Microbiology Commons^™

Proteômica Plasmática Quantitativa De Pacientes Sobreviventes E Não Sobreviventes De Covid-19 Internados No Hospital Revela Potenciais Biomarcadores Prognósticos E Alvos Terapêuticos, D C. Flora, A D. Valle, H Abs Pereira, T F. Garbieri, L. T. Grizzo, T J. Dionisio, A L. Leite, D Mc Rosa, C F. Santos, M Ar Buzalaf

Nebraska Center for Virology: Faculty Publications

O desenvolvimento de novas abordagens que permitam a avaliação precoce de quais casos de COVID-19 provavelmente se tornarão críticos e a descoberta de novos alvos terapêuticos são importantes. Neste estudo de coorte, foi avaliado o perfil proteômico e laboratorial do plasma de 163 pacientes internados no Hospital Estadual de Bauru (Bauru, SP, Brasil) entre 4 de maio e 4 de julho de 2020, que foram diagnosticados com COVID-19 por RT-PCR a partir de amostras de swab nasofaríngeo amostras. Amostras de plasma foram coletadas na admissão para análises laboratoriais de rotina e análise proteôomica quantitativa shotgun livre de marcadores. De acordo …

Genome Sequence Of Sn1, A Bacteriophage That Infects Sphaerotilus Natans And Pseudomonas Aeruginosa, K.M. Damitha Gunathilake, Denise M. Tremblay, Pier-Luc Plante, Ellen Jensen, Kenneth Nickerson, Sylvain Moineau

Kenneth Nickerson Papers

Phage SN1 infects Sphaerotilus natans and Pseudomonas aeruginosa strains. Its genome consists of 61,858 bp (64.3% GC) and 89 genes, including 32 with predicted functions. SN1 genome is very similar to Pseudomonas phage M6, which contains hypermodified thymidines. Genome analyses revealed similar base-modifying genes as those found in M6.

Phage SN1 was isolated in 1979 from activated sludge samples obtained from a wastewater treatment plant (Lincoln, Nebraska, USA) using S. natans ATCC 13338 as the host (1, 2). An early study showed that the siphophage SN1 has unusual bases in its genome as confirmed by cellulose thin-layer chromatography (1). Its …

Molecular Mechanisms Underlying Mucosal Attachment And Colonization By Clostridioides Difficile, Ben Sidner

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Clostridioides difficile is a Gram-positive, spore-forming, anaerobic bacterium which causes gastrointestinal disease and is a leading cause of nosocomial infections. Although infection typically occurs following antibiotic therapy, in recent years there has been an increase in infections which are not preceded by antibiotic use. Additionally, community-associated infections and rates of disease recurrence have increased. While it is understood that a healthy gastrointestinal microbiota provides protection against infection, the molecular mechanisms which underly C. difficile's ability to colonize and persist in the gut are mostly unknown. Building on work from others that suggests C. difficile associates with the outer mucus …

Methanogen Metabolic Flexibility, Sean R. Carr

School of Biological Sciences: Dissertations, Theses, and Student Research

Methanogens are obligately anaerobic archaea which produce methane as a byproduct of their respiration. They are found across a wide diversity of environments and play an important role in cycling carbon in anaerobic spaces and the removal of harmful fermentation byproducts which would otherwise inhibit other organisms. Methanogens subsist on low-energy substrates which requires them to utilize a highly efficient central metabolism which greatly favors respiratory byproducts over biomass. This metabolic strategy creates high substrate:product conversion ratios which is industrially relevant for the production of biomethane, but may also allow for the production of value-added commodities. Particularly of interest are …

Discovering Novel Polyextremotolerant Fungi And Determining Their Ecological Role Within The Biological Soil Crust Consortium, Erin C. Carr

School of Biological Sciences: Dissertations, Theses, and Student Research

The ecological niche of polyextremotolerant fungi within oligotrophic ecosystems such as biological soil crusts has not yet been determined. These fungi persist in locations where nutrients are depleted while simultaneously surrounded by autotrophic microbes such as algae and cyanobacteria. Yet it has not been shown that they are engaging in any exchange of nutrients the way lichens do. However, there is seemingly no other way for these fungi to obtain vital nutrients, such as carbon or nitrogen, other than from these microbes. Here we have isolated polyextremotolerant fungi from cold desert biological soil crusts which are a microbial biofilm that …

