Microbiology Commons^™

College Of Natural Sciences Newsletter, February 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 2

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3-4 Media Coverage of CNS
Page 5- 6 Local Boy Scouts Earn Their Chemistry Merit Badges
Page 7-8 Mount Vernon Teacher Wins 2022 South Dakota Outstanding Physical Science Teacher Award
Page 9 Middle Schoolers Visit SDSU
Page 10 Microbiology Club Tours POET
Page 11 53rd Geography Convention
Page 12 Open PRAIRIE Data

Conformational Flexibility And Local Frustration In The Functional States Of The Sars-Cov-2 Spike B.1.1.7 And B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism Of Functional Dynamics And Protein Stability, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Structural and functional studies of the SARS-CoV-2 spike proteins have recently determined distinct functional states of the B.1.1.7 and B.1.351 spike variants, providing a molecular framework for understanding the mechanisms that link the effect of mutations with the enhanced virus infectivity and transmissibility. A detailed dynamic and energetic analysis of these variants was undertaken in the present work to quantify the effects of different mutations on functional conformational changes and stability of the SARS-CoV-2 spike protein. We employed the efficient and accurate coarse-grained (CG) simulations of multiple functional states of the D614G mutant, B.1.1.7 and B.1.351 spike variants to characterize …

The Coxsackievirus And Adenovirus Receptor Has A Short Half-Life In Epithelial Cells, Poornima Kotha Lakshmi Narayan, James M. Readler, Mahmoud S. Alghamri, Trisha L. Brockman, Ray Yan, Priyanka Sharma, Vladislav Snitsarev, Katherine J.D.A Excoffon, Abimbola O. Kolawole

Department of Biology Faculty Scholarship and Creative Works

The coxsackievirus and adenovirus receptor (CAR) is an essential cellular protein that is involved in cell adhesion, cell signaling, and viral infection. The 8-exon encoded isoform (CAREx8) resides at the apical surface of polarized epithelia, where it is accessible as a receptor for adenovirus entering the airway lumen. Given its pivotal role in viral infection, it is a target for antiviral strategies. To understand the regulation of CAREx8 and determine the feasibility of receptor down regulation, the half-life of total and apical localized CAREx8 was determined and correlated with adenovirus transduction. Total and apical CAREx8 has a relatively short half-life …

An Exploratory Study On The Microbiome Of Northern And Southern Populations Of Ixodes Scapularis Ticks Predicts Changes And Unique Bacterial Interactions, Deepak Kumar, Latoyia P. Downs, Abdulsalam Adegoke, Erika Machtinger, Kelly Oggenfuss, Richard S. Ostfeld, Monica Embers, Shahid Karim

Faculty Publications

The black-legged tick (Ixodes scapularis) is the primary vector of Borrelia burgdorferi, the causative agent of Lyme disease in North America. However, the prevalence of Lyme borreliosis is clustered around the Northern States of the United States of America. This study utilized a metagenomic sequencing approach to compare the microbial communities residing within Ix. scapularis populations from northern and southern geographic locations in the USA. Using a SparCC network construction model, we performed potential interactions between members of the microbial communities from Borrelia burgdorferi–infected tissues of unfed and blood-fed ticks. A significant difference in bacterial composition …

Trait Energy And Fatigue May Be Connected To Gut Bacteria Among Young Physically Active Adults: An Exploratory Study, Ali Boolani, Karyn M. Gallivan, Kristin S. Ondrak, Courtney J. Christopher, Hector F. Castro, Shawn R. Campagna, Christopher M. Taylor, Meng Luo, Scot E. Dowd, Matthew Lee Smith, Lauri O. Byerley

School of Medicine Faculty Publications

Recent scientific evidence suggests that traits energy and fatigue are two unique unipolar moods with distinct mental and physical components. This exploratory study investigated the correlation between mental energy (ME), mental fatigue (MF), physical energy (PE), physical fatigue (PF), and the gut microbiome. The four moods were assessed by survey, and the gut microbiome and metabolome were determined from 16 S rRNA analysis and untargeted metabolomics analysis, respectively. Twenty subjects who were 31 ± 5 y, physically active, and not obese (26.4 ± 4.4 kg/m2) participated. Bacteroidetes (45%), the most prominent phyla, was only negatively correlated with PF. The second …

