Evidence for symmetric chromosomal inversions around the replication origin in bacteria.

BackgroundWhole-genome comparisons can provide great insight into many aspects of biology. Until recently, however, comparisons were mainly possible only between distantly related species. Complete genome sequences are now becoming available from multiple sets of closely related strains or species.ResultsBy comparing the recently completed genome sequences of Vibrio cholerae, Streptococcus pneumoniae and Mycobacterium tuberculosis to those of closely related species - Escherichia coli, Streptococcus pyogenes and Mycobacterium leprae, respectively - we have identified an unusual and previously unobserved feature of bacterial genome structure. Scatterplots of the conserved sequences (both DNA and protein) between each pair of species produce a distinct X-shaped pattern, which we call an X-alignment. The key feature of these alignments is that they have symmetry around the replication origin and terminus; that is, the distance of a particular conserved feature (DNA or protein) from the replication origin (or terminus) is conserved between closely related pairs of species. Statistically significant X-alignments are also found within some genomes, indicating that there is symmetry about the replication origin for paralogous features as well.ConclusionsThe most likely mechanism of generation of X-alignments involves large chromosomal inversions that reverse the genomic sequence symmetrically around the origin of replication. The finding of these X-alignments between many pairs of species suggests that chromosomal inversions around the origin are a common feature of bacterial genome evolution

The shadows of risk and inequality within salutogenic coastal waters

This is the author accepted manuscript. The final version is available from Routledge via the link in this recordEconomic and Social Research Council (ESRC

Effect of insulin-like growth factor I on HIV type 1 long terminal repeat-driven chloramphenicol acetyltransferase expression

In this study, we have investigated the ability of insulin-like growth factor I (IGF-I) to inhibit HIV long terminal repeat (LTR)-driven gene expression. Using COS 7 cells cotransfected with tat and an HIV LTR linked to a chloramphenicol acetyltransferase (CAT) reporter, we observed that physiological levels of IGF-I (10-9 M) significantly inhibited CAT expression in a concentration- and time-dependent manner. IGF-I did not inhibit C AT expression in COS 7 cells transfected with pSVCAT, and did not affect CAT expression in the absence of cotransfection with tat . Transfection of HIV-1 proviral DNA into COS 7 cells +/- IGF-I resulted in a significant decrease ( p 0.05) in infectious virion production. Both IGF-I and Ro24-7429 inhibited LTR-driven C AT expression, while TNF- alpha -enhanced CAT expression was not affected by IGF-I. On the other hand, a plasmid encoding parathyroid hormone-related peptide exhibited dramatic additivity of inhibition of CAT expression in COS 7 cells. Finally, we show that in Jurkat or U937 cells cotransfected with HIVLTRCAT/tat, IGF-I significantly inhibited CAT expression. Further, interleukin 4 showed in U937 cells inhibition of CAT expression that was not additive to IGF-I induced inhibition. Our data demonstrate that IGF-I can specifically inhibit HIVLTRCAT expression. This inhibition may occur at the level of the tat /TAR interaction. Finally, this IGF-I effect is seen in target cell lines and similar paths of inhibition may be involved in the various cell types employed. <br /

Peer support for discharge from inpatient to community mental health services: Study protocol clinical trial (SPIRIT Compliant).

INTRODUCTION: In the period shortly after discharge from inpatient to community mental health care, people are at increased risk of self-harm, suicide, and readmission to hospital. Discharge interventions including peer support have shown potential, and there is some evidence that community-based peer support reduces readmissions. However, systematic reviews of peer support in mental health services indicate poor trial quality and a lack of reporting of how peer support is distinctive from other mental health support. This study is designed to establish the clinical and cost effectiveness of a peer worker intervention to support discharge from inpatient to community mental health care, and to address issues of trial quality and clarity of reporting of peer support interventions. METHODS: This protocol describes an individually randomized controlled superiority trial, hypothesizing that people offered a peer worker discharge intervention in addition to usual follow-up care in the community are less likely to be readmitted in the 12 months post discharge than people receiving usual care alone. A total of 590 people will be recruited shortly before discharge from hospital and randomly allocated to care as usual plus the peer worker intervention or care as usual alone. Manualized peer support provided by trained peer workers begins in hospital and continues for 4 months in the community post discharge. Secondary psychosocial outcomes are assessed at 4 months post discharge, and service use and cost outcomes at 12 months post discharge, alongside a mixed methods process evaluation. DISCUSSION: Clearly specified procedures for sequencing participant allocation and for blinding assessors to allocation, plus full reporting of outcomes, should reduce risk of bias in trial findings and contribute to improved quality in the peer support evidence base. The involvement of members of the study team with direct experience of peer support, mental distress, and using mental health services, in coproducing the intervention and designing the trial, ensures that we theorize and clearly describe the peer worker intervention, and evaluate how peer support is related to any change in outcome. This is an important methodological contribution to the evidence base. TRIAL REGISTRATION: This study was prospectively registered as ISRCTN 10043328 on November 28, 2016

An investigation of the impact of using different methods for network meta-analysis: A protocol for an empirical evaluation

