Microbiology Commons^™

Place Cells Dynamically Refine Grid Cell Activities To Reduce Error Accumulation During Path Integration In A Continuous Attractor Model, Jose A Fernandez-Leon, Ahmet Kerim Uysal, Daoyun Ji

Faculty, Staff and Students Publications

Navigation is one of the most fundamental skills of animals. During spatial navigation, grid cells in the medial entorhinal cortex process speed and direction of the animal to map the environment. Hippocampal place cells, in turn, encode place using sensory signals and reduce the accumulated error of grid cells for path integration. Although both cell types are part of the path integration system, the dynamic relationship between place and grid cells and the error reduction mechanism is yet to be understood. We implemented a realistic model of grid cells based on a continuous attractor model. The grid cell model was …

Next-Generation Sequencing Shows Increasing Temperatures Affect Stream Fungal Communities, Regan Hodgson

Electronic Theses and Dissertations

Under climate change predictions, surface air temperature is expected to continue to rise and will likely affect functioning of stream ecosystems and microbial communities. Aquatic hyphomycetes are key fungal decomposers of plant litter in headwater streams controlling carbon, energy, and nutrient flows to higher trophic levels. This project addressed the effects of temperature on stream fungal communities in two recently conducted experiments (microcosm and streamside channel studies) using Illumina sequencing. The objectives were to determine (1) if temperature affects community structure of stream fungi based on relative abundances of ITS2 rDNA sequences, (2) if the effects of temperature on aquatic …

Potential Use Of Pgpr Based Biofertilizer For Improving The Nutrient Availability In Soil And Agronomic Efficiency Of Upland Rice, Rahma Tia Harahap, Diyan Herdiyantoro, Mieke Rochimi Setiawati, Isna Niar Rahmatul Azizah, Tualar Simarmata

Jurnal Kultivasi

Present study aimed to perform literature review to investigate the current status and potential use of plant growth promoting rhizobacteria (PGPR) for enhancing the soil plant’s health, plant growth and productivity in sustainable ways. The Systematic Literature Review (SLR) methods was applied according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) on published scientific literature from 2012-2022. Results revealed that genus diversity of PGPR (Bacillus sp., Serratia sp., Streptomyces sp., Pseudomonas sp., and Burkholderia sp.) produce siderophore and phytohormones such as indole-3-acetic acid (IAA), gibberellin (GAs), auxin, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, organic acids, biocontrol agent that …

Predicting The Next Pandemic: Utilizing Wastewater-Based Epidemiology As A Novel Technique For Detecting Mpox Dna, Austin Tang, Michael Moshi, Hayley Baker, Ching-Lan Chang

Undergraduate Research Symposium Lightning Talks

Mpox cases are trending downward in Las Vegas, aligning with national trends. The study demonstrates that it is possible to extract mpox DNA directly from wastewater and quantify the genetic material using qPCR. This research indicates that WBE can be utilized to give a relative abundance of virual nucleic acids in wastewater, giving opportunities for early-warning systems and other public health interventions. Mpox remains a global threat to public health, continued surveillance of MPXV using wastewater is necessary to ensure that we can detect unusual spike in viral DNA level. Mpox detected in the wastewater samples will be sequences to …

Quantification Of Sars-Cov-2 Prevalence Using Wastewater Surveillance, Moonis Ghani, Hayley Baker, Nabih Ghani, Anthony Harrington, Ching-Lan Chang

Undergraduate Research Symposium Lightning Talks

SARS-CoV-2 RNA was successfully detected in the wastewater samples. PMMoV concentrations varied little, meaning it was a valid control. The diversity of SARS-CoV-2 concentrations indicated varying levels of infection within different parts of the community. PCR and WGS can help determine viral load and identify variants.

Evaluation Of Novel Litter Amendments For Use In The Commercial Broiler Industry, Jorge A. Urrutia

Theses and Dissertations

Poultry litter amendments (LA) are commonly used to maintain good litter quality; the most common ones; are acidifiers. However, concern over the lifespan of LA acidifiers (d) and corrosive nature revealed a need for alternative LA. Products of interest include biochar (BC), superabsorbent polymers (SAPs), and alum mud (AM). Experiment 1 was a screening study (n=17 treatments, no birds) conducted to determine the optimal application rate/method of BC, SAPs, and AM vs.commercial LA and a control. Most SAPs treatments measured metrics may be similar (i.e., bacteria, water activity) or better (pH) vs. commercial LA (PLT). High inclusions of novel LA …

Survival, Regrowth And Morphotype Formation Of Salmonella Strains After Exposure To High Or Low Concentrations Of First Generation Qac In Water, Grace Umutesi

Theses and Dissertations

This study determines the differences in survival of eight Salmonella strains concentration of BAC in water, followed by regrowth in high and low nutrition conditions containing sublethal concentration of BAC. Our results show strain difference in survival, persistence of Salmonella in BAC at different concentrations. All eight strains of Salmonella were non-recoverable when exposed to 40 to 48 µg/ml BAC for 1h in water. When exposed to 24 µg/ml of BAC for 1 h in water, S. Typhimurium ATCC 14028 and S. Heidelberg ATCC 8326 cells were non-detectable from the initial 7 log CFU/ml. S. Blockley 7175, S. Virchow 7207, …

