Sequence variability of Campylobacter temperate bacteriophages

<p>Abstract</p> <p>Background</p> <p>Prophages integrated within the chromosomes of <it>Campylobacter jejuni </it>isolates have been demonstrated very recently. Prior work with <it>Campylobacter </it>temperate bacteriophages, as well as evidence from prophages in other enteric bacteria, suggests these prophages might have a role in the biology and virulence of the organism. However, very little is known about the genetic variability of <it>Campylobacter </it>prophages which, if present, could lead to differential phenotypes in isolates carrying the phages versus those that do not. As a first step in the characterization of <it>C. jejuni </it>prophages, we investigated the distribution of prophage DNA within a <it>C. jejuni </it>population assessed the DNA and protein sequence variability within a subset of the putative prophages found.</p> <p>Results</p> <p>Southern blotting of <it>C. jejuni </it>DNA using probes from genes within the three putative prophages of the <it>C. jejuni </it>sequenced strain RM 1221 demonstrated the presence of at least one prophage gene in a large proportion (27/35) of isolates tested. Of these, 15 were positive for 5 or more of the 7 <it>Campylobacter </it>Mu-like phage 1 (CMLP 1, also designated <it>Campylobacter jejuni </it>integrated element 1, or CJIE 1) genes tested. Twelve of these putative prophages were chosen for further analysis. DNA sequencing of a 9,000 to 11,000 nucleotide region of each prophage demonstrated a close homology with CMLP 1 in both gene order and nucleotide sequence. Structural and sequence variability, including short insertions, deletions, and allele replacements, were found within the prophage genomes, some of which would alter the protein products of the ORFs involved. No insertions of novel genes were detected within the sequenced regions. The 12 prophages and RM 1221 had a % G+C very similar to <it>C. jejuni </it>sequenced strains, as well as promoter regions characteristic of <it>C. jejuni</it>. None of the putative prophages were successfully induced and propagated, so it is not known if they were functional or if they represented remnant prophage DNA in the bacterial chromosomes.</p> <p>Conclusion</p> <p>These putative prophages form a family of phages with conserved sequences, and appear to be adapted to <it>Campylobacter</it>. There was evidence for recombination among groups of prophages, suggesting that the prophages had a mosaic structure. In many of these properties, the Mu-like CMLP 1 homologs characterized in this study resemble temperate bacteriophages of enteric bacteria that are responsible for contributions to virulence and host adaptation.</p

Precision Astrometry with the Very Long Baseline Array: Parallaxes and Proper Motions for 14 Pulsars

Astrometry can bring powerful constraints to bear on a variety of scientific questions about neutron stars, including their origins, astrophysics, evolution, and environments. Using phase-referenced observations at the VLBA, in conjunction with pulsar gating and in-beam calibration, we have measured the parallaxes and proper motions for 14 pulsars. The smallest measured parallax in our sample is 0.13+-0.02 mas for PSR B1541+09, which has a most probable distance of 7.2+1.3-1.1 kpc. We detail our methods, including initial VLA surveys to select candidates and find in-beam calibrators, VLBA phase-referencing, pulsar gating, calibration, and data reduction. The use of the bootstrap method to estimate astrometric uncertainties in the presence of unmodeled systematic errors is also described. Based on our new model-independent estimates for distance and transverse velocity, we investigate the kinematics and birth sites of the pulsars and revisit models of the Galactic electron density distribution. We find that young pulsars are moving away from the Galactic plane, as expected, and that age estimates from kinematics and pulsar spindown are generally in agreement, with certain notable exceptions. Given its present trajectory, the pulsar B2045-16 was plausibly born in the open cluster NGC 6604. For several high-latitude pulsars, the NE2001 electron density model underestimates the parallax distances by a factor of two, while in others the estimates agree with or are larger than the parallax distances, suggesting that the interstellar medium is irregular on relevant length scales. The VLBA astrometric results for the recycled pulsar J1713+0747 are consistent with two independent estimates from pulse timing, enabling a consistency check between the different reference frames.Comment: 16 pages, 9 figures, 4 tables; results unchanged; revised version accepted by Ap

