Life Sciences Commons^™

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, …

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 …

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 …

Global Analysis Of High Cited Papers On “Impact Of Covid-19 On Mental Health” During 2020-21, Ghouse Modin Nabeesab Mamdapur Mr., Brij Mohan Gupta Dr., Sandeep Grover Dr.

Library Philosophy and Practice (e-journal)

A bibliometric analysis based on 160 highly cited papers extracted from the Scopus international database was carried out to provide insights into literature characteristics and publication performances of various participating actors on “Impact of COVID-19 on Mental Health”. Quantitative and qualitative Indicators were applied to measure the productivity and citation impact of most productive participating countries, organizations, authors, journals and significant keywords and to visualise and measure collaborative interaction among them using VOSviewer software. Results obtained from this study can provide valuable information for researchers and policy-makers to identify present and future hotspots in research on “Impact of COVID-19 on …

Mucormycosis (Black Fungus) Maiming Covid Patients: Scientometrics Analysis Through Prism Of Biblioshiny, Sivankalai S, K Sivasekaran

Library Philosophy and Practice (e-journal)

This study analyses the global level outlook of research publications on Mucormycosis output between the period of 1923 to 2021 (May) on different limitations including contribution of authors, communication channel, publications on Institutions, countries, Journals, cited articles and mode of languages. 4451 data was downloaded from core collection of Web of Science bibliographic database using the search term ‘Mucormycosis’ and limited the publications 1900 to 2021, first publication was started in 1923 onwards. 3798 institutions and 8562 different disciplines contributed and 2808 records are in Articles. 4451 records published by 17320 authors and 23552 collaborated authors, documents per author are …

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 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 …

Presence Of Antibody-Dependent Cellular Cytotoxicity (Adcc) Against Sars-Cov-2 In Covid-19 Plasma, For Yue Tso, Salum J. Lidenge, Lisa K. Poppe, Phoebe B. Pena, Sara R. Privatt, Sydney J. Bennett, John R. Ngowi, Julius Mwaiselage, Michael Belshan, Jacob A. Siedlik, Morgan A. Raine, Juan B. Ochoa, Julia Garcia-Diaz, Bobby Nossaman, Lyndsey Buckner, W Mark Roberts, Matthew J. Dean, Augusto C. Ochoa, John T. West, Charles Wood

Nebraska Center for Virology: Faculty Publications

Background Neutralizing-antibody (nAb) is the major focus of most ongoing COVID-19 vaccine trials. However, nAb response against SARS-CoV-2, when present, decays rapidly. Given the myriad roles of antibodies in immune responses, it is possible that antibodies could also mediate protection against SARS-CoV-2 via effector mechanisms such as antibody-dependent cellular cytotoxicity (ADCC), which we sought to explore here. Methods Plasma of 3 uninfected controls and 20 subjects exposed to, or recovering from, SARS CoV-2 infection were collected from U.S. and sub-Saharan Africa. Immunofluorescence assay was used to detect the presence of SARS-CoV-2 specific IgG antibodies in the plasma samples. SARS-CoV-2 specific …

Inhibition Of Zika Virus Replication By G-Quadruplex-Binding Ligands, Indian Institute Of Technology Indore, Aryamav Pattnaik, Bikash R. Sahoo, Uma Shankar, Asit K. Pattnaik, Amit Kumar, Debasis Nayak

Nebraska Center for Virology: Faculty Publications

Zika virus (ZIKV), a mosquito-transmitted Flavivirus, emerged in the last decade causing serious diseases and affecting human health globally. Currently, no licensed vaccines or antivirals are available to combat ZIKV, although several vaccine candidates are in the pipeline. In recent years, the presence of non-canonical G-quadruplex (GQ) secondary structures in viral genomes has ignited significant attention as potential targets for antiviral strategy. In this study, we identified several novel conserved potential GQ structures by analyzing published ZIKV genome sequences using an in-house algorithm. Biophysical and biochemical analysis of the RNA sequences containing these potential GQ sequences suggested the existence of …

Covid19 Disease Map, A Computational Knowledge Repository Of Virus–Host Interaction Mechanisms, Marek Ostaszewski, Tomáš Helikar, Bhanwar Lal Puniya, A Host Of Co-Authors, Covid-19 Disease Map Community

Department of Biochemistry: Faculty Publications

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, …

The 20th Anniversary Meeting Of The Rocky Mountain Virology Association, Joel Rovnak, Laura A. St Clair, Carley Mcalister, Chinemerem P. Ogbu, Jessica Smolenske, Randall J. Cohrs, Rushika Perera

Nebraska Center for Virology: Faculty Publications

Due to the COVID-19 pandemic and multiple devastating forest fires, the 2020 meeting of the Rocky Mountain Virology Association was held virtually. The three-day gathering featured talks describing recent advances in virology and prion research. The keynote presentation described the measles virus paradox of immune suppression and life-long immunity. Special invited speakers presented information concerning visualizing antiviral effector cell biology in mucosal tissues, uncovering the T-cell tropism of Epstein-Barr virus type 2, a history and current survey of coronavirus spike proteins, a summary of Zika virus vaccination and immunity, the innate immune response to flavivirus infections, a discussion concerning prion …

