Life Sciences Commons^™

Changing The Pathobiological Paradigm In Myelodysplastic Syndromes: The Nlrp3 Inflammasome Drives The Mds Phenotype, Ashley Basiorka

USF Tampa Graduate Theses and Dissertations

Note: Portions of this abstract have been previously published in the journal Blood, Basiorka et al. Blood. 2016 Oct 13, and has been reproduced in this manuscript with permission from the publisher.

Myelodysplastic syndromes (MDS) are genetically diverse hematopoietic stem cell malignancies that share a common phenotype of cytological dysplasia, ineffective hematopoiesis and aberrant myeloid lineage maturation. Apoptotic cell death potentiated by inflammatory cytokines has been considered a fundamental feature of MDS for over two decades. However, this non-inflammatory form of cell death cannot account for the inflammatory nature of these disorders. We report that a hallmark of lower-risk …

How Random Noise And A Graphical Convention Subverted Behavioral Scientists' Explanations Of Self-Assessment Data: Numeracy Underlies Better Alternatives, Edward Nuhfer, Steven Fleisher, Christopher Cogan, Karl Wirth, Eric Gaze

Numeracy

Despite nearly two decades of research, researchers have not resolved whether people generally perceive their skills accurately or inaccurately. In this paper, we trace this lack of resolution to numeracy, specifically to the frequently overlooked complications that arise from the noisy data produced by the paired measures that researchers employ to determine self-assessment accuracy. To illustrate the complications and ways to resolve them, we employ a large dataset (N = 1154) obtained from paired measures of documented reliability to study self-assessed proficiency in science literacy. We collected demographic information that allowed both criterion-referenced and normative-based analyses of self-assessment data. …

Permafrost Organic Carbon Mobilization From The Watershed To The Colville River Delta: Evidence From 14C Ramped Pyrolysis And Lignin Biomarkers, Xiaowen Zhang, Thomas S. Bianchi, Xingqian Cui, Brad E. Rosenheim, Chien-Lu Ping, Andrea J. M. Hanna, Mikhail Kanevskiy, Kathryn M. Schreiner, Mead A. Allison

Marine Science Faculty Publications

The deposition of terrestrial-derived permafrost particulate organic carbon (POC) has been recorded in major Arctic river deltas. However, associated transport pathways of permafrost POC from the watershed to the coast have not been well constrained. Here we utilized a combination of ramped pyrolysis-oxidation radiocarbon analysis (RPO ¹⁴C) along with lignin biomarkers, to track the linkages between soils and river and delta sediments. Surface and deep soils showed distinct RPO thermographs which may be related to degradation and organo-mineral interaction. Soil material in the bed load of the river channel was mostly derived from deep old permafrost. Both surface and …

Recommendations On The Use Of Ecosystem Modeling For Informing Ecosystem-Based Fisheries Management And Restoration Outcomes In The Gulf Of Mexico, Arnaud Grüss, Kenneth A. Rose, James Simons, Cameron H. Ainsworth, Elizabeth A. Babcock, David D. Chagaris, Kim De Mutsert, John Froeschke, Peter Himchak, Isaac C. Kaplan, Halie O’Farrell, Manuel J. Zetina Rejon

Marine Science Faculty Publications

Ecosystem-based fisheries management (EBFM) and ecosystem restoration are gaining momentum worldwide, including in U.S. waters of the Gulf of Mexico (GOM). Ecosystem models are valuable tools for informing EBFM and restoration activities. In this paper, we provide guidance and a roadmap for ecosystem modeling in the GOM region, with an emphasis on model development and use of model products to inform EBFM and the increasing investments in restoration. We propose eight “best practices” for ecosystem modeling efforts, including (1) identification of priority management questions, (2) scenarios as simulation experiments, (3) calibration and validation needs, (4) sensitivity and uncertainty analyses, (5) …

Floating Algae Blooms In The East China Sea, Lin Qi, Chuanmin Hu, Mengqiu Wang, Shaoling Shang, Cara Wilson