BACKGROUND: Network meta-analysis, a method to synthesise evidence from multiple treatments, has increased in popularity in the past decade. Two broad approaches are available to synthesise data across networks, namely, arm- and contrast-synthesis models, with a range of models that can be fitted within each. There has been recent debate about the validity of the arm-synthesis models, but to date, there has been limited empirical evaluation comparing results using the methods applied to a large number of networks. We aim to address this gap through the re-analysis of a large cohort of published networks of interventions using a range of network meta-analysis methods. METHODS: We will include a subset of networks from a database of network meta-analyses of randomised trials that have been identified and curated from the published literature. The subset of networks will include those where the primary outcome is binary, the number of events and participants are reported for each direct comparison, and there is no evidence of inconsistency in the network. We will re-analyse the networks using three contrast-synthesis methods and two arm-synthesis methods. We will compare the estimated treatment effects, their standard errors, treatment hierarchy based on the surface under the cumulative ranking (SUCRA) curve, the SUCRA value, and the between-trial heterogeneity variance across the network meta-analysis methods. We will investigate whether differences in the results are affected by network characteristics and baseline risk. DISCUSSION: The results of this study will inform whether, in practice, the choice of network meta-analysis method matters, and if it does, in what situations differences in the results between methods might arise. The results from this research might also inform future simulation studies

Synthesis and reactivity of an N-triphos Mo(0) dinitrogen complex

The preparation and reactivity of a novel molybdenum dinitrogen complex supported by a nitrogen-centred tripodal phosphine ligand (N-triphos, N(CH2PPh2)3, NP3Ph) are reported. Reaction of N-triphos with [MoX3(THF)3] (X = Cl, Br, I) gave the Mo(III) complex [MoX3(κ2-NP3Ph)(THF)] (1), where bidentate N-triphos coordination was observed. Reduction of this complex in the presence of dppm (bis(diphenylphosphino)methane) gave the dinitrogen complex [Mo(N2)(dppm)(κ3-NP3Ph)] (2), which exhibits moderate dinitrogen activation. An additional hydride complex, [Mo(H)2(dppm)(κ3-NP3Ph)] (4), was produced either as a minor side product during the reduction step, or as a major product by direct hydrogenation of the dinitrogen complex 2. The reactivity of the dinitrogen complex 2 with a range of Lewis acids was also investigated. At low temperatures, protic or borane Lewis acids (H+, BBr3 and tris(pentafluorophenyl)borane (BCF)) were found to coordinate to the apical nitrogen atom of the N-triphos ligand, with no conclusive evidence of any functionalisation of the dinitrogen ligand. Alkali metal Lewis acid addition to 2 resulted in the unexpected rearrangement of the N-triphos ligand to form [Mo(dppm)(PMePh2)(PCP)][B(C6F5)4] (7), where PCP, [Ph2PCNHCH2PPh2] is the carbenic ligand formed upon rearrangement from the reaction of 2 with M[B(C6F5)4] (M = Li, Na or K). Single crystal X-ray diffraction of complexes 1, 2, 4 and 7 provided structural confirmation of the N-triphos molybdenum complexes described

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our “reliable-overlap” algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps

A Statistical Method for Reassociating Human Tali and Calcanei from a Commingled Context.

In a commingled context, assessing that a talus and a calcaneus correspond to the same individual could become a primary step for accurately sorting human remains. For this purpose, the lengths and widths of the trochlea, posterior calcaneal articular surface, and posterior talar articular surface were measured in 197 individuals (105 males, 92 females) from the Athens Collection. A total of 12 highly accurate equations for reassociating tali and calcanei were developed, using simple and multiple linear regression analysis and they were found to be suitable for sorting commingled human remains. Bilateral asymmetry and sex did not have an effect on the accuracy of the method

Coordination of opposing sex-specific and core muscle groups regulates male tail posture during Caenorhabditis elegans male mating behavior

Background To survive and reproduce, animals must be able to modify their motor behavior in response to changes in the environment. We studied a complex behavior of Caenorhabditis elegans, male mating behavior, which provided a model for understanding motor behaviors at the genetic, molecular as well as circuit level. C. elegans male mating behavior consists of a series of six sub-steps: response to contact, backing, turning, vulva location, spicule insertion, and sperm transfer. The male tail contains most of the sensory structures required for mating, in addition to the copulatory structures, and thus to carry out the steps of mating behavior, the male must keep his tail in contact with the hermaphrodite. However, because the hermaphrodite does not play an active role in mating and continues moving, the male must modify his tail posture to maintain contact. We provide a better understanding of the molecular and neuro-muscular pathways that regulate male tail posture during mating. Results Genetic and laser ablation analysis, in conjunction with behavioral assays were used to determine neurotransmitters, receptors, neurons and muscles required for the regulation of male tail posture. We showed that proper male tail posture is maintained by the coordinated activity of opposing muscle groups that curl the tail ventrally and dorsally. Specifically, acetylcholine regulates both ventral and dorsal curling of the male tail, partially through anthelmintic levamisole-sensitive, nicotinic receptor subunits. Male-specific muscles are required for acetylcholine-driven ventral curling of the male tail but dorsal curling requires the dorsal body wall muscles shared by males and hermaphrodites. Gamma-aminobutyric acid activity is required for both dorsal and ventral acetylcholine-induced curling of the male tail and an inhibitory gamma-aminobutyric acid receptor, UNC-49, prevents over-curling of the male tail during mating, suggesting that cross-inhibition of muscle groups helps maintain proper tail posture. Conclusion Our results demonstrated that coordination of opposing sex-specific and core muscle groups, through the activity of multiple neurotransmitters, is required for regulation of male tail posture during mating. We have provided a simple model for regulation of male tail posture that provides a foundation for studies of how genes, molecular pathways, and neural circuits contribute to sensory regulation of this motor behavior