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Identification Of The Ps1 Thr147ile Variant In A Family With Very Early Onset Dementia And Expressive Aphasia, James Denvir, Shirley Neitch, Jun Fan, Richard M. Niles, Goran Boskovic, Bernard G. Schreurs, Donald A. Primerano, Daniel L. Alkon 2019 Marshall University

Identification Of The Ps1 Thr147ile Variant In A Family With Very Early Onset Dementia And Expressive Aphasia, James Denvir, Shirley Neitch, Jun Fan, Richard M. Niles, Goran Boskovic, Bernard G. Schreurs, Donald A. Primerano, Daniel L. Alkon

Jun Fan

Background: Early onset dementias have variable clinical presentations and are often difficult to diagnose. We established a family pedigree that demonstrated consistent recurrence of very early onset dementia in successive generations.

Objective and Method: In order to refine the diagnosis in this family, we sequenced the exomes of two affected family members and relied on discrete filtering to identify disease genes and the corresponding causal variants.

Results: Among the 720 nonsynonymous single nucleotide polymorphisms (SNPs) shared by two affected members, we found a C to T transition that gives rise to a Thr147Ile missense substitution in the presenilin 1 (PS1 ...


Targeted Therapy For The Future: The Use Of Novel Antimicrobial Peptides Against P. Aeurginosa, Matthew Froid 2019 University of Nebraska at Omaha

Targeted Therapy For The Future: The Use Of Novel Antimicrobial Peptides Against P. Aeurginosa, Matthew Froid

Student Research and Creative Activity Fair

Pathogenic bacteria, such as the gram-negative bacterium Pseudomonas aeruginosa, are becoming resistant to our current arsenal of antibiotics at an alarming rate. P. aeruginosa is a leading cause of nosocomial acquired infections and is a primary co-morbidity in patients with compromised immune systems. One potential source of new antibiotic agents is antimicrobial peptides. Antimicrobial peptides (AMPs) are small proteins, and some have shown a high degree of efficacy and broad-spectrum activity against both Gram-positive and Gram-negative bacteria. An experimental AMP that has been developed by Dr. Wang at UNMC, DASamp2, has shown to be effective against virulent bacteria, including P ...


Cyanobacterial And Algal Abundance And Biomass In Cave Biofilms And Relation To Environmental And Biofilm Parameters, Slađana Popović, Nataša Nikolić, Jelena Jovanović, Dragana Predojević, Ivana Trbojević, Ljiljana Manić, Gordana Subakov Simić 2019 University of Belgrade, Institute of Chemistry, Technolpgy and Metallurgy, Center for Ecology and Technoeconomics

Cyanobacterial And Algal Abundance And Biomass In Cave Biofilms And Relation To Environmental And Biofilm Parameters, Slađana Popović, Nataša Nikolić, Jelena Jovanović, Dragana Predojević, Ivana Trbojević, Ljiljana Manić, Gordana Subakov Simić

International Journal of Speleology

Due to life in extreme environments, cyanobacteria and algae from cave biofilms that form at the entrances or deep inside the cave around artificial lights are of increasing interest to many scientists. It is well-known that many phototrophic microorganisms are first to colonize exposed substrata and produce the organic matter on which other biofilm constituents relly. Many studies dealing with phototrophic microorganisms from biofilms focus on the diversity and community composition of cyanobacteria and algae, while quantitative assessments are rarely implemented. Biofilm sampling was conducted in Degurić and Vernjikica Cave located in Western and Eastern Serbia, respectively. Ecological parameters (temperature ...


Complete Genome Sequences Of Mycobacterium Smegmatis Phages Chewbacca, Reptar3000, And Riparian, Isolated In Las Vegas, Nevada, Alicia Salisbury, Erin Cassin, Kevin Ayala-Pineda, Nicolas Barroga, Vanessa Cadiz, Ramiro Cisneros, Joseph Fersini, Tiffany Jeanite, Jonathan Juste, Juvie Ines, Gabriel Leyva, Dyanne Macalinao, Spencer Muscelli, Sophia Nhan, Gustavo S. Reyes, Heather Rhoden, Rodney Tan, Erika Torres, Krystal Tran, Georgette Uriarte-Valle, Christopher Wallace, Simon Wong, Kurt Regner, Christy Strong, Philippos K. Tsourkas 2019 University of Nevada, Las Vegas

