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Complete Genome Sequences Of Chop, Delrio, And Grandslam, Three Gordonia Phages Isolated From Soil In Central Arkansas, Heidi N. Mathes, Elijah I. Christenson, John H. Crum, Emme M. Edmondson, Kassidy E. Gray, Luke W. Lawson, Lauren E. Lee, Michael P. Lee, Jackson A. Lipscomb, Morgan E. Masengale, Hannah G. Matthews, Charles M. Mcclain 4th, Tuesday N. Melton, Trace H. Morrow, Alexis M. Perry, David R. Rainwater, Grace E. Renois, Maryann F. Rettig, Duncan C. Troup, Allie J. Wilson, Nathan Reyna, Ruth Plymale Apr 2023

Complete Genome Sequences Of Chop, Delrio, And Grandslam, Three Gordonia Phages Isolated From Soil In Central Arkansas, Heidi N. Mathes, Elijah I. Christenson, John H. Crum, Emme M. Edmondson, Kassidy E. Gray, Luke W. Lawson, Lauren E. Lee, Michael P. Lee, Jackson A. Lipscomb, Morgan E. Masengale, Hannah G. Matthews, Charles M. Mcclain 4th, Tuesday N. Melton, Trace H. Morrow, Alexis M. Perry, David R. Rainwater, Grace E. Renois, Maryann F. Rettig, Duncan C. Troup, Allie J. Wilson, Nathan Reyna, Ruth Plymale

Articles

Chop, DelRio, and GrandSlam are phage with a Siphoviridae morphotype isolated from soil in Arkansas using the host Gordonia terrae 3612. All three are temperate, and their genomes share at least 96% nucleotide identity. These phage are assigned to cluster DI based on gene content similarity to other sequenced actinobacteriophage.


Circulating Exosomal Micrornas As Predictive Biomarkers Of Neoadjuvant Chemotherapy Response In Breast Cancer, Valentina K. Todorova, Stephanie D. Byrum, Allen J. Gies, Cade Haynie, Hunter Smith, Nathan S. Reyna, Issam Makhoul Feb 2022

Circulating Exosomal Micrornas As Predictive Biomarkers Of Neoadjuvant Chemotherapy Response In Breast Cancer, Valentina K. Todorova, Stephanie D. Byrum, Allen J. Gies, Cade Haynie, Hunter Smith, Nathan S. Reyna, Issam Makhoul

Articles

Background: Neoadjuvant chemotherapy (NACT) is an increasingly used approach for treatment of breast cancer. The pathological complete response (pCR) is considered a good predictor of disease-specific survival. This study investigated whether circulating exosomal microRNAs could predict pCR in breast cancer patients treated with NACT. Method: Plasma samples of 20 breast cancer patients treated with NACT were collected prior to and after the first cycle. RNA sequencing was used to determine microRNA profiling. The Cancer Genome Atlas (TCGA) was used to explore the expression patterns and survivability of the candidate miRNAs, and their potential targets based on the expression levels and …


Complete Genome Sequences Of Four Putatively Antibiotic-Producing Bacteria Isolated From Soil In Arkansas, Usa, Ruth Plymale, Griffin Hopkins, Taylor Johnson, Taylor Savage, Danielle Schaal Jan 2022

Complete Genome Sequences Of Four Putatively Antibiotic-Producing Bacteria Isolated From Soil In Arkansas, Usa, Ruth Plymale, Griffin Hopkins, Taylor Johnson, Taylor Savage, Danielle Schaal

Articles

Soil bacteria can be a valuable source of antimicrobial compounds. Here, we report the complete genomes of four soil bacteria that were isolated by undergraduate microbiology students as part of a course-based research experience. These genomes were assembled using a hybrid approach combining paired-end Illumina reads with Oxford Nanopore Technologies MinION reads.


