Life Sciences Commons^™

Diving Into Aquatic Microbial Ecology And Evolution With Anne Thompson, Anne Thompson

PDXPLORES Podcast

On this episode of PDXPLORES, Assistant Professor of Biology, Anne Thompson, discusses her award-winning research work studying the diverse ecology of microorganisms found in Earth’s oceans. Thompson’s research examines microbial mortality impacts on the structure of oceanic food webs, carbon flow, and cell interactions that create dynamic patterns of nutrient and energy abundance within diverse aquatic ecosystems.

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Exploring Extreme Viruses With Ken Stedman, Kenneth Stedman

PDXPLORES Podcast

In this episode of PDXPLORES, Ken Stedman, Professor of Biology at Portland State University, discusses his distinguished virology career. From discovering his love of extreme viruses at Max Planck Institute for Biochemistry in Munich, Germany, to heading the Advanced Molecular and Cell Biology Research Laboratory and the eXtreme Virus Lab, Steadman has investigated extreme virus structures, function, genetics, and evolution for more than 25 years. He is the co-founder of the research lab Center for Life in Extreme Environments as well as the Chief Scientific Officer of StoneStable, Inc. Adding to his scientific accomplishments and accolades, Professor Stedman …

Viruses In Astrobiology, Ignacio De La Higuera, Ester Lázaro

Biology Faculty Publications and Presentations

Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very …

A Small Rna Is Functional In Escherichia Fergusonii Despite Containing A Large Insertion., Austin P. Wright, H. Auguste Dutcher, Brianna Butler, Timothy J. Nice, Rahul Raghavan

Biology Faculty Publications and Presentations

Bacterial small RNAs (sRNAs) are important regulators of gene expression; however, the impact of natural mutations on sRNA functions has not been studied extensively. Here we show that the sRNA MgrR contains a unique 53 bp insertion in Escherichia fergusonii, a close relative of Escherichia coli and Salmonella enterica. The insertion is a repetitive extragenic palindromic (REP) sequence that could block transcription, but full-length MgrR is produced in E. fergusonii, showing that the insertion has not affected sRNA production. Additionally, despite containing the large insertion, the sRNA appears to be functional because deletion of mgrR made E. fergusonii …

Novel Small Rnas Expressed By Bartonella Bacilliformis Under Multiple Conditions Reveal Potential Mechanisms For Persistence In The Sand Fly Vector And Human Host, Shaun Wachter, Linda D. Hicks, Rahul Raghavan, Michael F. Minnick

Biology Faculty Publications and Presentations

Bartonella bacilliformis, the etiological agent of Carrión’s disease, is a Gram-negative, facultative intracellular alphaproteobacterium. Carrión’s disease is an emerging but neglected tropical illness endemic to Peru, Colombia, and Ecuador. B. bacilliformis is spread between humans through the bite of female phlebotomine sand flies. As a result, the pathogen encounters significant and repeated environmental shifts during its life cycle, including changes in pH and temperature. In most bacteria, small non-coding RNAs (sRNAs) serve as effectors that may post-transcriptionally regulate the stress response to such changes. However, sRNAs have not been characterized in B. bacilliformis, to date. We …

Direct Binding Of Tfeα Opens Dna Binding Cleft Of Rna Polymeras, Sung-Hoon Jun, Jaekyung Hyun, Hoyoung Kim, Michael S. Bartlett, Hyun-Soo Cho, Katsuhiko S. Murakami

Biology Faculty Publications and Presentations

Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFEα binary, and RNAPTFEα-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFEα bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it while maintaining the TFEα interactions with the RNAP mobile modules. The structures and photo-crosslinking results also suggest that the conserved aromatic residue in the extended winged-helix …

Host-Dependent Differences In Replication Strategy Of The Sulfolobus Spindle-Shaped Virus Strain Ssv9 (A.K.A., Ssvk1): Infection Profiles In Hosts Of The Family Sulfolobaceae, Ruben M. Ceballos, Coyne Gareth Drummond, Carson Len Stacy, Elizabeth Padillo-Crespo, Kenneth M. Stedman

