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Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into 'iVirus' on the CyVerse collaborative cyberinfrastructure. Here we substantially expand iVirus's functionality and accessibility, to iVirus 2.0, as follows. First, core iVirus apps were integrated into the Department of Energy's Systems Biology KnowledgeBase (KBase) to provide an additional analytical platform. Second, at CyVerse, 20 software tools (apps) were upgraded or added as new tools and capabilities. Third, nearly 20-fold more sequence reads were aggregated to capture new data and environments. Finally, documentation, as "live" protocols, was updated to maximize user interaction with and contribution to infrastructure development. Together, iVirus 2.0 serves as a uniquely central and accessible analytical platform for studying how viruses, particularly dsDNA viruses, impact diverse microbial ecosystems.

In plants, a subset of genes exhibit imprinting in endosperm tissue such that expression is primarily from the maternal or paternal allele. Imprinting may arise as a consequence of mechanisms for silencing of transposons during reproduction, and in some cases imprinted expression of particular genes may provide a selective advantage such that it is conserved across species. Separate mechanisms for the origin of imprinted expression patterns and maintenance of these patterns may result in substantial variation in the targets of imprinting in different species. Here we present deep sequencing of RNAs isolated from reciprocal crosses of four diverse maize genotypes, providing a comprehensive analysis that allows evaluation of imprinting at more than 95% of endosperm-expressed genes. We find that over 500 genes exhibit statistically significant parent-of-origin effects in maize endosperm tissue, but focused our analyses on a subset of these genes that had >90% expression from the maternal allele (69 genes) or from the paternal allele (108 genes) in at least one reciprocal cross. Over 10% of imprinted genes show evidence of allelic variation for imprinting. A comparison of imprinting in maize and rice reveals that 13% of genes with syntenic orthologs in both species exhibit conserved imprinting. Genes that exhibit conserved imprinting between maize and rice have elevated nonsynonymous to synonymous substitution ratios compared with other imprinted genes, suggesting a history of more rapid evolution. Together, these data suggest that imprinting only has functional relevance at a subset of loci that currently exhibit imprinting in maize.

Objective WHO and UNICEF recommend cup feeding for neonates unable to breastfeed in low-resource settings. In developed countries, cup feeding in lieu of bottle feeding in the neonatal period is hypothesized to improve breastfeeding outcomes for those initially unable to breastfeed. Our aim was to synthesize the entire body of evidence on cup feeding. Methods We searched domestic and international databases for original research. Our search criteria required original data on cup feeding in neonates published in English between January 1990 and December 2014. Results We identified 28 original research papers. Ten were randomized clinical trials, 7 non-randomized intervention studies, and 11 observational studies; 11 were conducted in developing country. Outcomes evaluated included physiologic stability, safety, intake, duration, spillage, weight gain, any and exclusive breastfeeding, length of hospital stay, compliance, and acceptability. Cup feeding appears to be safe though intake may be less and spillage greater relative to bottle or tube feeding. Overall, slightly higher proportions of cup fed versus bottle fed infants report any breastfeeding; a greater proportion of cup fed infants reported exclusive breastfeeding at discharge and beyond. Cup feeding increases breastfeeding in subgroups (e.g. those who intend to breastfeed or women who had a Caesarean section). Compliance and acceptability is problematic in certain settings. Conclusions Further research on long-term breastfeeding outcomes and in low-resource settings would be helpful. Research data on high risk infants (e.g. those with cleft palates) would be informative. Innovative cup feeding approaches to minimize spillage, optimize compliance, and increase breastfeeding feeding are needed., Author(s): Christy M. McKinney[sup.1] [sup.5] , Robin P. Glass[sup.2] , Patricia Coffey[sup.3] , Tessa Rue[sup.4] , Matthew G. Vaughn[sup.1] , Michael Cunningham[sup.5] Author Affiliations: (1) Oral Health Sciences, School of [...]

