Biology Commons^™

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 …

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

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 …

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

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

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

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 …

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 …

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

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 …

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 …

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 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.

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

Biology: Faculty Publications and Other Works

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.

Wilms Tumor 1b Defines A Wound-Specific Sheath Cell Subpopulation Associated With Notochord Repair, Juan Carlos Lopez-Baez, Daniel J. Simpson, Laura Lleras Forero, Zhiqiang Zeng, Hannah Brunsdon, Angela Salzano, Alessandro Brombin, Cameron Wyatt, Witold Rybski, Leonie F A Huitema, Rodney M. Dale, Koichi Kawakami, Christoph Englert, Tamir Chandra, Stefan Schulte-Merker, Nicholas D. Hastie, E Elizabeth Patton

Biology: Faculty Publications and Other Works

Regenerative therapy for degenerative spine disorders requires the identification of cells that can slow down and possibly reverse degenerative processes. Here, we identify an unanticipated wound-specific notochord sheath cell subpopulation that expresses Wilms Tumor (WT) 1b following injury in zebrafish. We show that localized damage leads to Wt1b expression in sheath cells, and that wt1b⁺cells migrate into the wound to form a stopper-like structure, likely to maintain structural integrity. Wt1b⁺sheath cells are distinct in expressing cartilage and vacuolar genes, and in repressing a Wt1b-p53 transcriptional programme. At the wound, wt1b⁺and entpd5⁺ cells constitute …

The Critically Endangered Forest Owlet Heteroglaux Blewitti Is Nested Within The Currently Recognized Athene Clade: A Century-Old Debate Addressed, Pankaj Koparde, Prachi Mehta, Sushma Reddy, Uma Ramakrishnan, Shomita Mukherjee, V. V. Robin

Biology: Faculty Publications and Other Works

Range-restricted species generally have specific niche requirements and may often have unique evolutionary histories. Unfortunately, many of these species severely lack basic research, resulting in poor conservation strategies. The phylogenetic relationship of the Critically Endangered Forest Owlet Heteroglaux blewitti has been the subject of a century-old debate. The current classifications based on non-phylogenetic comparisons of morphology place the small owls of Asia into three genera, namely, Athene, Glaucidium, and Heteroglaux. Based on morphological and anatomical data, H. blewitti has been alternatively hypothesized to belong within Athene, Glaucidium, or its own monotypic genus Heteroglaux. …

Stream Microbial Communities Show Resistance To Pharmaceutical Exposure, E. J. Rosi, H. A. Bechtold, D. Snow, M. Rojas, A. J. Reisinger, J. J. Kelly

Biology: Faculty Publications and Other Works

Residues of pharmaceuticals are increasingly detected in surface waters throughout the world. In four streams in Baltimore, Maryland, USA, we detected analgesics, stimulants, antihistamines, and antibiotics using passive organic samplers. We exposed biofilm communities in these streams to the common drugs caffeine, cimetidine, ciprofloxacin, and diphenhydramine. Respiration rates in the least urban stream were suppressed when exposed to these drugs, but biofilm functioning in the most urban stream was resistant to drug exposure. Exposure to the antibiotic ciprofloxacin altered bacterial community composition at all sites, with the greatest change occurring in the most urban stream. These results indicated that continuous …

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

Bioinformatics Faculty Publications

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 …

Role Of Micrornas In Impaired Gut Permeability Following Ethanol And Burn Injury, Niya Latrice Morris

Dissertations

Every year there are nearly 500,000 reported burn injuries in the United States; half of which occur under the influence of alcohol. Clinical studies have shown that burn patients who are intoxicated at the time of injury have a worse prognosis; including increased risk of multiple organ dysfunction syndrome (MODS) and sepsis. The etiology behind these pathological consequences of ethanol and burn injury remains to be elucidated. The Gut-lymph hypothesis of MODS theorizes that trauma (e.g. ethanol and burn injury) results in a redistribution of blood flow to protect more vital organs which leads to ischemia/hypoxia (diminished oxygen delivery) in …

Cryptic Diversification Of Two Widespread Species In Madagascar, Lynika Sharlice Strozier

Master's Theses

Using phylogenetic and phylogeographic tools to uncover hidden diversity within the genus Newtonia in Madagascar

Madagascar is known for its rich biodiversity and high level of endemic species that are found nowhere else. Cryptic diversification, defined as genetically and evolutionarily distinct species that are hard to detect because they are morphologically indistinguishable from their closest relatives, has been hypothesized to occur in many groups on Madagascar. Currently it is unclear to what extent this phenomenon occurs in birds because only a few studies have been conducted. My study examined the phylogenetic and phylogeographic patterns within a songbird genus, Newtonia, that …

Predicted Suitable Habitat Declines For Midwestern United States Amphibians Under Future Climate And Land-Use Change Scenarios, Brock Struecker, Joseph Milanovich

Biology: Faculty Publications and Other Works

With current declines of vertebrate taxa meeting or exceeding those of historic mass extinction events, there is a growing need to investigate the main drivers of losses. Two of the main drivers of declines are global climate and land-use changes, both affecting multiple groups of taxa. Amphibians are at great risk from these two drivers of change and investigations into the impact of future change could assist with the formation of conservation plans to mitigate losses. Forecasting changes in suitable habitat with ecological niche modeling serves as a useful tool to begin to understand how species may respond to anthropogenic …

Developmental Nonlinearity Drives Phenotypic Robustness, Rebecca M. Green, Jennifer L. Fish, Nathan M. Young, Francis J. Smith, Benjamin Roberts, Katie Dolan, Irene Choi, Courtney L. Leach, Paul Gordon, James M. Cheverud, Charles C. Roseman, Trevor J. Williams, Ralph S. Marcucio, Benedikt Hallgrímsson

Biology: Faculty Publications and Other Works

Robustness to perturbation is a fundamental feature of complex organisms. Mutations are the raw material for evolution, yet robustness to their effects is required for species survival. The mechanisms that produce robustness are poorly understood. Nonlinearities are a ubiquitous feature of development that may link variation in development to phenotypic robustness. Here, we manipulate the gene dosage of a signaling molecule, Fgf8, a critical regulator of vertebrate development. We demonstrate that variation in Fgf8 expression has a nonlinear relationship to phenotypic variation, predicting levels of robustness among genotypes. Differences in robustness are not due to gene expression variance or …

Inhibitory Or Excitatory? Optogenetic Interrogation Of The Functional Roles Of Gabaergic Interneurons In Epileptogenesis, Hui Ye

Biology: Faculty Publications and Other Works

Alteration in the excitatory/inhibitory neuronal balance is believed to be the underlying mechanism of epileptogenesis. Based on this theory, GABAergic interneurons are regarded as the primary inhibitory neurons, whose failure of action permits hyperactivity in the epileptic circuitry. As a consequence, optogenetic excitation of GABAergic interneurons is widely used for seizure suppression. However, recent evidence argues for the context-dependent, possibly “excitatory” roles that GABAergic cells play in epileptic circuitry. We reviewed current optogenetic approaches that target the “inhibitory” roles of GABAergic interneurons for seizure control. We also reviewed interesting evidence that supports the “excitatory” roles of GABAergic interneurons in epileptogenesis. …

Clinical And Genome-Wide Analysis Of Cisplatin-Induced Peripheral Neuropathy In Survivors Of Adult-Onset Cancer, M. Eileen Dolan, Omar El Charif, Heather E. Wheeler, Eric R. Gamazon, Shirin Ardeshir-Rouhani-Fard, Patrick Monahan, Darren R. Feldman, Roebrt J. Hamilton, David J. Vaughn, Clair J. Beard, Chunkit Fung, Jeri Kim, Sophie D. Fossa, Daniel L. Hertz, Taisei Mushiroda, Michiaki Kubo, Lawrence H. Einhorn, Nancy J. Cox, Louis B. Travis

Biology: Faculty Publications and Other Works

No abstract provided.

Non-Sister Sri Lankan White-Eyes (Genus Zosterops) Are A Result Of Independent Colonizations, Sushma Reddy, Nelum Wickramasinghe, V. V. Robin, Uma Ramakrishnan, Sampath S. Seneviratne

Biology: Faculty Publications and Other Works

Co-occurrence of closely related taxa on islands could be attributed to sympatric speciation or multiple colonization. Sympatric speciation is considered to be rare in small islands, however multiple colonizations are known to be common in both oceanic and continental islands. In this study we investigated the phylogenetic relatedness and means of origin of the two sympatrically co-occurring Zosterops white-eyes, the endemic Zosterops ceylonensis and its widespread regional congener Z. palpebrosus, in the island of Sri Lanka. Sri Lanka is a continental island in the Indian continental shelf of the Northern Indian Ocean. Our multivariate morphometric analyses confirmed the …

Kinematic Difference Between A Biological Cell And An Artificial Vesicle In A Strong Dc Electric Field – A “Shell” Membrane Model Study, Hui Ye

Biology: Faculty Publications and Other Works

Background

Cellular biomechanics can be manipulated by strong electric fields, manifested by the field-induced membrane deformation and migration (galvanotaxis), which significantly impacts normal cellular physiology. Artificial giant vesicles that mimic the phospholipid bilayer of the cell membrane have been used to investigate the membrane biomechanics subjected to electric fields. Under a strong direct current (DC) electric field, the vesicle membrane demonstrates various patterns of deformation, which depends on the conductivity ratio between the medium and the cytoplasm. The vesicle exhibits prolate elongation along the direction of the electric field if the cytoplasm is more conductive than the medium. Conversely, the …

New Genera And Species Of Fossil Marine Amioid Fishes (Actinopterygii, Holostei) From The Late Cretaceous Agoult Locality In Southeastern Morocco, Mark V. Wilson, Alison M. Murray, Terry C. Grande

Biology: Faculty Publications and Other Works

The document is Terry C. Grande's (et al.) abstract in the Society of Vertebrate Paleontology 77th Annual Meeting Program and Abstracts.

Utilizing Modular Labs In Human Anatomy And Physiology: Lessons Learned From A First Time Experience, Jennifer Zitzner

Biology: Faculty Publications and Other Works

Anatomy and physiology laboratory experiences build upon concepts that are presented in the lecture part of the course. Our anatomy and physiology laboratory class meets weekly for approximately three hours and includes a compilation of activities that are to be completed during the laboratory period. While exercises are built off of topics presented in lecture and predominantly hands-on in nature, many students were not taking advantage of the self-directed learning experiences, especially those employing anatomical models. Some students were content to simply take photographs of models with their cell phones and complete only the graded portions of the laboratory assignment …

Thermal Environment And Microhabitat Of Ornate Box Turtle Hibernacula, Joseph Milanovich, Brock Struecker, Stanislaw A. Warcholek, Leigh Anne Harden

Biology: Faculty Publications and Other Works

Box turtle populations are under significant threat from historic and current alterations of land-use where remaining populations often occur in remnant patches of suitable habitat surrounded by a heterogeneous mixture of anthropogenically altered, unsuitable habitat. Ornate box turtles Terrapene ornata are a prairie-dependent species, are considered Near Threatened by the International Union for Conservation of Nature (IUCN), and are Endangered or Threatened within many US states. Since their range exists largely in northern latitudes, aspects of hibernacula are particularly important for winter survival. How box turtles select hibernacula within prairies is likely of great importance to better understand which microhabitats …