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Articles 1 - 18 of 18
Full-Text Articles in Viruses
Delivering Crispr To The Hiv-1 Reservoirs, Theodore Gurrola, Samuel Effah, Ilker Sariyer, Will Dampier, Michael Nonnemacher, Brian Wigdahl
Delivering Crispr To The Hiv-1 Reservoirs, Theodore Gurrola, Samuel Effah, Ilker Sariyer, Will Dampier, Michael Nonnemacher, Brian Wigdahl
Kimmel Cancer Center Faculty Papers
Human immunodeficiency virus type 1 (HIV-1) infection is well known as one of the most complex and difficult viral infections to cure. The difficulty in developing curative strategies arises in large part from the development of latent viral reservoirs (LVRs) within anatomical and cellular compartments of a host. The clustered regularly interspaced short palindromic repeats/ CRISPR-associated protein 9 (CRISPR/Cas9) system shows remarkable potential for the inactivation and/or elimination of integrated proviral DNA within host cells, however, delivery of the CRISPR/Cas9 system to infected cells is still a challenge. In this review, the main factors impacting delivery, the challenges for delivery …
The Sars-Cov-2 Differential Genomic Adaptation In Response To Varying Uvindex Reveals Potential Genomic Resources For Better Covid-19 Diagnosis And Prevention, Naveed Iqbal, Muhammad Rafiq, Masooma Ali, Sanaullah Tareen, Maqsood Ahmad, Faheem Nawaz, Sumair Khan, Rida Riaz, Ting Yang, Ambrin Fatima
The Sars-Cov-2 Differential Genomic Adaptation In Response To Varying Uvindex Reveals Potential Genomic Resources For Better Covid-19 Diagnosis And Prevention, Naveed Iqbal, Muhammad Rafiq, Masooma Ali, Sanaullah Tareen, Maqsood Ahmad, Faheem Nawaz, Sumair Khan, Rida Riaz, Ting Yang, Ambrin Fatima
Department of Biological & Biomedical Sciences
Coronavirus disease 2019 (COVID-19) has been a pandemic disease reported in almost every country and causes life-threatening, severe respiratory symptoms. Recent studies showed that various environmental selection pressures challenge the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infectivity and, in response, the virus engenders new mutations, leading to the emergence of more virulent strains of WHO concern. Advance prediction of the forthcoming virulent SARS-CoV-2 strains in response to the principal environmental selection pressures like temperature and solar UV radiation is indispensable to overcome COVID-19. To discover the UV-solar radiation-driven genomic adaption of SARS-CoV-2, a curated dataset of 2,500 full-grade genomes from …
Microplastics In Freshly Fallen Snow: How May It Adversely Impact Human Health And Exacerbate The Covid-19 Crisis?, Ayesha Liaquat, Aleena Kashif, Sushma Rathi, Alishba Raza
Microplastics In Freshly Fallen Snow: How May It Adversely Impact Human Health And Exacerbate The Covid-19 Crisis?, Ayesha Liaquat, Aleena Kashif, Sushma Rathi, Alishba Raza
Medical College Documents
No abstract provided.
Resolving The Repression Pathway Of Virulence Gene Hila In Salmonella, Alexandra King, Lon Chubiz Phd, Brenda Pratte, Lauren Daugherty
Resolving The Repression Pathway Of Virulence Gene Hila In Salmonella, Alexandra King, Lon Chubiz Phd, Brenda Pratte, Lauren Daugherty
Undergraduate Research Symposium
Salmonella is a relatively abundant, virulent species of bacteria that is most known for spreading gastrointestinal diseases through food. These illnesses result in approximately 1.35 million infections, including over 25,000 hospitalizations each year, in the U.S. alone (CDC.gov). As antibiotic resistance becomes an increasingly urgent public health problem, the importance of developing alternative treatment methods is only becoming more crucial. One of the genes responsible for this virulence is known as hilA. HilA is the main transcriptional regulator of Salmonella Pathogenicity Island-1 gene (UniProt). SPI-1 plays an important role in the invasion of Salmonella into epithelial cells. The proteins encoded …
The Temperature-Dependent Conformational Ensemble Of Sars-Cov-2 Main Protease (Mpro), Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean Mcsweeney, Daniel A. Keedy
The Temperature-Dependent Conformational Ensemble Of Sars-Cov-2 Main Protease (Mpro), Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean Mcsweeney, Daniel A. Keedy
Publications and Research
The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or Mpro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of Mpro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded Mpro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for Mpro, including …
Editorial: Pathogens, Pathobionts, And Autoimmunity, Linda A. Spatz, Gregg J. Silverman, Judith A. James
Editorial: Pathogens, Pathobionts, And Autoimmunity, Linda A. Spatz, Gregg J. Silverman, Judith A. James
Publications and Research
No abstract provided.