Marine Science Faculty Publications

A floating algae bloom in the East China Sea was observed in Moderate Resolution Imaging Spectroradiometer (MODIS) imagery in May 2017. Using satellite imagery from MODIS, Visible Infrared Imaging Radiometer Suite, Geostationary Ocean Color Imager, and Ocean Land Imager, and combined with numerical particle tracing experiments and laboratory experiments, we examined the history of this bloom as well as similar blooms in previous years and attempted to trace the bloom source and identify the algae type. Results suggest that one bloom origin is offshore Zhejiang coast where algae slicks have appeared in satellite imagery almost every February–March since 2012. Following …

Calculating Surface Ocean Pco2 From Biogeochemical Argo Floats Equipped With Ph: An Uncertainty Analysis, N. L. Williams, L. W. Juranek, R. A. Feely, K. S. Johnson, J. L. Sarmiento, L. D. Talley, A. G. Dickson, A. R. Gray, R. Wanninkhof, J. L. Russell, S. C. Riser, Y. Takeshita

Marine Science Faculty Publications

More than 74 biogeochemical profiling floats that measure water column pH, oxygen, nitrate, fluorescence, and backscattering at 10 day intervals have been deployed throughout the Southern Ocean. Calculating the surface ocean partial pressure of carbon dioxide (pCO_2sw) from float pH has uncertainty contributions from the pH sensor, the alkalinity estimate, and carbonate system equilibrium constants, resulting in a relative standard uncertainty in pCO_2sw of 2.7% (or 11 µatm at pCO_2sw of 400 µatm). The calculated pCO2sw from several floats spanning a range of oceanographic regimes are compared to existing climatologies. In some locations, such as the …

Biogeochemical Sensor Performance In The Soccom Profiling Float Array, Kenneth S. Johnson, Joshua N. Plant, Luke J. Coletti, Hans W. Jannasch, Carole M. Sakamoto, Stephen C. Riser, Dana D. Swift, Nancy L. Williams, Emmanuel Boss, Nils Haëntjens, Lynne D. Talley, Jorge L. Sarmiento

Marine Science Faculty Publications

The Southern Ocean Carbon and Climate Observations and Modeling (SOCCOM) program has begun deploying a large array of biogeochemical sensors on profiling floats in the Southern Ocean. As of February 2016, 86 floats have been deployed. Here the focus is on 56 floats with quality-controlled and adjusted data that have been in the water at least 6 months. The floats carry oxygen, nitrate, pH, chlorophyll fluorescence, and optical backscatter sensors. The raw data generated by these sensors can suffer from inaccurate initial calibrations and from sensor drift over time. Procedures to correct the data are defined. The initial accuracy of …

An Ice Sheet Model Validation Framework For The Greenland Ice Sheet, Stephen F. Price, Matthew J. Hoffman, Jennifer A. Bonin, Ian M. Howat, Thomas Neumann, Jack Saba, Irina Tezaur, Jeffrey Guerber, Don P. Chambers, Katherine J. Evans, Joseph H. Kennedy, Jan Lenaerts, William H. Lipscomb, Mauro Perego, Andrew G. Salinger, Raymond S. Tuminaro, Michiel R. Van Den Broeke, Sophie M. Nowicki

Marine Science Faculty Publications

We propose a new ice sheet model validation framework – the Cryospheric Model Comparison Tool (CmCt) – that takes advantage of ice sheet altimetry and gravimetry observations collected over the past several decades and is applied here to modeling of the Greenland ice sheet. We use realistic simulations performed with the Community Ice Sheet Model (CISM) along with two idealized, non-dynamic models to demonstrate the framework and its use. Dynamic simulations with CISM are forced from 1991 to 2013, using combinations of reanalysis-based surface mass balance and observations of outlet glacier flux change. We propose and demonstrate qualitative and quantitative …

Importance Of Lateral Flux And Its Percolation Depth On Organic Carbon Export In Arctic Tundra Soil: Implications From A Soil Leaching Experiment, Xiaowen Zhang, Jack A. Hutchings, Thomas S. Bianchi, Yina Liu, Ana Arellano, Edward A. Schuur

