Magnetic structure of Yb2Pt2Pb: Ising moments on the Shastry-Sutherland lattice.

Neutron diffraction measurements were carried out on single crystals and powders of Yb2Pt2Pb, where Yb moments form two interpenetrating planar sublattices of orthogonal dimers, a geometry known as Shastry-Sutherland lattice, and are stacked along the c axis in a ladder geometry. Yb2Pt2Pb orders antiferromagnetically at TN=2.07K, and the magnetic structure determined from these measurements features the interleaving of two orthogonal sublattices into a 5×5×1 magnetic supercell that is based on stripes with moments perpendicular to the dimer bonds, which are along (110) and (−110). Magnetic fields applied along (110) or (−110) suppress the antiferromagnetic peaks from an individual sublattice, but leave the orthogonal sublattice unaffected, evidence for the Ising character of the Yb moments in Yb2Pt2Pb that is supported by point charge calculations. Specific heat, magnetic susceptibility, and electrical resistivity measurements concur with neutron elastic scattering results that the longitudinal critical fluctuations are gapped with ΔE≃0.07meV

BRG1 mutations found in human cancer cell lines inactivate Rb-mediated cell-cycle arrest

Eukaryotic organisms package DNA into chromatin for compact storage in the cell nucleus. However, this process promotes transcriptional repression of genes. To overcome the transcriptional repression, chromatin remodeling complexes have evolved that alter the configuration of chromatin packaging of DNA into nucleosomes by histones. The SWI/SNF chromatin remodeling complex uses energy from ATP hydrolysis to reposition nucleosomes and make DNA accessible to transcription factors. Recent studies showing mutations of BRG1, one of 2 mutually exclusive ATPase subunits, in human tumor cell lines and primary tissue samples have implicated a role for its loss in cancer development. While most of the mutations lead to complete loss of BRG1 protein expression, others result in single amino acid substitutions. To better understand the role of these BRG1 point mutations in cancer development, we characterized SWI/SNF function in human tumor cell lines with these mutations in the absence of BRM expression, the other ATPase component. We found that the mutant BRG1 proteins still interacted with the core complex members and appeared at the promoters of target genes. However, while these mutations did not affect CD44 and CDH1 expression, known targets of the SWI/SNF complex, they did abrogate Rb mediated cell cycle arrest. Therefore, our results implicate that these mutations disrupt the de novo chromatin remodeling activity of the complex without affecting the status of existing nucleosome positioning

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation

Mapping Meaning : Critical Cartographies for Participatory Water Management in Taita Hills, Kenya

Participation of local people is often neglected in natural resource management, which leads to failure to understand the social aspects and historical construction of environmental problems. Participatory mapping can enhance the communication of local spatial knowledge for management processes and challenge the official maps and other spatial representations produced by state authorities and scientists. In this study, we analyze what kind of social meanings can be revealed through a multimethod participatory mapping process focusing on water resources in Taita Hills, Kenya. The participatory mapping clearly complicates the simplified image of the physical science mappings, typically depicting natural water supply, by addressing the impacts of contamination, inadequate infrastructure, poverty, distance to the sources, and restrictions in their uses on people's access to water. Moreover, this shared exercise is able to trigger discussion on issues that cannot always be localized but still contribute to place making. Local historical accounts reveal the social and political drivers of the current water-related problems, making explicit the political ecology dynamics in the area.Peer reviewe

Ergatis: a web interface and scalable software system for bioinformatics workflows

Motivation: The growth of sequence data has been accompanied by an increasing need to analyze data on distributed computer clusters. The use of these systems for routine analysis requires scalable and robust software for data management of large datasets. Software is also needed to simplify data management and make large-scale bioinformatics analysis accessible and reproducible to a wide class of target users

A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines

<p>Abstract</p> <p>Background</p> <p>Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP) paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts.</p> <p>Results</p> <p>To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption). An add-on module ('NuBio') facilitates the creation of bioinformatics workflows by providing domain specific data-containers (<it>e.g</it>., for biomolecular sequences, alignments, structures) and functionality (<it>e.g</it>., to parse/write standard file formats).</p> <p>Conclusions</p> <p>PaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at <url>http://muralab.org/PaPy</url>, and includes extensive documentation and annotated usage examples.</p

The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community

The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data. All of these data are freely available at http://www.aspgd.org. We welcome feedback from users and the research community at [email protected]