Evaluation Of Protective Efficacy Of Viral Vector Based Swine Influenza Vaccine And A Method For B Cell Culture For Monoclonal Antibody Generation, Sushmita Kumari

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

Influenza A virus of the swine (IAV-S) is an economically important swine pathogen that has the potential to spread to humans, thus posing an ongoing public health concern due to its zoonotic potential. Hemagglutinin (HA), the most abundant viral envelope protein, is known to be the key protective antigen. Anti-HA antibodies alone, have been shown to prevent IAV infection. In this study we evaluated the feasibility of a recombinant tri segmented Pichinde virus (PICV) as a viral vector to deliver IAV-S hemagglutinin antigen in pigs. Four groups of weaned pigs (T01-04) were immunized twice with PBS, rPICV-GFP as a vector …

Genomic Analysis Of Metabolic Differences Found In Clostridium Perfringens That Cause Necrotic Enteritis In Poultry, Connor M. Aylor

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

Clostridium perfringens is a common member of gut microbiota in healthy animals, but can also be an important pathogen in human and veterinary medicine. It produces several protein toxins that contribute to both histotoxic and enteric diseases in animals. Necrotic enteritis in poultry has been associated with the NetB toxin of C. perfringens; however, this toxin alone is insufficient to cause disease in infected chickens. While considerable research has focused on the presence of toxins and virulence factors, little has been done to assess the function of metabolic factors on the ability of the bacteria to cause disease. …

Tiny Earth, Tinier Microbes: An Experiential Learning Approach To Antibiotic Discovery, Emily Kassing

Honors Program: Senior Projects (Public)

Antimicrobial resistance is one of the greatest global health challenges of the 21^st century as antibiotic discovery has slowed even as scientific knowledge about AMR has progressed. At the same time, science education has turned to active learning approaches like CUREs, or course-based undergraduate research experiences, to achieve educational objectives while engaging students in real-life research. The Tiny Earth Project is a global research initiative that seeks to crowdsource antibiotic discovery by recruiting undergraduate students to screen soil samples for antibiotic producers. The goal of this study was to determine the viability of translating the Tiny Earth programming to …

Determining Pairwise Interactions To Predict Species Interactions In A Complex Community Of Gut Bacteria., Makenzie Maroney

Honors Program: Senior Projects (Public)

The human gastrointestinal (GI) tract houses a diverse and expansive microbial community known as the microbiota. The relationship between the host and the microbiota is considered to be mutualistic, as trillions of bacteria that reside in the hospitable GI tract can assist in essential host functions, including contributing to metabolism and immunity against disease. An important subpopulation of the GI microbiota is the mucin-associated biofilm that is comprised of a dense layer of bacteria that forms on the GI mucin layer. The mucin layer provides an alternative niche to the GI lumen; the glycans of the mucin and the subsequent …

The Quest To Identify A New Virus Disease Of Sunflower From Nebraska, Robert M. Harveson, Maher Al Rwahnih, California Department Of Food And Agriculture, Alex Karasev, Tom J. Gulya, Jeff Bradshaw

Panhandle Research and Extension Center

Between 2010 and 2018, sunflower plants exhibiting virus-like symptoms, including stunting, mottling, and chlorotic ringspots on leaves, were observed from commercial fields and research plots from four sites within three distinct counties of western Nebraska (Box Butte, Kimball, and Scotts Bluff). Near identical symptoms from field samples were reproduced on seedlings mechanically in the greenhouse on multiple occasions, confirming the presence of a sap-transmissible virus from each site. Symptomatic greenhouse-inoculated plants from the 2010 and 2011 Box Butte samples tested negative for sunflower mosaic virus (SuMV), sunflower chlorotic mottle virus (SuCMoV), and all potyviruses in general by ELISA and RT-PCR. …

