Open Access. Powered by Scholars. Published by Universities.®

Organisms Commons

Open Access. Powered by Scholars. Published by Universities.®

1,050 Full-Text Articles 2,512 Authors 330,197 Downloads 104 Institutions

All Articles in Organisms

Faceted Search

1,050 full-text articles. Page 1 of 41.

Severity Of Disease And Mortality For Hospitalized Patients With Community-Acquired Viral Pneumonia Compared To Patients With Community-Acquired Bacterial Pneumonia, Richard Y. Kim, Thomas Chandler, Stephen P. Furmanek, Timothy Lee Wiemken, Rodrigo Cavallazzi 2019 University of Louisville

Severity Of Disease And Mortality For Hospitalized Patients With Community-Acquired Viral Pneumonia Compared To Patients With Community-Acquired Bacterial Pneumonia, Richard Y. Kim, Thomas Chandler, Stephen P. Furmanek, Timothy Lee Wiemken, Rodrigo Cavallazzi

The University of Louisville Journal of Respiratory Infections

Background: There exists a large body of literature to help identify, diagnose, treat, and manage community-acquired pneumonia (CAP). Despite this, there is little data that directly compares the clinical syndromes and complications of pure bacterial pneumonia to pure viral pneumonia. Our study compares the clinical presentation, morbidity and mortality of viral vs. bacterial etiologies of CAP.

Methods: This was a secondary data analysis of the Community-Acquired Pneumonia Organization (CAPO) international study database. Data was collected concerning patient demographics, physical examination findings, laboratory findings, radiological findings, severity of illness, and clinical outcomes and stratified according to the two study groups, CAVP ...


Principles For Enhancing Virus Capsid Capacity And Stability From A Thermophilic Virus Capsid Structure, Nicholas P. Stone, Gabriel Demo, Emily Agnello, Brian A. Kelch 2019 University of Massachusetts Medical School

Principles For Enhancing Virus Capsid Capacity And Stability From A Thermophilic Virus Capsid Structure, Nicholas P. Stone, Gabriel Demo, Emily Agnello, Brian A. Kelch

University of Massachusetts Medical School Faculty Publications

The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To elucidate how capsids maintain stability in an extreme environment, we used cryoelectron microscopy to determine the capsid structure of the thermostable phage P74-26. We find the P74-26 capsid exhibits an overall architecture that is very similar to those of other tailed bacteriophages, allowing us to directly compare structures to derive the structural basis for enhanced stability. Our structure reveals lasso-like interactions that appear to function like catch bonds. This architecture allows the capsid ...


Protective Versus Pathologic Pre-Exposure Cytokine Profiles In Dengue Virus Infection, Heather Friberg, Coreen M. Beaumier, Sangshin Park, Pamela P. Pazoles, Timothy P. Endy, Anuja Mathew, Jeffrey R. Currier, Richard G. Jarman, Kathryn B. Anderson, Steven Hatch, Stephen J. Thomas, Alan L. Rothman 2018 Walter Reed Army Institute of Research

Protective Versus Pathologic Pre-Exposure Cytokine Profiles In Dengue Virus Infection, Heather Friberg, Coreen M. Beaumier, Sangshin Park, Pamela P. Pazoles, Timothy P. Endy, Anuja Mathew, Jeffrey R. Currier, Richard G. Jarman, Kathryn B. Anderson, Steven Hatch, Stephen J. Thomas, Alan L. Rothman

Open Access Articles

BACKGROUND: Hyperendemic circulation of all four types of dengue virus (DENV-1-4) has expanded globally, fueling concern for increased incidence of severe dengue. While the majority of DENV infections are subclinical, epidemiologic studies suggest that type-cross-reactive immunity can influence disease outcome in subsequent infections. The mechanisms controlling these differential clinical outcomes remain poorly defined.

