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The Full Genome Sequence Of An Antarctic Microbe Constructed Using A Rapid, Portable Sequencer And A Hybrid Assembly, Bruce Wyatt Boles 2019 University of Tennessee, Knoxville

The Full Genome Sequence Of An Antarctic Microbe Constructed Using A Rapid, Portable Sequencer And A Hybrid Assembly, Bruce Wyatt Boles

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Microbial genomes contain combinations of nucleotides that code for genes which subsequently determines the function of the cell. This information provides significant insight into the unique niche of microbes from extreme environments. Here we use two sequencing technologies, the Oxford Nanopore MinION with accompanying software and Illumina HiSeq, to generate a hybrid genome for a Shewanella strain isolated from an Antarctic glacier. Bioinformatic programs, Albacore and SPAdes, allowed us to decrease the time of genome assembly while also obtaining a large quantity of information related to the Shewanella sp. Our combined approach yielded a high quality genome assembly 5.3 ...


What’S For Dinner? Different Carbon Compounds Influence Host Metabolism In A Model Roseobacter-Roseophage System, Kaylee Rae Jacobs 2019 University of Tennessee, Knoxville

What’S For Dinner? Different Carbon Compounds Influence Host Metabolism In A Model Roseobacter-Roseophage System, Kaylee Rae Jacobs

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Viruses that infect bacteria (temperate phages) engage in complex interactions with their hosts. These phages can have two life cycles: lytic and lysogenic. For the latter, the phage can integrate its genome into that of its host and harmlessly replicate alongside with it. Conversely, upon induction, these integrated viruses can excise from their host genome and initiate the lytic cycle. A current paradigm is that phage induction is in response to host cell stress. However, in the absence of stressors, a low level of induction in a population occurs. This poorly understood phenomenon is referred to as spontaneous prophage induction ...


Microbe Hunters: Searching For Anammox Bacteria In The Tennessee Aquarium, Claire Elbon 2019 University of Tennessee, Knoxville

Microbe Hunters: Searching For Anammox Bacteria In The Tennessee Aquarium, Claire Elbon

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Ammonium and nitrite are toxic metabolic waste products generated by aquatic macroorganisms. They are of particular concern in closed systems, such as commercial aquaria. Typically, biological filtration systems are employed to regulate levels of toxic N species as they are more cost-efficient compared to water removal and replacement. Microbial communities that reside in these systems play vital roles in transformation of toxic N species. Commonly, nitrite and ammonium are converted into nitrate via nitrification. However, even nitrate is toxic at higher concentrations. Bacteria belonging to the phylum Planctomycetes can transform ammonium and nitrite to N2 via anaerobic ammonium oxidation (anammox ...


Ultramicrobacteria Genome Database Project, Abdullah A. Salim, Tien Tran, Andrew Putt, Terry C. Hazen 2019 University of Tennessee, Knoxville

Ultramicrobacteria Genome Database Project, Abdullah A. Salim, Tien Tran, Andrew Putt, Terry C. Hazen

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Ultramicrobacteria (UMB) are a largely uncultured, globally abundant, and metabolically active group of bacteria. UMB have cell diameters ≤0.3μm, cell volumes ≤0.1 μm3, and small streamlined genomes. Recent findings indicate that UMB aid in bioremediation and nutrient cycling, but future investigations and comprehension of current findings are skewed by highly variable nomenclature and a lack of databases for functional, genomic, geochemical, or spatial data specific to candidate UMB. We aim to develop a user-friendly open-access database of various UMB candidates linked to an open-access online map where researchers can gather genomic, spatial, and geochemical data. Our comprehensive review ...


Microbial Abundance And The Pattern Of Escherichia Coli Antibiotic Sensitivity And Resistance In Deer Creek And The Potential Impact Of A Veterinarian Hospital’S Input, Sarah Boxer, tim gsell 2019 Governors State University

Microbial Abundance And The Pattern Of Escherichia Coli Antibiotic Sensitivity And Resistance In Deer Creek And The Potential Impact Of A Veterinarian Hospital’S Input, Sarah Boxer, Tim Gsell

GSU Research Day

The gram-negative bacteria, E. coli, is an indicator of fecal input for both point and non-point source origin. The veterinarian hospital located on Deer Creek may contribute to high antibiotic levels, which are known to select for resistant strains of bacteria living in impacted waters. The water running north of the veterinarian hospital was considered potentially antibiotic influenced as it was downstream of the site. The origin of the stream and sites upstream from the hospital were considered influent water. Sediments were also collected from these sites to determine if more long term resident E. coli were present with elevated ...


Lipoarabinomannan From Mycobacterium Smegmatis Stimulates An Inflammatory Response In Raw 264.7 Murine Macrophages, Aysha Zaman 2019 University of Lynchburg

Lipoarabinomannan From Mycobacterium Smegmatis Stimulates An Inflammatory Response In Raw 264.7 Murine Macrophages, Aysha Zaman

Student Scholar Showcase

Macrophages are a key leukocyte in defense against Mycobacterium tuberculosis infection. The precise mechanism by which M. tuberculosis evades host macrophage defenses remains unknown, so understanding how macrophages interact with cell wall components of mycobacteria is critical. Lipoarabinomannan (LAM) is a glycolipid Toll-like receptor-2 (TLR-2) ligand found on the cell wall of mycobacteria, and is thought to contribute to the cell wall structural integrity. When LAM binds to TLR on host leukocytes, this activates cellular responses and phagocytosis by host macrophages. Nitric oxide production can be used as a measure of inflammatory response and can be evaluated via nitrite response ...


Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney 2019 University of Lynchburg

Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney

Student Scholar Showcase

Pseudomonas putida GB-1 is a model organism for the study of manganese oxidation in bacteria, however, the frequency of co-localization of multiple known and suspected manganese oxidizing proteins, as well as their occurrence between species, is unknown. Eight different genes isolated from known manganese oxidizing bacteria (MnxG, MopA, McoA, PputGB1_2552, PputGB1_2553, MoxA, MofA, and Bacillus MnxG) were tested individually using BioPython and BLAST (Basic Local Alignment Search Tool) on multiple genomic databases. BLAST searches had an expect value cutoff of 1e-50, limiting gene homologs to those with high sequence similarity. The abundance of homologous genes across classes of proteobacteria point ...


Construction Of Recombinant Vaccinia Virus For Oncolyitc Therapy, Marlene L. Campos Guerrero 2019 Kansas State University

Construction Of Recombinant Vaccinia Virus For Oncolyitc Therapy, Marlene L. Campos Guerrero

Kansas State University Undergraduate Research Conference

Homologous recombination is a mechanism conducted to exchange nucleotides between two similar sequences, which allows researchers to knock out and add genetic sequences of their interest in vaccinia virus (VACV). In this study, a Western Reserve VACV strain with inserted genes encoding Red Florescence Protein (RFP) and Green Florescence Protein (GFP), will be targeted and replaced with the Thymidine Kinase gene, J2R as well as C11 gene, respectively. This will set the foundation for continual removal of genes as well as additions to make a virus that will more effectively target cancer cells without affecting healthy cells. To conduct this ...


Does Quorum Sensing Regulate The Conjugation Of The Two Co-Resident Megaplasmids Of Agrobacterium Tumefaciens 15955, Christopher Carter 2019 Kansas State University Libraries

Does Quorum Sensing Regulate The Conjugation Of The Two Co-Resident Megaplasmids Of Agrobacterium Tumefaciens 15955, Christopher Carter

Kansas State University Undergraduate Research Conference

While the effects of Agrobacterium tumefaciens can be easily observed and have been studied closely, the mechanisms for their virulence habits have not. Several studies have suggested the mechanisms for plasmid transfer and conjugation, particularly concerning plasmid Ti (pTi), the TraR (TraR1) regulator, and the quorum sensing (QS) system associated with it. Very little is known, however, about the second plasmid (pAt) present within the bacteria nor its regulatory QS systems. To further understand these mechanics of plasmid conjugation, we have devised a series of experiments in order to find connections between the conjugation of both pTi and pAt and ...


Assessment Of The Potential Use Of Recombinant Baculovirus-Expressed Lassa Virus Nucleoprotein As A Serodiagnostic Antigen, Sahiba Grover 2019 Kansas State University Libraries

Assessment Of The Potential Use Of Recombinant Baculovirus-Expressed Lassa Virus Nucleoprotein As A Serodiagnostic Antigen, Sahiba Grover

Kansas State University Undergraduate Research Conference

Lassa virus is an arenavirus causing a disseminated systemic primary viral infection. This virus causes Lassa fever which is a viral hemorrhagic fever endemic in West Africa and is responsible for the deaths of thousands of people each year. There is a possibility for the Lassa virus to be introduced into the US and used as a biological weapon with the potential to harm a large-scale population. Because of increasing international travel, a sizeable burden from the disease, and its potential use for biological warfare, it is necessary to develop sensitive diagnostic assays to accurately detect virus infections and mitigate ...


Agrobacterial Diversity And Competitive Interactions Within An Infected Sunflower, Veronica Mateo 2019 Kansas State University Libraries

Agrobacterial Diversity And Competitive Interactions Within An Infected Sunflower, Veronica Mateo

Kansas State University Undergraduate Research Conference

Agrobacterial Diversity and Competitive Interactions Within an Infected Sunflower

Veronica E. Mateo, Kansas State University

Faculty Advisor/Mentor: Thomas Platt, Ph.D., tgplatt@ksu.edu

Co-Author(s): Emireth Monarrez, Seward County Community College; Priscila Guzman, Kansas State University; Ashlee Herken, Kansas State University; Teresa Shippy, Kansas State University

Bacterial communities are highly diverse with each being distinct in composition. Agrobacterium tumefaciens is a common soilborne plant pathogen. Some A. tumefaciens strains can cause crown gall disease, in which infected plants develop a tumor. This bacterium disrupts the host plant by genetically transforming plant cells thereby manipulating the plant’s physiology ...


Determining The Role Of Cdr20291_0493 Sporulation Initiation In Clostridium Difficile, Carolina Bueno 2019 Kansas State University Libraries

Determining The Role Of Cdr20291_0493 Sporulation Initiation In Clostridium Difficile, Carolina Bueno

Kansas State University Undergraduate Research Conference

Our lab focuses on the gene regulatory networks of Clostridium difficilesporulation and toxins virulence factors. Spores are the major reason of the disease transmission; this is why it is important to understand how this spores are formed so drugs can be targeted to formation. Our objective is to identify the gene regulatory networks that control sporulation. The candidate target gene we are studying is CDR20291_0493 in C. difficileR20291 strain. We want to understand the role of this gene in sporulation initiation of C.difficile. We first created a mutant of CDR20291_0493 mutant R20291Dto look for sporulation phenotype and ...


You Are What You Eat At Any Age: Carbon And Nitrogen Analysis Of Mummies From An Ancient Egyptian Necropolis, Stephen Funk, R. Paul Evans 2019 Brigham Young University - Provo

You Are What You Eat At Any Age: Carbon And Nitrogen Analysis Of Mummies From An Ancient Egyptian Necropolis, Stephen Funk, R. Paul Evans

Library/Life Sciences Undergraduate Poster Competition 2019

The BYU Egypt Project at Fag el-Gamus necropolis and adjacent Seila Pyramid has studied over 700 mummies excavated over the past 30 years. The necropolis includes an open area with densely located vertical burial shafts and a hill with horizontal burial shafts. The chronological and dietary history of the mummies was assessed using stable isotopy and 14C analysis of accessible biological samples.


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 ...


Establishment Of Listeria Monocytogenes In The Gastrointestinal Tract, Morgan L. Davis, Steven C. Ricke, Janet R. Donaldson 2019 University of Arkansas, Fayetteville

Establishment Of Listeria Monocytogenes In The Gastrointestinal Tract, Morgan L. Davis, Steven C. Ricke, Janet R. Donaldson

Faculty Publications

Listeria monocytogenes is a Gram positive foodborne pathogen that can colonize the gastrointestinal tract of a number of hosts, including humans. These environments contain numerous stressors such as bile, low oxygen and acidic pH, which may impact the level of colonization and persistence of this organism within the GI tract. The ability of L. monocytogenes to establish infections and colonize the gastrointestinal tract is directly related to its ability to overcome these stressors, which is mediated by the efficient expression of several stress response mechanisms during its passage. This review will focus upon how and when this occurs and how ...


Anti-Drug Antibody Responses Impair Prophylaxis Mediated By Aav-Delivered Hiv-1 Broadly Neutralizing Antibodies, Matthew R. Gardner, Ina Fetzer, Lisa M. Kattenhorn, Meredith E. Davis-Gardner, Amber S. Zhou, Barnett Alfant, Jesse A. Weber, Hema R. Kondur, Jose M. Martinez-Navio, Sebastian P. Fuchs, Ronald C. Desrosiers, Guangping Gao, Jeffrey D. Lifson, Michael Farzan 2019 The Scripps Research Institute

Anti-Drug Antibody Responses Impair Prophylaxis Mediated By Aav-Delivered Hiv-1 Broadly Neutralizing Antibodies, Matthew R. Gardner, Ina Fetzer, Lisa M. Kattenhorn, Meredith E. Davis-Gardner, Amber S. Zhou, Barnett Alfant, Jesse A. Weber, Hema R. Kondur, Jose M. Martinez-Navio, Sebastian P. Fuchs, Ronald C. Desrosiers, Guangping Gao, Jeffrey D. Lifson, Michael Farzan

Open Access Articles

Adeno-associated virus (AAV) delivery of potent and broadly neutralizing antibodies (bNAbs is a promising approach for the prevention of HIV-1 infection. The immunoglobulin G (IgG)1 subtype is usually selected for this application, because it efficiently mediates antibody effector functions and has a somewhat longer half-life. However, the use of IgG1-Fc has been associated with the generation of anti-drug antibodies (ADAs) that correlate with loss of antibody expression. In contrast, we have shown that expression of the antibody-like molecule eCD4-Ig bearing a rhesus IgG2-Fc domain showed reduced immunogenicity and completely protected rhesus macaques from simian-HIV (SHIV)-AD8 challenges. To directly ...


A Human Papillomavirus-Independent Cervical Cancer Animal Model Reveals Unconventional Mechanisms Of Cervical Carcinogenesis, Chunbo He, Xiangmin Lv, Cong Huang, Peter C. Angeletti, Guohua Hua, Jixin Dong, Jin Zhou, Zhengfeng Wang, Bowen Ma, Xingcheng Chen, Paul F. Lambert, Bo R. Rueda, John S. Davis, Cheng Wang 2019 Massachusetts General Hospital & University of Nebraska Medical Center & Huazhong Agricultural University

A Human Papillomavirus-Independent Cervical Cancer Animal Model Reveals Unconventional Mechanisms Of Cervical Carcinogenesis, Chunbo He, Xiangmin Lv, Cong Huang, Peter C. Angeletti, Guohua Hua, Jixin Dong, Jin Zhou, Zhengfeng Wang, Bowen Ma, Xingcheng Chen, Paul F. Lambert, Bo R. Rueda, John S. Davis, Cheng Wang

Virology Papers

HPV infections are common in healthy women and only rarely cause cervical cancer, suggesting that individual genetic susceptibility may play a critical role in the establishment of persistent HPV infection and the development of cervical cancer. Here, we provide convincing in vitro and in vivo evidence showing that differential expression and activation of YAP1 oncogene determine individual susceptibility to HPV infection and cervical carcinogenesis. We found that hyperactivation of YAP1 in mouse cervical epithelium was sufficient to induce invasive cervical cancer. Cervical epithelial cell-specific HPV16 E6/E7 and YAP1 double-knockin mouse model demonstrated that high-risk HPV synergized with hyperactivated YAP1 ...


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 ...


A Comparative Analysis Of The Fermentation Capabilities Of Various Bifidobacterium Strains, Ella Oney 2019 University of Nebraska - Lincoln

A Comparative Analysis Of The Fermentation Capabilities Of Various Bifidobacterium Strains, Ella Oney

Honors Theses, University of Nebraska-Lincoln

Bifidobacterium is a genus of anaerobic bacteria that are commonly found to inhabit the gastrointestinal tract of many members of the animal kingdom. These microorganisms are adapted to obtain their carbon from the breakdown of complex carbohydrates. Marmosets, a mammal whose gut microbiome is inhabited by high levels of Bifidobacteria, consume gum Arabic as a major part of their diet. The purpose of this experiment is to determine whether Bifidobacterium strains isolated from the guts of marmosets are able to degrade and ferment this complex carbohydrate or one of its main constituents, arabinose. This was accomplished by inoculating isolates of ...


Viral Infection Or Ifn-Alpha Alters Mitotic Spindle Orientation By Modulating Pericentrin Levels, William M. McDougall, Jill Perreira, Hui-Fang Hung, Anastassiia Vertii, E. Xiaofei, Wendy Zimmerman, Timothy F. Kowalik, Stephen J. Doxsey, Abraham L. Brass 2019 University of Massachusetts Medical School

Viral Infection Or Ifn-Alpha Alters Mitotic Spindle Orientation By Modulating Pericentrin Levels, William M. Mcdougall, Jill Perreira, Hui-Fang Hung, Anastassiia Vertii, E. Xiaofei, Wendy Zimmerman, Timothy F. Kowalik, Stephen J. Doxsey, Abraham L. Brass

Open Access Articles

Congenital microcephaly occurs in utero during Zika virus (ZIKV) infection. The single-gene disorder, Majewski osteodysplastic primordial dwarfism type II (MOPDII), also leads to microcephaly and is concomitant with a decrease in the centrosomal protein, pericentrin (PCNT). This protein is a known contributor of mitotic spindle misorientation and ultimately, microcephaly. Similar to MOPDII, either viral infection or interferon (IFN)-alpha exposure reduced PCNT levels at the mitotic spindle poles. We unexpectedly found that infection of cells with any one of a diverse set of viruses, such as ZIKV, dengue virus, cytomegalovirus, influenza A virus, or hepatitis B virus, or treatment of ...


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