Connected to Give: Faith Communities

This is the third report in the "Connected to Give" series, and compares the relationship between the charitable giving behavior of American's from a variety of backgrounds, including their key demographics; an examination their motivations for giving; and the types of organizations to which they contribute

pYR4 From a Norwegian isolate of Yersinia ruckeri is a putative virulence plasmid encoding both a type IV pilus and a type IV secretion system

Enteric redmouth disease caused by the pathogen Yersinia ruckeri is a significant problem for fish farming around the world. Despite its importance, only a few virulence factors of Y. ruckeri have been identified and studied in detail. Here, we report and analyze the complete DNA sequence of pYR4, a plasmid from a highly pathogenic Norwegian Y. ruckeri isolate, sequenced using PacBio SMRT technology. Like the well-known pYV plasmid of human pathogenic Yersiniae, pYR4 is a member of the IncFII family. Thirty-one percent of the pYR4 sequence is unique compared to other Y. ruckeri plasmids. The unique regions contain, among others genes, a large number of mobile genetic elements and two partitioning systems. The G+C content of pYR4 is higher than that of the Y. ruckeri NVH_3758 genome, indicating its relatively recent horizontal acquisition. pYR4, as well as the related plasmid pYR3, comprises operons that encode for type IV pili and for a conjugation system (tra). In contrast to other Yersinia plasmids, pYR4 cannot be cured at elevated temperatures. Our study highlights the power of PacBio sequencing technology for identifying mis-assembled segments of genomic sequences. Comparative analysis of pYR4 and other Y. ruckeri plasmids and genomes, which were sequenced by second and the third generation sequencing technologies, showed errors in second generation sequencing assemblies. Specifically, in the Y. ruckeri 150 and Y. ruckeri ATCC29473 genome assemblies, we mapped the entire pYR3 plasmid sequence. Placing plasmid sequences on the chromosome can result in erroneous biological conclusions. Thus, PacBio sequencing or similar long-read methods should always be preferred for de novo genome sequencing. As the tra operons of pYR3, although misplaced on the chromosome during the genome assembly process, were demonstrated to have an effect on virulence, and type IV pili are virulence factors in many bacteria, we suggest that pYR4 directly contributes to Y. ruckeri virulence

The repeat structure of two paralogous genes, Yersinia ruckeri invasin (yrInv) and a "Y. ruckeri invasin-like molecule", (yrIlm) sheds light on the evolution of adhesive capacities of a fish pathogen

Inverse autotransporters comprise the recently identified type Ve secretion system and are exemplified by intimin from enterohaemorrhagic Escherichia coli and invasin from enteropathogenic Yersiniae. These proteins share a common domain architecture and promote bacterial adhesion to host cells. Here, we identified and characterized two putative inverse autotransporter genes in the fish pathogen Yersinia ruckeri NVH_3758, namely yrInv (for Y. ruckeri invasin) and yrIlm (for Y. ruckeri invasin-like molecule). When trying to clone the highly repetitive genes for structural and functional studies, we experienced problems in obtaining PCR products. PCR failures and the highly repetitive nature of inverse autotransporters prompted us to sequence the genome of Y. ruckeri NVH_3758 using PacBio sequencing, which produces some of the longest average read lengths available in the industry at this moment. According to our sequencing data, YrIlm is composed of 2603 amino acids (7812 bp) and has a molecular mass of 256.4 kDa. Based on the new genome information, we performed PCR analysis on four non-sequenced Y. ruckeri strains as well as the sequenced. Y. ruckeri type strain. We found that the genes are variably present in the strains, and that the length of yrIlm, when present, also varies. In addition, the length of the gene product for all strains, including the type strain, was much longer than expected based on deposited sequences. The internal repeats of the yrInv gene product are highly diverged, but represent the same bacterial immunoglobulin-like domains as in yrIlm. Using qRT-PCR, we found that yrIlm and yrInv are differentially expressed under conditions relevant for pathogenesis. In addition, we compared the genomic context of both genes in the newly sequenced Y. ruckeri strain to all available PacBio-sequenced Y. ruckeri genomes, and found indications of recent events of horizontal gene transfer. Taken together, this study demonstrates and highlights the power of Single Molecule Real-Time technology for sequencing highly repetitive proteins, and sheds light on the genetic events that gave rise to these highly repetitive genes in a commercially important fish pathogen