Marine Science Faculty Publications

Temperature rise in the Arctic is causing deepening of active layers and resulting in the mobilization of deep permafrost dissolved organic matter (DOM). However, the mechanisms of DOM mobilization from Arctic soils, especially upper soil horizons which are drained most frequently through a year, are poorly understood. Here we conducted a short-term leaching experiment on surface and deep organic active layer soils, from the Yukon River basin, to examine the effects of DOM transport on bulk and molecular characteristics. Our data showed a net release of DOM from surface soils equal to an average of 5% of soil carbon. Conversely, …

The Periodic Topography Of Ice Stream Beds: Insights From The Fourier Spectra Of Mega-Scale Glacial Lineations, Matteo Spagnolo, Timothy C. Bartholomaus, Chris D. Clark, Chris R. Stokes, Nigel Atkinson, Julian A. Dowdeswell, Jeremy C. Ely, Alastair G. C. Graham, Kelly A. Hogan, Edward C. King, Robert D. Larter, Stephen J. Livingstone, Hamish D. Pritchard

Marine Science Faculty Publications

Ice stream bed topography contains key evidence for the ways ice streams interact with, and are potentially controlled by, their beds. Here we present the first application of two-dimensional Fourier analysis to 22 marine and terrestrial topographies from 5 regions in Antarctica and Canada, with and without mega-scale glacial lineations (MSGLs). We find that the topography of MSGL-rich ice stream sedimentary beds is characterized by multiple, periodic wavelengths between 300 and 1200 m and amplitudes from decimeters to a few meters. This periodic topography is consistent with the idea that instability is a key element to the formation of MSGL …

Resemblance Profiles As Clustering Decision Criteria: Estimating Statistical Power, Error, And Correspondence For A Hypothesis Test For Multivariate Structure, Joshua P. Kilborn, David L. Jones, Ernst B. Peebles, David F. Naar

Marine Science Faculty Publications

Clustering data continues to be a highly active area of data analysis, and resemblance profiles are being incorporated into ecological methodologies as a hypothesis testing-based approach to clustering multivariate data. However, these new clustering techniques have not been rigorously tested to determine the performance variability based on the algorithm's assumptions or any underlying data structures. Here, we use simulation studies to estimate the statistical error rates for the hypothesis test for multivariate structure based on dissimilarity profiles (DISPROF). We concurrently tested a widely used algorithm that employs the unweighted pair group method with arithmetic mean (UPGMA) to estimate the proficiency …

Persistent Spatial Structuring Of Coastal Ocean Acidification In The California Current System, F. Chan, J. A. Barth, C. A. Blanchette, R. H. Byrne, F. Chavez, O. Cheriton, R. A. Feely, G. Friederich, B. Gaylord, T. Gouhier, S. Hacker, T. Hill, G. Hofmann, M. A. Mcmanus, B. A. Menge, K. J. Nielsen, A. Russell, E. Sanford, J. Sevadjian, L. Washburn

Marine Science Faculty Publications

The near-term progression of ocean acidification (OA) is projected to bring about sharp changes in the chemistry of coastal upwelling ecosystems. The distribution of OA exposure across these early-impact systems, however, is highly uncertain and limits our understanding of whether and how spatial management actions can be deployed to ameliorate future impacts. Through a novel coastal OA observing network, we have uncovered a remarkably persistent spatial mosaic in the penetration of acidified waters into ecologically-important nearshore habitats across 1,000 km of the California Current Large Marine Ecosystem. In the most severe exposure hotspots, suboptimal conditions for calcifying organisms encompassed up …

