Norovirus Epidemiology and Duration of Shedding in Michigan, 2007-2008

Background: In the United States, an estimated 23 million cases of norovirus (NoV) are reported each year, and although mortality is low, the morbidity and economic impact are substantial. Methods: RT-PCR and sequencing were used for identification of NoV genotypes obtained from outbreak and sporadic cases. RT Quant PCR was used to determine the viral load in fecal specimens. In order to rule out bacterial infection as the cause for acute gastroenteritis (AGE), bacterial culture for Salmonella, E.coli O157, Shigella, Campylobacter and Clostridium difficile was performed by standard laboratory procedures. The duration of NV shedding was investigated with longitudinal sampling in the sporadic cases and an evaluation of the association between viral load and days since clinical onset in the outbreak-associated cases. Results: We describe the epidemiology and strain identification for NoV circulating in Michigan during 2007-8 in concurrent sporadic and outbreak-associated cases. In 2007- 8, 138 norovirus outbreaks (3,437 cases) were reported to the MDCH. Among the 47 outbreak specimens sequenced, GI was identified in 14 (29.8%) and GII in 33 (70.2%). The predominant type was GII.4, found in 23 of the 33 (69.6%) GII specimens. The statistical analysis of outbreak-associated cases showed that neither NoV type nor number of days post-onset were associated with NoV log concentration. Among the sporadic cases, the repeated measures analysis of variance showed that NoV type (I or II) was not associated with log titer (P = 0.90), but that the number of weeks post-onset was statistically associated with declining log titer at p = 0.0005. Conclusion: We found no predominant strain difference between concurrent sporadic and outbreak-associated cases. Prevalent strains of NoV were shed in high concentration for at least two weeks past disease onset, suggesting that current public health recommendations for 2-3 days home isolation following clinical recovery may need to be lengthened

ADVANTG An Automated Variance Reduction Parameter Generator

The report is the descriptive journey of the ADVANTG An Automated Variance Reduction Parameter Generator

A Simple Genetic Architecture Underlies Morphological Variation in Dogs

The largest genetic study to date of morphology in domestic dogs identifies genes controlling nearly 100 morphological traits and identifies important trends in phenotypic variation within this species

New ABA-Hypersensitive Arabidopsis Mutants Are Affected in Loci Mediating Responses to Water Deficit and Dickeya dadantii Infection

On water deficit, abscisic acid (ABA) induces stomata closure to reduce water loss by transpiration. To identify Arabidopsis thaliana mutants which transpire less on drought, infrared thermal imaging of leaf temperature has been used to screen for suppressors of an ABA-deficient mutant (aba3-1) cold-leaf phenotype. Three novel mutants, called hot ABA-deficiency suppressor (has), have been identified with hot-leaf phenotypes in the absence of the aba3 mutation. The defective genes imparted no apparent modification to ABA production on water deficit, were inherited recessively and enhanced ABA responses indicating that the proteins encoded are negative regulators of ABA signalling. All three mutants showed ABA-hypersensitive stomata closure and inhibition of root elongation with little modification of growth and development in non-stressed conditions. The has2 mutant also exhibited increased germination inhibition by ABA, while ABA-inducible gene expression was not modified on dehydration, indicating the mutated gene affects early ABA-signalling responses that do not modify transcript levels. In contrast, weak ABA-hypersensitivity relative to mutant developmental phenotypes suggests that HAS3 regulates drought responses by both ABA-dependent and independent pathways. has1 mutant phenotypes were only apparent on stress or ABA treatments, and included reduced water loss on rapid dehydration. The HAS1 locus thus has the required characteristics for a targeted approach to improving resistance to water deficit. In contrast to has2, has1 exhibited only minor changes in susceptibility to Dickeya dadantii despite similar ABA-hypersensitivity, indicating that crosstalk between ABA responses to this pathogen and drought stress can occur through more than one point in the signalling pathway

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, management, and analysis. In this perspective, we present AnVIL, describe its ecosystem and interoperability with other platforms, and highlight how this platform and associated initiatives contribute to improved genomic data sharing efforts. The AnVIL is a federated cloud platform designed to manage and store genomics and related data, enable population-scale analysis, and facilitate collaboration through the sharing of data, code, and analysis results. By inverting the traditional model of data sharing, the AnVIL eliminates the need for data movement while also adding security measures for active threat detection and monitoring and provides scalable, shared computing resources for any researcher. We describe the core data management and analysis components of the AnVIL, which currently consists of Terra, Gen3, Galaxy, RStudio/Bioconductor, Dockstore, and Jupyter, and describe several flagship genomics datasets available within the AnVIL. We continue to extend and innovate the AnVIL ecosystem by implementing new capabilities, including mechanisms for interoperability and responsible data sharing, while streamlining access management. The AnVIL opens many new opportunities for analysis, collaboration, and data sharing that are needed to drive research and to make discoveries through the joint analysis of hundreds of thousands to millions of genomes along with associated clinical and molecular data types

Successful molecular detection studies require clear communication among diverse research partners

Molecular detection techniques are powerful tools used in ecological applications ranging from diet analyses to pathogen surveillance. Research partnerships that use these tools often involve collaboration among professionals with expertise in field biology, laboratory techniques, quantitative modeling, wildlife disease, and natural resource management. However, in many cases, each of these collaborators lacks specific knowledge about the approaches, decisions, methods, and terminology used by their research partners, which can impede effective communication and act as a barrier to the efficient use of molecular data for ecological inferences and subsequent conservation decision making. We outline a collaborative framework to assist colleagues with diverse types of expertise to effectively translate their scientific and management needs to research partners from other specialties. The molecular techniques used to detect organisms will continue to advance both in sophistication and in the breadth of ecological applications. Our objective is to enable ecologists to harness the full utility of these methods by developing effective collaborative partnerships

Abundant expression of maternal siRNAs is a conserved feature of seed development

Small RNAs are abundant in plant reproductive tissues, especially 24-nucleotide (nt) small interfering RNAs (siRNAs). Most 24-nt siRNAs are dependent on RNA Pol IV and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). In Brassica rapa, RdDM is required in the maternal sporophyte for successful seed development. Here, we demonstrate that a small number of siRNA loci account for over 90% of siRNA expression during B. rapa seed development. These loci exhibit unique characteristics with regard to their copy number and association with genomic features, but they resemble canonical 24-nt siRNA loci in their dependence on RNA Pol IV/RDR2 and role in RdDM. These loci are expressed in ovules before fertilization and in the seed coat, embryo, and endosperm following fertilization. We observed a similar pattern of 24-nt siRNA expression in diverse angiosperms despite rapid sequence evolution at siren loci. In the endosperm, siren siRNAs show a marked maternal bias, and siren expression in maternal sporophytic tissues is required for siren siRNA accumulation. Together, these results demonstrate that seed development occurs under the influence of abundant maternal siRNAs that might be transported to, and function in, filial tissues