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Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ligin Solamen, Kenneth W. Olsen, Catherine Putonti, Stefan M. Kanzok Dec 2018

Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ligin Solamen, Kenneth W. Olsen, Catherine Putonti, Stefan M. Kanzok

Biology: Faculty Publications and Other Works

We recently identified three novel thioredoxin-like genes in the genome of the protozoan parasite Plasmodium that belong to the Phosducin-like family of proteins (PhLP). PhLPs are small cytosolic proteins hypothesized to function in G-protein signaling and protein folding. Although PhLPs are highly conserved in eukaryotes from yeast to mammals, only a few representatives have been experimentally characterized to date. In addition, while PhLPs contain a thioredoxin domain, they lack a CXXC motif, a strong indicator for redox activity, and it is unclear whether members of the PhLP family are enzymatically active. Here, we describe PbPhLP-3 as the first phosducin-like protein …


Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Sean W. Powers, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ligin Solamen, Kenneth W, Olsen, Catherine Putonti, Stefan M. Kanzok Dec 2018

Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Sean W. Powers, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ligin Solamen, Kenneth W, Olsen, Catherine Putonti, Stefan M. Kanzok

Bioinformatics Faculty Publications

We recently identified three novel thioredoxin-like genes in the genome of the protozoan parasite Plasmodium that belong to the Phosducin-like family of proteins (PhLP). PhLPs are small cytosolic proteins hypothesized to function in G-protein signaling and protein folding. Although PhLPs are highly conserved in eukaryotes from yeast to mammals, only a few representatives have been experimentally characterized to date. In addition, while PhLPs contain a thioredoxin domain, they lack a CXXC motif, a strong indicator for redox activity, and it is unclear whether members of the PhLP family are enzymatically active. Here, we describe PbPhLP-3 as the first phosducin-like protein …


Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Sean W. Powers, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ken W. Olsen, Catherine Putonti, Stefan M. Kanzok Dec 2018

Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Sean W. Powers, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ken W. Olsen, Catherine Putonti, Stefan M. Kanzok

Chemistry: Faculty Publications and Other Works

We recently identified three novel thioredoxin-like genes in the genome of the protozoan parasite Plasmodium that belong to the Phosducin-like family of proteins (PhLP). PhLPs are small cytosolic proteins hypothesized to function in G-protein signaling and protein folding. Although PhLPs are highly conserved in eukaryotes from yeast to mammals, only a few representatives have been experimentally characterized to date. In addition, while PhLPs contain a thioredoxin domain, they lack a CXXC motif, a strong indicator for redox activity, and it is unclear whether members of the PhLP family are enzymatically active. Here, we describe PbPhLP-3 as the first phosducin-like protein …


Minimum Information About An Uncultivated Virus Genome (Miuvig), Simon Roux, Evelien M. Adriaenssens, Bas E. Dutilh, Eugene V. Koonin, Andrew M. Kropinski, Mart Krupovic, Jens H. Kuhn, Rob Lavigne, J Rodney Brister, Arvind Varsani, Clara Amid, Ramy K. Aziz, Seth R. Bordenstein, Peer Bork, Mya Breitbart, Guy R. Cochrane, Rebecca A. Daly, Christelle Desnues, Melissa B. Duhaime, Joanne B. Emerson, François Enault, Jed A. Fuhrman, Pascal Hingamp, Philip Hugenholtz, Bonnie L. Hurwitz, Natalie N. Ivanova, Jessica M. Labonté, Kyung-Bum Lee, Rex R. Malmstrom, Manuel Martinez-Garcia, Ilene Karsch Mizrachi, Hiroyuki Ogata, David Páez-Espino, Marie-Agnès Petit, Catherine Putonti, Thomas Rattei, Alejandro Reyes, Francisco Rodriguez-Valera, Karyna Rosario, Lynn Schriml, Frederik Schulz, Grieg F. Steward, Matthew B. Sullivan, Shinichi Sunagawa, Curtis A. Suttle, Ben Temperton, Susannah G. Tringe, Rebecca Vega Thurber, Nicole S. Webster, Katrine L. Whiteson, Steven W. Whilhelm, K Eric Wommack, Tanja Woyke, Kelly C. Wrighton, Pelin Yilmaz, Takashi Yoshida, Mark J. Young, Natalya Yutin, Lisa Zeigler Allen, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh Dec 2018