METHODOLOGY/PRINCIPAL FINDINGS: Blood samples were collected from a cohort of school-aged Thai children who subsequently experienced a subclinical DENV infection or developed dengue illness. PBMC collected prior to infection were stimulated in vitro with DENV and the secretion of 30 cytokines was measured using a multiplexed ...


Resistance From Afar: Distal Mutation V36m Allosterically Modulates The Active Site To Accentuate Drug Resistance In Hcv Ns3/4a Protease, Aysegul Ozen, Kuan-Hung Lin, Keith P. Romano, Davide Tavella, Alicia Newton, Christos J. Petropoulos, Wei Huang, Cihan Aydin, Celia A. Schiffer 2018 University of Massachusetts Medical School

Resistance From Afar: Distal Mutation V36m Allosterically Modulates The Active Site To Accentuate Drug Resistance In Hcv Ns3/4a Protease, Aysegul Ozen, Kuan-Hung Lin, Keith P. Romano, Davide Tavella, Alicia Newton, Christos J. Petropoulos, Wei Huang, Cihan Aydin, Celia A. Schiffer

University of Massachusetts Medical School Faculty Publications

Hepatitis C virus rapidly evolves, conferring resistance to direct acting antivirals. While resistance via active site mutations in the viral NS3/4A protease has been well characterized, the mechanism for resistance of non-active site mutations is unclear. R155K and V36M often co-evolve and while R155K alters the electrostatic network at the binding site, V36M is more than 13 Angstrom away. In this study the mechanism by which V36M confers resistance, in the context of R155K, is elucidated with drug susceptibility assays, crystal structures, and molecular dynamics (MD) simulations for three protease inhibitors: telaprevir, boceprevir and danoprevir. The R155K and R155K ...


Intron-Containing Rna From The Hiv-1 Provirus Activates Type I Interferon And Inflammatory Cytokines, Sean M. McCauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, Leonid Yurkovetskiy, William E. Diehl, Jeremy Luban 2018 University of Massachusetts Medical School

Intron-Containing Rna From The Hiv-1 Provirus Activates Type I Interferon And Inflammatory Cytokines, Sean M. Mccauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, Leonid Yurkovetskiy, William E. Diehl, Jeremy Luban

Open Access Articles

HIV-1-infected people who take drugs that suppress viremia to undetectable levels are protected from developing AIDS. Nonetheless, HIV-1 establishes proviruses in long-lived CD4(+) memory T cells, and perhaps other cell types, that preclude elimination of the virus even after years of continuous antiviral therapy. Here we show that the HIV-1 provirus activates innate immune signaling in isolated dendritic cells, macrophages, and CD4(+) T cells. Immune activation requires transcription from the HIV-1 provirus and expression of CRM1-dependent, Rev-dependent, RRE-containing, unspliced HIV-1 RNA. If rev is provided in trans, all HIV-1 coding sequences are dispensable for activation except those cis-acting sequences required ...


Orbit: A New Paradigm For Genetic Engineering Of Mycobacterial Chromosomes, Kenan C. Murphy, Samantha J. Nelson, Subhalaxmi Nambi, Kadamba Papavinasasundaram, Christina E. Baer, Christopher M. Sassetti 2018 University of Massachusetts Medical School

Orbit: A New Paradigm For Genetic Engineering Of Mycobacterial Chromosomes, Kenan C. Murphy, Samantha J. Nelson, Subhalaxmi Nambi, Kadamba Papavinasasundaram, Christina E. Baer, Christopher M. Sassetti

Open Access Articles

Two efficient recombination systems were combined to produce a versatile method for chromosomal engineering that obviates the need to prepare double-stranded DNA (dsDNA) recombination substrates. A synthetic "targeting oligonucleotide" is incorporated into the chromosome via homologous recombination mediated by the phage Che9c RecT annealase. This oligonucleotide contains a site-specific recombination site for the directional Bxb1 integrase (Int), which allows the simultaneous integration of a "payload plasmid" that contains a cognate recombination site and a selectable marker. The targeting oligonucleotide and payload plasmid are cotransformed into a RecT- and Int-expressing strain, and drug-resistant homologous recombinants are selected in a single step ...


