Microbiology Commons^™

A Mathematical Analysis Of An In-Vivo Ebola Virus Transmission Dynamics Model, Seleman Ismail, Adeline Peter Mtunya

Tanzania Journal of Science

Ebola virus (EBOV) infection is a hemorrhagic and hazardous disease, which is among the most shocking threats to human health causing a large number of deaths. Currently, there are no approved curative therapies for the disease. In this study, a mathematical model for in-vivo Ebola virus transmission dynamics was analyzed. The analysis of the model mainly focused on the sensitivity of basic reproductive number,  pertaining to the model parameters. Particularly, the sensitivity indices of all parameters of  were computed by using the forward normalized sensitivity index method. The results showed that a slight change in the infection rate immensely influences …

Factors Affecting The Epizootics Of Entomopathogenic Fungi-A Review, Mirza Abdul Qayyum, Huda Bilal, Unsar Naeem Ullah:, Habib Ali, Hasnain Raza, Muhammad Wajid

Journal of Bioresource Management

Entomopathogenic fungi (EPF) specifically infect and kill insects can serve as a potential biological control agent. Several biotic and abiotic factors affect their occurrence, persistence, and epizootics caused by them. In biotic factors, fungi characters (host range, latency, spore density and dispersal, mainly host-pathogen compatibility), insect host factors (behavioral, morphological, and physiological), plant-mediated effects (plant architecture, surface chemistry, and leaf topology) are included supports or causes the barrier to mycobiopesticide. Abiotic factors which affect the EPF field persistence are mainly environmental (temperature, sunlight, humidity, rainfall) physical and chemical soil properties (soil texture, pH, E.c, moisture, C/N content, and organic matter) …

Plastic Biodegradation Through Insects And Their Symbionts Microbes: A Review, Huda Bilal, Hasnain Raza, Haseena Bibi, Tehmina Bibi

Journal of Bioresource Management

Plastic waste has recently been identified as one of the most serious environmental issues, affecting all life forms, natural habitats, and the economy, and is one of the most serious global environmental problems, second only to climate change. Seeking alternative environmentally sustainable options, such as biodegradation instead of conventional disposal, is critical in the face of this challenge. However, there is currently a lack of information about the mechanisms and efficacy of plastic biodegradation. From this perspective, this study aims to illustrate the negative environmental impacts of the plastic waste. It also addresses the role of insects and gut microbiota …

A Nosy Neighbor: Purification And Functional Characterization Of Lpg2149, Ashley M. Holahan

The Journal of Purdue Undergraduate Research

Ubiquitination is a process that marks proteins for various cell-signaling pathways, namely protein degradation and other processes. Th ese pathways are essential in a wide array of cellular processes, including defense mechanisms against invading pathogens. Th e ubiquitination process is universally found in all eukaryotic organisms, including plants and animals, and thus plays a vital role in cellular homeostasis. Recently, more discoveries have been made on prokaryotic effector proteins that hijack the ubiquitination system even when they do not possess a ubiquitin system of their own. MavC, also known as lpg2147 (Gan, Nakayasu, Hollenbeck, & Luo, 2019; Puvar et al., …

Immunometabolic Dysregulation At The Intersection Of Obesity And Covid-19, Collins N. Khwatenge, Marquette Pate, Laura C. Miller, Yongming Sang

Agricultural and Environmental Sciences Faculty Research

Obesity prevails worldwide to an increasing effect. For example, up to 42% of American adults are considered obese. Obese individuals are prone to a variety of complications of metabolic disorders including diabetes mellitus, hypertension, cardiovascular disease, and chronic kidney disease. Recent meta-analyses of clinical studies in patient cohorts in the ongoing coronavirus-disease 2019 (COVID-19) pandemic indicate that the presence of obesity and relevant disorders is linked to a more severe prognosis of COVID-19. Given the significance of obesity in COVID-19 progression, we provide a review of host metabolic and immune responses in the immunometabolic dysregulation exaggerated by obesity and the …

Role Of Gut Microbiome In Covid-19: An Insight Into Pathogenesis And Therapeutic Potential, Ikram Hussain, Gabriel Liu Yuan Cher, Muhammad Abbas Abid, Muhammad Bilal Abid

Department of Pathology and Laboratory Medicine

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulted in an unprecedented global crisis. Although primarily a respiratory illness, dysregulated immune responses may lead to multi-organ dysfunction. Prior data showed that the resident microbial communities of gastrointestinal and respiratory tracts act as modulators of local and systemic inflammatory activity (the gut-lung axis). Evolving evidence now signals an alteration in the gut microbiome, brought upon either by cytokines from the infected respiratory tract or from direct infection of the gut, or both. Dysbiosis leads to a "leaky gut". The intestinal permeability then allows access to …

Biophysical Evaluation Of Rhesus Macaque Fc Gamma Receptors Reveals Similar Igg Fc Glycoform Preferences To Human Receptors, Andrew R. Crowley, Nana Yaw Osei-Owusu, Gillian Dekkers, Wenda Gao, Manfred Wuhrer, Diogo M. Magnani, Keith A. Reimann, Seth H. Pincus, Gestur Vidarsson, Margaret E. Ackerman

School of Medicine Faculty Publications

Rhesus macaques are a common non-human primate model used in the evaluation of human monoclonal antibodies, molecules whose effector functions depend on a conserved N-linked glycan in the Fc region. This carbohydrate is a target of glycoengineering efforts aimed at altering antibody effector function by modulating the affinity of Fcγ receptors. For example, a reduction in the overall core fucose content is one such strategy that can increase antibody-mediated cellular cytotoxicity by increasing Fc-FcγRIIIa affinity. While the position of the Fc glycan is conserved in macaques, differences in the frequency of glycoforms and the use of an alternate monosaccharide in …

Single-Cell Rna Sequencing Deconvolutes The In Vivo Heterogeneity Of Human Bone Marrow-Derived Mesenchymal Stem Cells, Zun Wang, Xiaohua Li, Junxiao Yang, Yun Gong, Huixi Zhang, Xiang Qiu, Ying Liu, Cui Zhou, Yu Chen, Jonathan Greenbaum, Liang Cheng, Yihe Hu, Jie Xie, Xucheng Yang, Yusheng Li, Martin R. Schiller

Life Sciences Faculty Research

Bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stromal cells that have a critical role in the maintenance of skeletal tissues such as bone, cartilage, and the fat in bone marrow. In addition to providing microenvironmental support for hematopoietic processes, BM-MSCs can differentiate into various mesodermal lineages including osteoblast/osteocyte, chondrocyte, and adipocyte that are crucial for bone metabolism. While BM-MSCs have high cell-to-cell heterogeneity in gene expression, the cell subtypes that contribute to this heterogeneity in vivo in humans have not been characterized. To investigate the transcriptional diversity of BM-MSCs, we applied single-cell RNA sequencing (scRNA-seq) on freshly isolated CD271+ …

A Bioinformatic And Biochemical Analysis Of Cruciviruses, George William Kasun

Dissertations and Theses

Cruciviruses are novel ssDNA viruses discovered through metagenomics and direct environmental DNA amplification and cloning. The genomes of cruciviruses suggest that gene transfer between RNA and DNA viruses occurred due to the presence of putative protein-encoding genes that are homologous to both ssRNA and ssDNA viruses. In order to gain a better understanding of this group of viruses both bioinformatic analyses and in vitro biochemical experiments were employed. The results of the bioinformatic analyses show that cruciviruses are a highly diverse group of ssDNA viruses. Their placement within established ssDNA phylogenies is difficult due to heterogeneity in their putative replication-associated …

College Of Natural Sciences Newsletter, October 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 10

Page 1 Dean's Message
Page 2 Awards and Recognition; Introducing Natural Sciences Student Ambassadors
Page 3 Media Coverage of CNS
Page 4 Spooky Science Outreach
Page 5 The BIG Event Outreach
Page 6 Geography Club Road Trip
Page 7 Aamlid Family Anatomy Lab
Page 8 Hobo Day Recap
Page 10 Open PRAIRIE Data; Grants Awarded in CNS

A Conserved Structural Role For The Walker-A Lysine In P-Loop Containing Kinases, Fatlum Hajredini, Ranajeet Ghose