Adenoviral-Vectored Centralized Consensus Hemagglutinin Vaccine Provides Broad Protection Against H2 Influenza A Virus, Erika M. Petro-Turnquist, Brianna L. Bullard, Matthew J. Pekarek, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

Several influenza pandemics have occurred in the past century, one of which emerged in 1957 from a zoonotic transmission of H2N2 from an avian reservoir into humans. This pandemic caused 2–4 million deaths and circulated until 1968. Since the disappearance of H2N2 from human populations, there has been waning immunity against H2, and this subtype is not currently incorporated into seasonal vaccines. However, H2 influenza remains a pandemic threat due to consistent circulation in avian reservoirs. Here, we describe a method of pandemic preparedness by creating an adenoviral-vectored centralized consensus vaccine design against human H2 influenza. We also assessed the …

The Application Of The Skin Virome For Human Identification, Ema H. Graham, Jennifer Clarke, Samodha Fernando, Joshua Herr, Michael Adamowicz

Nebraska Center for Virology: Faculty Publications

The use of skin virome offers a unique approach for human identification purposes in instances where a viable and statistically relevant human DNA profile is unavailable. The skin virome may act as an alternative DNA profile and/or an additional form of probative genetic material. To date, no study has attempted to investigate the human virome over a time series across various physical locations of the body to identify its diagnostic potential as a tool for human identification. For this study, we set out to evaluate the stability, diversity, and individualization of the human skin virome. An additional goal was to …

Expanding Mouse-Adapted Yamagata-Like Influenza B Viruses In Eggs Enhances In Vivo Lethality In Balb/C Mice, Matthew J. Pekarek, Erika M. Petro-Turnquist, Adam Rubrum, Richard J. Webby, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

Despite the yearly global impact of influenza B viruses (IBVs), limited host range has been a hurdle to developing a readily accessible small animal disease model for vaccine studies. Mouseadapting IBV can produce highly pathogenic viruses through serial lung passaging in mice. Previous studies have highlighted amino acid changes throughout the viral genome correlating with increased pathogenicity, but no consensus mutations have been determined. We aimed to show that growth system can play a role in mouse-adapted IBV lethality. Two Yamagata-lineage IBVs were serially passaged 10 times in mouse lungs before expansion in embryonated eggs or Madin–Darby canine kidney cells …

Genomic Analysis Of Acetoanaerobium Sp. Vlb-1, An Anaerobic Bacterium Isolated From Nebraska's Eastern Saline Wetlands, Claire Martin

Honors Program: Senior Projects (Public)

Through the analysis of genetic code, the genomic and physiological characteristics of an environmental anaerobic bacterial isolate, Acetoanaerobium sp. strain VLB-1, can be determined and significant pathways can be identified in its significance to the environment. This particular organism was isolated from the Eastern Saline Wetlands in Lincoln, NE. With this isolate, an investigation into elemental and amino acid cycling via the Stickland reaction and the Wood-Ljungdahl pathway was conducted to determine possible metabolic products. The Stickland reaction is a relatively newly discovered pathway, observed in the genus Clostridium. A. sticklandii is the main model for this method of …

Determinants Of Virus Variation, Evolution, And Host Adaptation, Katherine Latourrette, Hernan Garcia-Ruiz

Nebraska Center for Virology: Faculty Publications

Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral factors that contribute to virus evolution. To achieve or fine tune compatibility and successfully establish infection, viruses adapt to a particular host species or to a group of species. However, some viruses are better able to adapt to diverse hosts, vectors, and environments. Viruses generate genetic diversity through mutation, reassortment, and recombination. Plant viruses are exposed to …

Immunogenicity And Protective Efficacy Of A Recombinant Pichinde Viral-Vectored Vaccine Expressing Influenza Virus Hemagglutinin Antigen In Pigs, Sushmita Kumari, Jayeshbhai Chaudhari, Qinfeng Huang, Phillip Gauger, Marcelo Nunes De Almeida, Yuying Liang, Hinh Ly, Hiep Vu