Biology Faculty Publications and Presentations

The Sulfolobus Spindle-shaped Virus (SSV) system has become a model for studying thermophilic virus biology, including archaeal host-virus interactions and biogeography. Several factors make the SSV system amenable to studying archaeal genetic mechanisms (e.g., CRISPRs) as well as virus-host interactions in high temperature acidic environments. Previously, we reported that SSVs exhibited differential infectivity on allopatric vs. sympatric hosts. We also noticed a wide host range for virus strain SSV9 (a.k.a., SSVK1). For decades, SSVs have been described as “non-lytic” double-stranded DNA viruses that infect species of the genus Sulfolobus and release virions via budding rather than host lysis. In this …

Unveiling Crucivirus Diversity By Mining Metagenomic Data, Ignacio De La Higuera, George Kasun, Ellis L. Torrance, Alyssa A. Pratt, Amberlee Maluenda, Jonathan Colombet, Maxime Bisseux, Viviane Ravet, Anisha Dayaram, Daisy Stainton, Simona Kraberger, Peyman Zawar-Reza, Sharyn Goldstien, James V. Briskie, Robyn White, Helen Taylor, Christopher Gomez, David G. Ainley, Jon S. Harding, Rafaela S. Fontenele, Joshua Schreck, Simone Ribeiro, Stephen A. Oswald, Jennifer M. Arnold, François Enault, Arvind Varsani, Kenneth M. Stedman

Biology Faculty Publications and Presentations

The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESSDNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of …

An Uncultivated Virus Infecting A Symbiotic Nanoarchaeota In The Hot Springs Of Yellowstone National Park, Jacob H. Munson-Mcgee, Colleen Rooney, Mark J. Young

Computer Science Faculty Publications and Presentations

The Nanoarchaeota are small cells with reduced genomes that are found attached to and dependent on a second archaeal cell for their growth and replication. Initially found in marine hydrothermal environments and subsequently in terrestrial geothermal hot springs, the Nanoarchaeota species that have been described are obligate ectobionts, each with a different host species. However, no viruses have been described that infect the Nanoarchaeota. Here we identify a virus infecting Nanoarchaeota using a combination of viral metagenomic and bioinformatic approaches. This virus, tentatively named Nanoarchaeota Virus 1 (NAV1), consists of a 35.6kb circular DNA genome encoding for 52 proteins. We …

Genome Sequences Of Three Cruciviruses Found In The Willamette Valley (Oregon), Ignacio De La Higuera, Ellis L. Torrance, Alyssa A. Pratt, George Kasun, Amberlee Maluenda, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Cruciviruses are single-stranded DNA (ssDNA) viruses whose genomes suggest the possibility of gene transfer between DNA and RNA viruses. Many crucivirus genome sequences have been found in metagenomic data sets, although no crucivirus has been isolated. Here, we present the complete genome sequences of three cruciviruses recovered from environmental samples from Oregon.

Origin, Evolution, And Loss Of Bacterial Small Rnas, H. Auguste Dutcher, Rahul Raghavan

Biology Faculty Publications and Presentations

Despite the central role of bacterial noncoding small RNAs (sRNAs) in posttranscriptional regulation, little is understood about their evolution. Here we compile what has been studied to date and trace a life cycle of sRNAs—from their mechanisms of emergence, through processes of change and frequent neofunctionalization, to their loss from bacterial lineages. Because they possess relatively unrestrictive structural requirements, we find that sRNA origins are varied, and include de novo emergence as well as formation from preexisting genetic elements via duplication events and horizontal gene transfer. The need for only partial complementarity to their mRNA targets facilitates apparent rapid change, …

Bioassessment Of A Drinking Water Reservoir Using Plankton: High Throughput Sequencing Vs. Traditional Morphological Method, Wanli Gao, Zhaojin Chen, Yuying Li, Yangdong Pan, Jingya Zhu, Shijun Guo, Lanqun Hu, Jin Huang

Environmental Science and Management Faculty Publications and Presentations

Drinking water safety is increasingly perceived as one of the top global environmental issues. Plankton has been commonly used as a bioindicator for water quality in lakes and reservoirs. Recently, DNA sequencing technology has been applied to bioassessment. In this study, we compared the effectiveness of the 16S and 18S rRNA high throughput sequencing method (HTS) and the traditional optical microscopy method (TOM) in the bioassessment of drinking water quality. Five stations reflecting different habitats and hydrological conditions in Danjiangkou Reservoir, one of the largest drinking water reservoirs in Asia, were sampled May 2016. Non-metric multi-dimensional scaling (NMDS) analysis showed …