Publications and Research

Bacterial tyrosine kinases (BY-kinases) and shikimate kinases (SKs) comprise two structurally divergent P-loop containing enzyme families that share similar catalytic site geometries, most notably with respect to their Walker-A, Walker-B, and DxD motifs. We had previously demonstrated that in BY-kinases, a specific interaction between the Walker-A and Walker-B motifs, driven by the conserved “catalytic” lysine housed on the former, leads to a conformation that is unable to efficiently coordinate Mg²⁺•ATP and is therefore incapable of chemistry. Here, using enhanced sampling molecular dynamics simulations, we demonstrate that structurally similar interactions between the Walker-A and Walker-B motifs, also mediated by …

A Small Rna Is Functional In Escherichia Fergusonii Despite Containing A Large Insertion., Austin P. Wright, H. Auguste Dutcher, Brianna Butler, Timothy J. Nice, Rahul Raghavan

Biology Faculty Publications and Presentations

Bacterial small RNAs (sRNAs) are important regulators of gene expression; however, the impact of natural mutations on sRNA functions has not been studied extensively. Here we show that the sRNA MgrR contains a unique 53 bp insertion in Escherichia fergusonii, a close relative of Escherichia coli and Salmonella enterica. The insertion is a repetitive extragenic palindromic (REP) sequence that could block transcription, but full-length MgrR is produced in E. fergusonii, showing that the insertion has not affected sRNA production. Additionally, despite containing the large insertion, the sRNA appears to be functional because deletion of mgrR made E. fergusonii …

Neuron-Specific Mitochondrial Oxidative Stress Results In Epilepsy, Glucose Dysregulation And A Striking Astrocyte Response, Ruth E Fulton, Jennifer N Pearson-Smith, Christopher Q Huynh, Timothy Fabisiak, Li-Ping Liang, Stefanos Aivazidis, Brigit A High, Georgia Buscaglia, Timothy Corrigan, Robert Valdez, Takahiko Shimizu, Manisha N Patel

Faculty, Staff and Students Publications

Mitochondrial superoxide (O2.−) production is implicated in aging, neurodegenerative disease, and most recently epilepsy. Yet the specific contribution of neuronal O2.− to these phenomena is unclear. Here, we selectively deleted superoxide dismutase-2 (SOD2) in neuronal basic helix-loop-helix transcription factor (NEX)-expressing cells restricting deletion to a subset of excitatory principle neurons primarily in the forebrain (cortex and hippocampus). This resulted in nSOD2 KO mice that lived into adulthood (2-3 months) with epilepsy, selective loss of neurons, metabolic rewiring and a marked mitohormetic gene response. Surprisingly, expression of an astrocytic gene, glial fibrillary acidic protein (GFAP) was significantly increased relative …

Human Genital Antibody-Mediated Inhibition Of Chlamydia Trachomatis Infection And Evidence For Ompa Genotype-Specific Neutralization, Caleb M. Ardizzone, Hannah L. Albritton, Rebecca A. Lillis, Caitlyn E.L. Bagnetto, Li Shen, Lisa A. Cavacini, Pamela A. Kozlowski, Alison J. Quayle

School of Graduate Studies Faculty Publications

The endocervix, the primary site of Chlamydia trachomatis (Ct) infection in women, has a unique repertoire of locally synthesized IgG and secretory IgA (SIgA) with contributions from serum IgG. Here, we assessed the ability of genital and serum-derived IgG and IgA from women with a recent positive Ct test to neutralize Ct elementary bodies (EBs) and inhibit inclusion formation in vitro in human endocervical epithelial cells. We also determined if neutralization was influenced by the major outer membrane protein (MOMP) of the infecting strain, as indicated by ompA gene sequencing and genotyping. At equivalent low concentrations of Ct EB (D/UW-3/Cx …

Using Molecular Diagnostics To Develop Therapeutic Strategies For Carbapenem-Resistant Gram-Negative Infections, Fred C. Tenover

Biology Faculty Publications

Infections caused by multidrug-resistant Gram-negative organisms have become a global threat. Such infections can be very difficult to treat, especially when they are caused by carbapenemase-producing organisms (CPO). Since infections caused by CPO tend to have worse outcomes than non-CPO infections, it is important to identify the type of carbapenemase present in the isolate or at least the Ambler Class (i.e., A, B, or D), to optimize therapy. Many of the newer beta-lactam/beta-lactamase inhibitor combinations are not active against organisms carrying Class B metallo-enzymes, so differentiating organisms with Class A or D carbapenemases from those with Class B enzymes rapidly …

