Legionella pneumophila Exploits the CsrA Superfamily to Adapt to a Range of Stresses.

Legionella pneumophila persists in incredibly diverse environments including intracellularly in myriad protists and mammilian lung macrophages, and extracellularly in natural and engineered water systems. Success in a given condition requires efficient regulation of appropriate gene and protein expression. A central regulator of the switch between two distinct expression profiles associated with the replicative and the transmissive cell types is CsrA, a highly conserved protein among many bacterial species. Interestingly, each of 14 surveyed strains in the Legionella genus encode between four and seven paralogs of the csrA gene. Every strain encodes a copy of the canonical csrA, as well as the non-redundant newly described csrR, which is a direct target of CsrA repression and itself promotes long-term survival in tap water. In addition, each strain encodes a variety of other csrA paralogs always associated with type IV secretion systems (T4SSs) in legionellae-specific horizontally acquired genomic islands referred to as integrative and conjugative elements (ICEs). Bioinformatic analyses suggest that specific sequences of csrA-like genes are co-inherited with specific lineages of T4SSs. Ectopic expression of one of these ICE-associated csrA paralogs, csrT, resulted in repression of both ICE-dependent and core genome-associated fitness traits, such as resistance to hydrogen peroxide and cellular infectivity, respectfully. The observation that the core genome csrR and the ICE-associated csrT both demonstrated regulatory effects on fitness suggests that the Legionella genus extensively utilizes the csrA superfamily to control expression of genes and proteins to expand environmental versatility.PHDMicrobiology and ImmunologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113530/1/zackabb_1.pd

Hinged Dissections Exist

We prove that any finite collection of polygons of equal area has a common hinged dissection. That is, for any such collection of polygons there exists a chain of polygons hinged at vertices that can be folded in the plane continuously without self-intersection to form any polygon in the collection. This result settles the open problem about the existence of hinged dissections between pairs of polygons that goes back implicitly to 1864 and has been studied extensively in the past ten years. Our result generalizes and indeed builds upon the result from 1814 that polygons have common dissections (without hinges). We also extend our common dissection result to edge-hinged dissections of solid 3D polyhedra that have a common (unhinged) dissection, as determined by Dehn's 1900 solution to Hilbert's Third Problem. Our proofs are constructive, giving explicit algorithms in all cases. For a constant number of planar polygons, both the number of pieces and running time required by our construction are pseudopolynomial. This bound is the best possible, even for unhinged dissections. Hinged dissections have possible applications to reconfigurable robotics, programmable matter, and nanomanufacturing.Comment: 22 pages, 14 figure

Genome modeling system: A knowledge management platform for genomics

In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Search for gravitational-lensing signatures in the full third observing run of the LIGO-Virgo network

Gravitational lensing by massive objects along the line of sight to the source causes distortions of gravitational wave-signals; such distortions may reveal information about fundamental physics, cosmology and astrophysics. In this work, we have extended the search for lensing signatures to all binary black hole events from the third observing run of the LIGO--Virgo network. We search for repeated signals from strong lensing by 1) performing targeted searches for subthreshold signals, 2) calculating the degree of overlap amongst the intrinsic parameters and sky location of pairs of signals, 3) comparing the similarities of the spectrograms amongst pairs of signals, and 4) performing dual-signal Bayesian analysis that takes into account selection effects and astrophysical knowledge. We also search for distortions to the gravitational waveform caused by 1) frequency-independent phase shifts in strongly lensed images, and 2) frequency-dependent modulation of the amplitude and phase due to point masses. None of these searches yields significant evidence for lensing. Finally, we use the non-detection of gravitational-wave lensing to constrain the lensing rate based on the latest merger-rate estimates and the fraction of dark matter composed of compact objects

Search for eccentric black hole coalescences during the third observing run of LIGO and Virgo

Despite the growing number of confident binary black hole coalescences observed through gravitational waves so far, the astrophysical origin of these binaries remains uncertain. Orbital eccentricity is one of the clearest tracers of binary formation channels. Identifying binary eccentricity, however, remains challenging due to the limited availability of gravitational waveforms that include effects of eccentricity. Here, we present observational results for a waveform-independent search sensitive to eccentric black hole coalescences, covering the third observing run (O3) of the LIGO and Virgo detectors. We identified no new high-significance candidates beyond those that were already identified with searches focusing on quasi-circular binaries. We determine the sensitivity of our search to high-mass (total mass M>70 M⊙) binaries covering eccentricities up to 0.3 at 15 Hz orbital frequency, and use this to compare model predictions to search results. Assuming all detections are indeed quasi-circular, for our fiducial population model, we place an upper limit for the merger rate density of high-mass binaries with eccentricities 0<e≤0.3 at 0.33 Gpc−3 yr−1 at 90\% confidence level