immunity, Andrew Michael Burrage

Dissertations

Virus cell entry represents one of the earliest opportunities for a host to respond to infection. Understanding the processes of pathogen detection and restriction employed by the host, as well as strategies utilized by the virus itself to evade such processes, is critical in developing therapeutics to counter pathogenesis. Adenovirus (Ad) infections are self-limiting in healthy populations, but can be devastating to individuals with compromised immune systems. Currently, no specific antiviral treatments exist to combat Ad infections in susceptible populations. However, because Ad infections are not severe in healthy individuals, employing replication-defective Ads as vaccine vectors is generally regarded as …

Draft Genome For A Urinary Isolate Of Lactobacillus Crispatus, Travis Kyle Price, Majed Shaheen, Laurynas Kalesinskas, Kema Malki, Evann Elizabeth Hilt, Catherine Putonti, Alan J. Wolfe

Bioinformatics Faculty Publications

While Lactobacillus crispatus contributes to the stability of normal vaginal microbiota, its role in urinary health remains unclear. As part of an on-going attempt to characterize the female urinary microbiota, we report the genome sequence of an L. crispatus strain isolated from a woman displaying no lower urinary tract symptoms.

Land-Use And Algal Species Influence Bacterial Community Composition And Activity In Streams, Miguel Rojas

Master's Theses

Microbial biofilms can be found on virtually all submerged surfaces in aquatic habitats, including rivers and streams. Biofilms are complex, taxonomically diverse communities of microorganisms (including algae and bacteria) that colonize solid surfaces and support a wide range of metabolic activities. Biofilms are critical components of river and stream ecosystems because they are key drivers of nutrient cycling processes (including nitrogen cycling) and because they serve as an important food source for higher trophic levels. Biofilms in urban streams are subject to a number of anthropogenic stressors, but research on the ecology of urban biofilms and their response to stressors …

Controlling Microbial Safety Challenges Of Meat Using High Voltage Atmospheric Cold Plasma, Lu Han, Dana Ziuzina, Caitlin Marie Heslin, Daniela Boehm, Apurva Patange, David Millan-Sango, Vasilis Valdramidis, Patrick J. Cullen, Paula Bourke

Articles

Atmospheric cold plasma (ACP) is a non-thermal technology, effective against a wide range of pathogenic microorganisms. Inactivation efficacy results from plasma generated reactive species. These may interact with any organic components in a test matrix including the target microorganism, thus food components may exert a protective effect against the antimicrobial mode of action. The effect of an in-package high voltage ACP process applied in conjunction with common meat processing MAP gas compositions as well as bacteria type and meat model media composition have been investigated to determine the applicability of this technology for decontamination of safety challenges associated with meat …

Atmospheric Cold Plasma Interactions With Modified Atmosphere Packaging Inducer Gases For Safe Food Preservation., Lu Han, Daniela Boehm, Vladimir Milosavljević, Ester Amias, Patrick J. Cullen, Paula Bourke

Articles

Diverse microbiological challenges and pervasive microbial resistance drive technological development in food processing, where increasing process complexity and consumer demand for less processed goods leads to strong demand for effective decontamination. Atmospheric cold plasma (ACP) has wide potential for decontamination application in the food sector. We investigated the effect of Modified Atmosphere Packaging (MAP) gas mixtures on reactive species generated, their efficacy and mechanism of inactivation against Escherichia coli, Listeria monocytogenes and Staphylococcus aureus. Oxygen levels in the applied working gas had positive interactive effects on ROS generation, in-package inactivation efficacy in conjunction with post-treatment storage time. …

Lactobacillus Crispatus Produces A Bacteridical Molecule That Kills Uropathogenic E. Coli, Katherine Diebel

Master's Theses

As many as 1 in 2 women will have at least one urinary tract infection (UTI) in their lifetime. UTIs can cause complications in pregnancy and decrease quality of life, and their treatment and prevention are expensive. Uropathogenic E. coli (UPEC) is the primary cause of UTI. The probiotic and bactericidal capacities of gut and vaginal Lactobacillus isolates have been studied, but the same attention has not been paid to urinary strains. These urinary isolates of L. crispatus appear to have a greater killing capacity against UPEC and this bactericidal activity does not depend on the cells themselves, consistent with …

