Biology Commons^™

Examining New Phylogenetic Markers To Uncover The Evolutionary History Of Early-Diverging Fungi: Comparing Mcm7, Tsr1 And Rrna Genes For Single- And Multi-Gene Analyses Of The Kickxellomycotina, Eric D. Tretter, E. M. Johnson, Yan Wang, Prasanna Kandel, Merlin M. White

Biology Faculty Publications and Presentations

The recently recognised protein-coding genes MCM7 and TSR1 have shown significant promise for phylogenetic resolution within the Ascomycota and Basidiomycota, but have remained unexamined within other fungal groups (except for Mucorales). We designed and tested primers to amplify these genes across early-diverging fungal clades, with emphasis on the Kickxellomycotina, zygomycetous fungi with characteristic flared septal walls forming pores with lenticular plugs. Phylogenetic tree resolution and congruence with MCM7 and TSR1 were compared against those inferred with nuclear small (SSU) and large subunit (LSU) rRNA genes. We also combined MCM7 and TSR1 data with the rDNA data to …

Evolution Of A Higher Intracellular Oxidizing Environment In Caenorhabditis Elegans Under Relaxed Selection, Joanna Joyner-Matos, Kiley A. Hicks, Dustin Cousins, Michelle Keller, Dee R. Denver, Charles F. Baer, Suzanne Estes

Biology Faculty Publications and Presentations

We explored the relationship between relaxed selection, oxidative stress, and spontaneous mutation in a set of mutationaccumulation (MA) lines of the nematode Caenorhabditis elegans and in their common ancestor. We measured steady-state levels of free radicals and oxidatively damaged guanosine nucleosides in the somatic tissues of five MA lines for which nuclear genome base substitution and GC-TA transversion frequencies are known. The two markers of oxidative stress are highly correlated and are elevated in the MA lines relative to the ancestor; point estimates of the per-generation rate of mutational decay (DM) of these measures of oxidative stress are similar to …

Bromus Tectorum Litter Alters Photosynthetic Characteristics Of Biological Soil Crusts From A Semiarid Shrubland, Marcelo D. Serpe, Eric Roberts, David J. Eldridge, Roger Rosentreter

Biology Faculty Publications and Presentations

Invasion by the exotic annual grass Bromus tectorum has increased the cover and connectivity of fine litter in the sagebrush steppes of western North America. This litter tends to cover biological soil crusts, which could affect their metabolism and growth. To investigate this possible phenomenon, biological soil crusts dominated by either the moss Bryum argenteum or the lichen Diploschistes muscorum were covered with B.tectorum litter (litter treatment) or left uncovered (control treatment) and exposed to natural field conditions. After periods of five and ten months, we removed the litter and compared the photosynthetic performance of biological soil crusts …

A Pharm-Ecological Perspective Of Terrestrial And Aquatic Plant-Herbivore Interactions, Jennifer Sorensen Forbey, M. Denise Dearing, Elisabeth M. Gross, Colin M. Orians, Erik E. Sotka, William J. Foley

Biology Faculty Publications and Presentations

We describe some recent themes in the nutritional and chemical ecology of herbivores and the importance of a broad pharmacological view of plant nutrients and chemical defenses that we integrate as “Pharm-ecology”. The central role that dose, concentration, and response to plant components (nutrients and secondary metabolites) play in herbivore foraging behavior argues for broader application of approaches derived from pharmacology to both terrestrial and aquatic plant-herbivore systems. We describe how concepts of pharmacokinetics and pharmacodynamics are used to better understand the foraging phenotype of herbivores relative to nutrient and secondary metabolites in food. Implementing these concepts into the field …

Human Disturbance And Stage-Specific Habitat Requirements Influence Snowy Plover Site Occupancy During The Breeding Season, Alyson F. Webber, Julie A. Heath, Richard A. Fischer

Biology Faculty Publications and Presentations

Habitat use has important consequences for avian reproductive success and survival. In coastal areas with recreational activity, human disturbance may limit use of otherwise suitable habitat. Snowy plovers Charadrius nivosus have a patchy breeding distribution along the coastal areas on the Florida Panhandle, USA. Our goal was to determine the relative effects of seasonal human disturbance and habitat requirements on snowy plover habitat use. We surveyed 303 sites for snowy plovers, human disturbance, and habitat features between January and July 2009 and 2010. We made multiple visits during three different sampling periods that corresponded to snowy plover breeding: pre-breeding, incubation, …

Insights Into Archaeal Evolution And Symbiosis From The Genomes Of A Nanoarchaeon And Its Inferred Crenarchaeal Host From Obsidian Pool, Yellowstone National Park, Mircea Podar, Kira S. Makarova, David E. Graham, Yuri L. Wolf, Eugene V. Koonin, Anna-Louise Reysenbach

Biology Faculty Publications and Presentations

Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.