Centromere-binding protein B (CENP-B) is a widely conserved DNA binding factor associated with heterochromatin and centromeric satellite repeats (1). In fission yeast, CENP-B homologues have been shown to silence long terminal repeat (LTR) retrotransposons by recruiting histone deacetylases (2). However, CENP-B factors also have unexplained roles in DNA replication (3,4). Here we show that a molecular function of CENP-B is to promote replication-fork progression through the LTR. Mutants have increased genomic instability caused by replication-fork blockage that depends on the DNA binding factor switch-activating protein 1 (Sap1), which is directly recruited by the LTR. The loss of Sap1-dependent barrier activity allows the unhindered progression of the replication fork, but results in rearrangements deleterious to the retrotransposon. We conclude that retrotransposons influence replication polarity through recruitment of Sap1 and transposition near replication-fork blocks, whereas CENP-B counteracts this activity and promotes fork stability. Our results may account for the role of LTR in fragile sites, and for the association of CENP-B with pericentromeric heterochromatin and tandem satellite repeats., In fission yeast, CENP-B proteins are encoded by three homologues, autonomously replicating sequence binding protein 1 (abp1), cenp-B homologue 1 (cbh1) and cbh2, and were previously characterized as DNA binding [...]

We describe the application of a vector-based radius approach to optical bench radius measurements in the presence of imperfect stage motions. In this approach, the radius is defined using a vector equation and homogeneous transformation matrix formulism. This is in contrast to the typical technique, where the displacement between the confocal and cat's eye null positions alone is used to determine the test optic radius. An important aspect of the vector-based radius definition is the intrinsic correction for measurement biases, such as straightness errors in the stage motion and cosine misalignment between the stage and displacement gauge axis, which lead to an artificially small radius value if the traditional approach is employed. Measurement techniques and results are provided for the stage error motions, which are then combined with the setup geometry through the analysis to determine the radius of curvature for a spherical artifact. Comparisons are shown between the new vector-based radius calculation, traditional radius computation, and a low uncertainty mechanical measurement. Additionally, the measurement uncertainty for the vector-based approach is determined using Monte Carlo simulation and compared to experimental results. OCIS codes: 220.4840, 120.3180, 120.3940, 120.6650.

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2008.08.036 Byline: Fei Li (1), Maite Huarte (2), Mikel Zaratiegui (3), Matthew W. Vaughn (3), Yang Shi (2), Rob Martienssen (3), W. Zacheus Cande (1) Keywords: PROTEINS Abstract: In most eukaryotes, histone methylation patterns regulate chromatin architecture and function: methylation of histone H3 lysine-9 (H3K9) demarcates heterochromatin, whereas H3K4 methylation demarcates euchromatin. We show here that the S. pombe JmjC-domain protein Lid2 is a trimethyl H3K4 demethylase responsible for H3K4 hypomethylation in heterochromatin. Lid2 interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, which also functions in the RNA interference pathway. Disruption of the JmjC domain alone results in severe heterochromatin defects and depletion of siRNA, whereas overexpressing Lid2 enhances heterochromatin silencing. The physical and functional link between H3K4 demethylation and H3K9 methylation suggests that the two reactions act in a coordinated manner. Surprisingly, crossregulation of H3K4 and H3K9 methylation in euchromatin also requires Lid2. We suggest that Lid2 enzymatic activity in euchromatin is regulated through a dynamic interplay with other histone-modification enzymes. Our findings provide mechanistic insight into the coordination of H3K4 and H3K9 methylation. Author Affiliation: (1) Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA (2) Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA (3) Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA Article History: Received 11 December 2007; Revised 2 May 2008; Accepted 20 August 2008 Article Note: (miscellaneous) Published: October 16, 2008

Author(s): Zachary Lippman [1, 5]; Anne-Valérie Gendrel [2, 5]; Michael Black [3, 6]; Matthew W. Vaughn [1]; Neilay Dedhia [1]; W. Richard McCombie [1]; Kimberly Lavine [1]; Vivek Mittal [1]; [...]