Conserved Mrna-Granule Component Scd6 Targets Dhh1 To Repress Translation Initiation And Activates Dcp2-Mediated Mrna Decay In Vivo, Quira Zeidan, Feng He, Fan Zhang, Hongen Zhang, Allan Jacobson, Alan G. Hinnebusch 2018 Eunice Kennedy Shriver National Institute of Child Health and Development

Conserved Mrna-Granule Component Scd6 Targets Dhh1 To Repress Translation Initiation And Activates Dcp2-Mediated Mrna Decay In Vivo, Quira Zeidan, Feng He, Fan Zhang, Hongen Zhang, Allan Jacobson, Alan G. Hinnebusch

Open Access Articles

Scd6 protein family members are evolutionarily conserved components of translationally silent mRNA granules. Yeast Scd6 interacts with Dcp2 and Dhh1, respectively a subunit and a regulator of the mRNA decapping enzyme, and also associates with translation initiation factor eIF4G to inhibit translation in cell extracts. However, the role of Scd6 in mRNA turnover and translational repression in vivo is unclear. We demonstrate that tethering Scd6 to a GFP reporter mRNA reduces mRNA abundance via Dcp2 and suppresses reporter mRNA translation via Dhh1. Thus, in a dcp2Delta mutant, tethered Scd6 reduces GFP protein expression with little effect on mRNA abundance, whereas ...


General Decapping Activators Target Different Subsets Of Inefficiently Translated Mrnas, Feng He, Alper Celik, Chan Wu, Allan Jacobson 2018 University of Massachusetts Medical School

General Decapping Activators Target Different Subsets Of Inefficiently Translated Mrnas, Feng He, Alper Celik, Chan Wu, Allan Jacobson

Open Access Articles

The Dcp1-Dcp2 decapping enzyme and the decapping activators Pat1, Dhh1, and Lsm1 regulate mRNA decapping, but their mechanistic integration is unknown. We analyzed the gene expression consequences of deleting PAT1, LSM1, or DHH1, or the DCP2 C-terminal domain, and found that: i) the Dcp2 C-terminal domain is an effector of both negative and positive regulation; ii) rather than being global activators of decapping, Pat1, Lsm1, and Dhh1 directly target specific subsets of yeast mRNAs and loss of the functions of each of these factors has substantial indirect consequences for genome-wide mRNA expression; and iii) transcripts targeted by Pat1, Lsm1, and ...


Potent Cas9 Inhibition In Bacterial And Human Cells By Acriic4 And Acriic5 Anti-Crispr Proteins, Jooyoung Lee, Aamir Mir, Alireza Edraki, Bianca Garcia, Nadia Amrani, Hannah E. Lou, Ildar Gainetdinov, April Pawluk, Raed Ibraheim, Xin D. Gao, Pengpeng Liu, Alan R. Davidson, Karen L. Maxwell, Erik J. Sontheimer 2018 University of Massachusetts Medical School

Potent Cas9 Inhibition In Bacterial And Human Cells By Acriic4 And Acriic5 Anti-Crispr Proteins, Jooyoung Lee, Aamir Mir, Alireza Edraki, Bianca Garcia, Nadia Amrani, Hannah E. Lou, Ildar Gainetdinov, April Pawluk, Raed Ibraheim, Xin D. Gao, Pengpeng Liu, Alan R. Davidson, Karen L. Maxwell, Erik J. Sontheimer

Open Access Articles

In their natural settings, CRISPR-Cas systems play crucial roles in bacterial and archaeal adaptive immunity to protect against phages and other mobile genetic elements, and they are also widely used as genome engineering technologies. Previously we discovered bacteriophage-encoded Cas9-specific anti-CRISPR (Acr) proteins that serve as countermeasures against host bacterial immunity by inactivating their CRISPR-Cas systems (A. Pawluk, N. Amrani, Y. Zhang, B. Garcia, et al., Cell 167:1829-1838.e9, 2016, https://doi.org/10.1016/j.cell.2016.11.017). We hypothesized that the evolutionary advantages conferred by anti-CRISPRs would drive the widespread occurrence of these proteins in nature (K ...