Nebraska Center for Virology: Faculty Publications

Influenza A virus of swine (IAV-S) is an economically important swine pathogen. The IAV-S hemagglutinin (HA) surface protein is the main target for vaccine development. In this study, we evaluated the feasibility of using the recombinant tri-segmented Pichinde virus (rPICV) as a viral vector to deliver HA antigen to protect pigs against IAV-S challenge. Four groups of weaned pigs (T01–T04) were included in the study. T01 was injected with PBS to serve as a non-vaccinated control. T02 was inoculated with rPICV expressing green fluorescence protein (rPICV-GFP). T03 was vaccinated with rPICV expressing the HA antigen of the IAV-S H3N2 strain …

Farnesol Secretion As A Possible Driving Force For Maintaining Candida Albicans As A Diploid, Kenneth Nickerson, Cory Boone, Kory Parker

Kenneth Nickerson Papers

Candida albicans is a pathogenic dimorphic fungus which is invariably found as a diploid in patients. C. albicans secretes the sesquiterpene farnesol both as a quorum sensing molecule which blocks the yeast to hypha conversion and as a virulence factor for pathogenicity. 20-25 μM farnesol kills other competing yeasts and fungi, often by triggering apoptosis, and yet wild type diploid C. albicans tolerates 300-500 μM farnesol. The recent availability of 10 haploid strains of C. albicans (5 mating type aand 5 mating type α) allowed us to compare their production of and sensitivity to farnesol. On average, the heterozygous diploid …

Soil Microbial Community Dynamics In Response To Prescribed Extreme Fires Following Juniperus Virginiana Invasion In The Loess Canyons Of Nebraska, Julie A. Fowler

School of Natural Resources: Dissertations, Theses, and Student Research

In Nebraska and other regions of the Great Plains, the conifer Juniperus virginiana (eastern redcedar) is converting grasslands to dense woodlands. This is driven by the interacting drivers of fire suppression, altered grazing regimes, climate change and other anthropogenic factors, impacting the provisioning of ecosystem services. This vegetation state transition modifies water resource regulation and biogeochemical cycles leading to altered edaphic properties including soil microbial community composition. To restore these grasslands and control J. virginiana spread, prescribed extreme burns are implemented as a management tool through local prescribed burn associations. We hypothesized that the alternative state transition to dense J. …

Risk Based Simulations Of Sporeformers Population Throughout The Dairy Production And Processing Chain: Evaluating On-Farm Interventions In Nebraska Dairy Farms, Rhaisa A. Crespo Ramírez

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Sporeformer bacteria are ubiquitous in the farm environment. These bacteria produce enzymes that negatively affect the quality of dairy products representing a problem for the dairy industry. Two major issues associated with high levels of sporeformers in raw milk are shelf-life reduction of fluid milk and market limitations for milk powder. Specific attention has been given to the contamination of milk powders with sporeformers due to their ability to survive pasteurization and milk powder processing conditions. Hence, the control of sporeformers is crucial to benefit the whole dairy industry. Researchers have suggested that certain management practices could decrease sporeformers in …

Dietary Fiber Utilization In The Gut: The Role Of Human Gut Microbes In The Degradation And Consumption Of Xylose-Based Carbohydrates, Elizabeth Drey

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Xylans are a family of xylose-based polysaccharides naturally present in fruits, vegetables, and cereal grains. Resistant to digestion by host enzymes, xylans reach the large intestine intact, where they are utilized by members of the gut microbiome. They are initially hydrolyzed by primary degraders that utilize extracellular xylanases to cleave xylan into smaller oligomers. These xylooligosaccharides (XOS) can then either be further hydrolyzed by primary degraders or can cross-feed secondary consumers, including Bifidobacterium. While several Bifidobacterium species have metabolic systems for XOS, studies have shown these species grow poorly on longer XOS and xylan substrates. In this thesis, …