Oxidation Alters The Architecture Of The Phenylalanyl-Trna Synthetase Editing Domain To Confer Hyperaccuracy, Pooja Srinivas, Rebecca E. Steiner, Ian J. Pavelich, Ricardo Guerrera-Ferreira, Puneet Juneja, Michael Ibba, Christine M. Dunham

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNA^Phe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNA^Phe, despite these oxidized residues not …

Reactive Chlorine Species Reversibly Inhibit Dnab Protein Splicing In Mycobacteria, Christopher Lennon Dr, Daniel Wahl, J. R. Goetz, Joel Weinberger Ii

Faculty & Staff Research and Creative Activity

Intervening proteins, or inteins, are mobile genetic elements that are translated within host polypeptides and removed at the protein level by splicing. In protein splicing, a self-mediated reaction removes the intein, leaving a peptide bond in place. While protein splicing can proceed in the absence of external cofactors, several examples of conditional protein splicing (CPS) have emerged. In CPS, the rate and accuracy of splicing are highly dependent on environmental conditions. Because the activity of the intein-containing host protein is compromised prior to splicing and inteins are highly abundant in the microbial world, CPS represents an emerging form of posttranslational …

Novel Pilot Development Of A Closed-Loop Sustainable System Between Biogas Renewable Energy, Distilling, And Aquaculture By Vermiculture Of Stillage Wastes, Samuel C. Kessler

The Cardinal Edge

This study provides a mixed-methods approach in analyzing a potential closed-loop system between renewable biogas production from anaerobic digestion, vermiculture production, aquaculture production, and organic wastes with a particular focus on stillage wastes. Such system may hold significant promise for significantly reducing organic carbon and methane emissions from its components, and should be assessed for such. The 2021 IPCC report essentially identified methane reduction as the single fastest way to slow global warming (IPCC, 2021), making the study and implementation of methane-reducing systems and supportive policy for them critical. Knowledge gaps to implementing this system were qualitatively identified as disconnect …

The Sterilization Of Escherichia Coli With Black Diamond-Coated Silicon, Sarah M. Cawthon, Jesse L. Rozsa, Mark P. Running

The Cardinal Edge

In order to combat increasing levels of antimicrobial resistance, new antimicrobials are needed to successfully kill microbes. Silicon coated in black diamond is a material that is hypothesized to have antimicrobial properties. To test this hypothesis, Escherichia coli cells were placed on different black diamond-coated silicon surfaces and allowed to rest on each surface for 15 minutes, 30 minutes, and 1 hour. Cells were collected, and growth was assessed by counting colonies on plates or spectrophotometry growth curves. The results of this study indicated that the experimental samples have some antimicrobial or growth inhibition properties, but they may not be …

Phenotypic/Genotypic Profile Of Oxa-10-Like-Harboring, Carbapenem-Resistant Pseudomonas Aeruginosa: Using Validated Pharmacokinetic/Pharmacodynamic In Vivo Models To Further Evaluate Enzyme Functionality And Clinical Implications, Fred C. Tenover, Christian M. Gill, Adrian Brink, Chun Yat Chu, Jennifer Coetzee, George Dimopoulos, Clinton Moodley, Christoffel Johannes Opperman, Spyros Pournaras, Isabella A. Tickler, Hafsah Deepa Tootla, Sophia Vourli, David P. Nicolau

Biology Faculty Publications

In vitro MICs and in vivo pharmacodynamics of ceftazidime and cefepime human-simulated regimens (HSR) against modified carbapenem inactivation method (mCIM)-positive Pseudomonas aeruginosa isolates harboring different OXA-10-like subtypes were described. The murine thigh model assessed ceftazidime (2 g every 8 h [q8h] HSR) and cefepime (2 g and 1 g q8h HSR). Phenotypes were similar despite possessing OXA-10-like subtypes with differing spectra. Ceftazidime produced ≥1-log10 killing in all isolates. Cefepime activity was dose dependent and MIC driven. This approach may be useful in assessing the implications of β-lactamase variants.