Biology Commons^™

Cellular And Molecular Mechanism Underlying Alcohol Inhibition Of Bone Fracture Healing, Jonathan Michael Eby

Dissertations

Alcohol consumption is associated with increased risk taking and injuries leading to bone fracture. During bone fracture repair mesenchymal stem cells (MSCs) located at the site of injury differentiate into chondrocytes and osteoblasts to form a fracture callus. While most fractures heal without complication, studies show that alcohol abuse can lead to delayed fracture healing and fracture callus formation in both people and animals. Despite what is known about alcohol consumption in pre-injury pathologies like osteopenia and osteoporosis, the cellular and molecular mechanisms by which alcohol consumption inhibits fracture callus formation following orthopaedic injury remain to be elucidated. Here, we …

Investigating Dispersal Ability To Infer Diversification In The Birds Of Madagascar, Robert D. Lauer

Master's Theses

The objective of this study was to investigate whether dispersal ability, as measured by a proxy of hand-wing index 2, influenced diversification of the birds of Madagascar at two scales. Madagascar is home to several avian lineages that have diversified greatly while other lineages are only represented by a single species. a key question in evolutionary biology is why some of these lineages diversified while others did not. One way to address this is to examine what features of these lineages promotes their diversification. Recent studies have focused on the relative importance of dispersal ability to diversification at the continental …

Neuromodulation With Electromagnetic Stimulation For Seizure Suppression: From Electrode To Magnetic Coil, Hui Ye, Stephanie Kaszuba

Biology: Faculty Publications and Other Works

Non-invasive brain tissue stimulation with a magnetic coil provides several irreplaceable advantages over that with an implanted electrode, in altering neural activities under pathological situations. We reviewed clinical cases that utilized time-varying magnetic fields for the treatment of epilepsy, and the safety issues related to this practice. Animal models have been developed to foster understanding of the cellular/molecular mechanisms underlying magnetic control of epileptic activity. These mechanisms include (but are not limited to) (1) direct membrane polarization by the magnetic field, (2) depolarization blockade by the deactivation of ion channels, (3) alteration in synaptic transmission, and (4) interruption of ephaptic …

Genetic Regulatory Variation In Populations Informs Transcriptome Analysis In Rare Disease, Pejman Mohammadi, Stephane E. Castel, Beryl B. Cummings, Jonah Einson, Christina Sousa, Paul Hoffman, Sandra Donkervoort, Zhuoxun Jiang, Payam Mohassel, A. Reghan Foley, Heather E. Wheeler, Hae Kyung Im, Carsten G. Bonnemann, Daniel G. Macarthur, Tuuli Lappalainen

Biology: Faculty Publications and Other Works

Transcriptome data can facilitate the interpretation of the effects of rare genetic variants. Here, we introduce ANEVA (analysis of expression variation) to quantify genetic variation in gene dosage from allelic expression (AE) data in a population. Application of ANEVA to the Genotype-Tissues Expression (GTEx) data showed that this variance estimate is robust and correlated with selective constraint in a gene. Using these variance estimates in a dosage outlier test (ANEVA-DOT) applied to AE data from 70 Mendelian muscular disease patients showed accuracy in detecting genes with pathogenic variants in previously resolved cases and led to one confirmed and several potential …

Bacteriophages Of The Lower Urinary Tract, Andrea Garretto, Taylor Miller-Ensminger, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Phages are vital members of the microbiota, having critical roles in shaping bacterial metabolism and community structure. Although phages have been discovered in the urinary tract, such as phages that infect Escherichia coli, sampling them is challenging owing to low biomass, possible contamination when using non-invasive methods and the invasiveness of methods that reduce the potential for contamination. Phages could influence bladder health, but an understanding of the association between phage communities, bacterial populations and bladder health is in its infancy. However, evidence suggests that phages can defend the host against pathogenic bacteria and, therefore, modulation of the microbiome …

Microplastic Contamination In Karst Groundwater Systems, Samuel V. Panno, Walton R. Kelly, John Scott, Wei Zheng, Rachel E. Mcneish, Nancy Holm, Timothy Hoellein, Elizabeth L. Baranski

Biology: Faculty Publications and Other Works

Groundwater in karst aquifers constitutes about 25% of drinking water sources globally. Karst aquifers are open systems, susceptible to contamination by surface‐borne pollutants. In this study, springs and wells from two karst aquifers in Illinois, USA, were found to contain microplastics and other anthropogenic contaminants. All microplastics were fibers, with a maximum concentration of 15.2 particles/L. The presence of microplastic was consistent with other parameters, including phosphate, chloride and triclosan, suggesting septic effluent as a source. More studies are needed on microplastic sources, abundance, and impacts on karst ecosystems.

Ribosomal/Nucleolar Stress Induction Regulates Tert-Butyl Hydroperoxide (Tbhp) Mediated Oxidative Stress In Anopheles Gambiae Midguts, Brian B. Tarimo, Bernadette A. Hritzo, Henry Chun Hin Law, Dingyin Tao, Rebecca Pastrana-Mena, Stefan M. Kanzok, Joram J. Buza, Rhoel R. Dinglasan

Biology: Faculty Publications and Other Works

Objective

A fundamental understanding of redox homeostasis in Anopheles gambiae midgut cells under different oxidative conditions is missing. Such knowledge can aid in the development of new malaria transmission-blocking strategies aimed at disrupting natural homeostatic processes in the mosquito during Plasmodium parasite uptake (i.e. blood feeding). The aim of this study was to understand how the An. gambiae midgut regulates oxidative stress to reactive oxygen species (ROS), especially to a potent ROS-inducer such as tert-Butyl hydroperoxide (tBHP).

Results

Initial studies using quantitative immunoblot indicated that the expression of the classical antioxidant protein An. gambiae thioredoxin-1 (AgTrx-1) remained unchanged …

Characterization Of The Φctx-Like Pseudomonas Aeruginosa Phage Dobby Isolated From The Kidney Stone Microbiota, Genevieve Johnson, Alan J. Wolfe, Catherine Putonti

Biology: Faculty Publications and Other Works

Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of Pseudomonas aeruginosa cultured from a kidney stone. Dobby is capable of lysing clinical P. aeruginosa strains within our collection from the urinary tract. Sequencing was performed producing a 37 152 bp genome that closely resembles the temperate P. aeruginosa …

Phylogenetic Relationships Within The Primitive Acanthomorph Fish Genus Polymixia, With Changes To Species Composition And Geographic Distributions, W. Calvin Borden, Terry C. Grande, Mark Vh Wilson

Biology: Faculty Publications and Other Works

The genus Polymixia is the only survivor of a Late Cretaceous marine fish radiation and is often said to be the most primitive living acanthomorph (i.e., Polymixia possesses the greatest number of primitive character states for Acanthomorpha). Recent studies, including this one, place Polymixia as the sister to all other Paracanthopterygii. Despite its importance, most species of Polymixia are extremely difficult to discriminate on the basis of morphology. As a result, the number of valid species is uncertain. Moreover, there has never been a phylogenetic analysis of the genus. Thus, a molecular phylogenetic study was needed to clarify species boundaries …

Pseudomonas Diversity Within Urban Freshwaters, Mary Batrich, Laura Maskeri, Ryan Schubert, Brian Ho, Melanie Kohout, Malik Abdeljaber, Ahmed Abuhasna, Mutah Kholoki, Penelope Psihogios, Tahir Razzaq, Samrita Sawhney, Salah Siddiqui, Eyad Xoubi, Alexandria Cooper, Thomas Hatzopoulos, Catherine Putonti

Bioinformatics Faculty Publications

Freshwater lakes are home to bacterial communities with 1000s of interdependent species. Numerous high-throughput 16S rRNA gene sequence surveys have provided insight into the microbial taxa found within these waters. Prior surveys of Lake Michigan waters have identified bacterial species common to freshwater lakes as well as species likely introduced from the urban environment. We cultured bacterial isolates from samples taken from the Chicago nearshore waters of Lake Michigan in an effort to look more closely at the genetic diversity of species found there within. The most abundant genus detected was Pseudomonas, whose presence in freshwaters is often attributed …

Characterization Of The Φctx-Like Pseudomonas Aeruginosa Phage Dobby Isolated From The Kidney Stone Microbiota, Genevieve Johnson, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of Pseudomonas aeruginosa cultured from a kidney stone. Dobby is capable of lysing clinical P. aeruginosa strains within our collection from the urinary tract. Sequencing was performed producing a 37 152 bp genome that closely resembles the temperate P. aeruginosa …

Alcohol Induced Bacterial Changes In The Setting Of Colitis, Paulius Kuprys

Dissertations

Inflammatory bowel diseases (IBD) affect a large number of individuals around the world. This group of diseases is largely composed of two types: Crohn's disease (CD) and ulcerative colitis (UC). Upon development of IBD, patients experience cyclical episodes of inflammation, known as flares. Flare induction appears to arise from multiple factors, which can also vary on a person-to-person basis. Alcohol has been shown to trigger IBD flares and onset, though the underlying mechanism has not been established.Defining factors of the IBD intestinal environment include an altered microbiome, bacterial infiltration of the intestinal epithelium, and increased leakage of proinflammatory bacterial byproducts. …

Role Of Daxx As A Predictive Biomarker In Breast Cancer, Michelle Lucia Fernandez

Master's Theses

Breast cancer is the most commonly diagnosed form of cancer in women, besides skin cancer, and second only to lung cancer for cause of mortality. It is divided into three subtypes, depending on different molecular or pathologic characteristics, including estrogen or progesterone receptor-positive (ER/PR+), human epidermal growth factor receptor-2-positive (HER2+) and triple negative breast cancer (TNBC). There are several therapies used to target these subtypes, but there is still a chance that the cancer will recur into a more aggressive, resistant form even if the therapies were successful before. This recurrence is believed to be due to the Cancer Stem …

Daxx As A Restrictor Of Tumor Initiating Cell Survival In Er+ Breast Cancer And Its Therapeutic Implications, Daniel Seamus Peiffer

Dissertations

Breast cancer overall is the second most common cause of cancer related death in women, with one in eight women being diagnosed during their lifetime. Breast cancer itself is divided into subtypes based on the expression levels of the hormone receptors including the estrogen receptor (ER) and the progesterone receptor (PR), as well as expression of the growth factor receptor epidermal growth factor receptor 2 (HER2). ER+ breast cancer is the most common breast cancer diagnosis, and these tumors are defined as being initially dependent on activation of the receptor for growth. Based on this, targeted endocrine therapies (ETs) have …

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 …