Investigating The Regulatory Mechanisms By Which Arabinose And Sypa Control Biofilm Formation In Vibrio Fischeri, Sheila Paris

Master's Theses

Biofilms are surface-associated microbial communities surrounded by an extracellular matrix. Through biofilm formation, many pathogens and symbionts are able to colonize, survive, and persist in their host. A model system used to study biofilm formation is the symbiotic bacterium Vibrio fischeri, which colonizes its host, the squid Euprymna scolopes. Complex signaling between the squid and the bacteria is essential for the proper regulation of biofilm formation as well as for persistent colonization.

The signal(s) that promote host-relevant biofilm formation are as-yet unknown, but recently it was discovered that the sugar, L-arabinose, serves as a unique signal to promote biofilm formation …

Determination Of Cyclic-Di-Gmp- Controlled Gene Expression In A Pharmacologically Important Bacterium, Morgan A. Stark

Undergraduate Honors Thesis Projects

The second messenger molecule cyclic dimeric GMP (c-di-GMP) regulates a myriad of processes in gram-negative bacteria. However, less is known about the roles it plays in gram-positive bacteria. Differential gene expression in three strains of the gram-positive bacterium, Streptomyces coelicolor, is being studied using RNA sequencing and Real Time PCR to gain insight into c-di-GMP signaling. The rmdA rmdB (regulator of morphology and development) double mutant was compared to the wild type strain known as MT1110. The rmdA and rmdB genes are needed for the formation of aerial mycelium, an important step in the life cycle of Streptomyces coelicolor (Hull …

Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions, J. Harry Caufield

Theses and Dissertations

The emergence of genomics as a discrete field of biology has changed humanity’s understanding of our relationship with bacteria. Sequencing the genome of each newly-discovered bacterial species can reveal novel gene sequences, though the genome may contain genes coding for hundreds or thousands of proteins of unknown function (PUFs). In some cases, these coding sequences appear to be conserved across nearly all bacteria. Exploring the functional roles of these cases ideally requires an integrative, cross-species approach involving not only gene sequences but knowledge of interactions among their products. Protein interactions, studied at genome scale, extend genomics into the field of …

Response Of Soil Microbial Communities To Saltwater Intrusion In Tidal Freshwater Wetlands, Chansotheary Dang

Theses and Dissertations

Saltwater intrusion due to global change is expected to have a detrimental effect on the biogeochemistry of tidal freshwater wetlands. Of particular concern is that fact that salinization can alter the role of these ecosystems in the global carbon cycling by causing shifts in microbial metabolism that alter greenhouse gas emissions and increase carbon mineralization rates. However, our understanding of how wetland microbial community dynamics will respond to saltwater intrusion is limited. To address this knowledge gap and increase our understanding of how microbial communities in tidal freshwater wetlands change over time (1, 3, 12, and 49 weeks) under elevated …

Sulfate-Reducing Bacteria Community Analysis: Isco/Isb Coupled Remediation, Christopher K. Bartlett

Theses and Dissertations (Comprehensive)

Improved techniques for remediating groundwater systems are required for the more than 500,000 contaminated sites in North America. Many of these sites are the legacy of historical industrial operations, inappropriate disposal practices and accidental releases. The most widely observed contaminant at many of these sites is petroleum hydrocarbons (PHCs). Recently, remediation efforts that involve the sequential application of treatment technologies have gained widespread interest. One specific sequential technology application or treatment train employs the aggressive nature of a chemical oxidation followed by bioremediation for polishing. When persulfate is used as the chemical oxidant its natural degradation by-product is sulfate, an …

Central, Extraventricular And Atypical Neurocytomas: A Clinicopathologic Study Of 35 Cases From Pakistan Plus A Detailed Review Of The Published Literature, Zubair Ahmad, Nasir Ud Din, Aisha Memon, Mohammad Usman Tariq, Romana Idrees, Sheema Hasan

