Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase.

DNA strand exchange by serine recombinases has been proposed to occur by a large-scale rotation of halves of the recombinase tetramer. Here we provide the first direct physical evidence for the subunit rotation mechanism for the Hin serine invertase. Single-DNA looping assays using an activated mutant (Hin-H107Y) reveal specific synapses between two hix sites. Two-DNA "braiding" experiments, where separate DNA molecules carrying a single hix are interwound, show that Hin-H107Y cleaves both hix sites and mediates multi-step rotational relaxation of the interwinding. The variable numbers of rotations in the DNA braid experiments are in accord with data from bulk experiments that follow DNA topological changes accompanying recombination by the hyperactive enzyme. The relatively slow Hin rotation rates, combined with pauses, indicate considerable rotary friction between synapsed subunit pairs. A rotational pausing mechanism intrinsic to serine recombinases is likely to be crucial for DNA ligation and for preventing deleterious DNA rearrangements

Genotypic and phenotypic characterization of antimicrobial resistance in Neisseria gonorrhoeae: A cross-sectional study of isolates recovered from routine urine cultures in a high-incidence setting

ABSTRACT The objectives of this study were to perform genomic and phenotypic characterization of antimicrobial resistance in Neisseria gonorrhoeae isolates recovered from urine samples from patients in St. Louis, MO, USA. Sixty-four clinical isolates were banked over a 2-year period and subjected to antimicrobial susceptibility testing (AST) by Kirby-Bauer disk diffusion (penicillin, tetracycline, cefuroxime, and ciprofloxacin) and gradient diffusion (tetracycline, doxycycline, azithromycin, ceftriaxone, cefixime, ciprofloxacin, gemifloxacin, and delafloxacin). The medical records for the patients were evaluated to determine the demographics, location, and prescribed treatment regimen. Isolate draft genomes were assembled from Illumina shotgun sequencing data, and resistance determinants were identified by ResFinder and PointFinder. Of the 64 isolates, 97% were nonsusceptible to penicillin, with resistant isolates all containing the blaTEM-1b gene; 78 and 81% of isolates were nonsusceptible to tetracycline and doxycycline, respectively, with resistant isolates all containing the tet(M) gene. One isolate was classified as non-wild-type to azithromycin, and all isolates were susceptible to ceftriaxone; 89% of patients received this combination of drugs as first-line therapy. Six percent of isolates were resistant to ciprofloxacin, with most resistant isolates containing multiple gyrA and parC mutations. Correlation between disk and gradient diffusion AST devices was high for tetracycline and ciprofloxacin (R2 > 99% for both). The rates of N. gonorrhoeae antibiotic resistance in St. Louis are comparable to current rates reported nationally, except ciprofloxacin resistance was less common in our cohort. Strong associations between specific genetic markers and phenotypic susceptibility testing hold promise for the utility of genotype-based diagnostic assays to guide directed antibiotic therapy. IMPORTANCE Neisseria gonorrhoeae causes the sexually transmitted infection gonorrhea, which is most commonly diagnosed using a DNA-based detection method that does not require growth and isolation of N. gonorrhoeae in the laboratory. This is problematic because the rates of antibiotic resistance in N. gonorrhoeae are increasing, but without isolating the organism in the clinical laboratory, antibiotic susceptibility testing cannot be performed on strains recovered from clinical specimens. We observed an increase in the frequency of urine cultures growing N. gonorrhoeae after we implemented a total laboratory automation system for culture in our clinical laboratory. Here, we report on the rates of resistance to multiple historically used, first-line, and potential future-use antibiotics for 64 N. gonorrhoeae isolates. We found that the rates of antibiotic resistance in our isolates were comparable to national rates. Additionally, resistance to specific antibiotics correlated closely with the presence of genetic resistance genes, suggesting that DNA-based tests could also be designed to guide antibiotic therapy for treating gonorrhea

Current and Emerging Uses of Statins in Clinical Therapeutics: A Review

Statins, a class of cholesterol-lowering medications that inhibit 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase, are commonly administered to treat atherosclerotic cardiovascular disease. Statin use may expand considerably given its potential for treating an array of cholesterol-independent diseases. However, the lack of conclusive evidence supporting these emerging therapeutic uses of statins brings to the fore a number of unanswered questions including uncertainties regarding patient-to-patient variability in response to statins, the most appropriate statin to be used for the desired effect, and the efficacy of statins in treating cholesterol-independent diseases. In this review, the adverse effects, costs, and drug–drug and drug–food interactions associated with statin use are presented. Furthermore, we discuss the pleiotropic effects associated with statins with regard to the onset and progression of autoimmune and inflammatory diseases, cancer, neurodegenerative disorders, strokes, bacterial infections, and human immunodeficiency virus. Understanding these issues will improve the prognosis of patients who are administered statins and potentially expand our ability to treat a wide variety of diseases

