RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons.

DNA transcription initiates after an RNA polymerase (RNAP) molecule binds to the promoter of a gene. In bacteria, the canonical picture is that RNAP comes from the cytoplasmic pool of freely diffusing RNAP molecules. Recent experiments suggest the possible existence of a separate pool of polymerases, competent for initiation, which freely slide on the DNA after having terminated one round of transcription.

Recycling of bacterial RNA polymerase by the Swi2/Snf2 ATPase RapA.

Free-living bacteria have regulatory systems that can quickly reprogram gene transcription in response to changes in the cellular environment. The RapA ATPase, a prokaryotic homolog of the eukaryotic Swi2/Snf2 chromatin remodeling complex, may facilitate such reprogramming, but the mechanisms by which it does so are unclear. We used multiwavelength single-molecule fluorescence microscopy in vitro to examine RapA function in the transcription cycle.

Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA.

Unlabelled: Free-living bacteria have regulatory systems that can quickly reprogram gene transcription in response to changes in cellular environment. The RapA ATPase, a prokaryotic homolog of the eukaryote Swi2/Snf2 chromatin remodeling complex, may facilitate such reprogramming, but the mechanisms by which it does so is unclear. We used multi-wavelength single-molecule fluorescence microscopy in vitro to examine RapA function in the transcription cycle.

RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons.

Unlabelled: DNA transcription initiates after an RNA polymerase (RNAP) molecule binds to the promoter of a gene. In bacteria, the canonical picture is that RNAP comes from the cytoplasmic pool of freely diffusing RNAP molecules. Recent experiments suggest the possible existence of a separate pool of polymerases, competent for initiation, which freely slide on the DNA after having terminated one round of transcription.

Data for assessment of leached dissolved organic carbon in watersheds.

("Dissolved organic carbon leaching flux in a mixed agriculture and forest watershed in Rwanda" [1]). This article presents data of leached dissolved organic carbon (LDOC), stream water dissolved organic carbon), rainfall amount (Ra), rainfall intensity (Ri), rainfall soil storage (S), runoff (Q), and soil properties such as total organic carbon (TOC), total nitrogen (TN), cation exchange capacity (CEC), and soil texture data collected in the Rukarara River Watershed (RRW), a tropical watershed. All these data were used to analyze leached dissolved organic carbon (LDOC) fluxes in the watershed and their relationship with stream DOC.

Robustness in spatially driven bistability in signaling systems.

Biological systems are spatially organized. This microscopic heterogeneity has been shown to produce emergent complex behaviors such as bistability. Even though the connection between spatiality and dynamic response is essential to understand biological output, its robustness and extent has not been sufficiently explored.

Data for assessment of soil water extractable and percolation water dissolved organic carbon in watersheds.

("Sources of soil dissolved organic carbon in a mixed agricultural and forested watershed in Rwanda", [6]) This data article presents water extractable organic carbon (WEOC), percolation water dissolved organic carbon (pDOC), and mean antecedent precipitation indices (API) and mean antecedent temperature (MAT) data. The article also presents edaphic properties such soil texture elements, total organic carbon (TOC), total nitrogen (TN), cation exchange capacity (CEC), iron (Fe), and aluminum (Al). Additionally, the article presents topography attributes such including topographic position index (TPI) and curvature.

Inherited Chromosomally Integrated Human Herpesvirus 6 Demonstrates Tissue-Specific RNA Expression That Correlates with an Increased Antibody Immune Response.

Human herpesviruses 6A and 6B (HHV-6A and HHV-6B) are human viruses capable of chromosomal integration. Approximately 1% of the human population carries one copy of HHV-6A/B integrated into every cell in their body, referred to as inherited chromosomally integrated human herpesvirus 6A/B (iciHHV-6A/B). Whether iciHHV-6A/B is transcriptionally active and how it shapes the immunological response are still unclear.

Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling.

Background: CUT&RUN is an efficient epigenome profiling method that identifies sites of DNA binding protein enrichment genome-wide with high signal to noise and low sequencing requirements. Currently, the analysis of CUT&RUN data is complicated by its exceptionally low background, which renders programs designed for analysis of ChIP-seq data vulnerable to oversensitivity in identifying sites of protein binding.

Results: Here we introduce Sparse Enrichment Analysis for CUT&RUN (SEACR), an analysis strategy that uses the global distribution of background signal to calibrate a simple threshold for peak calling.

Data for dynamics analysis of riverine dissolved organic in watersheds.

This data article presents water stage, flow, and net primary productivity (NPP) data that were used to analyze the dynamics of the riverine dissolved organic carbon (DOC) dynamics in the Rukarara River watershed in Rwanda. We measured water stage data every 15 min and calculated daily averages used to estimate flow based on rating curves. The rating curves were produced using several measured contemporaneous water stage and flow data.

Patchy field sampling biases understanding of climate change impacts across the Arctic.

Effective societal responses to rapid climate change in the Arctic rely on an accurate representation of region-specific ecosystem properties and processes. However, this is limited by the scarcity and patchy distribution of field measurements. Here, we use a comprehensive, geo-referenced database of primary field measurements in 1,840 published studies across the Arctic to identify statistically significant spatial biases in field sampling and study citation across this globally important region.

Riverine dissolved organic carbon in Rukarara River Watershed, Rwanda.

Dissolved organic carbon (DOC) loading is rarely estimated in tropical watersheds. This study quantifies DOC loading in the Rukarara River Watershed (RRW), a Rwandan tropical forest and agricultural watershed, and evaluates its relationship with hydrological factors, land use and land cover (LULC), and topography to better understand the impact of stream DOC export on watershed carbon budgets. The annual average load for the study period was 977.

Environmental and Sanitary Conditions of Guanabara Bay, Rio de Janeiro.

Guanabara Bay is the second largest bay in the coast of Brazil, with an area of 384 km(2). In its surroundings live circa 16 million inhabitants, out of which 6 million live in Rio de Janeiro city, one of the largest cities of the country, and the host of the 2016 Olympic Games. Anthropogenic interference in Guanabara Bay area started early in the XVI century, but environmental impacts escalated from 1930, when this region underwent an industrialization process.

Orchestrating high-throughput genomic analysis with Bioconductor.

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists.

Parallel evolution of transcriptome architecture during genome reorganization.

Assembly of genes into operons is generally viewed as an important process during the continual adaptation of microbes to changing environmental challenges. However, the genome reorganization events that drive this process are also the roots of instability for existing operons. We have determined that there exists a statistically significant trend that correlates the proportion of genes encoded in operons in archaea to their phylogenetic lineage.

Integration and visualization of systems biology data in context of the genome.

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment.

Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome.

GTC: A web server for integrating systems biology data with web tools and desktop applications.

Gaggle Tool Creator (GTC) is a web application which provides access to public annotation, interaction, orthology, and genomic data for hundreds of organisms, and enables instant analysis of the data using many popular web-based and desktop applications.

Visualization of omics data for systems biology.

High-throughput studies of biological systems are rapidly accumulating a wealth of 'omics'-scale data. Visualization is a key aspect of both the analysis and understanding of these data, and users now have many visualization methods and tools to choose from. The challenge is to create clear, meaningful and integrated visualizations that give biological insight, without being overwhelmed by the intrinsic complexity of the data.