Minimum Information About An Uncultivated Virus Genome (Miuvig), Simon Roux, Evelien M. Adriaenssens, Bas E. Dutilh, Eugene V. Koonin, Andrew M. Kropinski, Mart Krupovic, Jens H. Kuhn, Rob Lavigne, J Rodney Brister, Arvind Varsani, Clara Amid, Ramy K. Aziz, Seth R. Bordenstein, Peer Bork, Mya Breitbart, Guy R. Cochrane, Rebecca A. Daly, Christelle Desnues, Melissa B. Duhaime, Joanne B. Emerson, François Enault, Jed A. Fuhrman, Pascal Hingamp, Philip Hugenholtz, Bonnie L. Hurwitz, Natalie N. Ivanova, Jessica M. Labonté, Kyung-Bum Lee, Rex R. Malmstrom, Manuel Martinez-Garcia, Ilene Karsch Mizrachi, Hiroyuki Ogata, David Páez-Espino, Marie-Agnès Petit, Catherine Putonti, Thomas Rattei, Alejandro Reyes, Francisco Rodriguez-Valera, Karyna Rosario, Lynn Schriml, Frederik Schulz, Grieg F. Steward, Matthew B. Sullivan, Shinichi Sunagawa, Curtis A. Suttle, Ben Temperton, Susannah G. Tringe, Rebecca Vega Thurber, Nicole S. Webster, Katrine L. Whiteson, Steven W. Whilhelm, K Eric Wommack, Tanja Woyke, Kelly C. Wrighton, Pelin Yilmaz, Takashi Yoshida, Mark J. Young, Natalya Yutin, Lisa Zeigler Allen, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh

Bioinformatics Faculty Publications

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative …


Life History And Habitat Of The Rare Patch-Nosed Salamander (Urspelerpes Brucei), Carlos D. Camp, Tyler L. Brock, Todd W. Pierson, Joseph Milanovich, John C. Maerz Dec 2018

Life History And Habitat Of The Rare Patch-Nosed Salamander (Urspelerpes Brucei), Carlos D. Camp, Tyler L. Brock, Todd W. Pierson, Joseph Milanovich, John C. Maerz

Biology: Faculty Publications and Other Works

We examined the life history and habitat characteristics for the Patch-nosed Salamander, Urspelerpes brucei. Body-size measurements of individuals captured using litter bags and by hand from 2008 to 2010 indicated that the larval period lasts at least 2 y, salamanders attain reproductive maturity at or shortly after metamorphosis, and adults have very little variation in body size. Occupied streams are characterized by small size, little water, and narrow, steep-walled ravines. Within occupied streams, larval capture rate was significantly and negatively related to mean water depth, underscoring the importance of protecting headwaters. We hypothesize that the only known population of U. …


A High-Fat Diet Alters Genome-Wide Dna Methylation And Gene Expression In Sm/J Mice, Madeline R. Keleher, Rabab Zaidi, Lauren Hicks, Shyam Shah, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud Dec 2018

A High-Fat Diet Alters Genome-Wide Dna Methylation And Gene Expression In Sm/J Mice, Madeline R. Keleher, Rabab Zaidi, Lauren Hicks, Shyam Shah, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud

Biology: Faculty Publications and Other Works

Background: While the genetics of obesity has been well defined, the epigenetics of obesity is poorly understood. Here, we used a genome-wide approach to identify genes with differences in both DNA methylation and expression associated with a high-fat diet in mice. Results: We weaned genetically identical Small (SM/J) mice onto a high-fat or low-fat diet and measured their weights weekly, tested their glucose and insulin tolerance, assessed serum biomarkers, and weighed their organs at necropsy. We measured liver gene expression with RNA-seq (using 21 total libraries, each pooled with 2 mice of the same sex and diet) and DNA methylation …


The Effect Of Dietary Fat On Behavior In Mice, Madeline R. Keleher, Rabab Zaidi, Kayna Patel, Amer Ahmed, Carlee Bettler, Cassondra Pavlatos, Shyam Shah, James M. Cheverud Dec 2018

The Effect Of Dietary Fat On Behavior In Mice, Madeline R. Keleher, Rabab Zaidi, Kayna Patel, Amer Ahmed, Carlee Bettler, Cassondra Pavlatos, Shyam Shah, James M. Cheverud

Biology: Faculty Publications and Other Works

Purpose Obesity is linked to cognitive dysfunction in humans and rodents, and its effects can be passed on to the next generation. However, the extent of these effects is not well understood. The purpose of this study was to determine the effect of a prenatal maternal high-fat diet and an individual high-fat diet in inbred mice. Methods We varied maternal diet and offspring diet to test the hypothesis that a high-fat diet would increase anxiety, reduce activity levels, and impair nest-building. First, we fed a high-fat (HF) or low-fat (LF) diet to genetically identical female Small (SM/J) mice and mated …


Relationships Between Neuronal Birthdates And Tonotopic Positions In The Mouse Cochlear Nucleus, Austin R. Shepard, Jennifer L. Scheffel, Wei-Ming Yu Nov 2018

Relationships Between Neuronal Birthdates And Tonotopic Positions In The Mouse Cochlear Nucleus, Austin R. Shepard, Jennifer L. Scheffel, Wei-Ming Yu