Results: The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deepbranching archaeal lineage. However, the Nst1 …

Migration Timing And Wintering Areas Of Three Species Of Flycatchers (Tyrannus) Breeding In The Great Plains Of North America, Alex E. Jahn, Victor R. Cueto, James W. Fox, Michael S. Husak, Daniel H. Kim, Diane V. Landoll, Jesús Pinto Ledezma, Heather K. Lepage, Douglas J. Levey, Michael T. Murphy, Rosalind B. Renfrew

Biology Faculty Publications and Presentations

Descriptions of intra- and interspecific variation in migratory patterns of closely related species are rare yet valuable because they can help assess how differences in ecology and life-history strategies drive the evolution of migration. We report data on timing and location of migration routes and wintering areas, and on migratory speed and phenology, of Eastern Kingbirds (Tyrannus tyrannus) from Nebraska and Oklahoma and of Western Kingbirds (T. verticalis) and Scissor-tailed Flycatchers (T. forficatus) from Oklahoma. Eastern Kingbirds primarily departed the breeding site in September, migrating to the Amazon Basin (Bolivia and Brazil), >6,400 km …

Sequencing And De Novo Transcriptome Assembly Of Brachypodium Sylvaticum (Poaceae), Samuel E. Fox, Justin Preece, Jeffrey A. Kimbrel, Gina L. Marchini, Abigail Sage, Ken Youens-Clark, Mitchell B. Cruzan, Pankaj Jaiswal

Biology Faculty Publications and Presentations

Premise of the study: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. Methods and Results: More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis), 104,950 (Spain), and 177,682 (Greece) transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum . The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium …

The Triggering Receptor Expressed On Myeloid Cells 2: “Trem-Ming” The Inflammatory Component Associated With Alzheimer's Disease, Troy T. Rohn

Biology Faculty Publications and Presentations

Alzheimer's disease (AD) is an age-related neurodegenerative disorder characterized by a progressive loss of memory and cognitive skills. Although much attention has been devoted concerning the contribution of the microscopic lesions, senile plaques, and neurofibrillary tangles to the disease process, inflammation has long been suspected to play a major role in the etiology of AD. Recently, a novel variant in the gene encoding the triggering receptor expressed on myeloid cells 2 (TREM2) has been identified that has refocused the spotlight back onto inflammation as a major contributing factor in AD. Variants in TREM2 triple one's risk of developing late-onset AD. …

Phytochemistry Predicts Habitat Selection By An Avian Herbivore At Multiple Spatial Scales, Graham G. Frye, John W. Connelly, David D. Musil, Jennifer S. Forbey

Biology Faculty Publications and Presentations

Animal habitat selection is a process that functions at multiple, hierarchically structured spatial scales. Thus multi-scale analyses should be the basis for inferences about factors driving the habitat selection process. Vertebrate herbivores forage selectively on the basis of phytochemistry, but few studies have investigated the influence of selective foraging (i.e., fine-scale habitat selection) on habitat selection at larger scales. We tested the hypothesis that phytochemistry is integral to the habitat selection process for vertebrate herbivores. We predicted that habitats selected at three spatial scales would be characterized by higher nutrient concentrations and lower concentrations of plant secondary metabolites (PSMs) than …

Distance And Sex Determine Host Plant Choice By Herbivorous Beetles, Daniel J. Ballhorn, Stefanie Kautz, Martin Heil

Biology Faculty Publications and Presentations

Background: Plants respond to herbivore damage with the release of volatile organic compounds (VOCs). This indirect defense can cause ecological costs when herbivores themselves use VOCs as cues to localize suitable host plants. Can VOCs reliably indicate food plant quality to herbivores?