Monitoring Biodiversity Change Through Effective Global Coordination, Laetitia M. Navarro, Néstor Fernández, Carlos Guerra, Rob Guralnick, W Daniel Kissling, Maria Cecilia Londoño, Frank Muller-Karger, Eren Turak, Patricia Balvanera, Mark J. Costello, Aurelie Delavaud, Gy El Serafy, Simon Ferrier, Ilse Geijzendorffer, Gary N. Geller, Walter Jetz, Eun-Shik Kim, Hyejin Kim, Corinne S. Martin, Melodie A. Mcgeoch, Tuyeni H. Mwampamba, Jeanne L. Nel, Emily Nicholson, Nathalie Pettorelli, Michael E. Schaepman, Andrew Skidmore, Isabel Sousa Pinto, Sheila Vergara, Petteri Vihervaara, Haigen Xu, Tetsukazu Yahara, Mike Gill, Henrique M. Pereira

Marine Science Faculty Publications

The ability to monitor changes in biodiversity, and their societal impact, is critical to conserving species and managing ecosystems. While emerging technologies increase the breadth and reach of data acquisition, monitoring efforts are still spatially and temporally fragmented, and taxonomically biased. Appropriate long-term information remains therefore limited. The Group on Earth Observations Biodiversity Observation Network (GEO BON) aims to provide a general framework for biodiversity monitoring to support decision-makers. Here, we discuss the coordinated observing system adopted by GEO BON, and review challenges and advances in its implementation, focusing on two interconnected core components — the Essential Biodiversity Variables as …

Local And Regional Stressors Interact To Drive A Salinization-Induced Outbreak Of Predators On Oyster Reefs, David L. Kimbro, J. Wilson White, Hanna Tillotson, Nikkie Cox, Megan Christopher, Owen Stokes-Cawley, Samantha Yuan, Timothy J. Pusack, Christopher D. Stallings

Marine Science Faculty Publications

Predator outbreaks are predicted to increasingly decimate economically and ecologically important prey populations because global climate change and food-web modifications frequently facilitate predators and stress prey. Natural systems are organized hierarchically, with processes operating at multiple scales giving rise to patterns of biodiversity, so predicting and managing outbreaks requires a framework that accounts for the effects of both local and regional stressors. Here, we used the comparative experimental approach to investigate whether the collapse of a nationally important oyster fishery in the Gulf of Mexico (Apalachicola Bay, Florida) could have been (1) caused proximally by a predator outbreak and (2) …

Sub-Ice Shelf Sediment Geochronology Utilizing Novel Radiocarbon Methodology For Highly Detrital Sediments, C. Subt, H. I. Yoon, K. C. Yoo, J. I. Lee, A. Leventer, Eugene W. Domack, Brad E. Rosenheim

Marine Science Faculty Publications

Sub-ice shelf sediments near Larsen C ice shelf (LIS-C) show fine-scale rhythmic laminations that could provide a near-continuous seasonal-resolution record of regional ice mass changes. Despite the great potential of these sediments, a dependable Late Quaternary chronology is difficult to generate, rendering the record incomplete. As with many marginal Antarctic sediments, in the absence of preserved carbonate microfossils, the reliability of radiocarbon chronologies depends on presence of high proportions of autochthonous organic carbon with minimized detrital organic carbon. Consequently, acid insoluble organic (AIO) ¹⁴C dating works best where high productivity drives high sediment accumulation rates, but can be problematic …

Nearshore Sediment Thickness, Fire Island, New York, Stanley D. Locker, Jennifer L. Miselis, Noreen A. Buster, Cheryl J. Hapke, Heidi M. Wadman, Jesse E. Mcninch, Arnell S. Forde, Chelsea A. Stalk

Marine Science Faculty Publications

Investigations of coastal change at Fire Island, New York (N.Y.), sought to characterize sediment budgets and determine geologic framework controls on coastal processes. Nearshore sediment thickness is critical for assessing coastal system sediment availability, but it is largely unquantified due to the difficulty of conducting geological or geophysical surveys across the nearshore. This study used an amphibious vessel to acquire chirp subbottom profiles. These profiles were used to characterize nearshore geology and provide an assessment of nearshore sediment volume. Two resulting sediment-thickness maps are provided: total Holocene sediment thickness and the thickness of the active shoreface. The Holocene sediment section …