Biology: Faculty Publications and Other Works

Tonotopy is a key anatomical feature of the vertebrate auditory system, but little is known about the mechanisms underlying its development. Since date of birth of a neuron correlates with tonotopic position in the cochlea, we investigated if it also correlates with tonotopic position in the cochlear nucleus (CN). In the cochlea, spiral ganglion neurons are organized in a basal to apical progression along the length of the cochlea based on birthdates, with neurons in the base (responding to high‐frequency sounds) born early around mouse embryonic day (E) 9.5–10.5, and those in the apex (responding to low‐frequency sounds) born late …


Mechanic Stress Generated By A Time-Varying Electromagnetic Field On Bone Surface, Hui Ye Oct 2018

Mechanic Stress Generated By A Time-Varying Electromagnetic Field On Bone Surface, Hui Ye

Biology: Faculty Publications and Other Works

Bone cells sense mechanical load, which is essential for bone growth and remodeling. In a fracture, this mechanism is compromised. Electromagnetic stimulation has been widely used to assist in bone healing, but the underlying mechanisms are largely unknown. A recent hypothesis suggests that electromagnetic stimulation could influence tissue biomechanics; however, a detailed quantitative understanding of EM-induced biomechanical changes in the bone is unavailable. This paper used a muscle/bone model to study the biomechanics of the bone under EM exposure. Due to the dielectric properties of the muscle/bone interface, a time-varying magnetic field can generate both compressing and shear stresses on …


S-Plot2: Rapid Visual And Statistical Analysis Of Genomic Sequences, Laurynas Kalesinskas, Evan Cudone, Yuriy Fofanov, Catherine Putonti Sep 2018

S-Plot2: Rapid Visual And Statistical Analysis Of Genomic Sequences, Laurynas Kalesinskas, Evan Cudone, Yuriy Fofanov, Catherine Putonti

Biology: Faculty Publications and Other Works

With the daily release of data from whole genome sequencing projects, tools to facilitate comparative studies are hard-pressed to keep pace. Graphical software solutions can readily recognize synteny by measuring similarities between sequences. Nevertheless, regions of dissimilarity can prove to be equally informative; these regions may harbor genes acquired via lateral gene transfer (LGT), signify gene loss or gain, or include coding regions under strong selection. Previously, we developed the software S-plot. This tool employed an alignment-free approach for comparing bacterial genomes and generated a heatmap representing the genomes’ similarities and dissimilarities in nucleotide usage. In prior studies, this tool …


Genetic Architecture Of Gene Expression Traits Across Diverse Populations, Lauren S. Mogil, Angela Andaleon, Alexa Badalamenti, Scott P. Dickinson, Xiuqing Guo, Jerome I. Rotter, W. Craig Johnson, Hae Kyung Im, Yongmei Liu, Heather E. Wheeler Aug 2018

Genetic Architecture Of Gene Expression Traits Across Diverse Populations, Lauren S. Mogil, Angela Andaleon, Alexa Badalamenti, Scott P. Dickinson, Xiuqing Guo, Jerome I. Rotter, W. Craig Johnson, Hae Kyung Im, Yongmei Liu, Heather E. Wheeler

Biology: Faculty Publications and Other Works

For many complex traits, gene regulation is likely to play a crucial mechanistic role. How the genetic architectures of complex traits vary between populations and subsequent effects on genetic prediction are not well understood, in part due to the historical paucity of GWAS in populations of non-European ancestry. We used data from the MESA (Multi-Ethnic Study of Atherosclerosis) cohort to characterize the genetic architecture of gene expression within and between diverse populations. Genotype and monocyte gene expression were available in individuals with African American (AFA, n = 233), Hispanic (HIS, n = 352), and European (CAU, n = 578) ancestry. …


Microplastic In Riverine Fish Is Connected To Species Traits, R. E. Mcneish, L. H. Kim, H. A. Barrett, S. A. Mason, J. J. Kelly, T. J. Hoellein Aug 2018

Microplastic In Riverine Fish Is Connected To Species Traits, R. E. Mcneish, L. H. Kim, H. A. Barrett, S. A. Mason, J. J. Kelly, T. J. Hoellein

Biology: Faculty Publications and Other Works

Microplastic is a contaminant of concern worldwide. Rivers are implicated as major pathways of microplastic transport to marine and lake ecosystems, and microplastic ingestion by freshwater biota is a risk associated with microplastic contamination, but there is little research on microplastic ecology within freshwater ecosystems. Microplastic uptake by fish is likely affected by environmental microplastic abundance and aspects of fish ecology, but these relationships have rarely been addressed. We measured the abundance and composition of microplastic in fish and surface waters from 3 major tributaries of Lake Michigan, USA. Microplastic was detected in fish and surface waters from all 3 …