Methodology: We determined the choice behavior of herbivorous beetles (Chrysomelidae: Gynandrobrotica guerreroensis and Cerotoma ruficornis) when facing lima bean plants (Fabaceae: Phaseolus lunatus) with different cyanogenic potential, which is an important constitutive direct defense. Expression of inducible indirect defenses was experimentally manipulated by jasmonic acid treatment at different concentrations. The long-distance responses of male and female beetles to …

Asian Primate Species Richness Correlates With Rainfall, Yi-Chen Wang, Amrita Srivathsan, Chen-Chieh Feng, Agus Salim, Myron Shekelle

Biology Faculty Publications and Presentations

Previous studies of meta-analyses found significantly positive correlations between primate species richness and rainfall for Africa, Madagascar and the Neotropics, with the exception of Asia, leaving the open question whether that anomaly is the result of sampling bias, biogeography, or some other factor. This study re-examines the question using modelled data, with primate species richness data from the Southeast Asian Mammals Databank and rainfall data from the Climatic Research Unit. Data processing with Geographical Information Systems resulted in 390 sample points. Reduced major axis and ordinary least squares regressions were employed to examine the relationship for six regions, including the …

Matrix Gla Protein Reinforces Angiogenic Resolution, Bikram Sharma, Allan R. Albig

Biology Faculty Publications and Presentations

Matrix Gla Protein (MGP) is an ECM molecule commonly associated with dysfunctions of large blood vessels such as arteriosclerosis and atherosclerosis. However, the exact role of MGP in the microvasculature is not clear. Utilizing a mouse MGP knockout model we found that MGP suppresses angiogenic sprouting from mouse aorta restricts microvascular density in cardiac and skeletal muscle, and is an endogenous inhibitor of tumor angiogenesis. Similarly, morpholino based knockdown of MGP in zebrafish embryos caused a progressive loss of luminal structures in intersegmental vessels, a phenotype reminiscent of Dll4/Notch inhibition. Accordingly, MGP suppressed Notch-dependent Hes-1 promoter activity and expression of …

Caspase-Cleaved Glial Fibrillary Acidic Protein Within Cerebellar White Matter Of The Alzheimer's Disease Brain, Troy T. Rohn, Lindsey W. Catlin, Wayne W. Poon

Biology Faculty Publications and Presentations

Although the cerebellum is generally thought of as an area spared of Alzheimer's disease (AD) pathology, recent evidence suggests that balance and mobility dysfunction may be magnified in affected individuals. In the present study, we sought to determine the degree of pathological changes within the cerebellum utilizing an antibody that specifically detects caspase-cleaved GFAP within degenerating astrocytes. Compared to control subjects, application of this antibody, termed the GFAP caspase-cleavage product (GFAPccp) antibody, revealed widespread labeling in cerebellar white matter with little staining observed in grey matter. Staining was observed within damaged astrocytes, was often localized near blood vessels and co-localized …

Nullomer Derived Anticancer Peptides (Nullops): Differential Lethal Effects On Normal And Cancer Cells In Vitro, Abdelkrim Alileche, Jayita Goswami, William Bourland, Mike Davis, Greg Hampikian

Biology Faculty Publications and Presentations

We demonstrate the first use of the nullomer (absent sequences) approach to drug discovery and development. Nullomers are the shortest absent sequences determined in a species, or group of species. By identifying the shortest absent peptide sequences from the NCBI databases, we screened several potential anti-cancer peptides. In order to improve cell penetration and solubility we added short poly arginine tails (5Rs), and initially solubilized the peptides in1M trehalose. The results for one of the absent sequences 9R (RRRRRNWMWC), and its scrambled version 9S1R (RRRRRWCMNW) are reported here. We refer to these peptides derived from nullomers as PolyArgNulloPs. A control …

When Dna Won't Work, Rick Visser, Greg Hampikian

Biology Faculty Publications and Presentations

Within the criminal justice system, DNA (deoxyribonucleic acid) evidence has often been heralded as the gold standard of forensic science. In a 2009 U.S. Supreme Court decision, Chief Justice Roberts wrote that "DNA testing has an unparalleled ability both to exonerate the wrongly convicted and to identify the guilty. It has the potential to significantly improve both the criminal justice system and police investigative practices." The phrases “unparalleled ability” and “significantly improve” reflect the high standard that DNA has attained in both forensic science and the entire criminal justice system.

Forensic DNA technology has a major advantage over other forensic …

Cephalopod Genomics: A Plan Of Strategies And Organization, Caroline B. Albertin, Laure Bonnaud, C. Titus Brown, Wendy J. Crookes-Goodson, Rute R. Da Fonseca, Carlo Di Cristo, Brian P. Dilkes, Eric Edsinger-Gonzales, Robert M. Freeman Jr., Roger T. Hanlon, Kristen M. Koenig, Annie R. Lindgren, Mark Q. Martindale, Patrick Minx, Leonid L. Moroz, Marie-Therese Nödl, Spencer V. Nyholm, Atsushi Ogura, Judit R. Pungor, Joshua J. C. Rosenthal, Erich M. Schwarz, Shuichi Shigeno, Jan M. Strugnell, Tim Wollesen, Guojie Zhang, Clifton W. Ragsdale