EFFECTS OF MANAGEMENT PRACTICES ON GRASSLAND BIRDS: HORNED LARK

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 4,000 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species’ breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management is posted at the Web site mentioned below

STAGES: the Space Telescope A901/2 Galaxy Evolution Survey

We present an overview of the Space Telescope A901/2 Galaxy Evolution Survey (STAGES). STAGES is a multiwavelength project designed to probe physical drivers of galaxy evolution across a wide range of environments and luminosity. A complex multi-cluster system at z~0.165 has been the subject of an 80-orbit F606W HST/ACS mosaic covering the full 0.5x0.5 (~5x5 Mpc^2) span of the supercluster. Extensive multiwavelength observations with XMM-Newton, GALEX, Spitzer, 2dF, GMRT, and the 17-band COMBO-17 photometric redshift survey complement the HST imaging. Our survey goals include simultaneously linking galaxy morphology with other observables such as age, star-formation rate, nuclear activity, and stellar mass. In addition, with the multiwavelength dataset and new high resolution mass maps from gravitational lensing, we are able to disentangle the large-scale structure of the system. By examining all aspects of environment we will be able to evaluate the relative importance of the dark matter halos, the local galaxy density, and the hot X-ray gas in driving galaxy transformation. This paper describes the HST imaging, data reduction, and creation of a master catalogue. We perform Sersic fitting on the HST images and conduct associated simulations to quantify completeness. In addition, we present the COMBO-17 photometric redshift catalogue and estimates of stellar masses and star-formation rates for this field. We define galaxy and cluster sample selection criteria which will be the basis for forthcoming science analyses, and present a compilation of notable objects in the field. Finally, we describe the further multiwavelength observations and announce public access to the data and catalogues.Comment: 29 pages, 22 figures; accepted to MNRAS. Full data release available at http://www.nottingham.ac.uk/astronomy/stage

STAGES: the Space Telescope A901/2 Galaxy Evolution Survey

We present an overview of the Space Telescope A901/2 Galaxy Evolution Survey (STAGES). STAGES is a multiwavelength project designed to probe physical drivers of galaxy evolution across a wide range of environments and luminosity. A complex multicluster system at z∼ 0.165 has been the subject of an 80-orbit F606W Hubble Space Telescope (HST)/Advanced Camera for Surveys (ACS) mosaic covering the full span of the supercluster. Extensive multiwavelength observations with XMM-Newton, GALEX, Spitzer, 2dF, Giant Metrewave Radio Telescope and the 17-band COMBO-17 photometric redshift survey complement the HST imaging. Our survey goals include simultaneously linking galaxy morphology with other observables such as age, star formation rate, nuclear activity and stellar mass. In addition, with the multiwavelength data set and new high-resolution mass maps from gravitational lensing, we are able to disentangle the large-scale structure of the system. By examining all aspects of an environment we will be able to evaluate the relative importance of the dark matter haloes, the local galaxy density and the hot X-ray gas in driving galaxy transformation. This paper describes the HST imaging, data reduction and creation of a master catalogue. We perform the Sérsic fitting on the HST images and conduct associated simulations to quantify completeness. In addition, we present the COMBO-17 photometric redshift catalogue and estimates of stellar masses and star formation rates for this field. We define galaxy and cluster sample selection criteria, which will be the basis for forthcoming science analyses, and present a compilation of notable objects in the field. Finally, we describe the further multiwavelength observations and announce public access to the data and catalogue

MSH3 polymorphisms and protein levels affect CAG repeat instability in huntington's disease mice

Expansions of trinucleotide CAG/CTG repeats in somatic tissues are thought to contribute to ongoing disease progression through an affected individual's life with Huntington's disease or myotonic dystrophy. Broad ranges of repeat instability arise between individuals with expanded repeats, suggesting the existence of modifiers of repeat instability. Mice with expanded CAG/CTG repeats show variable levels of instability depending upon mouse strain. However, to date the genetic modifiers underlying these differences have not been identified. We show that in liver and striatum the R6/1 Huntington's disease (HD) (CAG)~100 transgene, when present in a congenic C57BL/6J (B6) background, incurred expansion-biased repeat mutations, whereas the repeat was stable in a congenic BALB/cByJ (CBy) background. Reciprocal congenic mice revealed the Msh3 gene as the determinant for the differences in repeat instability. Expansion bias was observed in congenic mice homozygous for the B6 Msh3 gene on a CBy background, while the CAG tract was stabilized in congenics homozygous for the CBy Msh3 gene on a B6 background. The CAG stabilization was as dramatic as genetic deficiency of Msh2. The B6 and CBy Msh3 genes had identical promoters but differed in coding regions and showed strikingly different protein levels. B6 MSH3 variant protein is highly expressed and associated with CAG expansions, while the CBy MSH3 variant protein is expressed at barely detectable levels, associating with CAG stability. The DHFR protein, which is divergently transcribed from a promoter shared by the Msh3 gene, did not show varied levels between mouse strains. Thus, naturally occurring MSH3 protein polymorphisms are modifiers of CAG repeat instability, likely through variable MSH3 protein stability. Since evidence supports that somatic CAG instability is a modifier and predictor of disease, our data are consistent with the hypothesis that variable levels of CAG instability associated with polymorphisms of DNA repair genes may have prognostic implications for various repeat-associated diseases