Multiethnic Meta-Analysis Identifies Ancestry-Specific And Cross-Ancestry Loci For Pulmonary Function, Annah B. Wyss, Tamar Sofer, Mi Kyeong Lee, Natalie Terzikhan, Jennifer N. Nguyen, Lies Lahousse, Jeanne C. Latourelle, Albert Vernon Smith, Traci M. Bartz, Mary F. Feitosa, Wei Gao, Tarunveer S. Ahluwalia, Wenbo Tang, Christopher Oldmeadow, Qing Duan, Kim De Jong, Mary K. Wojczynski, Xin-Qun Wang, Raymond Noordam, Fernando Pires Hartwig, Victoria E. Jackson, Tianyuan Wang, Ma'en Obeidat, Brain D. Hobbs, Tianxiao Huan, Hongsheng Gui, Margaret M. Parker, Donglei Hu, Lauren S. Mogil, Gleb Kichaev, Jianping Jin, Mariaelisa Graff, Tamara B. Harris, Ravi Kalhan, Susan R. Heckbert, Lavinia Paternoster, Kristin M. Burkart, Yongmei Liu, Elizabeth G. Holliday, James G. Wilson, Judith M. Vonk, Jason L. Sanders, R. Graham Barr, Renee De Mutsert, Ana Maria Baptista Menezes, Hieab H. H. Adams, Maarten Van Den Berge, Roby Joehanes, Albert M. Levin, Jennifer Liberto, Lenore J. Launer, Alanna C. Morrison, Colleen M. Sitlani, Juan C. Celedon, Stephen B. Kritchevsky, Rodney J. Scott, Kaare Christensen, Jerome I. Rotter, Tobias N. Bonten, Fernando Cesar Wehrmeister, Yohan Bossé, Shujie Xio, Sam Oh, Nora Franceschini, Jennifer A. Brody, Robert C. Kaplan, Kurt Lohman, Mark Mcevoy, Michael A. Province, Frits R. Rosendaal, Kent D. Taylor, David C. Nickle, L. Keoki Williams, Esteban G. Burchard, Heather E. Wheeler, Don D. Sin, Wilmundur Gudnason, Kari E. North, Myriam Fornage, Bruce M. Psaty, Richard H. Myers, George O'Connor, Torben Hansen, Cathy C. Laurie, Patricia A. Cassano, Joohon Sung, Woo Jin Kim, John R. Attia, Leslie Lange, H. Marike Boezen, Bharat Thyagarajan, Stephen S. Rich, Dennis O. Mook-Kanamori, Bernardo Lessa Horta, André G. Uitterlinden, Hae Kyung Im, Michael H. Cho, Guy G. Brusselle, Sina A. Gharib, Josée Dupuis, Ani Manichaikul, Stephanie J. London Jul 2018

Multiethnic Meta-Analysis Identifies Ancestry-Specific And Cross-Ancestry Loci For Pulmonary Function, Annah B. Wyss, Tamar Sofer, Mi Kyeong Lee, Natalie Terzikhan, Jennifer N. Nguyen, Lies Lahousse, Jeanne C. Latourelle, Albert Vernon Smith, Traci M. Bartz, Mary F. Feitosa, Wei Gao, Tarunveer S. Ahluwalia, Wenbo Tang, Christopher Oldmeadow, Qing Duan, Kim De Jong, Mary K. Wojczynski, Xin-Qun Wang, Raymond Noordam, Fernando Pires Hartwig, Victoria E. Jackson, Tianyuan Wang, Ma'en Obeidat, Brain D. Hobbs, Tianxiao Huan, Hongsheng Gui, Margaret M. Parker, Donglei Hu, Lauren S. Mogil, Gleb Kichaev, Jianping Jin, Mariaelisa Graff, Tamara B. Harris, Ravi Kalhan, Susan R. Heckbert, Lavinia Paternoster, Kristin M. Burkart, Yongmei Liu, Elizabeth G. Holliday, James G. Wilson, Judith M. Vonk, Jason L. Sanders, R. Graham Barr, Renee De Mutsert, Ana Maria Baptista Menezes, Hieab H. H. Adams, Maarten Van Den Berge, Roby Joehanes, Albert M. Levin, Jennifer Liberto, Lenore J. Launer, Alanna C. Morrison, Colleen M. Sitlani, Juan C. Celedon, Stephen B. Kritchevsky, Rodney J. Scott, Kaare Christensen, Jerome I. Rotter, Tobias N. Bonten, Fernando Cesar Wehrmeister, Yohan Bossé, Shujie Xio, Sam Oh, Nora Franceschini, Jennifer A. Brody, Robert C. Kaplan, Kurt Lohman, Mark Mcevoy, Michael A. Province, Frits R. Rosendaal, Kent D. Taylor, David C. Nickle, L. Keoki Williams, Esteban G. Burchard, Heather E. Wheeler, Don D. Sin, Wilmundur Gudnason, Kari E. North, Myriam Fornage, Bruce M. Psaty, Richard H. Myers, George O'Connor, Torben Hansen, Cathy C. Laurie, Patricia A. Cassano, Joohon Sung, Woo Jin Kim, John R. Attia, Leslie Lange, H. Marike Boezen, Bharat Thyagarajan, Stephen S. Rich, Dennis O. Mook-Kanamori, Bernardo Lessa Horta, André G. Uitterlinden, Hae Kyung Im, Michael H. Cho, Guy G. Brusselle, Sina A. Gharib, Josée Dupuis, Ani Manichaikul, Stephanie J. London