Complete Genome Sequences Of Mycobacterium Smegmatis Phages Chewbacca, Reptar3000, And Riparian, Isolated In Las Vegas, Nevada, Alicia Salisbury, Erin Cassin, Kevin Ayala-Pineda, Nicolas Barroga, Vanessa Cadiz, Ramiro Cisneros, Joseph Fersini, Tiffany Jeanite, Jonathan Juste, Juvie Ines, Gabriel Leyva, Dyanne Macalinao, Spencer Muscelli, Sophia Nhan, Gustavo S. Reyes, Heather Rhoden, Rodney Tan, Erika Torres, Krystal Tran, Georgette Uriarte-Valle, Christopher Wallace, Simon Wong, Kurt Regner, Christy Strong, Philippos K. Tsourkas

Life Sciences Faculty Publications

Here, we present the complete genome sequences of Mycobacterium smegmatis phages Chewbacca, Reptar3000, and Riparian, isolated from soil in Las Vegas, NV. The phages were isolated and annotated by undergraduate students enrolled in the Phage Discovery course offered by the School of Life Sciences at the University of Nevada, Las Vegas


Comparison Of Microbial Communities In The Sediments And Water Columns Of Frozen Cryoconite Holes In The Mcmurdo Dry Valleys, Antarctica, Pacifica Sommers, John Lawrence Darcy, Dorota L. Porazinska, Eli M.S. Gendron, Andrew G. Fountain, Felix Zamora, Kim Vincent, Kaelin M. Cawley, Adam J. Solon, Lara Vimercati, Jenna Ryder, Steven K. Schmidt 2019 University of Colorado at Boulder

Comparison Of Microbial Communities In The Sediments And Water Columns Of Frozen Cryoconite Holes In The Mcmurdo Dry Valleys, Antarctica, Pacifica Sommers, John Lawrence Darcy, Dorota L. Porazinska, Eli M.S. Gendron, Andrew G. Fountain, Felix Zamora, Kim Vincent, Kaelin M. Cawley, Adam J. Solon, Lara Vimercati, Jenna Ryder, Steven K. Schmidt

University Libraries Open Access Fund Supported Publications

Although cryoconite holes, sediment-filled melt holes on glacier surfaces, appear small and homogenous, their microbial inhabitants may be spatially partitioned. This partitioning could be particularly important for maintaining biodiversity in holes that remain isolated for many years, such as in Antarctica. We hypothesized that cryoconite holes with greater species richness and biomass should exhibit greater partitioning between the sediments and water, promoting greater biodiversity through spatial niche partitioning. We tested this hypothesis by sampling frozen cryoconite holes along a gradient of biomass and biodiversity in the Taylor Valley, Antarctica, where ice-lidded cryoconite holes are a ubiquitous feature of glaciers. We ...


Data Evidencing Slow Anaerobic Digestion In Emergency Treatment And Disposal Of Infectious Animal Carcasses, Jacek A. Koziel, Heekwon Ahn, Thomas D. Glanville, Timothy S. Frana, J. (Hans) van Leeuwen, Lam T. Nguyen 2019 Iowa State University

Data Evidencing Slow Anaerobic Digestion In Emergency Treatment And Disposal Of Infectious Animal Carcasses, Jacek A. Koziel, Heekwon Ahn, Thomas D. Glanville, Timothy S. Frana, J. (Hans) Van Leeuwen, Lam T. Nguyen

Agricultural and Biosystems Engineering Publications

Burial of infectious and potentially infectious livestock and poultry animals is the most common response to an emergency situation. The data set summarizes 22-week-long experiment that simulates the environment found within conventional burial trenches for emergency disposal of animal carcasses, worldwide, sometimes with a topical application of quicklime as it is required in the Republic of Korea. This data set shows the rarely presented evidence of the extremely slow decay of animal carcasses. Besides visual evidence of no visible breakdown of carcass material, i.e., carcass (or carcass quarters and coarse cuts) still resembled the initial material at the end ...