Carbon Regeneration In The Cariaco Basin, Venezuela, Arístides Marquez, Andrew Dale, Luis Troccoli Ghinaglia, Fabiola López Monroy, William Senior, Aida Ríos, Frank Muller Karger, Yrene Astor, Ramón Varela

Marine Science Faculty Publications

The carbon regeneration in the water column of the Cariaco Basin (Venezuela) was investigated using a regression model of total alkalinity (TA) and the concentration of total inorganic carbon (TCO₂). Primary productivity (PP) was determined from the inorganic carbon fraction assimilated by phytoplankton and the variation of the 22 and 23ºC isotherm was used as an indicator of coastal upwelling. The results indicate that CO₂ levels were lowest (1962 µmol/kg) at the surface and increased to 2451 µmol/kg below the oxic-anoxic redox interface. The vertical regeneration distribution of carbon was dominated (82%) by organic carbon originating from …

A Family Of Genus-Specific Rnas In Tandem With Dna-Binding Proteins Control Expression Of The Bada Major Virulence Factor Gene In Bartonella Henselae, Nhan Tu, Ronan K. Carroll, Andy Weiss, Lindsey N. Shaw, Gael Nicolas, Sarah Thomas, Amorce Lima, Udoka Okaro, Burt Anderson

Molecular Biosciences Faculty Publications

Bartonella henselae is a gram-negative zoonotic bacterium that causes infections in humans including endocarditis and bacillary angiomatosis. B. henselae has been shown to grow as large aggregates and form biofilms in vitro. The aggregative growth and the angiogenic host response requires the trimeric autotransporter adhesin BadA. We examined the transcriptome of the Houston-1 strain of B. henselae using RNA-seq revealing nine novel, highly-expressed intergenic transcripts (Bartonella regulatory transcript, Brt1-9). The Brt family of RNAs is unique to the genus Bartonella and ranges from 194 to 203 nucleotides with high homology and stable predicted secondary structures. Immediately downstream of each …

Changing Measurements Or Changing Movements? Sampling Scale And Movement Model Identifiability Across Generations Of Biologging Technology, Leah R. Johnson, Philipp H. Boersch-Supan, Richard A. Phillips, Sadie J. Ryan

Integrative Biology Faculty and Staff Publications

Animal movement patterns contribute to our understanding of variation in breeding success and survival of individuals, and the implications for population dynamics. Over time, sensor technology for measuring movement patterns has improved. Although older technologies may be rendered obsolete, the existing data are still valuable, especially if new and old data can be compared to test whether a behavior has changed over time. We used simulated data to assess the ability to quantify and correctly identify patterns of seabird flight lengths under observational regimes used in successive generations of wet/dry logging technology. Care must be taken when comparing data collected …

Genetic And Epigenetic Variation In Spartina Alterniflora Following The Deepwater Horizon Oil Spill, Marta Robertson, Aaron Schrey, Ashley Shayter, Christina J. Moss, Christina Richards

Integrative Biology Faculty and Staff Publications

Catastrophic events offer unique opportunities to study rapid population response to stress in natural settings. In concert with genetic variation, epigenetic mechanisms may allow populations to persist through severe environmental challenges. In 2010, the Deepwater Horizon oil spill devastated large portions of the coastline along the Gulf of Mexico. However, the foundational salt marsh grass, Spartina alterniflora, showed high resilience to this strong environmental disturbance. Following the spill, we simultaneously examined the genetic and epigenetic structure of recovering populations of S. alterniflora to oil exposure. We quantified genetic and DNA methylation variation using amplified fragment length polymorphism and methylation …

Microbe Biogeography Tracks Water Masses In A Dynamic Oceanic Frontal System, Anni Djurhuus, Philipp H. Boersch-Supan, Svein-Ole Mikalse, Alex D. Rogers