Genome-Wide Screening Of Potential Rnase Y-Processed Mrnas In The M49 Serotype Streptococcus Pyogenes Nz131, Zhiyun Chen, Rahul Raghavan, Fengxia Qi, Justin Merritt, Jens Kreth

Biology Faculty Publications and Presentations

RNase Y is a major endoribonuclease in Group A streptococcus (GAS) and other Gram‐positive bacteria. Our previous study showed that RNase Y was involved in mRNA degradation and processing in GAS. We hypothesized that mRNA processing regulated the expression of important GAS virulence factors via altering their mRNA stabilities and that RNase Y mediated at least some of the mRNA‐processing events. The aims of this study were to (1) identify mRNAs that were processed by RNase Y and (2) confirm the mRNA‐processing events. The transcriptomes of Streptococcus pyogenes NZ131 wild type and its RNase Y mutant (Δrny) were …

Simplified Reversed Chloroquines To Overcome Malaria Resistance To Quinoline-Based Drugs, Bornface Gunsaru, Steven J. Burgess, Westin Morrill, Jane X. Kelly, Shawheen Shomloo, Martin J. Smilkstein, Katherine May Liebman, David H. Peyton

Chemistry Faculty Publications and Presentations

Building on our earlier work of attaching a chemosensitizer (reversal agent) to a known drug pharmacophore, we have now expanded the structure-activity relationship study to include simplified versions of the chemosensitizer. The change from two aromatic rings in this head group to a single ring does not appear to detrimentally affect the antimalarial activity of the compounds. Data from in vitro heme binding and beta-hematin inhibition assays suggest that the single aromatic RCQ compounds retain activities against Plasmodium falciparum similar to those of CQ, although other mechanisms of action may be relevant to their activities.

Accumulation And Expression Of Multiple Antibiotic Resistance Genes In Arcobacter Cryaerophilus That Thrives In Sewage, Jess A. Millar, Rahul Raghavan

Biology Faculty Publications and Presentations

We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also …

Peering Below The Diffraction Limit: Robust And Specific Sorting Of Viruses With Flow Cytometry, Shea T. Lance, David J. Sukovich, Kenneth M. Stedman, Adam R. Abate

Biology Faculty Publications and Presentations

Background: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population. Specific sorting opens new avenues in the study of uncultivable viruses, including recovering the full genomes of viruses based on genetic fragments in metagenomes, or identifying the …

Group I Intron Internal Guide Sequence Binding Strength As A Component Of Ribozyme Network Formation, Elizabeth Satterwhite, Jessica Anne Mellor Yeates, Niles Lehman

Chemistry Faculty Publications and Presentations

Origins-of-life research requires searching for a plausible transition from simple chemicals to larger macromolecules that can both hold information and catalyze their own production. We have previously shown that some group I intron ribozymes possess the ability to help synthesize other ribozyme genotypes by recombination reactions in small networks in an autocatalytic fashion. By simplifying these recombination reactions, using fluorescent anisotropy, we quantified the thermodynamic binding strength between two nucleotides of two group I intron RNA fragments for all 16 possible genotype combinations. We provide evidence that the binding strength (K_D) between the 3-nucleotide internal guide sequence …

Mitochondrial Dna Sequence And Lack Of Response To Anoxia In The Annual Killifish Austrofundulus Limnaeus, Josiah T. Wagner, Florisela H. Chavez, Jason E. Podrabsky

Biology Faculty Publications and Presentations

The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in regions of Venezuela, South America. Permanent populations of A. limnaeus are maintained by production of stress-tolerant embryos that are able to persist in the desiccated sediment. Previous work has demonstrated that A. limnaeus have a remarkable ability to tolerate extended periods of anoxia and desiccating conditions. After considering temperature, A. limnaeus embryos have the highest known tolerance to anoxia when compared to any other vertebrate yet studied. Oxygen is completely essential for the process of oxidative phosphorylation by mitochondria, the intracellular organelle responsible for the majority of adenosine triphosphate production. Thus, …