Characterizing The Amino Acid Activation Center Of The Naturally Editing-Deficient Aminoacyl-Trna Synthetase Phers In Mycoplasma Mobile, Nien-Ching Han, Arundhati Kavoor, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

To ensure correct amino acids are incorporated during protein synthesis, aminoacyl-tRNA synthetases (aaRSs) employ proofreading mechanisms collectively referred to as editing. Although editing is important for viability, editing-deficient aaRSs have been identified in host-dependent organisms. In Mycoplasma mobile, editing-deficient PheRS and LeuRS have been identified. We characterized the amino acid activation site of MmPheRS and identified a previously unknown hyperaccurate mutation, L287F. Additionally, we report that m-Tyr, an oxidation byproduct of Phe which is toxic to editing-deficient cells, is poorly discriminated by MmPheRS activation and is not subjected to editing. Furthermore, expressing MmPheRS and the hyperaccurate variants renders …

Heterologous Production Of Plant Secondary Metabolites Resveratrol And Caffeic Acid In E.Coli And Synechocystis Sp. Pcc 6803, Yong Xue

Theses and Dissertations

Caffeic acid and resveratrol are polyphenol compounds produced by plants as secondary metabolites to protect against biotic and abiotic stresses. In the last decades, numerous studies have demonstrated the beneficial effects of these compounds on human health as anticancer, antioxidant, anti-virus and anti-inflammatory agents. In plants, both caffeic acid and resveratrol are synthesized either from phenylalanine or tyrosine. Recently, heterologous production of phenylpropanoids using genetically engineered bacteria is gaining more and more attentions from industry because it can dramatically improve the yield with reduced costs. The major aim of the work is to explore the possibility of using Synechocystis or …

Distribution Of Serotypes And Antibiotic Resistance Of Invasive Pseudomonas Aeruginosa In A Multi-Country Collection, Shamima Nasrin, Nicolas Hegerle, Shaichi Sen, Joseph Nkeze, Sunil Sen, Jasnehta Permala-Booth, Myeongjin Choi, James Sinclair, Milagritos D. Tapia, Sadia Shakoor

Department of Pathology and Laboratory Medicine

Background: Pseudomonas aeruginosa is an opportunistic pathogen that causes a wide range of acute and chronic infections and is frequently associated with healthcare-associated infections. Because of its ability to rapidly acquire resistance to antibiotics, P. aeruginosa infections are difficult to treat. Alternative strategies, such as a vaccine, are needed to prevent infections. We collected a total of 413 P. aeruginosa isolates from the blood and cerebrospinal fluid of patients from 10 countries located on 4 continents during 2005-2017 and characterized these isolates to inform vaccine development efforts. We determined the diversity and distribution of O antigen and flagellin types and …

Thrombospondin-1 Expression And Modulation Of Wnt And Hippo Signaling Pathways During The Early Phase Of Trypanosoma Cruzi Infection Of Heart Endothelial Cells, Ashutosh Arun, Kayla J. Rayford, Ayorinde Cooley, Tanu Rana, Girish Rachakonda, Fernando Villalta, Siddharth Pratap, Maria F. Lima, Nader Sheibani, Pius N. Nde

Publications and Research

The protozoan parasite, Trypanosoma cruzi, causes severe morbidity and mortality in afflicted individuals. Approximately 30% of T. cruzi infected individuals present with cardiac pathology. The invasive forms of the parasite are carried in the vascular system to infect other cells of the body. During transportation, the molecular mechanisms by which the parasite signals and interact with host endothelial cells (EC) especially heart endothelium is currently unknown. The parasite increases host thrombospondin-1 (TSP1) expression and activates the Wnt/β-catenin and hippo signaling pathways during the early phase of infection. The links between TSP1 and activation of the signaling pathways and …

Clinical Performance Of The Xpert® Ct/Ng Test For Detection Of Chlamydia Trachomatis And Neisseria Gonorrhoeae: A Multicenter Evaluation In Chinese Urban Hospitals, Fred C. Tenover, Yan Han, Mei-Qin Shi, Qing-Ping Jiang, Wen-Jing Le, Xiao-Lin Qin, Han-Zhen Xiong, He-Ping Zheng, Yi-Wei Tang, Yue-Ping Yin

Biology Faculty Publications

Background: We aimed to evaluate the clinical performance of the GeneXpert® (Xpert) CT/NG assay for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) using urine and cervical swabs collected from patients in China.

Methods: This study was conducted from September 2016 to September 2018 in three Chinese urban hospitals. The results from the Xpert CT/NG test were compared to those from the Roche cobas® 4800 CT/NG test. Discordant results were confirmed by DNA sequence analysis.

Results: In this study, 619 first void urine (FVU) specimens and 1,042 cervical swab specimens were included in the final dataset. There were …

Design Of A Synthetic Temperature-Activated Epigenetic Biocontainment System, Owen Rivers Page

Theses and Dissertations

The need for an internal control to govern engineered strain survival is becoming apparent when considering the biosafety and ethics within biotechnological research. Using understudied regulatory elements known as RNA thermometers (RNATs) that can modulate protein translation based on temperature changes and a Type II restriction modification system, we posit the creation of a synthetic temperature-activated epigenetic biocontainment system, termed the ‘sentinel switch’. We have mined a wide variety of bacteria from Yersinia pestis to Synechocystis sp. looking for novel RNATs. A complementary synthetic biology approach based on library generation and screening of chimeric RNATs (ChRNATs) was also conducted. RNATs …

Phage Hunters: The Discovery Of Two Novel Bacteriophages That Infect Gordonia Rubripertincta, Sarah Ballarin, Neel Balusa, Melissa Bell, Samia Caballero, Joshua Chan, Maria Farez, Ashley J. Guillen-Tapia, Nashrah Pierre-Louis, Victoria Polishuk, Bhavya Soni, Julie Torruellas Garcia, Katie E. Crump

Sea-Phages

Antibiotic resistance is a global healthcare concern because it poses a threat to effectively treating bacterial infections and the need for alternative therapeutics are urgently required. Phage therapy, which uses viruses to treat bacterial infections, is a promising alternative to conventional antibiotics. Phages have also been widely used in the food industry to prevent microbial growth on certain foods and are currently being explored as a method for bioremediation of oil spills and wastewater treatment. Although phages are ubiquitous in nature, many have yet to be discovered. Through the SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) program …

The Use Of Probiotic Applications In Early Life Stages To Mitigate Batrachochytrium Dendrobatidis Infections In Rana Luteiventris (Columbia Spotted Frogs), Autumn N. Holley

2022 Symposium

Chytridiomycosis, an amphibian skin disease caused by a chytrid fungal pathogen, Batrachochytrium dendrobatidis (Bd), has been linked to global amphibian declines. Some amphibian populations are resistant to severe infection due to symbiotic antifungal skin bacteria, but attempts to develop probiotics from these bacteria have been inconsistently successful because bacteria fail to persist on the skin. Studies have largely been conducted on adult and juvenile amphibians, despite amphibians having fewer known mechanisms for microbiome regulation prior to metamorphosis. We hypothesize that probiotics will persist longer and thus be more effective against pathogen infection if they are applied at an early life …

Interrelationships Of Systemic Changes In Hepatic Encephalopathy, Els Reuvekamp

Biology and Microbiology Graduate Students Plan B Research Projects

Hepatic encephalopathy is a temporary decline in mental function that is often associated with liver disease and/or portal-systemic disease. Hepatic encephalopathy (HE) symptoms can range from minor cognitive declines to coma and are known to result from excess ammonia accumulations in the blood stream subsequent to liver failure. While HE is known to result from hepatobiliary disorder, many of the physiological process underlying its development and progression remain to be elucidated. Recent studies have identified neurological, metabolic, and microbiome changes implicated in the disease state of HE. In this review, the roles of traditional pharmaceutical interventions and newly developing understandings …