Effect Of Macrograzers (Campostoma Spp. And Faxonius Spp.) On Periphyton In Ozark Streams With Considerations Given To Macrograzer Biomass, Phosphorus, And Season: Mensurative And Manipulative Studies, Kayla R. Sayre 2018 University of Arkansas, Fayetteville

Effect Of Macrograzers (Campostoma Spp. And Faxonius Spp.) On Periphyton In Ozark Streams With Considerations Given To Macrograzer Biomass, Phosphorus, And Season: Mensurative And Manipulative Studies, Kayla R. Sayre

Theses and Dissertations

Nutrient and benthic algal biomass relationships can guide numeric nutrient criteria development in lotic systems. However, herbivorous macrograzers may confound this relationship by reducing the slope of the positive relationship between nutrients and periphyton biomass in streams. I conducted a mensurative field study to determine if stoneroller and crayfish abundance related to algal biomass at varying nutrient concentrations and manipulated macrograzer presence with electrical exclosures in streams to examine macrograzer effects on algal biomass and understand whether these effects on periphyton varied with total phosphorus (TP) or season. Macrograzer density was quantified across a TP gradient (n=15 streams; range ...


Bacterial Abundance And Resistance In Ground Beef Varieties, Savannah Kumar, Sarah M. Boomer 2018 Western Oregon University

Bacterial Abundance And Resistance In Ground Beef Varieties, Savannah Kumar, Sarah M. Boomer

PURE Insights

Raw ground beef purchased at supermarkets across America have one thing in common: they harbor bacteria, some of which are drug resistant and can be detrimental to public health. To understand the impact of farming and processing practices on the quantity of bacteria and drug resistance, organic and regular beef were assessed using MacConkey media. Bacterial colonies were sorted according to lactose utilization, with positive colonies representing fecal E. coli. Lactose negative colonies were further characterized into one of two groups (fecal Hafnia-like or soil Pseudomonas) using a variety of metabolic tests (oxidase, sulfur, indole). Advanced metabolic testing showed that ...


Cryptococcus Neoformans Cda1 And Its Chitin Deacetylase Activity Are Required For Fungal Pathogenesis, Rajendra Upadhya, Lorina G. Baker, Woei C. Lam, Charles A. Specht, Maureen J. Donlin, Jennifer K. Lodge 2018 Washington University

Cryptococcus Neoformans Cda1 And Its Chitin Deacetylase Activity Are Required For Fungal Pathogenesis, Rajendra Upadhya, Lorina G. Baker, Woei C. Lam, Charles A. Specht, Maureen J. Donlin, Jennifer K. Lodge

Open Access Articles

Chitin is an essential component of the cell wall of Cryptococcus neoformans conferring structural rigidity and integrity under diverse environmental conditions. Chitin deacetylase genes encode the enyzmes (chitin deacetylases [Cdas]) that deacetylate chitin, converting it to chitosan. The functional role of chitosan in the fungal cell wall is not well defined, but it is an important virulence determinant of C. neoformans Mutant strains deficient in chitosan are completely avirulent in a mouse pulmonary infection model. C. neoformans carries genes that encode three Cdas (Cda1, Cda2, and Cda3) that appear to be functionally redundant in cells grown under vegetative conditions. Here ...


Deciphering The Molecular Basis Of Mycobacteria And Lipoglycan Recognition By The C-Type Lectin Dectin-2, Alexiane Decout, Devinder Kaur, Jerome Nigou 2018 University of Toulouse

Deciphering The Molecular Basis Of Mycobacteria And Lipoglycan Recognition By The C-Type Lectin Dectin-2, Alexiane Decout, Devinder Kaur, Jerome Nigou

Open Access Articles

Dectin-2 is a C-type lectin involved in the recognition of several pathogens such as Aspergillus fumigatus, Candida albicans, Schistosoma mansonii, and Mycobacterium tuberculosis that triggers Th17 immune responses. Identifying pathogen ligands and understanding the molecular basis of their recognition is one of the current challenges. Purified M. tuberculosis mannose-capped lipoarabinomannan (ManLAM) was shown to induce signaling via Dectin-2, an activity that requires the (alpha1 --> 2)-linked mannosides forming the caps. Here, using isogenic M. tuberculosis mutant strains, we demonstrate that ManLAM is a bona fide and actually the sole ligand mediating bacilli recognition by Dectin-2, although M. tuberculosis produces a ...


No Evidence For Kin Protection In The Expression Of Sickness Behaviors In House Mice, Patricia C. Lopes, Per Block, Alice Pontiggia, Anna K. Lindholm, Barbara König 2018 Chapman University

No Evidence For Kin Protection In The Expression Of Sickness Behaviors In House Mice, Patricia C. Lopes, Per Block, Alice Pontiggia, Anna K. Lindholm, Barbara König

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

When infected, animals change their behaviors in several ways, including by decreasing their activity, their food and water intake, and their interest in social interactions. These behavioral alterations are collectively called sickness behaviors and, for several decades, the main hypotheses put forward to explain this phenomenon were that engaging in sickness behaviors facilitated the fever response and improved the likelihood of host survival. However, a new hypothesis was recently proposed suggesting that engaging in sickness behaviors may serve to protect kin. We tested this kin protection hypothesis by combining a field and a laboratory experiment in house mice. In both ...


Vancomycin Delays Clindamycin-Induced Fatality In The Hamster Model Of Clostridioides [Clostridium] Difficile Infection, Amelia E. Fox-King, Chrisabelle Mefferd, Jacqueline R. Phan, Nancy O. Nou, Ernesto Abel-Santos, Brian P. Hedlund 2018 University of Nevada, Las Vegas

Vancomycin Delays Clindamycin-Induced Fatality In The Hamster Model Of Clostridioides [Clostridium] Difficile Infection, Amelia E. Fox-King, Chrisabelle Mefferd, Jacqueline R. Phan, Nancy O. Nou, Ernesto Abel-Santos, Brian P. Hedlund

LSAMP Poster Presentations

Antibiotics can leave the host gut microbiome susceptible to Clostridioides [Clostridium] difficile colonization and lethal toxin production. For instance, clindamycin-induced susceptibility to C. difficile infection (CDI) results in rapid fatality in hamster models, yet vancomycin has been shown to offer increased survival in hamsters challenged with C. difficile. We aim to develop an antibiotic treatment that will facilitate CDI susceptibility without prompt fatality in hamster models. An antibiotic regimen starting with a continuous vancomycin treatment along with a single clindamycin dosage is thought to reduce the major disruption in the indigenous gut microbiome and prevent clindamycin-induced death. Quantitative polymerase chain ...


Simulating Antibiotic Resistance In The Computer Lab And Biology Lab: Ideas For Undergraduate Projects, Anne E. Yust 2018 The New School

Simulating Antibiotic Resistance In The Computer Lab And Biology Lab: Ideas For Undergraduate Projects, Anne E. Yust

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Implementing Strategies To Reduce Central Line-Associated Blood Stream Infections On An Inpatient Pediatric Unit, Sherryann St. Pierre, Nicole Manchester, Jessica Howe, Melanie Lord, Mark Parker, Suneela Nayak, Ruth Hanselman, Stephen Tyzik, Amy Sparks, Barbara Bush Children's Hospital 2018 Maine Medical Center

Implementing Strategies To Reduce Central Line-Associated Blood Stream Infections On An Inpatient Pediatric Unit, Sherryann St. Pierre, Nicole Manchester, Jessica Howe, Melanie Lord, Mark Parker, Suneela Nayak, Ruth Hanselman, Stephen Tyzik, Amy Sparks, Barbara Bush Children's Hospital

Operational Excellence

STRATEGIES TO REDUCE CENTRAL LINE ASSOCIATED BLOODSTREAM INFECTIONS

Every central line associated bloodstream infection (CLABSI) leads to poor outcomes, increased mortality and increased healthcare costs. A pediatric care team in an academic tertiary medical center set a goal to reduce the number of these infections on their unit.