Coxiella Burnetii And Leishmania Mexicana Residing Within Similar Parasitophorous Vacuoles Elicit Disparate Host Responses, Jess A. Millar, Raquel Valdés, Fenil Kacharia, Scott M. Landfear, Eric D. Cambronne, Rahul Raghavan, Lynn Soong, Emilio Luis Malchiodi

Biology Faculty Publications and Presentations

Coxiella burnetii is a bacterium that thrives in an acidic parasitophorous vacuole (PV) derived from lysosomes. Leishmania mexicana, a eukaryote, has also independently evolved to live in a morphologically similar PV. As Coxiella and Leishmania are highly divergent organisms that cause different diseases, we reasoned that their respective infections would likely elicit distinct host responses despite producing phenotypically similar parasite-containing vacuoles. The objective of this study was to investigate, at the molecular level, the macrophage response to each pathogen. Infection of THP-1 (human monocyte/macrophage) cells with Coxiella and Leishmania elicited disparate host responses. At 5 days post-infection, when …

Effects Of Sex And Mycorrhizal Fungi On Gas Exchange In The Dioecious Salt Marsh Grass Distichlis Spicata, Kassandra Reuss-Schmidt, Todd N. Rosenstiel, Sally R. Rogers, Allie G. Simpson, Sarah M. Eppley

Biology Faculty Publications and Presentations

Premise of research. In dioecious plant species, males and females often differ in physiology, and mycorrhizal fungal relationships are likely to influence these differences. However, few data are available on the potential role of mycorrhizal fungi in altering sex-specific physiology and population sex ratios of dioecious plant species.

Methodology. In this study, we measured leaf gas exchange in a multifactorial greenhouse experiment with and without mycorrhizal fungal additions and under field conditions in Distichlis spicata, a dioecious C4 salt marsh grass, displaying extreme spatial sex ratio variation.

Pivotal results. We found a significant interaction between gas exchange, plant sex, and …

Spring Thaw Ionic Pulses Boost Nutrient Availability And Microbial Growth In Entombed Antarctic Dry Valley Cryoconite Holes, Jon Telling, Alexandre M. Anesio, Martyn Tranter, Andrew G. Fountain, Thomas H. Nylen, Jon Hawkings, Virendra B. Singh, Preeti Kaur, Michaela Musilova, Jemma L. Wadham

Geology Faculty Publications and Presentations

The seasonal melting of ice entombed cryoconite holes on McMurdo Dry Valley glaciers provides oases for life in the harsh environmental conditions of the polar desert where surface air temperatures only occasionally exceed 0°C during the Austral summer. Here we follow temporal changes in cryoconite hole biogeochemistry on Canada Glacier from fully frozen conditions through the initial stages of spring thaw toward fully melted holes. The cryoconite holes had a mean isolation age from the glacial drainage system of 3.4 years, with an increasing mass of aqueous nutrients (dissolved organic carbon, total nitrogen, total phosphorus) with longer isolation age. During …

Structural Insights Into The Architecture Of The Hyperthermophilic Fusellovirus Ssv1, Kenneth M. Stedman, Melissa Deyoung, Mitul Saha, Michael B. Sherman, Marc C. Morais

Biology Faculty Publications and Presentations

The structure and assembly of many icosahedral and helical viruses are well-characterized. However, the molecular basis for the unique spindle-shaped morphology of many viruses that infect Archaea remains unknown. To understand the architecture and assembly of these viruses, the spindle-shaped virus SSV1 was examined using cryo-EM, providing the first 3D-structure of a spindle-shaped virus as well as insight into SSV1 biology, assembly and evolution. Furthermore, a geometric framework underlying the distinct spindle-shaped structure is proposed.