Biology Faculty Publications and Presentations

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an …

Phylogeny Of A Neotropical Clade In The Gesneriaceae: More Tales Of Convergent Evolution, John L. Clark, Minde M. Funke, Aaron M. Duffy, James F. Smith

Biology Faculty Publications and Presentations

The Gesneriaceae is a family known for convergent evolution of complex floral forms. As a result, defining genera and resolving evolutionary relationships among such genera using morphological data alone has been challenging and often does not accurately reflect monophyletic lineages. The tribe Episcieae is the most diverse within Neotropical Gesneriaceae in terms of its number of species and morphological diversity. As a result, defining genera using floral characters has been historically troublesome. Here we investigate relationships among genera of the tribe using an array of chloroplast DNA, nuclear ribosomal genes, and low-copy nuclear genes to provide resolution for the monophyly …

Identification Of An Amino-Terminal Fragment Of Apolipoprotein E4 That Localizes To Neurofibrillary Tangles Of The Alzheimer’S Disease Brain, Troy T. Rohn, Lindsey W. Catlin, Kendra G. Coonse, Jeffrey W. Habig

Biology Faculty Publications and Presentations

Although the risk factor for harboring the apolipoprotein E4 (apoE4) allele in late-onset Alzheimer’s disease (AD) is well known, the mechanism by which apoE4 contributes to AD pathogenesis has yet to be clarified. Preferential cleavage of the ApoE4 isoform relative to other polymorphic forms appears to be significant, as the resulting fragments are associated with hallmarks of AD. To examine the possible role of apoE4 proteolysis in AD, we designed a site-directed antibody directed at position D172, which would yield a predicted amino-terminal fragment previously identified in AD brain extracts. Western blot analysis utilizing this novel antibody, termed the amino-terminal …

Phylotranscriptomics To Bring The Understudied Into The Fold: Monophyletic Ostracoda, Fossil Placement, And Pancrustacean Phylogeny, Todd H. Oakley, Joanna M. Wolfe, Annie R. Lindgren, Alexander K. Zaharoff

Biology Faculty Publications and Presentations

An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. However, many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often undersampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing expressed sequence tag, mitochondrial genome, nuclear genome, and ribosomal DNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We …

Landscape Of Transcription In Human Cells, Jainab Khatun

Biology Faculty Publications and Presentations

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, …

An Integrated Encyclopedia Of Dna Elements In The Human Genome, Jainab Khatun

Biology Faculty Publications and Presentations

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence …

Oncostatin M Promotes Mammary Tumor Metastasis To Bone And Osteolytic Bone Degradation, Celeste Bolin, Ken Tawara, Caleb Sutherland, Jeff Redshaw, Patrick S. Aranda, Jim Moselhy, Robin Anderson, Cheryl Jorcyk

Biology Faculty Publications and Presentations

Oncostatin M (OSM) is an interleukin-6 (IL-6) family cytokine that has been implicated in a number of biological processes including inflammation, hematopoiesis, immune responses, development, and bone homeostasis. Recent evidence suggests that OSM may promote breast tumor invasion and metastasis. We investigated the role of OSM in the formation of bone metastases in vivo using the 4T1.2 mouse mammary tumor model in which OSM expression was knocked down using shRNA (4T1.2-OSM). 4T1.2-OSM cells were injected orthotopically into Balb/c mice, resulting in a greater than 97% decrease in spontaneous metastasis to bone compared to control cells. Intratibial injection of these same …

Long Noncoding Rnas Are Rarely Translated In Two Human Cell Lines, Jainab Khatun, Brian Risk, Morgan Giddings

Biology Faculty Publications and Presentations

Data from the Encyclopedia of DNA Elements (ENCODE) project show over 9640 human genome loci classified as long noncoding RNAs (lncRNAs), yet only ~100 have been deeply characterized to determine their role in the cell. To measure the protein-coding output from these RNAs, we jointly analyzed two recent data sets produced in the ENCODE project: tandem mass spectrometry (MS/MS) data mapping expressed peptides to their encoding genomic loci, and RNA-seq data generated by ENCODE in long polyA+ and polyA– fractions in the cell lines K562 and GM12878. We used the machinelearning algorithm RuleFit3 to regress the peptide data against RNA …