Metagenomic Analysis Of Root-Associated Microbiome Of Healthy And Taproot Decline-Affected Soybeans And Identification Of Healthy Soybean Root Endophytes With Protective Activity Against The Causal Agent, Xylaria Necrophora, Uyen Wesser

Theses and Dissertations

Plant roots are associated with a diverse microbial community of bacteria and fungi. The root microbiome communities associate with the root surface or penetrate the superficial layers of root tissues. It is of high agronomic interest to characterize root microbiomes and identify microbes with beneficial effects on plant defense against pathogens. Soybean taproot decline (TRD) is an emerging soil-borne disease caused by a fungus classified as Xylaria necrophora, challenging to control and with devastating effects on yield. Our group has initiated a study of the soybean root microbiome with three primary experiments: (I) perform a comparative study of root …

Effects Of Microcystin-Lr On Channel Catfish (Ictalurus Punctatus) Susceptibility To Microbial Pathogens (Aeromonas Hydrophila And Edwardsiella Piscicida), Alison Marchant

Theses and Dissertations

Microcystin-LR is a hepatotoxin produced by cyanobacteria. Aeromonas hydrophila and Edwardsiella piscicida infections are leading causes of losses in market-sized channel catfish (Ictalurus punctatus). These older fish should have natural immunity in place and a predisposing factor is likely a prerequisite for these disease outbreaks. While microcystin-LR rarely causes mortality in warm-water aquaculture, we believe it may be a predisposing factor that leads to bacterial disease outbreaks during the summer months due to its ability to damage the liver. Our study investigated microcystin-LR’s effects on channel catfish susceptibility to these pathogens. We found that a sublethal dose of microcystin-LR induced …

Molecular And Phenotypic Characterization Of Escherichia Coli Isolated From Broiler Chicken Flocks In Mississippi, Priyanka Devkota

Theses and Dissertations

Avian pathogenic Escherichia coli (APEC) is the causative agent of colibacillosis. APEC causes significant economic losses to the poultry industry. In this study, 66 E. coli isolates were collected from broiler flocks across Mississippi and categorized as clinical and non-clinical isolates. Genotypic and phenotypic characterization of virulence factors and antimicrobial resistance profiles of these E. coli were examined. The data disclosed a higher prevalence of virulence genes in clinical isolates than in non-clinical isolates. High differences on the genotypic and phenotypic antimicrobial resistance among clinical and non-clinical isolates were observed. Whole genome sequences of avian E. coli elaborated a diverse …

The Expanding Marine Built Environment And Biofilm Formation Processes, Rachel Mugge

Dissertations

The marine built environment (i.e., places or things made or modified by humans) in the northern Gulf of Mexico is rapidly expanding and includes over 2,000 known historic shipwrecks, nearly 4,100 artificial reefs, and other built structures for natural resource extraction, marine aquaculture, renewable energy generation, munitions dumping areas, and commercial and recreational activities. While these structures have the potential to develop into artificial reefs, acting as biodiversity hotspots that provide food and shelter and facilitate organism transport, it is unclear how they affect biodiversity and ecosystem function in the marine environment. The success of artificial reefs to become ecosystems …

Genotype Classification Of Moraxella Bovis Using Maldi-Tof Ms Profiles, Hannah G. Olson, John Dustin Loy, Michael L. Clawson, Emily L. Wynn, Matthew M. Hille

Nebraska Center for Virology: Faculty Publications

Moraxella bovis (M. bovis) is regarded as a causative agent of infectious bovine keratoconjunctivitis (IBK), the most common ocular disease of cattle. Recently, whole genome sequencing identified the presence of two distinct genotypes within M. bovis that differ in chromosome content, potential virulence factors, as well as prophage and plasmid profiles. It is unclear if the genotypes equally associate with IBK or if one is more likely to be isolated from IBK lesions. We utilized 39 strains of M. bovis that had previously undergone whole genome sequencing and genotype classification to determine the utility of matrix-assisted laser desorption/ionization …

Application Of Organic Fertilizer And Phosphate Solubilizing Bacteria To Increase The Growth And Yield Of Potatoes In Andisol, Agustina Erlinda Marpaung, Bina Karo, Susilawati Barus, Rina Christina Hutabarat, Rasiska Tarigan

Jurnal Kultivasi

Andisol has low phosphate (P) nutrient content due to high P fixation by allophane minerals, which affects crop production. The application of organic fertilizers and phosphate solubilizing bacteria can increase the availability of P in the soil in order to increase the production of potato plants. This study aimed to evaluate the effect of different types of organic fertilizer and phosphate solubilizing bacteria (PSB) on potato production. The research was conducted from August to November 2020 in the installation of research and assessment of agricultural technology Berastagi, Karo Regency, with an altitude of ± 1,340 m above sea level and …

