Viral Outbreak in Corals Associated with an In Situ Bleaching Event: Atypical Herpes-Like Viruses and a New Megavirus Infecting Symbiodinium.

Previous studies of coral viruses have employed either microscopy or metagenomics, but few have attempted to comprehensively link the presence of a virus-like particle (VLP) to a genomic sequence. We conducted transmission electron microscopy imaging and virome analysis in tandem to characterize the most conspicuous viral types found within the dominant Pacific reef-building coral genus Acropora. Collections for this study inadvertently captured what we interpret as a natural outbreak of viral infection driven by aerial exposure of the reef flat coincident with heavy rainfall and concomitant mass bleaching.

Extensive Transcriptome Changes During Natural Onset and Release of Vegetative Bud Dormancy in Populus.

To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. To understand vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant axillary buds from Populus trees growing under natural conditions. Of 44,441 Populus gene models analyzed using NimbleGen microarrays, we found that 1,362 (3.

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones.

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO[Formula: see text], NO[Formula: see text], Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.

Incorporation of Non-Canonical Amino Acids.

In this chapter we discuss the strengths, caveats and technical considerations of three approaches for reprogramming the chemical composition of selected amino acids within a membrane protein. In vivo nonsense suppression in the Xenopus laevis oocyte, evolved orthogonal tRNA and aminoacyl-tRNA synthetase pairs and protein ligation for biochemical production of semisynthetic proteins have been used successfully for ion channel and receptor studies. The level of difficulty for the application of each approach ranges from trivial to technically demanding, yet all have untapped potential in their application to membrane proteins.

Evidence for genes associated with the ability of Mycobacterium avium subsp. hominissuis to escape apoptotic macrophages.

Mycobacterium avium subsp. hominissuis (MAH) is an environmental bacteria that infects immunocompromised humans. MAH cases are increasing in incidence, making it crucial to gain knowledge of the pathogenic mechanisms associated with the bacterium.

Antibodies against invasive phenotype-specific antigens increase Mycobacterium avium subspecies paratuberculosis translocation across a polarized epithelial cell model and enhance killing by bovine macrophages.

Johne's disease, caused by Mycobacterium avium subspecies paratuberculosis (MAP), is a severe chronic enteritis which affects large populations of ruminants globally. Prevention strategies to combat the spread of Johne's disease among cattle herds involve adhering to strict calving practices to ensure young susceptible animals do not come in contact with MAP-contaminated colostrum, milk, or fecal material. Unfortunately, the current vaccination options available are associated with high cost and suboptimal efficacy.

The salinity signature of the cross-shelf exchanges in the Southwestern Atlantic Ocean: Numerical simulations.

A high-resolution model is used to characterize the dominant patterns of sea surface salinity (SSS) variability generated by the freshwater discharges of the Rio de la Plata (RdlP) and the Patos/Mirim Lagoon in the southwestern Atlantic region. We identify three dominant modes of SSS variability. The first two, which have been discussed in previous studies, represent the seasonal and the interannual variations of the freshwater plumes over the continental shelf.

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant.

While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass spectrometry-based proteomics approach to identify proteins in fecal samples collected on days of life 13-21 from an infant born at 28 weeks gestation. No prior studies have coupled strain-resolved community metagenomics to proteomics for such a purpose.

Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality.

To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytical tools. With the advent of high throughput sequencing technologies, obtaining genome-wide population genetic data has become easier than ever before.

Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison.

Microbial communities are responsible for the bulk of biogeochemical processing in temporary headwater streams, yet there is still relatively little known about how community structure and function respond to periodic drying. Moreover, the ability to sample temporary habitats can be a logistical challenge due to the limited capability to measure and predict the timing, intensity and frequency of wet-dry events. Unsurprisingly, published datasets on microbial community structure and function are limited in scope and temporal resolution and vary widely in the molecular methods applied.

Greater decision-making competence is associated with greater expected-value sensitivity, but not overall risk taking: an examination of concurrent validity.

Decision-making competence reflects individual differences in the susceptibility to committing decision-making errors, measured using tasks common from behavioral decision research (e.g., framing effects, under/overconfidence, following decision rules).

Decision-making competence predicts domain-specific risk attitudes.

Decision-making competence (DMC) reflects individual differences in rational responding across several classic behavioral decision-making tasks. Although it has been associated with real-world risk behavior, less is known about the degree to which DMC contributes to specific components of risk attitudes. Utilizing a psychological risk-return framework, we examined the associations between risk attitudes and DMC.

Altimeter-derived seasonal circulation on the southwest Atlantic shelf: 27°-43°S.

Altimeter sea surface height (SSH) fields are analyzed to define and discuss the seasonal circulation over the wide continental shelf in the SW Atlantic Ocean (27°-43°S) during 2001-2012. Seasonal variability is low south of the Rio de la Plata (RdlP), where winds and currents remain equatorward for most of the year. Winds and currents in the central and northern parts of our domain are also equatorward during autumn and winter but reverse to become poleward during spring and summer.

Isolating the effects of storm events on arctic aquatic bacteria: temperature, nutrients, and community composition as controls on bacterial productivity.

Storm events can pulse nutrients and carbon from soils and provide an important subsidy to food webs in oligotrophic streams and lakes. Bacterial nutrient limitation and the potential response of stream aquatic bacteria to storm events was investigated in arctic tundra environments by manipulating both water temperature and inorganic nutrient concentrations in short (up to 4 days) and long duration (up to 2 weeks) laboratory mesocosm experiments. Inorganic N and P additions increased bacterial production ((14)C-labeled leucine uptake) up to seven times over controls, and warmer incubation temperatures increased the speed of this response to added nutrients.

Introducing a sensor to measure budburst and its environmental drivers.

Budburst is a key adaptive trait that can help us understand how plants respond to a changing climate from the molecular to landscape scale. Despite this, acquisition of budburst data is constrained by a lack of information at the plant scale on the environmental stimuli associated with the release of bud dormancy. Additionally, to date, little effort has been devoted to phenotyping plants in natural populations due to the challenge of accounting for the effect of environmental variation.

Cases of ergotism in livestock and associated ergot alkaloid concentrations in feed.

Ergot-induced disease in humans was known long before Biblical times and has been the root cause for countless human epidemics spanning from the early fourteenth century to the late sixteenth century. In contrast, many of these same ergot alkaloids have been utilized for their medicinal properties to mitigate migraine headaches and have had indications as anti-carcinogens. Although ergot alkaloids have been used for centuries by humans, basic pharmacokinetic data has not been documented for clinical disease in livestock.

Barred owls and landscape attributes influence territory occupancy of northern spotted owls.

We used multi-season occupancy analyses to model 2 fates of northern spotted owl territories in relation to habitat amount, habitat fragmentation, and the presence of barred owls in Washington State, USA, 1989-2005. Local colonization is the probability a territory unoccupied by a spotted owl in year would be occupied in year  + 1, and local extinction is the probability a territory that was occupied by a spotted owl in year would be unoccupied in year  + 1. We found a negative relationship between local extinction probability and amount of late-seral forest edge.

VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera).

We have developed VitisCyc, a grapevine-specific metabolic pathway database that allows researchers to (i) search and browse the database for its various components such as metabolic pathways, reactions, compounds, genes and proteins, (ii) compare grapevine metabolic networks with other publicly available plant metabolic networks, and (iii) upload, visualize and analyze high-throughput data such as transcriptomes, proteomes, metabolomes etc. using OMICs-Viewer tool. VitisCyc is based on the genome sequence of the nearly homozygous genotype PN40024 of Vitis vinifera "Pinot Noir" cultivar with 12X v1 annotations and was built on BioCyc platform using Pathway Tools software and MetaCyc reference database.

Genetic resources for methane production from biomass described with the Gene Ontology.

Methane (CH4) is a valuable fuel, constituting 70-95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea.

An efficient technique for Bayesian modeling of family data using the BUGS software.

Linear mixed models have become a popular tool to analyze continuous data from family-based designs by using random effects that model the correlation of subjects from the same family. However, mixed models for family data are challenging to implement with the BUGS (Bayesian inference Using Gibbs Sampling) software because of the high-dimensional covariance matrix of the random effects. This paper describes an efficient parameterization that utilizes the singular value decomposition of the covariance matrix of random effects, includes the BUGS code for such implementation, and extends the parameterization to generalized linear mixed models.

On the reproductive success of early-generation hatchery fish in the wild.

Large numbers of hatchery salmon spawn in wild populations each year. Hatchery fish with multiple generations of hatchery ancestry often have heritably lower reproductive success than wild fish and may reduce the fitness of an entire population. Whether this reduced fitness also occurs for hatchery fish created with local- and predominantly wild-origin parents remains controversial.