Biology: Faculty Publications and Other Works

Nearly 100 loci have been identified for pulmonary function, almost exclusively in studies of European ancestry populations. We extend previous research by meta-analyzing genome-wide association studies of 1000 Genomes imputed variants in relation to pulmonary function in a multiethnic population of 90,715 individuals of European (N = 60,552), African (N = 8429), Asian (N = 9959), and Hispanic/Latino (N = 11,775) ethnicities. We identify over 50 additional loci at genome-wide significance in ancestry-specific or multiethnic meta-analyses. Using recent fine-mapping methods incorporating functional annotation, gene expression, and differences in linkage disequilibrium between ethnicities, we further shed light …


Pseudomonas Pb1-Like Phages: Whole Genomes From Metagenomes Offer Insight Into An Abundant Group Of Bacteriophages, Siobhan C. Watkins, Emily Sible, Catherine Putonti Jun 2018

Pseudomonas Pb1-Like Phages: Whole Genomes From Metagenomes Offer Insight Into An Abundant Group Of Bacteriophages, Siobhan C. Watkins, Emily Sible, Catherine Putonti

Biology: Faculty Publications and Other Works

Despite the abundance, ubiquity and impact of environmental viruses, their inherent genomic plasticity and extreme diversity pose significant challenges for the examination of bacteriophages on Earth. Viral metagenomic studies have offered insight into broader aspects of phage ecology and repeatedly uncover genes to which we are currently unable to assign function. A combined effort of phage isolation and metagenomic survey of Chicago’s nearshore waters of Lake Michigan revealed the presence of Pbunaviruses, relatives of the Pseudomonas phage PB1. This prompted our expansive investigation of PB1-like phages. Genomic signatures of PB1-like phages and Pbunaviruses were identified, permitting the unambiguous distinction between …


Detecting Viral Genomes In The Female Urinary Microbiome, Andrea Garretto, Krystal Thomas-White, Alan J. Wolfe, Catherine Putonti Jun 2018

Detecting Viral Genomes In The Female Urinary Microbiome, Andrea Garretto, Krystal Thomas-White, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Viruses are the most abundant component of the human microbiota. Recent evidence has uncovered a rich diversity of viruses within the female bladder, including both bacteriophages and eukaryotic viruses. We conducted whole-genome sequencing of the bladder microbiome of 30 women: 10 asymptomatic ‘healthy’ women and 20 women with an overactive bladder. These metagenomes include sequences representative of human, bacterial and viral DNA. This analysis, however, focused specifically on viral sequences. Using the bioinformatic tool virMine, we discovered sequence fragments, as well as complete genomes, of bacteriophages and the eukaryotic virus JC polyomavirus. The method employed here is a critical proof …


Relationships Of Native And Exotic Strains Of Phragmites Australis To Wetland Ecosystem Properties, John Kelly, L. A. Volesky, S. Iqbal, P. Geddes Jun 2018

Relationships Of Native And Exotic Strains Of Phragmites Australis To Wetland Ecosystem Properties, John Kelly, L. A. Volesky, S. Iqbal, P. Geddes

Biology: Faculty Publications and Other Works

Invasions by exotic plant species like Phragmites australis can affect wetlands and the services they provide, including denitrification. Native and exotic Phragmites strains were genetically verified in 2002 but few studies have compared their ecosystem effects. We compared relationships between native and exotic Phragmites and environmental attributes, soil nutrient concentrations, and abundance and activity of soil denitrifying bacteria. There were no significant differences for any measured variables between sites with exotic and native strains. However, there were significant positive correlations between native Phragmites stem density and soil nutrient concentrations and denitrification rates. Furthermore, denitrifying bacterial abundance was positively correlated with …


The Evolution Of Molecular Compatibility Between Bacteriophage Φx174 And Its Host, Alexander Kula, Joseph Saelens, Alyxandria M. Schubert, Michael Travisano, Catherine Putonti May 2018