The s ---> d gamma decay in and beyond the Standard Model

The New Physics sensitivity of the s ---> d gamma transition and its accessibility through hadronic processes are thoroughly investigated. Firstly, the Standard Model predictions for the direct CP-violating observables in radiative K decays are systematically improved. Besides, the magnetic contribution to epsilon prime is estimated and found subleading, even in the presence of New Physics, and a new strategy to resolve its electroweak versus QCD penguin fraction is identified. Secondly, the signatures of a series of New Physics scenarios, characterized as model-independently as possible in terms of their underlying dynamics, are investigated by combining the information from all the FCNC transitions in the s ---> d sector.Comment: 54 pages, 14 eps figure

Associated Higgs production with top quarks at the Large Hadron Collider: NLO QCD corrections

We present in detail the calculation of the O(alpha_s^3) inclusive total cross section for the process pp -> t-tbar-h, in the Standard Model, at the CERN Large Hadron Collider with center-of-mass energy sqrt(s_H)=14 TeV. The calculation is based on the complete set of virtual and real O(alpha_s) corrections to the parton level processes q-qbar -> t-tbar-h and gg -> t-tbar-h, as well as the tree level processes (q,qbar)g -> t-tbar-h-(q,qbar). The virtual corrections involve the computation of pentagon diagrams with several internal and external massive particles, first encountered in this process. The real corrections are computed using both the single and the two cutoff phase space slicing method. The next-to-leading order QCD corrections significantly reduce the renormalization and factorization scale dependence of the Born cross section and moderately increase the Born cross section for values of the renormalization and factorization scales above m_t.Comment: 70 pages, 12 figures, RevTeX4: one word changed in the abstract, one sentence reworded in the introduction. To appear in Phys. Rev.

Paleogenome reveals genetic contribution of extinct giant panda to extant populations

Historically, the giant panda was widely distributed from northern China to southwestern Asia. As a result of range contraction and fragmentation, extant individuals are currently restricted to fragmented mountain ranges on the eastern margin of the Qinghai-Tibet plateau, where they are distributed among three major population clusters. However, little is known about the genetic consequences of this dramatic range contraction. For example, were regions where giant pandas previously existed occupied by ancestors of present-day populations, or were these regions occupied by genetically distinct populations that are now extinct? If so, is there any contribution of these extinct populations to the genomes of giant pandas living today? To investigate these questions, we sequenced the nuclear genome of an ∼5,000-year-old giant panda from Jiangdongshan, Tengchong County in Yunnan Province, China. We find that this individual represents a genetically distinct population that diverged prior to the diversification of modern giant panda populations. We find evidence of differential admixture with this ancient population among modern individuals originating from different populations as well as within the same population. We also find evidence for directional gene flow, which transferred alleles from the ancient population into the modern giant panda lineages. A variable proportion of the genomes of extant individuals is therefore likely derived from the ancient population represented by our sequenced individual. Although extant giant panda populations retain reasonable genetic diversity, our results suggest that this represents only part of the genetic diversity this species harbored prior to its recent range contractions

Immediate and long-term impact of the COVID-19 pandemic on delivery of surgical services

Background The ongoing pandemic is having a collateral health effect on delivery of surgical care to millions of patients. Very little is known about pandemic management and effects on other services, including delivery of surgery. Methods This was a scoping review of all available literature pertaining to COVID‐19 and surgery, using electronic databases, society websites, webinars and preprint repositories. Results Several perioperative guidelines have been issued within a short time. Many suggestions are contradictory and based on anecdotal data at best. As regions with the highest volume of operations per capita are being hit, an unprecedented number of operations are being cancelled or deferred. No major stakeholder seems to have considered how a pandemic deprives patients with a surgical condition of resources, with patients disproportionally affected owing to the nature of treatment (use of anaesthesia, operating rooms, protective equipment, physical invasion and need for perioperative care). No recommendations exist regarding how to reopen surgical delivery. The postpandemic evaluation and future planning should involve surgical services as an essential part to maintain appropriate surgical care for the population during an outbreak. Surgical delivery, owing to its cross‐cutting nature and synergistic effects on health systems at large, needs to be built into the WHO agenda for national health planning. Conclusion Patients are being deprived of surgical access, with uncertain loss of function and risk of adverse prognosis as a collateral effect of the pandemic. Surgical services need a contingency plan for maintaining surgical care in an ongoing or postpandemic phase.publishedVersio