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
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, …
On The Inadequacy Of Species Distribution Models For Modelling The Spread Of Sars-Cov-2: Response To Araújo And Naimi, Joseph D. Chipperfield, Blas M. Benito, Robert B. O'Hara, Richard J. Telford, Colin J. Carlson
On The Inadequacy Of Species Distribution Models For Modelling The Spread Of Sars-Cov-2: Response To Araújo And Naimi, Joseph D. Chipperfield, Blas M. Benito, Robert B. O'Hara, Richard J. Telford, Colin J. Carlson
Public Health Resources
The ongoing pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing significant damage to public health and economic livelihoods, and is putting significant strains on healthcare services globally. This unfolding emergency has prompted the preparation and dissemination of the article “Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate” by Araújo and Naimi (2020). The authors present the results of an ensemble forecast made from a suite of species distribution models (SDMs), where they attempt to predict the suitability of the climate for the spread of SARS-CoV-2 over the coming months. They argue that climate is …
Ictv Virus Taxonomy Profile: Hypoviridae, Nobuhiro Suzuki, Said A. Ghabrial, Kook-Hyung Kim, Michael Pearson, Shin-Yi L. Marzano, Hajime Yaegashi, Jiatao Xie, Lihua Guo, Hideki Kondo, Igor Koloniuk, Bradley I. Hillman, Ictv Report Consortium
Ictv Virus Taxonomy Profile: Hypoviridae, Nobuhiro Suzuki, Said A. Ghabrial, Kook-Hyung Kim, Michael Pearson, Shin-Yi L. Marzano, Hajime Yaegashi, Jiatao Xie, Lihua Guo, Hideki Kondo, Igor Koloniuk, Bradley I. Hillman, Ictv Report Consortium
Plant Pathology Faculty Publications
The Hypoviridae, comprising one genus, Hypovirus, is a family of capsidless viruses with positive-sense, ssRNA genomes of 9.1–12.7 kb that possess either a single large ORF or two ORFs. The ORFs appear to be translated from genomic RNA by non-canonical mechanisms, i.e. internal ribosome entry site-mediated and stop/restart translation. Hypoviruses have been detected in ascomycetous or basidiomycetous filamentous fungi, and are considered to be replicated in host Golgi-derived, lipid vesicles that contain their dsRNA as a replicative form. Some hypoviruses induce hypovirulence to host fungi, while others do not. This is a summary of the current ICTV report …
Transmembrane Domains Of Highly Pathogenic Viral Fusion Proteins Exhibit Trimeric Association In Vitro, Stacy R. Webb, Stacy E. Smith, Michael G. Fried, Rebecca Ellis Dutch
Transmembrane Domains Of Highly Pathogenic Viral Fusion Proteins Exhibit Trimeric Association In Vitro, Stacy R. Webb, Stacy E. Smith, Michael G. Fried, Rebecca Ellis Dutch
Molecular and Cellular Biochemistry Faculty Publications
Enveloped viruses require viral fusion proteins to promote fusion of the viral envelope with a target cell membrane. To drive fusion, these proteins undergo large conformational changes that must occur at the right place and at the right time. Understanding the elements which control the stability of the prefusion state and the initiation of conformational changes is key to understanding the function of these important proteins. The construction of mutations in the fusion protein transmembrane domains (TMDs) or the replacement of these domains with lipid anchors has implicated the TMD in the fusion process. However, the structural and molecular details …
Ictv Virus Taxonomy Profile: Partitiviridae, Eeva J. Vainio, Sotaro Chiba, Said A. Ghabrial, Edgar Maiss, Marilyn Roossinck, Sead Sabanadzovic, Nobuhiro Suzuki, Jiatao Xie, Max Nibert, Ictv Report Consortium
Ictv Virus Taxonomy Profile: Partitiviridae, Eeva J. Vainio, Sotaro Chiba, Said A. Ghabrial, Edgar Maiss, Marilyn Roossinck, Sead Sabanadzovic, Nobuhiro Suzuki, Jiatao Xie, Max Nibert, Ictv Report Consortium
Plant Pathology Faculty Publications