Guano Among Bat Species From Two Regions Shows Influence Of Geography And Diet On Bacterial Community, Rahma Ahmed, Thomas Mcelroy, Shannon Whitney, Lydia Moore

Symposium of Student Scholars

Studies of bat guano have shown that the diversity and structure of associated microbial communities can be related to factors such as host phylogeny, life history and reproductive stage, geography, and diet. Many insectivorous bat species in the southeastern U.S. have generalist diets that may shift seasonally to take advantage of abundant prey species or maximize caloric intake. Seasonal shifts in prey availability or consumption should be reflected in a guano microbiome change. We also expected to detect distinct guano microbiomes within species. Within species, distinct microbial communities related to geography, and finally life history and reproductive stage. We compared …

Alternative Precautionary Measures Yielding Lower C. Diff Infection Rates In Healthcare Facilities, Matthew Kramer

Symposium of Student Scholars

Background: An international healthcare concern is the persistent spread of Clostridium difficile, a Gram-positive spore forming bacterium that is responsible for the most common hospital-acquired infection, amongst patients.

Objective: A systematic review was performed to summarize evidence that the interventions utilized in healthcare facilities which indicate a patient’s precautionary status are insufficient, outdated, and commonly lead to infection in neighboring patient rooms. Databases such as PubMed, NCBI, Google Scholar, and APHA’s Medical Care were searched, covering the period from 2017-2022. Studies were included if their focus concentrated on C. diff and the precautionary measures taken by employees at healthcare …

Detecting Bacterial Species From Ancient Human Skeletal Samples, Ariel Owens, Daisy Mcgrath, Tsai-Tien Tseng

Symposium of Student Scholars

Diagnosis of tuberculosis (TB) via morphological analysis is difficult and often inconsistent. With next-generation sequencing (NGS), ancient host microbiomes can be subjected to metagenomic analyses for the detection of TB in silico. Suitable bioinformatic workflows are needed for reliable ancient DNA (aDNA) analysis of causative agents. This study aims to enhance available bioinformatic screening methods to create more suitable bioinformatic processes and generate insights in relation to TB.

This research utilizes publicly available NGS data accessed through the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). Initial quality control steps included adapter trimming with Trim …

Isolation And Characterization Of Chi-Like Salmonella Bacteriophages Infecting Two Salmonella Enterica Serovars, Typhimurium And Enteritidis, Addisu D. Teklemariam, Mona G. Alharbi, Rashad R. Al-Hindi, Ibrahim Alotibi, Abdullah A. Aljaddawi, Sheren A. Azhari, Ahmed Esmael

Nebraska Center for Virology: Faculty Publications

Salmonella enterica Serovar Typhimurium and Salmonella enterica Serovar Enteritidis are well-known pathogens that cause foodborne diseases in humans. The emergence of antibiotic-resistant Salmonella serovars has caused serious public health problems worldwide. In this study, two lysogenic phages, STP11 and SEP13, were isolated from a wastewater treatment plant in Jeddah, KSA. Transmission electron microscopic images revealed that both phages are new members of the genus “Chivirus” within the family Siphoviridae. Both STP11 and SEP13 had a lysis time of 90 min with burst sizes of 176 and 170 PFU/cell, respectively. The two phages were thermostable (0 ^◦C …

Activity Disruption Causes Degeneration Of Entorhinal Neurons In A Mouse Model Of Alzheimer’S Circuit Dysfunction, Rong Zhao, Stacy D Grunke, Caleb A Wood, Gabriella A Perez, Melissa Comstock, Ming-Hua Li, Anand K Singh, Kyung-Won Park, Joanna L Jankowsky

Faculty, Staff and Students Publications

Neurodegenerative diseases are characterized by selective vulnerability of distinct cell populations; however, the cause for this specificity remains elusive. Here, we show that entorhinal cortex layer 2 (EC2) neurons are unusually vulnerable to prolonged neuronal inactivity compared with neighboring regions of the temporal lobe, and that reelin + stellate cells connecting EC with the hippocampus are preferentially susceptible within the EC2 population. We demonstrate that neuronal death after silencing can be elicited through multiple independent means of activity inhibition, and that preventing synaptic release, either alone or in combination with electrical shunting, is sufficient to elicit silencing-induced degeneration. Finally, we …

The Future Of Microbiome Research, Anna Vietmeier

D.U.Quark

No abstract provided.

Assessing Selective Export Of Fluorescent Ssa4 Reporters, Caroline Firmin, Rebecca Adams

Science University Research Symposium (SURS)

The process of creating proteins from mRNA is necessary for cell viability. Importantly, the proteins that are generated are differentially regulated so that the cell makes specific proteins in response to its environment. For example, mRNA is selectively exported during stress conditions to allow response to this stress. During heat shock at 42°C, in which proteins are denatured, the gene SSA4 encodes a selectively transported protein chaperone that allows refolding of denatured proteins. This study sought to explore the mechanisms of this selective export. To do this, I analyzed the expression of a fluorescent reporter wherein GFP is expressed with …