Evidence for alignment of the rotation and velocity vectors in pulsars

We present strong observational evidence for a relationship between the direction of a pulsar's motion and its rotation axis. We show carefully calibrated polarization data for 25 pulsars, 20 of which display linearly polarized emission from the pulse longitude at closest approach to the magnetic pole. Such data allow determination of the position angle of the linear polarisation which in turn reflects the position angle of the rotation axis. Of these 20 pulsars, 10 show an offset between the velocity vector and the polarisation position angle which is either less than 10\degr or more than 80\degr, a fraction which is very unlikely by random chance. We believe that the bimodal nature of the distribution arises from the presence of orthogonal polarisation modes in the pulsar radio emission. In some cases this orthogonal ambiguity is resolved by observations at other wavelengths so that we conclude that the velocity vector and the rotation axis are aligned at birth. Strengthening the case is the fact that 4 of the 5 pulsars with ages less than 3 Myr show this relationship, including the Vela pulsar. We discuss the implications of these findings in the context of the Spruit & Phinney (1998)\nocite{sp98} model of pulsar birth-kicks. We point out that, contrary to claims in the literature, observations of double neutron star systems do not rule out aligned kick models and describe a possible observational test involving the double pulsar system.Comment: MNRAS, In Pres

A novel interfacial polymerization approach towards synthesis of graphene oxide-incorporated thin film nanocomposite membrane with improved surface properties

The conventional interfacial polymerization (IP) technique that requires a rubber roller in removing amine aqueous solution is likely to cause uneven distribution of nanomaterials on microporous substrate during thin film nanocomposite (TFN) membrane fabrication. A novel IP technique was developed in this work to pre-coat the substrate with graphene oxide (GO) nanosheets followed by vacuum filtration of amine aqueous solution through the substrate before initiating polyamide cross-linking process. This novel technique was also employed to fabricate a composite membrane that contained no nanomaterials. The results showed that the GO-incorporated TFN membrane exhibited 71.7% and 129.4% higher pure water flux compared to the composite membranes without GO incorporation that were synthesized using conventional and filtration IP technique, respectively. The water enhancement of the TFN membrane could be attributed to the existence of hydrophilic GO that was distributed evenly throughout the substrate surface coupled with the formation of porous selective layer that reduced water transport resistance. Besides exhibiting promising rejection against divalent ions, the newly developed TFN membrane also showed significantly lower water flux deterioration in filtrating bovine serum albumin and Reactive Black 5 solution. The enhanced membrane antifouling resistance was mainly due to the improved membrane surface properties that minimize deposition and adsorption of foulants on the TFN membrane surface

Pulsar spin-velocity alignment from single and binary neutron star progenitors

The role of binary progenitors of neutron stars in the apparent distribution of space velocities and spin-velocity alignment observed in young pulsars is studied. A Monte-Carlo synthesis of pulsar population from single and binary stars with different assumptions about the NS natal kick model (direction distribution, amplitude, and kick reduction in binary progenitors which experienced mass exchange due to Roche lobe overflow with initial masses on the main sequence from the range 8-11 $M_\odot$) is performed. The calculated spin-velocity alignment distributions are compared with observational data obtained from radio polarization measurements. The observed space velocity of pulsars is found to be mostly shaped by the natal kick velocity form and its amplitude; the fraction of binaries is not important here for reasonably large kicks. The distribution of kick direction relative to the spin axis during the formation of a NS is found to affect strongly the spin-velocity correlation of pulsars. Comparison with observed pulsar spin-velocity angles favours a sizeable fraction of binary progenitors and the kick-spin angle $\sim 5-20^\circ$. The form of the initial binary mass ratio distribution does not affect our results.Comment: 20 pages, 8 figures; Submitted to MNRA