Host Cell Responses To Zika Virus Infection, Bikash Ranjan Sahoo

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

The re-emergence of Zika virus (ZIKV) in 2015 as a significant human pathogen causing neurological diseases in infants as well as adults is a serious global health concern. A clear understanding of the mechanisms involved in ZIKV replication in infected host cells as well as the host responses to virus infection are keys to the development of therapeutic strategies against ZIKV. Studies conducted in this dissertation demonstrate that ZIKV infection induces the activation of mTOR signaling cascade that promotes viral protein accumulation and infectious progeny production. While both mTORC1 and mTORC2 are essential for ZIKV replication, the observation that depletion …

Sterol Biosynthesis In Four Green Algae: A Bioinformatic Analysis Of The Ergosterol Versus Phytosterol Decision Point, Adam Voshall, Nakeirah T.M. Christie, Suzanne L. Rose, Maya Khasin, James L. Van Etten, Jennifer E. Markham, Wayne Riekhof, Kenneth Nickerson

Kenneth Nickerson Papers

Animals and fungi produce cholesterol and ergosterol, respectively, while plants produce the phytosterols stigmasterol, campesterol, and β-sitosterol in various combinations. The recent sequencing of many algal genomes allows the detailed reconstruction of the sterol metabolic pathways. Here, we characterized sterol synthesis in two sequenced Chlorella spp., the free-living C. sorokiniana, and symbiotic C. variabilis NC64A. Chlamydomonas reinhardtii was included as an internal control and Coccomyxa subellipsoidea as a plant-like outlier. We found that ergosterol was the major sterol produced by Chlorella spp. and C. reinhardtii, while C. subellipsoidea produced the three phytosterols found in plants. In silico analysis of the …

Novel Scalable And Simplified System To Generate Microglia-Containing Cerebral Organoids From Human Induced Pluripotent Stem Cells, Brittany Bodnar, Yongang Zhang, Jinbiao Liu, Yuan Lin, Peng Wang, Zhengyu Wei, Sami Saribas, Yuanjun Zhu, Fang Li, Xu Wang, Wenli Yang, Qingsheng Li, Wen-Zhe Ho, Wenhui Hu

Nebraska Center for Virology: Faculty Publications

Human cerebral organoid (CO) is a three-dimensional (3D) cell culture system that recapitulates the developing human brain. While CO has proved an invaluable tool for studying neurological disorders in a more clinically relevant matter, there have still been several shortcomings including CO variability and reproducibility as well as lack of or underrepresentation of certain cell types typically found in the brain. As the technology to generate COs has continued to improve, more efficient and streamlined protocols have addressed some of these issues. Here we present a novel scalable and simplified system to generate microglia-containing CO (MCO). We characterize the cell …

Development Of Vaccines And Antivirals Against Zika Virus, Aryamav Pattnaik

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

The re-emergence of Zika virus (ZIKV), an arbovirus, poses a major global human health concern because of its ability to cause congenital abnormalities and neurological diseases. While many candidate vaccines and antiviral drugs are in the developmental pipeline, none have been approved for use against ZIKV infection. This dissertation describes the characterization of one vaccine and two antiviral drug candidates against ZIKV infection. A bacterial ferritin-based nanoparticle vaccine, termed zDIII-F, is designed to display multiple copies of ZIKV E protein domain III on its surface. These stable nanoparticles are shown to induce robust antibody-mediated protection against lethal ZIKV infection in …

Protective Role Of Palmitoleate Against Zika Virus-Induced Apoptosis In Placental Trophoblasts, Philma Glora Muthuraj

College of Education and Human Sciences: Dissertations, Theses, and Student Research

Zika virus (ZIKV) infection in pregnant women causes congenital Zika syndrome which involves birth defects such as intrauterine growth restriction (IUGR), retinal defects and microcephaly in the fetus. ZIKV infection results in placental pathology which plays a crucial role in disease transmission from mother to fetus. Currently, there is no Food and Drug Administration (FDA) approved vaccine or therapeutic drug against ZIKV. In this thesis, we have elucidated the cell signaling pathways connected to ZIKV-induced apoptosis in trophoblasts and also the protective effect of palmitoleate against ZIKV-induced apoptosis. First, we demonstrated the molecular mechanism behind ZIKV-induced apoptosis using an in …