The Evolution Of Molecular Compatibility Between Bacteriophage Φx174 And Its Host, Alexander Kula, Joseph Saelens, Alyxandria M. Schubert, Michael Travisano, Catherine Putonti

Bioinformatics Faculty Publications

Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic …


Identification Of Raw As A Regulator Of Glial Development, Diana Luong, Luselena Perez, Jennifer Mierisch May 2018

Identification Of Raw As A Regulator Of Glial Development, Diana Luong, Luselena Perez, Jennifer Mierisch

Biology: Faculty Publications and Other Works

Glial cells perform numerous functions to support neuron development and function, including axon wrapping, formation of the blood brain barrier, and enhancement of synaptic transmission. We have identified a novel gene, raw, which functions in glia of the central and peripheral nervous systems in Drosophila. Reducing Raw levels in glia results in morphological defects in the brain and ventral nerve cord, as well as defects in neuron function, as revealed by decreased locomotion in crawling assays. Examination of the number of glia along peripheral nerves reveals a reduction in glial number upon raw knockdown. The reduced number of …


The Evolution Of Molecular Compatibility Between Bacteriophage Φx174 And Its Host, Alexander Kula, Joseph Saelens, Jennifer Cox, Alyxandria M. Schubert, Michael Travisano, Catherine Putonti May 2018

The Evolution Of Molecular Compatibility Between Bacteriophage Φx174 And Its Host, Alexander Kula, Joseph Saelens, Jennifer Cox, Alyxandria M. Schubert, Michael Travisano, Catherine Putonti

Biology: Faculty Publications and Other Works

Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic …


Caspase-3 Suppresses Diethylnitrosamine-Induced Hepatocyte Death, Compensatory Proliferation And Hepatocarcinogenesis Through Inhibiting P38 Activation, Na Shang, Thomas Bank, Xianzhong Ding, Peter W. Breslin, Jun Li, Baomin Shi, Wei Qiu May 2018

Caspase-3 Suppresses Diethylnitrosamine-Induced Hepatocyte Death, Compensatory Proliferation And Hepatocarcinogenesis Through Inhibiting P38 Activation, Na Shang, Thomas Bank, Xianzhong Ding, Peter W. Breslin, Jun Li, Baomin Shi, Wei Qiu

Biology: Faculty Publications and Other Works

It is critical to understand the molecular mechanisms of hepatocarcinogenesis in order to prevent or treat hepatocellular carcinoma (HCC). The development of HCC is commonly associated with hepatocyte death and compensatory proliferation. However, the role of Caspase-3, a key apoptotic executor, in hepatocarcinogenesis is unknown. In this study, we used Caspase-3-deficient mice to examine the role of Caspase-3 in hepatocarcinogenesis in a chemical (diethylnitrosamine, DEN)-induced HCC model. We found that Caspase-3 deficiency significantly increased DEN-induced HCC. Unexpectedly, Caspase-3 deficiency increased apoptosis induced by DEN and the subsequent compensatory proliferation. Intriguingly, we discovered that Caspase-3 deficiency increased the activation of …


Exploring The Phenotypic Consequences Of Tissue Specific Gene Expression Variation Inferred From Gwas Summary Statistics, Alvaro N. Barbeira, Scott P. Dickinson, Rodrigo Bonazzola, Jiamao Zheng, Heather E. Wheeler, Jason M. Torres, Eric S. Torstenson, Kaanan P. Shah, Tzintzuni Garcia, Todd L. Edwards, Eli A. Stahl, Laura M. Huckins, Gtex Consortium, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im May 2018

Exploring The Phenotypic Consequences Of Tissue Specific Gene Expression Variation Inferred From Gwas Summary Statistics, Alvaro N. Barbeira, Scott P. Dickinson, Rodrigo Bonazzola, Jiamao Zheng, Heather E. Wheeler, Jason M. Torres, Eric S. Torstenson, Kaanan P. Shah, Tzintzuni Garcia, Todd L. Edwards, Eli A. Stahl, Laura M. Huckins, Gtex Consortium, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im

Biology: Faculty Publications and Other Works

Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression to compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy and general robustness to misspecified reference sets. We apply this framework to 44 GTEx tissues and 100+ phenotypes from GWAS and meta-analysis studies, creating a growing public catalog of associations that seeks to capture the effects of gene expression variation on human phenotypes. Replication in an independent cohort is shown. Most of the associations are tissue specific, suggesting context specificity of the trait etiology. …


Bacteriophages Of The Urinary Microbiome, Taylor Miller-Ensminger, Andrea Garretto, Jonathon Brenner, Krystal Thomas-White, Adriano Zambom, Alan J. Wolfe, Catherine Putonti May 2018