Integrative Biology Faculty and Staff Publications

Dispersal limitation, not just environmental selection, plays an important role in microbial biogeography. The distance–decay relationship is thought to be weak in habitats where dispersal is high, such as in the pelagic environment, where ocean currents facilitate microbial dispersal. Most studies of microbial community composition to date have observed little geographical heterogeneity on a regional scale (100 km). We present a study of microbial communities across a dynamic frontal zone in the southwest Indian Ocean and investigate the spatial structure of the microbes with respect to the different water masses separated by these fronts. We collected 153 samples of free-living …

Diverse Landscapes Beneath Pine Island Glacier Influence Ice Flow, Robert G. Bingham, David G. Vaughan, Edward C. King, Damon Davies, Stephen L. Cornford, Andrew M. Smith, Robert J. Arthern, Alex M. Brisbourne, Rydt, Jan De Rydt, Alastair G. C. Graham, Matteo Spagnolo, Oliver J. Marsh, David E. Shean

Marine Science Faculty Publications

The retreating Pine Island Glacier (PIG), West Antarctica, presently contributes ~5–10% of global sea-level rise. PIG’s retreat rate has increased in recent decades with associated thinning migrating upstream into tributaries feeding the main glacier trunk. To project future change requires modelling that includes robust parameterisation of basal traction, the resistance to ice flow at the bed. However, most ice-sheet models estimate basal traction from satellite-derived surface velocity, without a priori knowledge of the key processes from which it is derived, namely friction at the ice-bed interface and form drag, and the resistance to ice flow that arises as ice deforms …

Major Advance Of South Georgia Glaciers During The Antarctic Cold Reversal Following Extensive Sub-Antarctic Glaciation, Alastair G. C. Graham, Gerhard Kuhn, Ove Meisel, Claus-Dieter Hillenbrand, Dominic A. Hodgson, Werner Ehrmann, Lukas Wacker, Paul Wintersteller, Santos Ferreira, Dos Santos Ferreira, Miriam Römer, Duanne White, Gerhard Bohrmann

Marine Science Faculty Publications

The history of glaciations on Southern Hemisphere sub-polar islands is unclear. Debate surrounds the extent and timing of the last glacial advance and termination on sub-Antarctic South Georgia in particular. Here, using sea-floor geophysical data and marine sediment cores, we resolve the record of glaciation offshore of South Georgia through the transition from the Last Glacial Maximum to Holocene. We show a sea-bed landform imprint of a shelf-wide last glacial advance and progressive deglaciation. Renewed glacier resurgence in the fjords between c. 15,170 and 13,340 yr ago coincided with a period of cooler, wetter climate known as the Antarctic Cold …

Limited Grounding-Line Advance Onto The West Antarctic Continental Shelf In The Easternmost Amundsen Sea Embayment During The Last Glacial Period, Johann P. Klages, Gerhard Kuhn, Claus-Dieter Hillenbrand, James A. Smith, Alastair G. C. Graham, Frank O. Nitsche, Thomas Frederichs, Patrycja E. Jernas, Karsten Gohl, Lukas Wacker

Marine Science Faculty Publications

Precise knowledge about the extent of the West Antarctic Ice Sheet (WAIS) at the Last Glacial Maximum (LGM; c. 26.5–19 cal. ka BP) is important in order to 1) improve paleo-ice sheet reconstructions, 2) provide a robust empirical framework for calibrating paleo-ice sheet models, and 3) locate potential shelf refugia for Antarctic benthos during the last glacial period. However, reliable reconstructions are still lacking for many WAIS sectors, particularly for key areas on the outer continental shelf, where the LGM-ice sheet is assumed to have terminated. In many areas of the outer continental shelf around Antarctica, direct geological data for …

Stable And Radiocarbon Isotopic Composition Of Dissolved Organic Matter In The Gulf Of Mexico, B. D. Walker, E. R. M. Druffel, J. Kolasinski, B. J. Roberts, X. Xu, B. E. Rosenheim