Transitioning Cell Culture Cure Labs From Campus To Online: Novel Strategies For A Novel Time, Jaime L. Sabel, Kendra Wright, Jacob J. Adler, Gary Bates, La Shall Bates, Sumali Pandey, Amanda M. Simons, Sarah J. Swerdlow, Nathan S. Reyna, Lori Hensley Mar 2021

Transitioning Cell Culture Cure Labs From Campus To Online: Novel Strategies For A Novel Time, Jaime L. Sabel, Kendra Wright, Jacob J. Adler, Gary Bates, La Shall Bates, Sumali Pandey, Amanda M. Simons, Sarah J. Swerdlow, Nathan S. Reyna, Lori Hensley

Articles

Course-based undergraduate research experiences (CUREs) provide a way for students to gain research experience in a classroom setting. Few examples of cell culture CUREs or online CUREs exist in the literature. The Cell Biology Education Consortium (CBEC) provides a network and resources for instructors working to incorporate cell-culture based research into the classroom. In this article, we provide examples from six instructors from the CBEC network on how they structure their cell-culture CUREs and how they transitioned the labs to online in the spring semester of 2020. We intend for these examples to provide instructors with ideas for strategies to …


Novel Role For The Golgi Membrane Protein Tmem165 In Control Of Migration And Invasion For Breast Carcinoma, Pavitra Murali, Blake P. Johnson, Zhongpeng Lu, Leslie Climer, Danielle A. Scott, Francois Foulquier, Gabriela Oprea-Ilies, Vladimir Lupashin, Richard R. Drake, Karen L. Abbott Jul 2020

Novel Role For The Golgi Membrane Protein Tmem165 In Control Of Migration And Invasion For Breast Carcinoma, Pavitra Murali, Blake P. Johnson, Zhongpeng Lu, Leslie Climer, Danielle A. Scott, Francois Foulquier, Gabriela Oprea-Ilies, Vladimir Lupashin, Richard R. Drake, Karen L. Abbott

Articles

The TMEM165 gene encodes for a multiple pass membrane protein localized in the Golgi that has been linked to congenital disorders of glycosylation. The TMEM165 protein is a putative ion transporter that regulates H+/Ca++/Mn++ homeostasis and pH in the Golgi. Previously, we identified TMEM165 as a potential biomarker for breast carcinoma in a glycoproteomic study using late stage invasive ductal carcinoma tissues with patient-matched adjacent normal tissues. The TMEM165 protein was not detected in non-malignant matched breast tissues and was detected in invasive ductal breast carcinoma tissues by mass spectrometry. Our hypothesis is that the TMEM165 protein confers a growth …


Glioma-Derived Exosomes Drive The Differentiation Of Neural Stem Cells To Astrocytes, Krishna D. Sharma, Danielle Schaal, Rajshekhar A. Kore, Rabab N. Hamzah, Sahitya Chetan Pandanaboina, Abdallah Hayar, Robert J. Griffin, Malathi Srivatsan, Nathan S. Reyna, Jennifer Yanhua Xie Jul 2020

Glioma-Derived Exosomes Drive The Differentiation Of Neural Stem Cells To Astrocytes, Krishna D. Sharma, Danielle Schaal, Rajshekhar A. Kore, Rabab N. Hamzah, Sahitya Chetan Pandanaboina, Abdallah Hayar, Robert J. Griffin, Malathi Srivatsan, Nathan S. Reyna, Jennifer Yanhua Xie

Articles

Exosomes appear to be effective inter-cellular communicators delivering several types of molecules, such as proteins and RNAs, suggesting that they could influence neural stem cell (NSC) differentiation. Our RNA sequencing studies demonstrated that the RNAs related to cell proliferation and astrocyte differentiation were upregulated in human mesenchymal stem cells (hMSC) when co-cultured with exosomes obtained from the culture medium of human glioma cells (U87). Metallothionein 3 and elastin genes, which are related to cell proliferation, increased 10 and 7.2 fold, respectively. Expression of genes for astrocyte differentiation, such as tumor growth factor alpha, induced protein 3 of the NOTCH1 family, …


Genomic Diversity Of Bacteriophages Infecting Microbacterium Spp, Deborah Jacobs-Sera, Nathan S. Reyna, Lawrence A. Abad, Richard M. Alvey, Kirk R. Anders, Haley G. Aull, Suparna S. Bhalla, Lawrence S. Blumer, David W. Bollivar, J. Alfred Bonilla, Kristen A. Butela, Roy J. Coomans, Steven G. Cresawn, Tom D'Elia, Arturo Diaz, Ashley M. Divens, Nicholas P. Edgington, Gregory D. Frederick, Maria D. Gainey, Rebecca A. Garlena, Kenneth W. Grant, Susan M.R. Gurney, Heather L. Hendrickson, Lee E. Hughes, Margaret A. Kenna, Karen K. Klyczek, Hari Kotturi, Travis N. Mavrich, Angela L. Mckinney, Evan C. Merkhofer, Jordan Moberg Parker, Sally D. Molloy, Denise L. Monti, Dana A. Pape-Zambito Jun 2020

Genomic Diversity Of Bacteriophages Infecting Microbacterium Spp, Deborah Jacobs-Sera, Nathan S. Reyna, Lawrence A. Abad, Richard M. Alvey, Kirk R. Anders, Haley G. Aull, Suparna S. Bhalla, Lawrence S. Blumer, David W. Bollivar, J. Alfred Bonilla, Kristen A. Butela, Roy J. Coomans, Steven G. Cresawn, Tom D'Elia, Arturo Diaz, Ashley M. Divens, Nicholas P. Edgington, Gregory D. Frederick, Maria D. Gainey, Rebecca A. Garlena, Kenneth W. Grant, Susan M.R. Gurney, Heather L. Hendrickson, Lee E. Hughes, Margaret A. Kenna, Karen K. Klyczek, Hari Kotturi, Travis N. Mavrich, Angela L. Mckinney, Evan C. Merkhofer, Jordan Moberg Parker, Sally D. Molloy, Denise L. Monti, Dana A. Pape-Zambito

Articles

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, …


Generation Of A Fully Human Scfv That Binds Tumor-Specific Glycoforms, Zhongpeng Lu, Kalika Kamat, Blake P. Johnson, Catherin C. Yin, Nathalie Scholler, Karen L. Abbott Dec 2019

Generation Of A Fully Human Scfv That Binds Tumor-Specific Glycoforms, Zhongpeng Lu, Kalika Kamat, Blake P. Johnson, Catherin C. Yin, Nathalie Scholler, Karen L. Abbott

Articles

Tumor-specific glycosylation changes are an attractive target for the development of diagnostic and therapeutic applications. Periostin is a glycoprotein with high expression in many tumors of epithelial origin including ovarian cancer. Strategies to target the peptide portion of periostin as a diagnostic or therapeutic biomarker for cancer are limited due to increased expression of periostin in non-cancerous inflammatory conditions. Here, we have screened for antibody fragments that recognize the tumor-specific glycosylation present on glycoforms of periostin containing bisecting N-glycans in ovarian cancer using a yeast-display library of antibody fragments, while subtracting those that bind to the periostin protein with glycoforms …


Hypoxia-Derived Exosomes Induce Putative Altered Pathways In Biosynthesis And Ion Regulatory Channels In Glioblastoma Cells, Rajshekhar A. Kore, Jacob L. Edmondson, Samir V. Jenkins, Azemat Jamshidi-Parsian, Ruud P.M. Dings, Nathan S. Reyna, Robert J. Griffin Jul 2018

Hypoxia-Derived Exosomes Induce Putative Altered Pathways In Biosynthesis And Ion Regulatory Channels In Glioblastoma Cells, Rajshekhar A. Kore, Jacob L. Edmondson, Samir V. Jenkins, Azemat Jamshidi-Parsian, Ruud P.M. Dings, Nathan S. Reyna, Robert J. Griffin

Articles

Hypoxia, a hallmark characteristic of glioblastoma (GBM) induces changes in the transcriptome and the proteome of tumor cells. We discovered that hypoxic stress produces significant qualitative and quantitative changes in the protein content of secreted exosomes from GBM cells. Among the proteins found to be selectively elevated in hypoxic exosomes were protein-lysine 6-oxidase (LOX), thrombospondin-1 (TSP1), vascular derived endothelial factor (VEGF) and a disintegrin and metalloproteinase with thrombospondin motifs 1 (ADAMTS1), well studied contributors to tumor progression, metastasis and angiogenesis. Our findings demonstrate that hypoxic exosomes induce differential gene expression in recipient glioma cells. Glioma cells stimulated with hypoxic exosomes …


Genome Sequences Of Four Cluster P Mycobacteriophages, Erin L. Doyle, Christy L. Fillman, Nathan S. Reyna, Ruth C. Plymale, Deborah M. Tobiason, Daniel E. Westholm, Jonathan L. Askins, Brittany P. Backus, Ashlynn C. Baker, Harrison S. Ballard, Paul J. Bisesi, Logan Bond, Deanna Byrnes, Hannah Carlstedt, Kinnon S. Dodson, Megan J. Fallert, Kyla J. Foster, Daniel N. Games, Tristan R. Grams, Nancy A. Guild, Autumn Hurd, Nicholas Iwata, Cassidy R. Kepler, Lucinda R. Krenzke, Kelly Luekens, Jackie Lewis, Cali Mcentee, Justin C. Mcgee, Noah Nalley, Jade Prochaska, Reid G. Rogers, Jessica B. Schipper, Kelsey Snyder Jan 2018

Genome Sequences Of Four Cluster P Mycobacteriophages, Erin L. Doyle, Christy L. Fillman, Nathan S. Reyna, Ruth C. Plymale, Deborah M. Tobiason, Daniel E. Westholm, Jonathan L. Askins, Brittany P. Backus, Ashlynn C. Baker, Harrison S. Ballard, Paul J. Bisesi, Logan Bond, Deanna Byrnes, Hannah Carlstedt, Kinnon S. Dodson, Megan J. Fallert, Kyla J. Foster, Daniel N. Games, Tristan R. Grams, Nancy A. Guild, Autumn Hurd, Nicholas Iwata, Cassidy R. Kepler, Lucinda R. Krenzke, Kelly Luekens, Jackie Lewis, Cali Mcentee, Justin C. Mcgee, Noah Nalley, Jade Prochaska, Reid G. Rogers, Jessica B. Schipper, Kelsey Snyder

Articles

Four bacteriophages infecting Mycobacterium smegmatis mc2155 (three belonging to subcluster P1 and one belonging to subcluster P2) were isolated from soil and sequenced. All four phages are similar in the left arm of their genomes, but the P2 phage differs in the right arm. All four genomes contain features of temperate phages.


The Glycosyltransferase Gnt-Iii Activates Notch Signaling And Drives Stem Cell Expansion To Promote The Growth And Invasion Of Ovarian Cancer, Heba Allam, Blake P. Johnson, Mao Zhang, Zhongpeng Lu, Martin J. Cannon, Karen L. Abbott Sep 2017

The Glycosyltransferase Gnt-Iii Activates Notch Signaling And Drives Stem Cell Expansion To Promote The Growth And Invasion Of Ovarian Cancer, Heba Allam, Blake P. Johnson, Mao Zhang, Zhongpeng Lu, Martin J. Cannon, Karen L. Abbott

Articles

Glycosylation changes associated with cellular transformation can facilitate the growth and progression of tumors. Previously we discovered that the gene Mgat3 encoding the glycosyltransferase GnT-III is elevated in epithelial ovarian carcinomas (EOCs) and leads to the production of abnormal truncated N-linked glycan structures instead of the typical bisected forms. In this study, we are interested in discovering how these abnormal glycans impact the growth and progression of ovarian cancer. We have discovered using stable shRNA gene suppression that GnT-III expression controls the expansion of side-population cells, also known as cancer stem cells. More specifically, we found that GnT-III expression regulates …


Rapid Verification Of Terminators Using The Pgr-Blue Plasmid And Golden Gate Assembly, Jace C. Bradshaw, Allea Belle Gongola, Nathan S. Reyna Apr 2016

Rapid Verification Of Terminators Using The Pgr-Blue Plasmid And Golden Gate Assembly, Jace C. Bradshaw, Allea Belle Gongola, Nathan S. Reyna

Articles

The goal of this protocol is to allow for the rapid verification of bioinformatically identified terminators. Further, the plasmid (pGR-Blue) is designed specifically for this protocol and allows for the quantification of terminator efficiency. As a proof of concept, six terminators were bioinformatically identified in the mycobacteriophage Bernal13. Once identified, terminators were then made as oligonucleotides with the appropriate sticky ends and annealed together. Using Golden Gate Assembly (GGA), terminators were then cloned into pGR-Blue. Under visible light, false positive colonies appear blue and positively transformed colonies are white/yellow. After induction of an arabinose inducible promoter (pBad) with arabinose, colony …


Comparative Genomics Of Cluster O Mycobacteriophages, Steven G. Cresawn, Nathan S. Reyna, Ruth Plymale, Welkin H. Pope, Deborah Jacobs-Sera, Charles A. Bowman, Daniel A. Russell, Rebekah M. Dedrick, Tamarah Adair, Kirk R. Anders, Sarah Ball, David Bollivar, Caroline Breitenberger, Sandra H. Burnett, Kristen Butela, Deanna Byrnes, Sarah Carzo, Kathleen A. Cornely, Trevor Cross, Richard L. Daniels, David Dunbar, Ann M. Findley, Chris R. Gissendanner, Urszula P. Golebiewska, Grant A. Hartzog, J. Robert Hatherill, Lee E. Hughes, Chernoh S. Jalloh, Carla De Los Santos, Kevin Ekanem, Sphindile L. Khambule, Rodney A. King, Christina King-Smith, Karen Klyczek, Greg P. Krukonis Mar 2015

Comparative Genomics Of Cluster O Mycobacteriophages, Steven G. Cresawn, Nathan S. Reyna, Ruth Plymale, Welkin H. Pope, Deborah Jacobs-Sera, Charles A. Bowman, Daniel A. Russell, Rebekah M. Dedrick, Tamarah Adair, Kirk R. Anders, Sarah Ball, David Bollivar, Caroline Breitenberger, Sandra H. Burnett, Kristen Butela, Deanna Byrnes, Sarah Carzo, Kathleen A. Cornely, Trevor Cross, Richard L. Daniels, David Dunbar, Ann M. Findley, Chris R. Gissendanner, Urszula P. Golebiewska, Grant A. Hartzog, J. Robert Hatherill, Lee E. Hughes, Chernoh S. Jalloh, Carla De Los Santos, Kevin Ekanem, Sphindile L. Khambule, Rodney A. King, Christina King-Smith, Karen Klyczek, Greg P. Krukonis

Articles

Mycobacteriophages - viruses of mycobacterial hosts - are genetically diverse but morphologically are all classified in the Caudovirales with double-stranded DNA and tails. We describe here a group of five closely related mycobacteriophages - Corndog, Catdawg, Dylan, Firecracker, and YungJamal - designated as Cluster O with long flexible tails but with unusual prolate capsids. Proteomic analysis of phage Corndog particles, Catdawg particles, and Corndog-infected cells confirms expression of half of the predicted gene products and indicates a non-canonical mechanism for translation of the Corndog tape measure protein. Bioinformatic analysis identifies 8-9 strongly predicted SigA promoters and all five Cluster O …


Emergent Fungal Entomopathogen Does Not Alter Density Dependence In A Viral Competitor, Andrew M. Liebhold, Ruth Plymale, Joseph S. Elkinton, Ann E. Hajek Jun 2013

Emergent Fungal Entomopathogen Does Not Alter Density Dependence In A Viral Competitor, Andrew M. Liebhold, Ruth Plymale, Joseph S. Elkinton, Ann E. Hajek

Articles

Population cycles in forest Lepidoptera often result from recurring density-dependent epizootics of entomopathogens. While these systems are typically dominated by a single pathogen species, insects are often infected by multiple pathogens, yet little is known how pathogens interact to affect host dynamics. The apparent invasion of northeastern North America by the fungal entomopathogen Entomophaga maimaiga some time prior to 1989 provides a unique opportunity to evaluate such interactions. Prior to the arrival of E. maimaga, the oscillatory dynamics of host gypsy moth, Lymantria dispar, populations were apparently driven by epizootics of a nucleopolyhedrovirus. Subsequent to its emergence, E. …


Comparing Two Methods For Quantifying Soil-Borne Entomophaga Maimaiga Resting Spores, Ann E. Hajek, Ruth C. Plymale, James R. Reilly Aug 2012

Comparing Two Methods For Quantifying Soil-Borne Entomophaga Maimaiga Resting Spores, Ann E. Hajek, Ruth C. Plymale, James R. Reilly

Articles

To improve usability of methods for quantifying environmentally persistent entomophthoralean resting spores in soil, we modified and tested two methods using resting spores (azygospores) of the gypsy moth pathogen Entomophaga maimaiga. Both methods were effective for recovering resting spores at concentrations >100 resting spores/g dry soil. While a modification of a method originally described by Weseloh and Andreadis (2002) recovered more resting spores than a modified method based on Percoll density gradients, the ability to estimate true densities from counts was similar for both methods. Regression equations are provided for predicting true resting spore densities from counts, with R 2 …


Plant-Mediated Alteration Of The Peritrophic Matrix And Baculovirus Infection In Lepidopteran Larvae, Ruth C. Plymale, Michael J. Grove, Diana Cox-Foster, Nancy Ostiguy, Kelli Hoover Apr 2008

Plant-Mediated Alteration Of The Peritrophic Matrix And Baculovirus Infection In Lepidopteran Larvae, Ruth C. Plymale, Michael J. Grove, Diana Cox-Foster, Nancy Ostiguy, Kelli Hoover

Articles

The peritrophic matrix (PM) lines the midgut of most insects, providing protection to the midgut epithelial cells while permitting passage of nutrients and water. Herein, we provide evidence that plant-mediated alteration of the PM contributes to the well-documented inhibition of fatal infection by Autographa californica multiple nucleopolyhedrovirus (AcMNPV) of Heliothis virescens F. larvae fed cotton foliage. We examined the impact of the PM on pathogenesis using a viral construct expressing a reporter gene (AcMNPV-hsp70/ lacZ) orally inoculated into larvae with either intact PMs or PMs disrupted by Trichoplusia ni granulovirus occlusion bodies containing enhancin, known to degrade insect intestinal mucin. …


Induction Of Systemic Acquired Resistance In Cotton Foliage Does Not Adversely Affect The Performance Of An Entomopathogen, Ruth C. Plymale, Gary W. Felton, Kelli Hoover Jul 2007

Induction Of Systemic Acquired Resistance In Cotton Foliage Does Not Adversely Affect The Performance Of An Entomopathogen, Ruth C. Plymale, Gary W. Felton, Kelli Hoover

Articles

Baculoviral efficacy against lepidopteran larvae is substantially impacted by the host plant. Here, we characterized how baculoviral pathogenicity to cotton-fed Heliothis virescens larvae is affected by induction of systemic acquired resistance (SAR). Numerous studies have shown that SAR induced by the plant elicitor benzo-(1,2,3)-thiadiazole-7- carbothioic acid S-methyl ester (BTH) can protect against plant pathogens, but reports on the impacts of SAR on chewing herbivores or on natural enemies of herbivores are few. We found that BTH application significantly increased foliar peroxidase activity, condensed tannin levels, and total phenolic levels but did not alter dihydroxyphenolic levels. Consumption of BTH-treated foliage did …


Evaluation Of Marker-Assisted Introgression Of Yield Qtl Alleles Into Adapted Soybean, Nathan S. Reyna, C.H. Sneller Jul 2001

Evaluation Of Marker-Assisted Introgression Of Yield Qtl Alleles Into Adapted Soybean, Nathan S. Reyna, C.H. Sneller

Articles

Genetic diversity is limited in southern elite soybean [Glycine max (L.) Merrill]. Introgression of diverse alleles for yield may increase the rate of yield improvement. Beneficial yield alleles at three quantitative trait loci (QTL) from the northern cultivar Archer have been tagged with molecular markers. The objective of this research was to assess the value of the three Archer alleles for increased yield in southern environments and genetic backgrounds. Four sets of near isogenic lines (NIL) for each quantitative trait locus (QTL) were derived from heterozygous F6 plants identified from the crosses of Archer X Asgrow A5403 and …