Department of Pathology and Laboratory Medicine

Background: Central neurocytomas are rare neuronal neoplasms with a favorable prognosis. They are typically located in the lateral ventricles of the brain and mostly histologically correspond to WHO grade II with a Mib 1 labelling index of 2 % and are designated as "atypical neurocytomas.AIM: The aim of our study was to describe the common as well as unusual morphologic features and the role of various immunohistochemical stains in the diagnosis of these rare tumors.MATERIALS AND Methods: We retrieved and reviewed 35 cases diagnosed between 2001 and 2015.Results: Sixty percent of patients were males, and the mean age was 26 …

Errors In Surgical Pathology Reports: A Study From A Major Center In Pakistan, Zubair Ahmad, Romana Idrees, Nasir Uddin, Arsalan Ahmed, Saira Fatima

Department of Pathology and Laboratory Medicine

Background:
Errors in surgical pathology diagnosis can have serious consequences for the patient. Since the final product of a surgical pathology lab is the report, errors can be picked by reviewing reports of cases.AIM: To determine the frequency and types of error in surgical pathology reports of cases signed out in 2014 in a laboratory in Karachi, Pakistan.
Material and Methods:
All surgical pathology reports in which changes were made in the original report after sign out and an amended report was issued were included. Errors included: (1) misinterpretations; (2) missing critical information; (3) erroneous critical information; (4) misidentification; and …

Flaviviruses As A Cause Of Undifferentiated Fever In Sindh Province, Pakistan: A Preliminary Report, Erum Khan, Joveria Q. Farooqi, Kelli L. Barr, Dhani Prakoso, Amna Nasir, Akbar Kanji, Sadia Shakoor, Faisal Riaz Malik, Rumina Hasan, John A. Lednicky

Department of Pathology and Laboratory Medicine

Arboviral diseases are expanding worldwide, yet global surveillance is often limited due to diplomatic and cultural barriers between nations. With human encroachment into new habitats, mosquito-borne viruses are also invading new areas. The actual prevalence of expanding arboviruses is unknown in Pakistan due to inappropriate diagnosis and poor testing for arboviral diseases. The primary objective of this study was to document evidence of flavivirus infections as the cause of undifferentiated fever in Pakistan. Through a cooperative effort between the USA and Pakistan, patient exposure to dengue virus (DENV), West Nile virus (WNV), and Japanese encephalitis virus (JEV) was examined in …

Sporadic Early Onset Colorectal Cancer In Pakistan: A Case- Control Analysis Of Microsatellite Instability, Sabeehuddin Siddique, Kanwal Tariq, Sobia Rafiq, Ahmed Raheem, Rashida Ahmed, Munira Shabbir-Moosajee, Kulsoom Ghias

Department of Pathology and Laboratory Medicine

Background: Early onset sporadic colorectal cancer (CRC) is a biologically and clinically distinct entity hypothesized to exhibit differences in histological features and microsatellite instability (MSI) as compared to typical onset CRC. This study compared the MSI status, mismatch repair enzyme deficiency and clinicopathological features of early onset (aged ≤45 years) with controls (>45 years).
Materials and Methods: A total of 30 cases and 30 controls were analyzed for MSI status using the Bethesda marker panel. Using antibodies against hMLH1, hMSH2 and hMSH6, mismatch repair protein expression was assessed by immunohistochemistry. Molecular characteristics were correlated with clinicopathological features.
Results: …

Arbuscular Mycorrhizal Fungi Of Northern White Cedar (Thuja Occidentalis L.): Habitat Effects On Fungal Communities And Inoculum Effects On Plant Growth On Acid Peat Soils, Guswarni Anwar

Dissertations, Master's Theses and Master's Reports

The relationship of arbuscular mycorrhizal (AM) fungi with northern white cedar (NWC) was examined from the perspective of both fundamental questions about habitat specificity in the root fungal community, as well as applied questions regarding AM fungal efficacy in NWC restoration in peat soils. I performed two experiments testing the effects of AM fungi on survival, growth, and nutrition of NWC seedlings; and one molecular study to determine the habitat effects on community composition of NWC root-associated fungi. First, a greenhouse AM inoculation experiment was conducted in factorial combination with fertilization and liming to examine conditional effectiveness of AM fungal …