Bacteriophages Of The Urinary Microbiome, Taylor Miller-Ensminger, Andrea Garretto, Jonathon Brenner, Krystal Thomas-White, Adriano Zambom, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Bacterial viruses (bacteriophages) play a significant role in microbial community dynamics. Within the human gastrointestinal tract, for instance, associations amongst bacteriophages (phages), microbiota stability, and human health have been discovered. In contrast to the gastrointestinal tract, the phages associated with the urinary microbiota are largely unknown. Preliminary metagenomic surveys of the urinary virome indicate a rich diversity of novel lytic phage sequences, at an abundance far outnumbering eukaryotic viruses. These surveys, however, exclude the lysogenic phages residing within the bacteria of the bladder. To characterize this phage population, we examined 181 genomes representative of the phylogenetic diversity of bacterial species …


Culturing Of Female Bladder Bacteria Reveals An Interconnected Urogenital Microbiota, Krystal Thomas-White, Samuel C. Forster, Nitin Kumar, Michelle Van Kuiken, Catherine Putonti, Mark D. Stares, Evann E. Hilt, Travis K. Price, Alan J. Wolfe, Trevor D. Lawley Apr 2018

Culturing Of Female Bladder Bacteria Reveals An Interconnected Urogenital Microbiota, Krystal Thomas-White, Samuel C. Forster, Nitin Kumar, Michelle Van Kuiken, Catherine Putonti, Mark D. Stares, Evann E. Hilt, Travis K. Price, Alan J. Wolfe, Trevor D. Lawley

Biology: Faculty Publications and Other Works

Metagenomic analyses have indicated that the female bladder harbors an indigenous microbiota. However, there are few cultured reference strains with sequenced genomes available for functional and experimental analyses. Here we isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women. This culture collection spans 78 species, representing approximately two thirds of the bacterial diversity within the sampled bladders, including Proteobacteria, Actinobacteria, and Firmicutes. Detailed genomic and functional comparison of the bladder microbiota to the gastrointestinal and vaginal microbiotas demonstrates similar vaginal and bladder microbiota, with functional capacities that are distinct from those observed in the gastrointestinal microbiota. Whole-genome …


Culturing Of Female Bladder Bacteria Reveals An Interconnected Urogenital Microbiota, Krystal Thomas-White, Samuel C. Forster, Nitin Kumar, Michelle Van Kuiken, Catherine Putonti, Mark D. Stares, Evann E. Hilt, Travis K. Price, Alan J. Wolfe, Trevor D. Lawley Apr 2018

Culturing Of Female Bladder Bacteria Reveals An Interconnected Urogenital Microbiota, Krystal Thomas-White, Samuel C. Forster, Nitin Kumar, Michelle Van Kuiken, Catherine Putonti, Mark D. Stares, Evann E. Hilt, Travis K. Price, Alan J. Wolfe, Trevor D. Lawley

Bioinformatics Faculty Publications

Metagenomic analyses have indicated that the female bladder harbors an indigenous microbiota. However, there are few cultured reference strains with sequenced genomes available for functional and experimental analyses. Here we isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women. This culture collection spans 78 species, representing approximately two thirds of the bacterial diversity within the sampled bladders, including Proteobacteria, Actinobacteria, and Firmicutes. Detailed genomic and functional comparison of the bladder microbiota to the gastrointestinal and vaginal microbiotas demonstrates similar vaginal and bladder microbiota, with functional capacities that are distinct from those observed in the gastrointestinal microbiota. Whole-genome …


Inhibition Of Insulin‐Like Growth Factor 1 Receptor Enhances The Efficacy Of Sorafenib In Inhibiting Hepatocellular Carcinoma Cell Growth And Survival, Fang Wang, Thomas Bank, George Malnassy, Maribel Arteaga, Na Shang, Annika Dalheim, Xianzhong Ding, Scott J. Cotler, Mitchell F. Denning, Michael I. Nishimura, Peter Breslin, Wei Qiu Apr 2018

Inhibition Of Insulin‐Like Growth Factor 1 Receptor Enhances The Efficacy Of Sorafenib In Inhibiting Hepatocellular Carcinoma Cell Growth And Survival, Fang Wang, Thomas Bank, George Malnassy, Maribel Arteaga, Na Shang, Annika Dalheim, Xianzhong Ding, Scott J. Cotler, Mitchell F. Denning, Michael I. Nishimura, Peter Breslin, Wei Qiu

Biology: Faculty Publications and Other Works

Hepatocellular carcinoma (HCC) is the fifth most common primary cancer and second largest cause of cancer‐related death worldwide. The first‐line oral chemotherapeutic agent sorafenib only increases survival in patients with advanced HCC by less than 3 months. Most patients with advanced HCC have shown limited response rates and survival benefits with sorafenib. Although sorafenib is an inhibitor of multiple kinases, including serine/threonine‐protein kinase c‐Raf, serine/threonine‐protein kinase B‐Raf, vascular endothelial growth factor receptor (VEGFR)‐1, VEGFR‐2, VEGFR‐3, and platelet‐derived growth factor receptor β, HCC cells are able to escape from sorafenib treatment using other pathways that the drug insufficiently inhibits. The aim …