The Partitiviridae is a family of small, isometric, non-enveloped viruses with bisegmented double-stranded (ds) RNA genomes of 3–4.8 kbp. The two genome segments are individually encapsidated. The family has five genera, with characteristic hosts for members of each genus: either plants or fungi for genera Alphapartitivirus and Betapartitivirus, fungi for genus Gammapartitivirus, plants for genus Deltapartitivirus and protozoa for genus Cryspovirus. Partitiviruses are transmitted intracellularly via seeds (plants), oocysts (protozoa) or hyphal anastomosis, cell division and sporogenesis (fungi); there are no known natural vectors. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) …
Ictv Virus Taxonomy Profile: Chrysoviridae, Said A. Ghabrial, José R. Castón, Robert H. A. Coutts, Bradley I. Hillman, Daohong Jiang, Dae-Hyun Kim, Hiromitsu Moriyama, Ictv Report Consortium
Ictv Virus Taxonomy Profile: Chrysoviridae, Said A. Ghabrial, José R. Castón, Robert H. A. Coutts, Bradley I. Hillman, Daohong Jiang, Dae-Hyun Kim, Hiromitsu Moriyama, Ictv Report Consortium
Plant Pathology Faculty Publications
The Chrysoviridae is a family of small, isometric, non-enveloped viruses (40 nm in diameter) with segmented dsRNA genomes (typically four segments). The genome segments are individually encapsidated and together comprise 11.5–12.8 kbp. The single genus Chrysovirus includes nine species. Chrysoviruses lack an extracellular phase to their life cycle; they are transmitted via intracellular routes within an individual during hyphal growth, in asexual or sexual spores, or between individuals via hyphal anastomosis. There are no known natural vectors for chrysoviruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Chrysoviridae, which …
Virus-Mediated Suppression Of Host Non-Self Recognition Facilitates Horizontal Transmission Of Heterologous Viruses, Songsong Wu, Jiasen Cheng, Yanping Fu, Tao Chen, Daohong Jiang, Said A. Ghabrial, Jiatao Xie
Virus-Mediated Suppression Of Host Non-Self Recognition Facilitates Horizontal Transmission Of Heterologous Viruses, Songsong Wu, Jiasen Cheng, Yanping Fu, Tao Chen, Daohong Jiang, Said A. Ghabrial, Jiatao Xie
Plant Pathology Faculty Publications
Non-self recognition is a common phenomenon among organisms; it often leads to innate immunity to prevent the invasion of parasites and maintain the genetic polymorphism of organisms. Fungal vegetative incompatibility is a type of non-self recognition which often induces programmed cell death (PCD) and restricts the spread of molecular parasites. It is not clearly known whether virus infection could attenuate non-self recognition among host individuals to facilitate its spread. Here, we report that a hypovirulence-associated mycoreovirus, named Sclerotinia sclerotiorum mycoreovirus 4 (SsMYRV4), could suppress host non-self recognition and facilitate horizontal transmission of heterologous viruses. We found that cell death in …
Photosynthetic Bacterium Rhodopseudomonas Palustris Gj-22 Induces Systemic Resistance Against Viruses, Pin Su, Xinqiu Tan, Chenggang Li, Deyong Zhang, Ju’E Cheng, Songbai Zhang, Xuguo Zhou, Qingpin Yan, Jing Peng, Zhuo Zhang, Yong Liu, Xiangyang Lu
Photosynthetic Bacterium Rhodopseudomonas Palustris Gj-22 Induces Systemic Resistance Against Viruses, Pin Su, Xinqiu Tan, Chenggang Li, Deyong Zhang, Ju’E Cheng, Songbai Zhang, Xuguo Zhou, Qingpin Yan, Jing Peng, Zhuo Zhang, Yong Liu, Xiangyang Lu
Entomology Faculty Publications
Photosynthetic bacteria (PSB) have been extensively used in agriculture to promote plant growth and to improve crop quality. Their potential application in plant disease management, however, is largely overlooked. In this study, the PSB strain Rhodopseudomonas palustris GJ-22 was investigated for its ability to induce resistance against a plant virus while promoting plant growth. In the field, a foliar spray of GJ-22 suspension protected tobacco plants against tobacco mosaic virus (TMV). Under axenic conditions, GJ-22 colonized the plant phyllosphere and induced resistance against TMV. Additionally, GJ-22 produced two phytohormones, indole-3-acetic acid and 5-aminolevulinic acid, which promote growth and germination in …
Anomaly Detection In Host Signaling Pathways For The Early Prognosis Of Acute Infection, Kun Wang, Stanley Langevin, Corey S. O'Hern, Mark D. Shattuck, Serenity Ogle, Adriana Forero, Juliet Morrison, Richard Slayden, Michael G. Katze, Michael Kirby