The Nuclear Hormone Receptor Nhr-86 Controls Anti-Pathogen Responses In C. Elegans, Nicholas D. Peterson, Hilary K. Cheesman, Pengpeng Liu, Sarah M. Anderson, Kyle J. Foster, Richa Chhaya, Paola N. Perrat, Jose Thekkiniath, Qiyuan Yang, Cole M. Haynes, Read Pukkila-Worley 2019 University of Massachusetts Medical School

The Nuclear Hormone Receptor Nhr-86 Controls Anti-Pathogen Responses In C. Elegans, Nicholas D. Peterson, Hilary K. Cheesman, Pengpeng Liu, Sarah M. Anderson, Kyle J. Foster, Richa Chhaya, Paola N. Perrat, Jose Thekkiniath, Qiyuan Yang, Cole M. Haynes, Read Pukkila-Worley

Open Access Articles

Nuclear hormone receptors (NHRs) are ligand-gated transcription factors that control adaptive host responses following recognition of specific endogenous or exogenous ligands. Although NHRs have expanded dramatically in C. elegans compared to other metazoans, the biological function of only a few of these genes has been characterized in detail. Here, we demonstrate that an NHR can activate an anti-pathogen transcriptional program. Using genetic epistasis experiments, transcriptome profiling analyses and chromatin immunoprecipitation-sequencing, we show that, in the presence of an immunostimulatory small molecule, NHR-86 binds to the promoters of immune effectors to activate their transcription. NHR-86 is not required for resistance to ...


Interferon-Induced Transmembrane Protein 3 Blocks Fusion Of Sensitive But Not Resistant Viruses By Partitioning Into Virus-Carrying Endosomes, Krishna C. Suddala, Christine C. Lee, Paul Meraner, Mariana Marin, Ruben M. Markosyan, Tanay M. Desai, Fredric S. Cohen, Abraham L. Brass, Gregory B. Melikyan 2019 Emory University

Interferon-Induced Transmembrane Protein 3 Blocks Fusion Of Sensitive But Not Resistant Viruses By Partitioning Into Virus-Carrying Endosomes, Krishna C. Suddala, Christine C. Lee, Paul Meraner, Mariana Marin, Ruben M. Markosyan, Tanay M. Desai, Fredric S. Cohen, Abraham L. Brass, Gregory B. Melikyan

Open Access Articles

Late endosome-resident interferon-induced transmembrane protein 3 (IFITM3) inhibits fusion of diverse viruses, including Influenza A virus (IAV), by a poorly understood mechanism. Despite the broad antiviral activity of IFITM3, viruses like Lassa virus (LASV), are fully resistant to its inhibitory effects. It is currently unclear whether resistance arises from a highly efficient fusion machinery that is capable of overcoming IFITM3 restriction or the ability to enter from cellular sites devoid of this factor. Here, we constructed and validated a functional IFITM3 tagged with EGFP or other fluorescent proteins. This breakthrough allowed live cell imaging of virus co-trafficking and fusion with ...


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 ...


Strain-Specific Protein Interaction And Localization Of Two Strains Of Potato Yellow Dwarf Virus And Functional Domains Of Their Matrix Protein, Chanyong Jang 2019 University of Kentucky

Strain-Specific Protein Interaction And Localization Of Two Strains Of Potato Yellow Dwarf Virus And Functional Domains Of Their Matrix Protein, Chanyong Jang

Theses and Dissertations--Plant Pathology

Potato yellow dwarf virus (PYDV) is the type species of the genus nucleorhabdovirus which is typified by its nucleotropic characters of the members. The virus accomplishes its replication and morphogenesis in the nuclei of infected cells. Two strains, Constricta strain (CYDV) and Sanguinolenta strain (SYDV) have been described at the level of vector-specificity. CYDV is vectored by Agallia constricta and SYDV is transmitted by Aceratagllia sanguinolenta. The full-length genome of CYDV was sequenced. The 12,792 nt antisense genome encodes seven open reading frames in the order of, nucleocapsid protein (N), unknown protein (X), phosphoprotein (P), movement protein (Y), matrix ...


Persistent Viral Reservoirs In Lymphoid Tissues In Siv-Infected Rhesus Macaques Of Chinese-Origin On Suppressive Antiretroviral Therapy, Summer Siddiqui, Stefanie Perez, Yong Gao, Lara Doyle-Meyers, Brian T. Foley, Qingsheng Li, Binhua Ling 2019 Tulane National Primate Research Center

Persistent Viral Reservoirs In Lymphoid Tissues In Siv-Infected Rhesus Macaques Of Chinese-Origin On Suppressive Antiretroviral Therapy, Summer Siddiqui, Stefanie Perez, Yong Gao, Lara Doyle-Meyers, Brian T. Foley, Qingsheng Li, Binhua Ling

Virology Papers

Understanding HIV latent reservoirs in tissues is essential for the development of new strategies targeting these sites for eradication. Here, we assessed the size of latent reservoirs and the source of residual viruses in multiple lymphoid tissues of SIV-infected and fully suppressed rhesus macaques of Chinese-origin (cRMs). Eight cRMs were infected with SIVmac251 and treated with tenofovir and emtricitabine daily for 24 weeks initiated 4 weeks post-infection. Four of the eight animals reached sustained full viral suppression with undetectable viremia. The levels of cell-associated SIV DNA varied in peripheral blood mononuclear cells (PBMCs) and multiple lymphoid tissues, but with higher ...


Metabolic Engineering For Biocatalyst Robustness To Organic Inhibitors, Liam Royce, Laura R. Jarboe 2019 Iowa State University

Metabolic Engineering For Biocatalyst Robustness To Organic Inhibitors, Liam Royce, Laura R. Jarboe

Chemical and Biological Engineering Publications

Microbial production of biorenewable fuels and chemicals is often limited by inhibition of the biocatalyst, either by increasing concentrations of the product compound or by contaminant compounds in the biomass‐derived sugars. This inhibition can interfere with economically viable production. Here we discuss typical mechanisms of inhibition and methods for improving biocatalyst robustness. Inhibition often takes the form of inhibition of enzyme activity, depletion of cofactor pools, and membrane damage; methods are discussed for mitigating each of these types of inhibition. Various evolutionary schemes have been developed and implemented on a variety of inhibitory compounds, including butanol, acetic acid, furfural ...


Relationship Between The Cervical Microbiome, Hiv Status, And Precancerous Lesions, Cameron Klein, Daniela Gonzalez, Kandali Samwel, Crispin Kahesa, Julius Mwaiselage, Nirosh Aluthge, Samodha Fernando, John T. West, Charles Wood, Peter C. Angeletti 2019 University of Nebraska - Lincoln

Relationship Between The Cervical Microbiome, Hiv Status, And Precancerous Lesions, Cameron Klein, Daniela Gonzalez, Kandali Samwel, Crispin Kahesa, Julius Mwaiselage, Nirosh Aluthge, Samodha Fernando, John T. West, Charles Wood, Peter C. Angeletti

Virology Papers

Nearly all cervical cancers are causally associated with human papillomavirus (HPV). The burden of HPV-associated dysplasias in sub-Saharan Africa is influenced by HIV. To investigate the role of the bacterial microbiome in cervical dysplasia, cytobrush samples were collected directly from cervical lesions of 144 Tanzanian women. The V4 hypervariable region of the 16S rRNA gene was amplified and deep sequenced. Alpha diversity metrics (Chao1, PD whole tree, and operational taxonomic unit [OTU] estimates) displayed significantly higher bacterial richness in HIV-positive patients (P = 0.01) than in HIV-negative patients. In HIV-positive patients, there was higher bacterial richness in patients with high-grade ...


Near-Atomic Structure Of A Giant Virus, Qianglin Fang, Dongjie Zhu, Irina Agarkova, Jagat Adhikari, Thomas Klose, Yue Liu, Zhenguo Chen, Yingyuan Sun, Michael L. Gross, James L. Van Etten, Xinzheng Zhang, Michael G. Rossmann 2019 Purdue University

Near-Atomic Structure Of A Giant Virus, Qianglin Fang, Dongjie Zhu, Irina Agarkova, Jagat Adhikari, Thomas Klose, Yue Liu, Zhenguo Chen, Yingyuan Sun, Michael L. Gross, James L. Van Etten, Xinzheng Zhang, Michael G. Rossmann

Virology Papers

Although the nucleocytoplasmic large DNA viruses (NCLDVs) are one of the largest group of viruses that infect many eukaryotic hosts, the near-atomic resolution structures of these viruses have remained unknown. Here we describe a 3.5 Å resolution icosahedrally averaged capsid structure of Paramecium bursaria chlorella virus 1 (PBCV-1). This structure consists of 5040 copies of the major capsid protein, 60 copies of the penton protein and 1800 minor capsid proteins of which there are 13 different types. The minor capsid proteins form a hexagonal network below the outer capsid shell, stabilizing the capsid by binding neighboring capsomers together. The ...


A Poxvirus Pseudokinase Represses Viral Dna Replication Via A Pathway Antagonized By Its Paralog Kinase, Annabel T. Olson, Zhigang Wang, Amber B. Rico, Matthew S. Wiebe 2019 University of Nebraska - Lincoln

A Poxvirus Pseudokinase Represses Viral Dna Replication Via A Pathway Antagonized By Its Paralog Kinase, Annabel T. Olson, Zhigang Wang, Amber B. Rico, Matthew S. Wiebe

Virology Papers

Poxviruses employ sophisticated, but incompletely understood, signaling pathways that engage cellular defense mechanisms and simultaneously ensure viral factors are modulated properly. For example, the vaccinia B1 protein kinase plays a vital role in inactivating the cellular antiviral factor BAF, and likely orchestrates other pathways as well. In this study, we utilized experimental evolution of a B1 deletion virus to perform an unbiased search for suppressor mutations and identify novel pathways involving B1. After several passages of the ΔB1 virus we observed a robust increase in viral titer of the adapted virus. Interestingly, our characterization of the adapted viruses reveals that ...


Development And Evaluation Of Nonradioactive Methods For Monitoring T Lymphocyte Response To Equine Arteritis Virus (Eav) In Horses, Annet Kyomuhangi 2019 University of Kentucky

Development And Evaluation Of Nonradioactive Methods For Monitoring T Lymphocyte Response To Equine Arteritis Virus (Eav) In Horses, Annet Kyomuhangi

Theses and Dissertations--Veterinary Science

Target cell lysis is the hallmark of immune effector responses of cytotoxic T lymphocytes (CTL), natural killer (NK) cells, and monocytes. The most commonly used assay to measure target cell lysis is the 51Cr release assay and is considered the ‘gold standard’. However, this assay has many disadvantages that limit its use by most laboratories. Thus, several alternative assays have been developed. Some of these alternative assays are more sensitive, easy to perform and do not use radioactive elements.

In this study, four of these assays were evaluated for their ability to detect antigen- specific CTL responses in equine blood ...


Detection Of Beta-Lactamase Variants In Municipal Wastewater And Fresh Water, Sunil Pandey 2019 Eastern Illinois University

Detection Of Beta-Lactamase Variants In Municipal Wastewater And Fresh Water, Sunil Pandey

Masters Theses

The occurrence and spread of antibiotic-resistant genes (ARGs) are pressing public health problems worldwide. A key factor contributing to the spread of ARGs is lateral gene transfer. Wastewater treatment plants (WWTPs) are measured hot spots of microbial diversity and resistance because they receive polluted wastewater from diverse sources and contain a variety of different environments with dense bacterial loads. Due to the overuse of antibiotics the genetic capacities of microbes have profited. This helps every source of resistance gene and every means of horizontal gene transmission to develop the multiple mechanism of resistance to each antibiotic used clinically, agriculturally, or ...


Temporal Dynamics Of Bacterial Communities In Soil And Leachate Water After Swine Manure Application, Elizabeth L. Rieke, Michelle L. Soupir, Thomas B. Moorman, Fan Yang, Adina C. Howe 2018 Iowa State University

Temporal Dynamics Of Bacterial Communities In Soil And Leachate Water After Swine Manure Application, Elizabeth L. Rieke, Michelle L. Soupir, Thomas B. Moorman, Fan Yang, Adina C. Howe

Agricultural and Biosystems Engineering Publications

Application of swine manure to agricultural land allows recycling of plant nutrients, but excess nitrate, phosphorus and fecal bacteria impact surface and drainage water quality. While agronomic and water quality impacts are well studied, little is known about the impact of swine manure slurry on soil microbial communities. We applied swine manure to intact soil columns collected from plots maintained under chisel plow or no-till with corn and soybean rotation. Targeted 16S-rRNA gene sequencing was used to characterize and to identify shifts in bacterial communities in soil over 108 days after swine manure application. In addition, six simulated rainfalls were ...


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 ...


The Effects Of Inulin And Galactooligosaccharides On The Production Of Reuterin By Lactobacillus Reuteri, Micah Dwight Forshee 2018 Olivet Nazarene University

The Effects Of Inulin And Galactooligosaccharides On The Production Of Reuterin By Lactobacillus Reuteri, Micah Dwight Forshee

ELAIA

The microbiome is a dynamic community that can positively and negatively influence host health. Lactobacillus reuteri is a probiotic that has received much attention for its ability to inhibit pathogens such as Salmonella typhimurium, Escherichia coli, and Clostridium difficile. It does so by its unique ability to metabolize glycerol into the antimicrobial compound 3-HPA, which is commonly referred to as reuterin. The ability to secrete reuterin is dependent not only on glycerol availability but also the concentration of glucose. In fact, there appears to be a “goldilocks” ratio between glucose and glycerol as either too much or too little glucose ...


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