Age-related increase of kynurenine enhances miR29b-1-5p to decrease both CXCL12 signaling and the epigenetic enzyme Hdac3 in bone marrow stromal cells

Mechanisms leading to age-related reductions in bone formation and subsequent osteoporosis are still incompletely understood. We recently demonstrated that kynurenine (KYN), a tryptophan metabolite, accumulates in serum of aged mice and induces bone loss. Here, we report on novel mechanisms underlying KYN's detrimental effect on bone aging. We show that KYN is increased with aging in murine bone marrow mesenchymal stem cells (BMSCs). KYN reduces bone formation via modulating levels of CXCL12 and its receptors as well as histone deacetylase 3 (Hdac3). BMSCs responded to KYN by significantly decreasing mRNA expression levels of CXCL12 and its cognate receptors, CXCR4 and ACKR3, as well as downregulating osteogenic gene RUNX2 expression, resulting in a significant inhibition in BMSCs osteogenic differentiation. KYN's effects on these targets occur by increasing regulatory miRNAs that target osteogenesis, specifically miR29b-1-5p. Thus, KYN significantly upregulated the anti-osteogenic miRNA miR29b-1-5p in BMSCs, mimicking the up-regulation of miR-29b-1-5p in human and murine BMSCs with age. Direct inhibition of miR29b-1-5p by antagomirs rescued CXCL12 protein levels downregulated by KYN, while a miR29b-1-5p mimic further decreased CXCL12 levels. KYN also significantly downregulated mRNA levels of Hdac3, a target of miR-29b-1-5p, as well as its cofactor NCoR1. KYN is a ligand for the aryl hydrocarbon receptor (AhR). We hypothesized that AhR mediates KYN's effects in BMSCs. Indeed, AhR inhibitors (CH-223191 and 3',4'-dimethoxyflavone [DMF]) partially rescued secreted CXCL12 protein levels in BMSCs treated with KYN. Importantly, we found that treatment with CXCL12, or transfection with an miR29b-1-5p antagomir, downregulated the AhR mRNA level, while transfection with miR29b-1-5p mimic significantly upregulated its level. Further, CXCL12 treatment downregulated IDO, an enzyme responsible for generating KYN. Our findings reveal novel molecular pathways involved in KYN's age-associated effects in the bone microenvironment that may be useful translational targets for treating osteoporosis

Low-frequency deep brain stimulation reveals resonant beta-band evoked oscillations in the pallidum of Parkinson’s Disease patients

IntroductionEvidence suggests that spontaneous beta band (11–35 Hz) oscillations in the basal ganglia thalamocortical (BGTC) circuit are linked to Parkinson’s disease (PD) pathophysiology. Previous studies on neural responses in the motor cortex evoked by electrical stimulation in the subthalamic nucleus have suggested that circuit resonance may underlie the generation of spontaneous and stimulation-evoked beta oscillations in PD. Whether these stimulation-evoked, resonant oscillations are present across PD patients in the internal segment of the globus pallidus (GPi), a primary output nucleus in the BGTC circuit, is yet to be determined.MethodsWe characterized spontaneous and stimulation-evoked local field potentials (LFPs) in the GPi of four PD patients (five hemispheres) using deep brain stimulation (DBS) leads externalized after DBS implantation surgery.ResultsOur analyses show that low-frequency (2–4 Hz) stimulation in the GPi evoked long-latency (>50 ms) beta-band neural responses in the GPi in 4/5 hemispheres. We demonstrated that neural sources generating both stimulation-evoked and spontaneous beta oscillations were correlated in their frequency content and spatial localization.DiscussionOur results support the hypothesis that the same neuronal population and resonance phenomenon in the BGTC circuit generates both spontaneous and evoked pallidal beta oscillations. These data also support the development of closed-loop control systems that modulate the GPi spontaneous oscillations across PD patients using beta band stimulation-evoked responses