Genome Sequence Of A Virulent African Swine Fever Virus Isolated In 2020 From A Domestic Pig In Northern Vietnam, Quang Lam Truong, Thi Lan Nguyen, Thi Hoa Nguyen, Jishu Shi, Hiep Lai Xuan Vu, Thi Lan Huong Lai, Van Giap Nguyen

Nebraska Center for Virology: Faculty Publications

This study reports the genome sequence of an isolated African swine fever (ASF) virus (VNUA-ASFV-05L1/HaNam) obtained at the fourth passage on pulmonary alveolar macrophages. The virus was isolated during a typical acute ASF outbreak in pigs in a northern province of Vietnam in 2020.

Codon Bias Can Determine Sorting Of A Potassium Channel Protein, Anja J. Engel, Marina Kithil, Markus Langhans, Oliver Rauh, Matea Cartolano, James L. Van Etten, Anna Moroni, Gerhard Thiel

Nebraska Center for Virology: Faculty Publications

Due to the redundancy of the genetic code most amino acids are encoded by multiple synonymous codons. It has been proposed that a biased frequency of synonymous codons can affect the function of proteins by modulating distinct steps in transcription, translation and folding. Here, we use two similar prototype K⁺ channels as model systems to examine whether codon choice has an impact on protein sorting. By monitoring transient expression of GFP-tagged channels in mammalian cells, we find that one of the two channels is sorted in a codon and cell cycle-dependent manner either to mitochondria or the secretory pathway. …

Identification Of A Chlorovirus Pbcv-1 Protein Involved In Degrading The Host Cell Wall During Virus Infection, Irina V. Agarkova, Leslie C. Lane, David D. Dunigan, Cristian F. Quispe, Garry A. Duncan, Elad Milrot, Abraham Minsky, Ahmed Esmael, Jayadri S. Ghosh, James L. Van Etten

Nebraska Center for Virology: Faculty Publications

Chloroviruses are unusual among viruses infecting eukaryotic organisms in that they must, like bacteriophages, penetrate a rigid cell wall to initiate infection. Chlorovirus PBCV-1 infects its host, Chlorella variabilis NC64A by specifically binding to and degrading the cell wall of the host at the point of contact by a virus-packaged enzyme(s). However, PBCV-1 does not use any of the five previously characterized virus-encoded polysaccharide degrading enzymes to digest the Chlorella host cell wall during virus entry because none of the enzymes are packaged in the virion. A search for another PBCV-1-encoded and virion-associated protein identified protein A561L. The fourth domain …

Process Interventions For Improving The Microbiological Safety Of Low Moisture Food Ingredients, Tushar Verma

Department of Food Science and Technology: Dissertations, Theses, and Student Research

The recurrence of Salmonella in low moisture foods and the implementation of the FSMA rule requires a need to validate legacy and novel processing technologies. In this dissertation, a legacy thermal (extrusion), a novel thermal (radiofrequency (RF) heating), and a non-thermal (chlorine dioxide) technology, were evaluated as intervention technologies for Salmonella in low moisture foods. The twin-screw extruder was performed at different levels of screw speeds, temperatures, moisture contents, and fat contents to understand the impact of processing conditions on Salmonella inactivation in oat flour. At temperature >65°C, the Salmonella population was below the detection limit. At 55°C, Salmonella reduction …

Characterization Of Novel Chlorovirus Glycosyltransferases That Synthesize Atypical Glycans, Eric A. Noel

School of Biological Sciences: Dissertations, Theses, and Student Research

Giant dsDNA chloroviruses encode a diverse repertoire of glycosyltransferases (GTases) and methyltransferases (MTases) that biosynthesize unusual, methylated sugars independent of their host chlorella-like green algae prompting a reexamination of glycobiology systems. Unlike most other viruses, the prototype chlorovirus PBCV-1 encodes most, if not all, of the machinery required to glycosylate its major capsid protein (MCP). The structures of the four N-linked glycans do not resemble any other glycans in the three domains of life. Here, we investigated the potential involvement of chlorovirus- encoded putative GTases and MTases in glycosylation of the viral MCP. First, we aimed to generate site-directed …