Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states

Background: At the beginning of the transcription process, the RNA polymerase (RNAP) core enzyme requires a sigma-factor to recognize the genomic location at which the process initiates. Although the crucial role of sigma-factors has long been appreciated and characterized for many individual promoters, we do not yet have a genome-scale assessment of their function. Results: Using multiple genome-scale measurements, we elucidated the network of s-factor and promoter interactions in Escherichia coli. The reconstructed network includes 4,724 sigma-factor-specific promoters corresponding to transcription units (TUs), representing an increase of more than 300% over what has been previously reported. The reconstructed network was used to investigate competition between alternative sigma-factors (the sigma(70) and sigma(38) regulons), confirming the competition model of sigma substitution and negative regulation by alternative s-factors. Comparison with sigma-factor binding in Klebsiella pneumoniae showed that transcriptional regulation of conserved genes in closely related species is unexpectedly divergent. Conclusions: The reconstructed network reveals the regulatory complexity of the promoter architecture in prokaryotic genomes, and opens a path to the direct determination of the systems biology of their transcriptional regulatory networks

Will all scientists working on snails and the diseases they transmit please stand up?

Copyright © 2012 Adema et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.No abstract available

Whole Genome Analysis of a Schistosomiasis-Transmitting Freshwater Snail.

Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization\u27s goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biomphalaria glabrata, a lophotrochozoan protostome, and provide timely and important information on snail biology. We describe aspects of phero-perception, stress responses, immune function and regulation of gene expression that support the persistence of B. glabrata in the field and may define this species as a suitable snail host for S. mansoni. We identify several potential targets for developing novel control measures aimed at reducing snail-mediated transmission of schistosomiasis

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

Janssen S, McDonald D, Gonzalez A, et al. Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. mSystems. 2018;3(3):e00021-18

JWST mirror and actuator performance at cryo-vacuum

The James Webb Space Telescope (JWST) telescope’s Secondary Mirror Assembly (SMA) and eighteen Primary Mirror Segment Assemblies (PMSAs) are each actively controlled in rigid body position via six hexapod actuators. Each of the PMSAs additionally has a radius of curvature actuator. The mirrors are stowed to the mirror support structure to survive the launch environment and then must be deployed 12.5 mm to reach the nominally deployed position before the Wavefront Sensing & Control (WFSC) alignment and phasing process begins. JWST requires testing of the full optical system in a Cryogenic Vacuum (CV) environment before launch. The cryo vacuum test campaign was executed in Chamber A at the Johnson Space Center (JSC) in Houston Texas. The test campaign consisted of an ambient vacuum test, a cooldown test, a cryo stable test at 65 Kelvin, a warmup test, and finally a second ambient vacuum test. Part of that test campaign was the functional and performance testing of the hexapod actuators on the flight mirrors. This paper will describe the testing that was performed on all 132 hexapod and radius of curvature actuators. The test campaign first tests actuators individually then tested how the actuators perform in the hexapod system. Telemetry from flight sensors on the actuators and measurements from external metrology devices such as interferometers, photogrammetry systems and image analysis was used to demonstrate the performance of the JWST actuators. The mirror move commanding process was exercised extensively during the JSC CV test and many examples of accurately commanded moves occurred. The PMSA and SMA actuators performed extremely well during the JSC CV test, and we have demonstrated that the actuators are fully functional both at ambient and cryo temperatures and that the mirrors will go to their commanded positions with the accuracy needed to phase and align the telescope

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

Minich JJ, Zhu Q, Janssen S, et al. KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. mSystems. 2018;3(3):e00218-17

Land management explains major trends in forest structure and composition over the last millennium in California's Klamath Mountains

For millennia, forest ecosystems in California have been shaped by fire from both natural processes and Indigenous land management, but the notion of climatic variation as a primary controller of the pre-colonial landscape remains pervasive. Understanding the relative influence of climate and Indigenous burning on the fire regime is key because contemporary forest policy and management are informed by historical baselines. This need is particularly acute in California, where 20th-century fire suppression, coupled with a warming climate, has caused forest densification and increasingly large wildfires that threaten forest ecosystem integrity and management of the forests as part of climate mitigation efforts. We examine climatic versus anthropogenic influence on forest conditions over 3 millennia in the western Klamath Mountains—the ancestral territories of the Karuk and Yurok Tribes—by combining paleoenvironmental data with Western and Indigenous knowledge. A fire regime consisting of tribal burning practices and lightning were associated with long-term stability of forest biomass. Before Euro-American colonization, the long-term median forest biomass was between 104 and 128 Mg/ha, compared to values over 250 Mg/ha today. Indigenous depopulation after AD 1800, coupled with 20th-century fire suppression, likely allowed biomass to increase, culminating in the current landscape: a closed Douglas fir–dominant forest unlike any seen in the preceding 3,000 y. These findings are consistent with precontact forest conditions being influenced by Indigenous land management and suggest large-scale interventions could be needed to return to historic forest biomass levels

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types