Sub-Antarctic And High Antarctic Notothenioid Fishes: Ecology And Adaptational Biology Revealed By The Icefish 2004 Cruise Of Rvib Nathaniel B. Palmer, H. William Detrich Iii, Bradley A. Buckley, Daniel F. Doolittle, Christopher D. Jones, Susanne J. Lockhart

Biology Faculty Publications and Presentations

The goal of the ICEFISH 2004 cruise, which was conducted on board RVIB Nathaniel B. Palmer and traversed the transitional zones linking the South Atlantic to the Southern Ocean, was to compare the evolution, ecology, adaptational biology, community structure, and population dynamics of Antarctic notothenioid fishes relative to the cool/temperate notothenioids of the sub-Antarctic. To place this work in a comprehensive ecological context, cruise participants surveyed the benthos and geology of the biogeographic provinces and island shelves on either side of the Antarctic Polar Front (or Antarctic Convergence). Genome-enabled comparison of the responses of cold-living and temperate notothenioids to heat …

Differential Virus Host-Ranges Of The Fuselloviridae Of Hyperthermophilic Archaea: Implications For Evolution In Extreme Environments, Ruben M. Ceballos, Caleb D. Marceau, Joshua O. Marceau, Steven Morris, Adam J. Clore, Kenneth M. Stedman

Biology Faculty Publications and Presentations

An emerging model for investigating virus-host interactions in hyperthermophilic Archaea is the Fusellovirus-Sulfolobus system. The host, Sulfolobus, is a hyperthermophilic acidophile endemic to sulfuric hot springs worldwide. The Fuselloviruses, also known as Sulfolobus Spindle-shaped Viruses (SSVs), are "lemon" or "spindle"-shaped double-stranded DNA viruses, which are also found worldwide. Although a few studies have addressed the host-range for the type virus, Sulfolobus Spindle-shaped Virus 1 (SSV1), using common Sulfolobus strains, a comprehensive host-range study for SSV-Sulfolobus systems has not been performed. Herein, we examine six bona fide SSV strains (SSV1, SSV2, SSV3, SSVL1, SSVK1, SSVRH) and their respective infection characteristics on …

Predicting Occupancy Of Wintering Migratory Birds: Is Microhabitat Information Necessary?, Christopher J. W. Mcclure, Brian W. Rolek, Geoffrey E. Hill

Biology Faculty Publications and Presentations

Information regarding microhabitat, here defined as small-scale vegetation structure, is often useful in predicting use of habitat by birds. Quantifying microhabitat, however, is expensive and labor intensive compared to assessment of habitat at a larger scale, possibly from remotely sensed imagery. To assess the importance of microhabitat information in constructing predictive models of habitat occupancy, we compared occupancy models built on the basis of macro- and microhabitat together and separately. We based our models on counts of wintering migratory bird species and vegetation surveys within Tuskegee National Forest, Alabama, completed during winter 2009. Models built from macrohabitat data only outperformed …

In Vivo Quantification Reveals Extensive Natural Variation In Mitochondrial Form And Function In Caenorhabditis Briggsae, Kiley Ann Hicks, Dana K. Howe, Aubrey Leung, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among- isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential …

The Breeding Biology Of The Northern Pygmy Owl: Do The Smallest Of The Small Have An Advantage?, John F. Deshler, Michael T. Murphy

Biology Faculty Publications and Presentations

We explored the breeding biology of the Northern Pygmy-Owl (Glaucidium gnoma) from 2007 to 2009 in a forested reserve in Portland, Oregon. Large body size is often assumed to give animals reproductive advantages, and we tested whether body size affected timing of breeding and examined variation in diet, breeding date, clutch size, and reproductive success to explore whether the presumed benefits of large body size are evident in this species. The average size of 13 clutches was 5.8, and nest success was high (92%); 22 successful nests fledged an average of 5.2 young. Dates of first laying varied …

Antisense Transcription Is Pervasive But Rarely Conserved In Enteric Bacteria, Rahul Raghavan, D. B. Sloan, H. Ochman

Biology Faculty Publications and Presentations

Noncoding RNAs, including antisense RNAs (asRNAs) that originate from the complementary strand of protein-coding genes, are involved in the regulation of gene expression in all domains of life. Recent application of deep-sequencing technologies has revealed that the transcription of asRNAs occurs genome-wide in bacteria. Although the role of the vast majority of asRNAs remains unknown, it is often assumed that their presence implies important regulatory functions, similar to those of other noncoding RNAs. Alternatively, many antisense transcripts may be produced by chance transcription events from promoter-like sequences that result from the degenerate nature of bacterial transcription factor binding sites. To …