Anomaly Detection In Host Signaling Pathways For The Early Prognosis Of Acute Infection, Kun Wang, Stanley Langevin, Corey S. O'Hern, Mark D. Shattuck, Serenity Ogle, Adriana Forero, Juliet Morrison, Richard Slayden, Michael G. Katze, Michael Kirby
Publications and Research
Clinical diagnosis of acute infectious diseases during the early stages of infection is critical to administering the appropriate treatment to improve the disease outcome. We present a data driven analysis of the human cellular response to respiratory viruses including influenza, respiratory syncytia virus, and human rhinovirus, and compared this with the response to the bacterial endotoxin, Lipopolysaccharides (LPS). Using an anomaly detection framework we identified pathways that clearly distinguish between asymptomatic and symptomatic patients infected with the four different respiratory viruses and that accurately diagnosed patients exposed to a bacterial infection. Connectivity pathway analysis comparing the viral and bacterial diagnostic …
A Pan-Dengue Virus Reverse Transcription-Insulated Isothermal Pcr Assay Intended For Point-Of-Need Diagnosis Of Dengue Virus Infection By Use Of The Pockit Nucleic Acid Analyzer, Yun Young Go, R. P. V. Jayanthe Rajapakse, Senanayake A. M. Kularatne, Pei-Yu Alison Lee, Keun Bon Ku, Sangwoo Nam, Pin-Hsing Chou, Yun-Long Tsai, Yu-Lun Liu, Hsiao-Fen Grace Chang, Hwa-Tang Thomas Wang, Udeni B. R. Balasuriya
A Pan-Dengue Virus Reverse Transcription-Insulated Isothermal Pcr Assay Intended For Point-Of-Need Diagnosis Of Dengue Virus Infection By Use Of The Pockit Nucleic Acid Analyzer, Yun Young Go, R. P. V. Jayanthe Rajapakse, Senanayake A. M. Kularatne, Pei-Yu Alison Lee, Keun Bon Ku, Sangwoo Nam, Pin-Hsing Chou, Yun-Long Tsai, Yu-Lun Liu, Hsiao-Fen Grace Chang, Hwa-Tang Thomas Wang, Udeni B. R. Balasuriya
Maxwell H. Gluck Equine Research Center Faculty Publications
Dengue virus (DENV) infection is considered a major public health problem in developing tropical countries where the virus is endemic and continues to cause major disease outbreaks every year. Here, we describe the development of a novel, inexpensive, and user-friendly diagnostic assay based on a reverse transcription-insulated isothermal PCR (RT-iiPCR) method for the detection of all four serotypes of DENV in clinical samples. The diagnostic performance of the newly established pan-DENV RT-iiPCR assay targeting a conserved 3′ untranslated region of the viral genome was evaluated. The limit of detection with a 95% confidence was estimated to be 10 copies of …
Expansion Of The Chlorovirus Genus By Studies On Virus Natural History And Chlorella Host Metabolism, Cristian F. Quispe
Expansion Of The Chlorovirus Genus By Studies On Virus Natural History And Chlorella Host Metabolism, Cristian F. Quispe
School of Biological Sciences: Dissertations, Theses, and Student Research
Inland waters cover about 2.5 percent of our planet and harbor huge numbers of known and unknown microorganisms including viruses. Viruses likely play dynamic, albeit largely undocumented roles in regulating microbial communities and in recycling nutrients in the ecosystem. Phycodnaviruses are a genetically diverse, yet morphologically similar, group of large dsDNA-containing viruses (160- to 560-kb) that inhabit aquatic environments. Members of the genus Chlorovirus are common in freshwater. They replicate in eukaryotic, single-celled, chlorella-like green algae that normally exist as endosymbionts of protists in nature. Very little is known about the natural history of the chloroviruses and how they achieve …
Enhanced Expression Of Codon Optimized Mycobacterium Avium Subsp. Paratuberculosis Antigens In Lactobacillus Salivarius, Christopher D. Johnston, John P. Bannatine, Rodney Govender, Lorraine Endersen, Daniel Pletzer, Helge Weingart, Aidan Coffey, Jim O'Mahony, Roy D. Sleator
Enhanced Expression Of Codon Optimized Mycobacterium Avium Subsp. Paratuberculosis Antigens In Lactobacillus Salivarius, Christopher D. Johnston, John P. Bannatine, Rodney Govender, Lorraine Endersen, Daniel Pletzer, Helge Weingart, Aidan Coffey, Jim O'Mahony, Roy D. Sleator
Department of Biological Sciences Publications
It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants …