Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome

<p>Abstract</p> <p>Background</p> <p>Infection of cattle with <it>Mycobacterium avium </it>subspecies <it>paratuberculosis </it>(<it>M. ap</it>) causes severe economic losses to the dairy industry in the USA and worldwide. In an effort to better examine diversity among <it>M. ap </it>strains, we used optical mapping to profile genomic variations between strains of <it>M. ap </it>K-10 (sequenced strain) and <it>M. ap </it>ATCC 19698 (type strain).</p> <p>Results</p> <p>The assembled physical restriction map of <it>M. ap </it>ATCC 19698 showed a genome size of 4,839 kb compared to the sequenced K-10 genome of 4,830 kb. Interestingly, alignment of the optical map of the <it>M. ap </it>ATCC 19698 genome to the complete <it>M. ap </it>K-10 genome sequence revealed a 648-kb inversion around the origin of replication. However, Southern blotting, PCR amplification and sequencing analyses of the inverted region revealed that the genome of <it>M. ap </it>K-10 differs from the published sequence in the region starting from 4,197,080 bp to 11,150 bp, spanning the origin of replication. Additionally, two new copies of the coding sequences > 99.8% were identified, identical to the MAP0849c and MAP0850c genes located immediately downstream of the MAP3758c gene.</p> <p>Conclusion</p> <p>The optical map of <it>M. ap </it>ATCC 19698 clearly indicated the miss-assembly of the sequenced genome of <it>M. ap </it>K-10. Moreover, it identified 2 new genes in <it>M. ap </it>K-10 genome. This analysis strongly advocates for the utility of physical mapping protocols to complement genome sequencing projects.</p

Critical speeding-up in a local dynamics for the random-cluster model

We study the dynamic critical behavior of the local bond-update (Sweeny) dynamics for the Fortuin-Kasteleyn random-cluster model in dimensions d=2,3, by Monte Carlo simulation. We show that, for a suitable range of q values, the global observable S_2 exhibits "critical speeding-up": it decorrelates well on time scales much less than one sweep, so that the integrated autocorrelation time tends to zero as the critical point is approached. We also show that the dynamic critical exponent z_{exp} is very close (possibly equal) to the rigorous lower bound \alpha/\nu, and quite possibly smaller than the corresponding exponent for the Chayes-Machta-Swendsen-Wang cluster dynamics.Comment: LaTex2e/revtex4, 4 pages, includes 5 figure

Cluster simulations of loop models on two-dimensional lattices

We develop cluster algorithms for a broad class of loop models on two-dimensional lattices, including several standard O(n) loop models at n \ge 1. We show that our algorithm has little or no critical slowing-down when 1 \le n \le 2. We use this algorithm to investigate the honeycomb-lattice O(n) loop model, for which we determine several new critical exponents, and a square-lattice O(n) loop model, for which we obtain new information on the phase diagram.Comment: LaTex2e, 4 pages; includes 1 table and 2 figures. Totally rewritten in version 2, with new theory and new data. Version 3 as published in PR

Marine Deep Biosphere Microbial Communities Assemble in Near-Surface Sediments in Aarhus Bay

Analyses of microbial diversity in marine sediments have identified a core set of taxa unique to the marine deep biosphere. Previous studies have suggested that these specialized communities are shaped by processes in the surface seabed, in particular that their assembly is associated with the transition from the bioturbated upper zone to the nonbioturbated zone below. To test this hypothesis, we performed a fine-scale analysis of the distribution and activity of microbial populations within the upper 50 cm of sediment from Aarhus Bay (Denmark). Sequencing and qPCR were combined to determine the depth distributions of bacterial and archaeal taxa (16S rRNA genes) and sulfate-reducing microorganisms (SRM) (dsrB gene). Mapping of radionuclides throughout the sediment revealed a region of intense bioturbation at 0–6 cm depth. The transition from bioturbated sediment to the subsurface below (7 cm depth) was marked by a shift from dominant surface populations to common deep biosphere taxa (e.g., Chloroflexi and Atribacteria). Changes in community composition occurred in parallel to drops in microbial activity and abundance caused by reduced energy availability below the mixed sediment surface. These results offer direct evidence for the hypothesis that deep subsurface microbial communities present in Aarhus Bay mainly assemble already centimeters below the sediment surface, below the bioturbation zone

A look at the consumption behaviours along Ghana’s slave routes.

This study examines the consumption behaviours of four types of visitors to sites associated with the Transatlantic Slave Trade in Ghana. A questionnaire was used to elicit information regarding sites they intended or actually visited, perceived differences regarding site experiences and impressions of the heritage product itself. The results show that visitors were highly selective in their consumption patterns, although the sites in the country’s south were the major attractions and generators for all purposes. There is evidence that trip motive and connection to slavery influence consumption behaviour, as some visitors are willing to invest effort, expense and time to consume truly unique learning experiences. The findings were interpreted as evidence that site managers may need to design strategies using visitor profile and consumption patterns to deliver a coordinated and integrated appeal to the target visitor group

Multiscale characterisation of chimneys/pipes: Fluid escape structures within sedimentary basins

Evaluation of seismic reflection data has identified the presence of fluid escape structures cross-cutting overburden stratigraphy within sedimentary basins globally. Seismically-imaged chimneys/pipes are considered to be possible pathways for fluid flow, which may hydraulically connect deeper strata to the seabed. The properties of fluid migration pathways through the overburden must be constrained to enable secure, long-term subsurface carbon dioxide (CO2) storage. We have investigated a site of natural active fluid escape in the North Sea, the Scanner pockmark complex, to determine the physical characteristics of focused fluid conduits, and how they control fluid flow. Here we show that a multi-scale, multi-disciplinary experimental approach is required for complete characterisation of fluid escape structures. Geophysical techniques are necessary to resolve fracture geometry and subsurface structure (e.g., multi-frequency seismics) and physical parameters of sediments (e.g., controlled source electromagnetics) across a wide range of length scales (m to km). At smaller (mm to cm) scales, sediment cores were sampled directly and their physical and chemical properties assessed using laboratory-based methods. Numerical modelling approaches bridge the resolution gap, though their validity is dependent on calibration and constraint from field and laboratory experimental data. Further, time-lapse seismic and acoustic methods capable of resolving temporal changes are key for determining fluid flux. Future optimisation of experiment resource use may be facilitated by the installation of permanent seabed infrastructure, and replacement of manual data processing with automated workflows. This study can be used to inform measurement, monitoring and verification workflows that will assist policymaking, regulation, and best practice for CO2 subsurface storage operations

Long-distance attachments and implications for tourism development: the case of the Western Ukrainian diaspora

This study analyzes the perspectives of roots tourism through the experiences of Western Ukrainian diaspora members. Their sense of attachment to the ancestral homeland and their visits to the places of origin are investigated, together with the views by tour operators specialized in roots tourism and public authorities dealing with tourism in the region, evaluating the actual or potential impact in terms of tourism development opportunities. The peculiar history of this territory makes it a distinct research target, with dynamics that are different from the rest of the country. The desire to turn Western Ukraine into a solid tourist destination and the aim of stimulating economic development in a region that is still struggling to re-emerge from its marginality are widespread and form a fertile basis for the growth of diaspora tourism as a solid asset. Lights and shadows emerge from the diaspora tourists’ experiences and perceptions. Specialized tour operators clearly see the enhancement of this form of tourism as an important business opportunity, while public authorities are not currently focusing on this segment, preferring general tourism promotion

Efficacy of artesunate-amodiaquine and artemether-lumefantrine fixed-dose combinations for the treatment of uncomplicated Plasmodium falciparum malaria among children aged six to 59 months in Nimba County, Liberia: an open-label randomized non-inferiority trial.

Prospective efficacy monitoring of anti-malarial treatments is imperative for timely detection of resistance development. The in vivo efficacy of artesunate-amodiaquine (ASAQ) fixed-dose combination (FDC) was compared to that of artemether-lumefantrine (AL) among children aged six to 59 months in Nimba County, Liberia, where Plasmodium falciparum malaria is endemic and efficacy data are scarce

Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes

Type 2 diabetes (T2D) is a very common disease in humans. Here we conduct a meta-analysis of genome-wide association studies (GWAS) with ~16 million genetic variants in 62,892 T2D cases and 596,424 controls of European ancestry. We identify 139 common and 4 rare variants associated with T2D, 42 of which (39 common and 3 rare variants) are independent of the known variants. Integration of the gene expression data from blood (n = 14,115 and 2765) with the GWAS results identifies 33 putative functional genes for T2D, 3 of which were targeted by approved drugs. A further integration of DNA methylation (n = 1980) and epigenomic annotation data highlight 3 genes (CAMK1D, TP53INP1, and ATP5G1) with plausible regulatory mechanisms, whereby a genetic variant exerts an effect on T2D through epigenetic regulation of gene expression. Our study uncovers additional loci, proposes putative genetic regulatory mechanisms for T2D, and provides evidence of purifying selection for T2D-associated variants