The team’s research showed that daily bathing greatly decreases CLABSI. Their baseline metrics demonstrated an unacceptable level of those with central lines being bathed. A root cause analysis revealed that patient and family refusal was the leading cause for those who did not bathe.

A performance improvement plan was initiated that ...


Adapting Cell-Free Protein Synthesis As A Platform Technology For Education, Grace W. Chu, Max Z. Levine, Nicole E. Gregorio, Javin P. Oza 2018 California State University, Los Angeles

Adapting Cell-Free Protein Synthesis As A Platform Technology For Education, Grace W. Chu, Max Z. Levine, Nicole E. Gregorio, Javin P. Oza

STAR (STEM Teacher and Researcher) Presentations

Cell-free protein synthesis (CFPS) has emerged as an enabling biotechnology for research and biomanufacturing as it allows for the production of protein without the need for a living cell. Applications of CFPS include the construction of libraries for functional genomics and structural biology, the production of personalized medicine, and the expression of virus-like particles. The absence of a cell wall provides an open platform for direct manipulation of the reaction conditions and biological machinery. This project focuses on adapting the CFPS biotechnology to the classroom, making a hands-on bioengineering approach to learning protein synthesis accessible to students grades K-16 through ...


Upregulation Of Hla-E By Dengue And Not Zika Viruses, Elena Drews, Awadalkareem Adam, Phone Htoo, Elizabeth Townsley, Anuja Mathew 2018 University of Massachusetts Medical School

Upregulation Of Hla-E By Dengue And Not Zika Viruses, Elena Drews, Awadalkareem Adam, Phone Htoo, Elizabeth Townsley, Anuja Mathew

Open Access Articles

Introduction: The most severe form of dengue virus (DENV) illness, dengue haemorrhagic fever, is characterised by plasma leakage and increased vascular permeability.

Objectives: Given the critical role that endothelial cells play in the pathogenesis of DENV, we wanted to determine whether infection with DENV altered the expression of MHC class I related genes including HLA-E.

Results: In this study, we provide evidence that HLA-E but not MICA/B or HLA-G is upregulated by all four serotypes of DENV in an endothelial cell line human microvascular endothelial cells (HMEC)-1. In contrast, Zika virus (ZIKV), a related flavivirus, where plasma leakage ...


All-In-One Adeno-Associated Virus Delivery And Genome Editing By Neisseria Meningitidis Cas9 In Vivo, Raed Ibraheim, Chun-Qing Song, Aamir Mir, Nadia Amrani, Wen Xue, Erik J. Sontheimer 2018 University of Massachusetts Medical School

All-In-One Adeno-Associated Virus Delivery And Genome Editing By Neisseria Meningitidis Cas9 In Vivo, Raed Ibraheim, Chun-Qing Song, Aamir Mir, Nadia Amrani, Wen Xue, Erik J. Sontheimer

RNA Therapeutics Institute Publications

BACKGROUND: Clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) have recently opened a new avenue for gene therapy. Cas9 nuclease guided by a single-guide RNA (sgRNA) has been extensively used for genome editing. Currently, three Cas9 orthologs have been adapted for in vivo genome engineering applications: Streptococcus pyogenes Cas9 (SpyCas9), Staphylococcus aureus Cas9 (SauCas9), and Campylobacter jejuni (CjeCas9). However, additional in vivo editing platforms are needed, in part to enable a greater range of sequences to be accessed via viral vectors, especially those in which Cas9 and sgRNA are combined into a single vector genome.

RESULTS: Here ...


Digital Commons powered by bepress