High Prevalence Of Pre-Existing Serological Cross-Reactivity Against Severe Acute Respiratory Syndrome Coronavirus-2 (Sars-Cov-2) In Sub-Saharan Africa, For Yue Tso, Salum J. Lidenge, Phoebe B. Peña, Ashley A. Clegg, John R. Ngowi, Julius Mwaiselage, Owen Ngalamika, Peter Julius, John T. West, Charles Wood

Nebraska Center for Virology: Faculty Publications

Objective: Significant morbidity and mortality have occurred in the USA, Europe, and Asia due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), whereas the numbers of infections and deaths in sub-Saharan Africa (SSA) have remained comparatively low. It has been hypothesized that exposure of the population in SSA to other coronaviruses prior to the COVID-19 pandemic resulted in some degree of cross-protection against SARS-CoV-2 infection and pathogenesis. We evaluated this hypothesis by comparing SARS-CoV-2 cross-reactive antibodies in pre-pandemic plasma samples collected from SSA and the USA.

Method: Pre-COVID-19 pandemic plasma samples from SSA and the USA were collected and tested by …

High Prevalence Of Pre-Existing Serological Cross-Reactivity Against Severe Acute Respiratory Syndrome Coronavirus-2 (Sars- Cov-2) In Sub-Saharan Africa, For Yue Tso, Salum Lidenge, Phoebe B. Peña, Ashley A. Clegg, John R. Ngowi, Julius Mwaiselage, Owen Ngalamika, Peter Julius, John T. West, Charles Wood

Nebraska Center for Virology: Faculty Publications

Objective: Significant morbidity and mortality have occurred in the USA, Europe, and Asia due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), whereas the numbers of infections and deaths in sub-Saharan Africa (SSA) have remained comparatively low. It has been hypothesized that exposure of the population in SSA to other coronaviruses prior to the COVID-19 pandemic resulted in some degree of cross-protection against SARS-CoV-2 infection and pathogenesis. We evaluated this hypothesis by comparing SARS-CoV-2 cross-reactive antibodies in pre-pandemic plasma samples collected from SSA and the USA.

Method: Pre-COVID-19 pandemic plasma samples from SSA and the USA were collected and tested by …

Strategies Targeting Hemagglutinin As A Universal Influenza Vaccine, Brianna L. Bullard, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

Influenza virus has significant viral diversity, both through antigenic drift and shift, which makes development of a vaccine challenging. Current influenza vaccines are updated yearly to in- clude strains predicted to circulate in the upcoming influenza season, however this can lead to a mismatch which reduces vaccine efficacy. Several strategies targeting the most abundant and im- munogenic surface protein of influenza, the hemagglutinin (HA) protein, have been explored. These strategies include stalk-directed, consensus-based, and computationally derived HA immunogens. In this review, we explore vaccine strategies which utilize novel antigen design of the HA protein to improve cross-reactive immunity for development …

Chlorovirus Pbcv-1 Multidomain Protein A111/114r Has Three Glycosyltransferase Functions Involved In The Synthesis Of Atypical N-Glycans, Eric Noel, Anna Notaro, Immacolata Speciale, Garry A. Duncan, Cristina De Castro, James L. Van Etten

Nebraska Center for Virology: Faculty Publications

The structures of the four N-linked glycans from the prototype chlorovirus PBCV-1 major capsid protein do not resemble any other glycans in the three domains of life. All known chloroviruses and antigenic variants (or mutants) share a unique conserved central glycan core consisting of five sugars, except for antigenic mutant virus P1L6, which has four of the five sugars. A combination of ge- netic and structural analyses indicates that the protein coded by PBCV-1 gene a111/114r, conserved in all chloroviruses, is a glycosyltransferase with three putative domains of approximately 300 amino acids each. Here, in addition to in silico sequence …

Zika Virus Infection Induces Endoplasmic Reticulum Stress And Apoptosis In Placental Trophoblasts, Philma Glora Muthuraj, Prakask K. Sahoo, Madison Kraus, Taylor Bruett, Arun S. Annamalai, Aryamav Pattnaik, Asit K. Pattnaik, Siddappa N. Byrareddy, Sathish Kumar Natarajan

Nebraska Center for Virology: Faculty Publications

Zika virus (ZIKV) infection to a pregnant woman can be vertically transmitted to the fetus via the placenta leading to Congenital Zika syndrome. This is characterized by microcephaly, retinal defects, and intrauterine growth retardation. ZIKV induces placental trophoblast apoptosis leading to severe abnormalities in the growth and development of the fetus. However, the molecular mechanism behind ZIKV-induced apoptosis in placental trophoblasts remains unclear. We hypothesize that ZIKV infection induces endoplasmic reticulum (ER) stress in the trophoblasts, and sustained ER stress results in apoptosis. HTR-8 (HTR-8/SVneo), a human normal immortalized trophoblast cell and human choriocarcinoma-derived cell lines (JEG-3 and JAR) were …