Implicit Regularization and Renormalization of QCD

We apply the Implicit Regularization Technique (IR) in a non-abelian gauge theory. We show that IR preserves gauge symmetry as encoded in relations between the renormalizations constants required by the Slavnov-Taylor identities at the one loop level of QCD. Moreover, we show that the technique handles divergencies in massive and massless QFT on equal footing.Comment: (11 pages, 2 figures

Hot Exoplanet Atmospheres Resolved with Transit Spectroscopy (HEARTS) VIII. Nondetection of sodium in the atmosphere of the aligned planet KELT-10b

We searched for potential atmospheric species in KELT-10b, focusing on sodium doublet lines (Na i; 589 nm) and the Balmer alpha line (H $\alpha$; 656 nm) in the transmission spectrum. Furthermore, we measured the planet-orbital alignment with the spin of its host star. We used the Rossiter-McLaughlin Revolutions technique to analyze the local stellar lines occulted by the planet during its transit. We used the standard transmission spectroscopy method to probe the planetary atmosphere, including the correction for telluric lines and the Rossiter-McLaughlin effect on the spectra. We analyzed two new light curves jointly with the public photometry observations. We do not detect signals in the Na i and H $\alpha$ lines within the uncertainty of our measurements. We derive the 3-sigma upper limit of excess absorption due to the planetary atmosphere corresponding to equivalent height Rp to 1.8Rp (Na i) and 1.9Rp (H $\alpha$). The analysis of the Rossiter-McLaughlin effect yields the sky-projected spin-orbit angle of the system $\lambda$ = -5.2 $\pm$ 3.4 and the stellar projected equatorial velocity $v_{eq} \sin{i_\star}$ = 2.58 $\pm$ 0.12 km/s. Photometry results are compatible within 1 -sigma with previous studies. We found no evidence of Na i and H $\alpha$, within the precision of our data, in the atmosphere of KELT-10b. Our detection limits allow us to rule out the presence of neutral sodium or excited hydrogen in an escaping extended atmosphere around KELT-10b. We cannot confirm the previous detection of Na i at lower altitudes with VLT/UVES. We note, however, that the Rossiter-McLaughlin effect impacts the transmission spectrum on a smaller scale than the previous detection with UVES. Analysis of the planet-occulted stellar lines shows the sky-projected alignment of the system, which is likely truly aligned due to tidal interactions of the planet with its cool (Teff < 6250 K) host star.Comment: Accepted in A&

TESS Discovery of an ultra-short-period planet around the nearby M dwarf LHS 3844

Data from the newly-commissioned \textit{Transiting Exoplanet Survey Satellite} (TESS) has revealed a "hot Earth" around LHS 3844, an M dwarf located 15 pc away. The planet has a radius of $1.32\pm 0.02$ $R_\oplus$ and orbits the star every 11 hours. Although the existence of an atmosphere around such a strongly irradiated planet is questionable, the star is bright enough ($I=11.9$, $K=9.1$) for this possibility to be investigated with transit and occultation spectroscopy. The star's brightness and the planet's short period will also facilitate the measurement of the planet's mass through Doppler spectroscopy.Comment: 10 pages, 4 figures. Submitted to ApJ Letters. This letter makes use of the TESS Alert data, which is currently in a beta test phase, using data from the pipelines at the TESS Science Office and at the TESS Science Processing Operations Cente

Regularization Independent Analysis of the Origin of Two Loop Contributions to N=1 Super Yang-Mills Beta Function

We present a both ultraviolet and infrared regularization independent analysis in a symmetry preserving framework for the N=1 Super Yang-Mills beta function to two loop order. We show explicitly that off-shell infrared divergences as well as the overall two loop ultraviolet divergence cancel out whilst the beta function receives contributions of infrared modes.Comment: 7 pages, 2 figures, typos correcte

On the equivalence between Implicit Regularization and Constrained Differential Renormalization

Constrained Differential Renormalization (CDR) and the constrained version of Implicit Regularization (IR) are two regularization independent techniques that do not rely on dimensional continuation of the space-time. These two methods which have rather distinct basis have been successfully applied to several calculations which show that they can be trusted as practical, symmetry invariant frameworks (gauge and supersymmetry included) in perturbative computations even beyond one-loop order. In this paper, we show the equivalence between these two methods at one-loop order. We show that the configuration space rules of CDR can be mapped into the momentum space procedures of Implicit Regularization, the major principle behind this equivalence being the extension of the properties of regular distributions to the regularized ones.Comment: 16 page