Non-Invasive Biomarkers For The Diagnosis Of Endometriosis And Polycystic Ovary Syndrome, Chandana Kamaraj

Biology and Microbiology Graduate Students Plan B Research Projects

Benign gynecological disorders can affect a high percentage of women of reproductive age, ages 15-44 years. These conditions can affect the lifestyle of the individual and can be associated with infertility. The gold standard to identify and diagnose endometriosis requires invasive surgical procedures, while the Rotterdam Criteria is used to identify and diagnose polycystic ovary syndrome. The purpose of this paper is to discuss, describe, and characterize potential non-invasive biomarkers that are present in various pathological stages of both endometriosis and polycystic ovary syndrome. These biomarkers include CA125, Serum galectin-9, hsa-miRNA-154-5p, miRNA-93, miRNA-320 and ET-1, miRNA-222, miRNA-146a, and miR-30c used …

The Isolation And Characterization Of Bacteriophage Hasitha, Gillian Brown

Mahurin Honors College Capstone Experience/Thesis Projects

Microbacteriophage Hasitha is a virus that infects Microbacterium foliorum, a bacterium associated with grasses that was first discovered in Germany. Hasitha was isolated from an enriched compost sample and is of particular interest due to its unusual growth pattern. Most bacteriophages require actively growing host cells to produce new phage progeny. However, Hasitha can infect and kill stationary (non-replicating) bacterial cells. We discovered this unusual characteristic through a fortuitous observation of infected lawns that were allowed to incubate in the lab workspace for approximately one month. During this time, a noticeable “halo” grew around the initial site of infection …

Decolorization Of Synthetic Textile Dyes By Fungal Endophytes Isolated From The Leaves Of Philippine Mangrove (Avicennia Marina), Steve P. Obanan, Resureccion B. Sadaba, Pamela Alva-Gatchalian, Annabelle V. Cadiz, Evelyn M. Basilio, Dennis B. Bela-Ong

Biology Faculty Publications

Textile dyes in wastewater can be harmful pollutants when released into the environment without treatment. Biodegradation of textile dye effluents by different microbes, including fungi, has become popular as an alternative to physicochemical methods. The mangrove Avicennia marina is known to harbor endophytic fungi which have the potential to carry out dye degradation. Therefore, this study assessed the ability to decolorize synthetic dyes of endophytic fungi isolated from the leaves of A. marina. Of the nine fungal endophytes, Aspergillus niger, Syncephalastrum racemosum and Penicillium citrinum exhibited the highest mycelial growths in solid media, while all endophytes adsorbed Congo red. Through …

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. …

Clostridioides Difficile Motility In Defined Culture Media And Its Response To Nutrients, Mary Ishak

Honors Undergraduate Theses

In recent years, Clostridiodes difficile has caused a sharp increase in hospital-acquired infections. Patients on multiple courses of antibiotics experience a general clearing of normal gut microbiota, leading to dysbiosis and an opportunity for C. difficile to colonize the colon. Understanding which nutrients produce optimal respiratory metabolism in C. difficile will help to determine the reasoning behind whether the microbe invests its energy into various cellular processes, such as motility. Different C. difficile strains were first cultured in BHIS broth (brain-heart infusion, supplemented) and CDMM broth (C. difficile minimal media) before being used to inoculate soft agar wells. The …

Novel Microbe-Resistant Clay Dressing For Healing Burn Wounds, Kasey L. Rigby

Honors Undergraduate Theses

Every year, about 550,000 patients receive medical attention for minor and major burns in the United States.¹ In 2020, it was estimated that 11 million people worldwide suffered from burn injuries, with 150,000 of those burns being fatal.² Burns are among the most painful and debilitating recalcitrant wounds that can often turn terminal when infection occurs. The different grades for burns that we aim to treat are first, second, and third degrees.² Each burn type is susceptible to secondary infection that can be life threatening, and as a result, are extensively treated with antimicrobial agents.2 At present, …