Gene Co-Occurrence Networks Reflect Bacteriophage Ecology And Evolution, Jason W. Shapiro, Catherine Putonti Mar 2018

Gene Co-Occurrence Networks Reflect Bacteriophage Ecology And Evolution, Jason W. Shapiro, Catherine Putonti

Biology: Faculty Publications and Other Works

Bacteriophages are the most abundant and diverse biological entities on the planet, and new phage genomes are being discovered at a rapid pace. As more phage genomes are published, new methods are needed for placing these genomes in an ecological and evolutionary context. Phages are difficult to study by phylogenetic methods, because they exchange genes regularly, and no single gene is conserved across all phages. Here, we demonstrate how gene-level networks can provide a high-resolution view of phage genetic diversity and offer a novel perspective on virus ecology. We focus our analyses on virus host range and show how network …


Gene Co-Occurrence Networks Reflect Bacteriophage Ecology And Evolution, Jason W. Shapiro, Catherine Putonti Mar 2018

Gene Co-Occurrence Networks Reflect Bacteriophage Ecology And Evolution, Jason W. Shapiro, Catherine Putonti

Bioinformatics Faculty Publications

Bacteriophages are the most abundant and diverse biological entities on the planet, and new phage genomes are being discovered at a rapid pace. As more phage genomes are published, new methods are needed for placing these genomes in an ecological and evolutionary context. Phages are difficult to study by phylogenetic methods, because they exchange genes regularly, and no single gene is conserved across all phages. Here, we demonstrate how gene-level networks can provide a high-resolution view of phage genetic diversity and offer a novel perspective on virus ecology. We focus our analyses on virus host range and show how network …


Maternal High-Fat Diet Associated With Altered Gene Expression, Dna Methylation, And Obesity Risk In Mouse Offspring, Madeline Rose Keleher, Rabab Zaidi, Shyam Shah, M. Elsa Oakley, Cassondra Pavlatos, Samir El Idrissi, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud Feb 2018

Maternal High-Fat Diet Associated With Altered Gene Expression, Dna Methylation, And Obesity Risk In Mouse Offspring, Madeline Rose Keleher, Rabab Zaidi, Shyam Shah, M. Elsa Oakley, Cassondra Pavlatos, Samir El Idrissi, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud

Biology: Faculty Publications and Other Works

We investigated maternal obesity in inbred SM/J mice by assigning females to a high-fat diet or a low-fat diet at weaning, mating them to low-fat-fed males, cross-fostering the offspring to low-fat-fed SM/J nurses at birth, and weaning the offspring onto a high-fat or low-fat diet. A maternal high-fat diet exacerbated obesity in the high-fat-fed daughters, causing them to weigh more, have more fat, and have higher serum levels of leptin as adults, accompanied by dozens of gene expression changes and thousands of DNA methylation changes in their livers and hearts. Maternal diet particularly affected genes involved in RNA processing, immune …


Draft Genome Sequence Of The Siderophore-Degrading Soil Bacterium Mesorhizobium Loti Strain Lu, Domenic Castignetti, Nathaniel Polley, Catherine Putonti Feb 2018

Draft Genome Sequence Of The Siderophore-Degrading Soil Bacterium Mesorhizobium Loti Strain Lu, Domenic Castignetti, Nathaniel Polley, Catherine Putonti

Bioinformatics Faculty Publications

Here, we present the draft genome of Mesorhizobium loti strain LU, a soil bacterium capable of degrading the trihydroxamate siderophore deferrioxamine B to its constituent monohydroxamic acids. Genome size was 6,399,828 bp, with a GC content of 61.5%. This draft genome consists of 35 scaffolds, with an N50 of 389,921 bp.


Draft Genome Sequence Of An Active Heterotrophic Nitrifier-Denitrifier, Cupriavidus Pauculus Um1, Catherine Putonti, Nathaniel Polley, Domenic Castignetti Feb 2018

Draft Genome Sequence Of An Active Heterotrophic Nitrifier-Denitrifier, Cupriavidus Pauculus Um1, Catherine Putonti, Nathaniel Polley, Domenic Castignetti

Bioinformatics Faculty Publications

Here, we present the draft genome sequence of Cupriavidus pauculus UM1, a metal-resistant heterotrophic nitrifier-denitrifier capable of synthesizing nitrite from pyruvic oxime. The size of the genome is 7,402,815 bp with a GC content of 64.8%. This draft assembly consists of 38 scaffolds.