Marine Science Faculty Publications

Dissolved organic carbon (DOC) is of primary importance to marine ecosystems and the global carbon cycle. Stable carbon (δ¹³C) and radiocarbon (Δ¹⁴C) isotopic measurements are powerful tools for evaluating DOC sources and cycling. However, the isotopic signature of DOC in the Gulf of Mexico (GOM) remains almost completely unknown. Here we present the first DOC Δ¹⁴C and δ¹³C depth profiles from the GOM. Our results suggest the Mississippi River exports large amounts of DOC with an anthropogenic “bomb” Δ¹⁴C signature. Riverine DOC is removed and recycled offshore, and some marine …

Parasite Microbiome Project: Systematic Investigation Of Microbiome Dynamics Within And Across Parasite-Host Interactions, Nolwenn M. Dheilly, Daniel Bolnick, Seth Bordenstein, Paul J. Brindley, Cédric Figuères, Edward C. Holmes, Joaquín Martínez Martínez, Anna J. Phillips, Robert Poulin, Karyna Rosario

Marine Science Faculty Publications

Understanding how microbiomes affect host resistance, parasite virulence, and parasite-associated diseases requires a collaborative effort between parasitologists, microbial ecologists, virologists, and immunologists. We hereby propose the Parasite Microbiome Project to bring together researchers with complementary expertise and to study the role of microbes in host-parasite interactions. Data from the Parasite Microbiome Project will help identify the mechanisms driving microbiome variation in parasites and infected hosts and how that variation is associated with the ecology and evolution of parasites and their disease outcomes. This is a call to arms to prevent fragmented research endeavors, encourage best practices in experimental approaches, and …

Ictv Virus Taxonomy Profile: Circoviridae, Mya Breitbart, Eric Delwart, Karyna Rosario, Joaquim Segales, Arvind Varsani

Marine Science Faculty Publications

The family Circoviridae comprises viruses with small, circular, single-stranded DNA (ssDNA) genomes, including the smallest known animal viruses. Members of this family are classified into two genera, Circovirus and Cyclovirus, which are distinguished by the position of the origin of replication relative to the coding regions and the length of the intergenic regions. Within each genus, the species demarcation threshold is 80 % genome-wide nucleotide sequence identity. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Circoviridae, which is available at www.ictv.global/report/circoviridae.

Diverse And Highly Recombinant Anelloviruses Associated With Weddell Seals In Antarctica, Elizabeth Fahsbender, Jennifer M. Burns, Stacy Kim, Simona Kraberger, Greg Frankfurter, Mya Breitbart

Marine Science Faculty Publications

The viruses circulating among Antarctic wildlife remain largely unknown. In an effort to identify viruses associated withWeddell seals (Leptonychotes weddellii) inhabiting the Ross Sea, vaginal and nasal swabs, and faecal samples were collectedbetween November 2014 and February 2015. In addition, a Weddell seal kidney and South Polar skua (Stercorariusmaccormicki) faeces were opportunistically sampled. Using high throughput sequencing, we identified and recovered 152anellovirus genomes that share 63–70% genome-wide identities with other pinniped anelloviruses. Genome-wide pairwisecomparisons coupled with phylogenetic analysis revealed two novel anellovirus species, tentatively named torque tenoLeptonychotes weddellii virus (TTLwV) -1 and -2. TTLwV-1 (n¼133, genomes encompassing 40 genotypes) is …

Genome Sequence Of Euphorbia Mosaic Virus From Passionfruit And Euphorbia Heterophylla In Florida, J. E. Polston, M. A. Londoño, A. L. Cohen, M. Padilla-Rodriguez, K. Rosario, Mya Breitbart

Marine Science Faculty Publications

Euphorbia mosaic virus (EuMV) was found in a symptomatic passionfruit (Passiflora edulis) plant from Homestead, Florida, USA, as well as in the symptomatic weed Euphorbia heterophylla. This is the first identification of EuMV in Florida and the United States and the first report of a natural infection of passionfruit by EuMV.

Virus Taxonomy In The Age Of Metagenomics, Peter Simmonds, Mike Adams, Mária Benkő, Mya Breitbart, J. Rodney Brister, Eric Carstens

Marine Science Faculty Publications

The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the …