Novel Cul3 Binding Proteins Function To Remodel E3 Ligase Complexes, Wananit Wimuttisuk, Mark West, Brittney Davidge, Kebing Yu, Arthur Salomon, Jeffrey D. Singer

Biology Faculty Publications and Presentations

Background: Cullins belong to a family of scaffold proteins that assemble multi-subunit ubiquitin ligase complexes to recruit protein substrates for ubiquitination via unique sets of substrate adaptor, such as Skp1 or Elongin B, and a substrate-binding protein with a conserved protein-protein interacting domain, such as leucine-rich repeats (LRR), a WD40 domain, or a zinc-finger domain. In the case of the Cullin3 (Cul3), it forms a BTB-Cul3-Rbx1 (BCR) ubiquitin ligase complex where it is believed that a BTB domain-containing protein performs dual functions where it serves as both the substrate adaptor and …

Taxis Toward Hydrogen Gas By Methanococcus Maripaludis, Kristen A. Brileya, James M. Connolly, Carey Downey, Robin Gerlach, Matthew W. Fields

Biology Faculty Publications and Presentations

Knowledge of taxis (directed swimming) in the Archaea is currently expanding through identification of novel receptors, effectors, and proteins involved in signal transduction to the flagellar motor. Although the ability for biological cells to sense and swim toward hydrogen gas has been hypothesized for many years, this capacity has yet to be observed and demonstrated. Here we show that the average swimming velocity increases in the direction of a source of hydrogen gas for the methanogen, Methanococcus maripaludis using a capillary assay with anoxic gas-phase control and time-lapse microscopy. The results indicate that a methanogen couples motility to hydrogen concentration …

Reversible Inactivation And Desiccation Tolerance Of Silicified Viruses, James R. Laidler, Jessica A. Shugart, Sherry L. Cady, Keith S. Bahjat, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Long-distance host-independent virus dispersal is poorly understood, especially for viruses found in isolated ecosystems. To
demonstrate a possible dispersal mechanism, we show that bacteriophage T4, archaeal virus Sulfolobus spindle-shaped virus Kamchatka, and vaccinia virus are reversibly inactivated by mineralization in silica under conditions similar to volcanic hot
springs. In contrast, bacteriophage PRD1 is not silicified. Moreover, silicification provides viruses with remarkable desiccation
resistance, which could allow extensive aerial dispersal.

Mesoaciditoga Lauensis Gen. Nov., Sp. Nov., A Moderate Thermoacidophilic Thermotogales From A Deep-Sea Hydrothermal Vent, Anna-Louise Reysenbach, Yitai Liu, Annie R. Lindgren, Issac D. Wagner, Christine Demko Sislak, Anchelique Mets, Stefan Schouten

Biology Faculty Publications and Presentations

A novel moderately thermophilic, heterotrophic bacterium was isolated from a deep-sea hydrothermal vent deposit from the Mariner field along the Eastern Lau Spreading Center, Southwestern Pacific. Cells were short motile rods (about 0.4 μm-0.8 μm) that occurred singly or in pairs and were surrounded by a sheath-like membrane or ‘toga’. The cells grew between 45 and 65°C (optimum 57-60°C), pH 4.1-6.0 (optimum pH 5.5-5.7) and optimally at 3% (w/v) NaCl. The isolate grew on a range of carbon and proteinaceous substrates and reduced sulfur. The G + C content of the DNA was about 45 mol%. Phylogenetic analysis of the …

Metagenome Sequence Analysis Of Filamentous Microbial Communities Obtained From Geochemically Distinct Geothermal Channels Reveals Specialization Of Three Aquificales Lineages, Cristina Takacs-Vesbach, William P. Inskeep, Zackary J. Jay, Markus J. Herrgard, Douglas B. Rusch, Susannah G. Tringe, Mark A. Kozubal, Natsuko Hamamura, Richard E. Macur, Bruce W. Fouke, Anna-Louise Reysenbach, Timothy R. Mcdermott, Ryan Dem. Jennings, Nicolas W. Hengartner, Gary Xie

Biology Faculty Publications and Presentations

The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems world- wide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal “filamentous streamer” communities (∼40 Mbp per site), which targeted three different groups of Aquificales found in Yellow- stone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobac- ulum (Aquificaceae) populations, whereas the circum-neutral pH (6.5–7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circum-neutral sites with undetectable …

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 …

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 …

A Novel Virus Genome Discovered In An Extreme Environment Suggests Recombination Between Unrelated Groups Of Rna And Dna Viruses, Geoffrey S. Diemer, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Background: Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis.

Results: Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar …