A novel NGS library preparation method to characterize native termini of fragmented DNA.

Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5' and 3') of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80-90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA

The Evolution of Cuspy Triaxial Galaxies Harboring Central Black Holes

We use numerical simulations to study the evolution of triaxial elliptical galaxies with central black holes. In contrast to earlier numerical studies which used galaxy models with central density ``cores,'' our galaxies have steep central cusps, like those observed in real ellipticals. As a black hole grows in these cuspy triaxial galaxies, the inner regions become rounder owing to chaos induced in the orbit families which populate the model. At larger radii, however, the models maintain their triaxiality, and orbital analyses show that centrophilic orbits there resist stochasticity over many dynamical times. While black hole induced evolution is strong in the inner regions of these galaxies, and reaches out beyond the nominal ``sphere of influence'' of a black hole, our simulations do not show evidence for a rapid {\it global} transformation of the host. The triaxiality of observed elliptical galaxies is therefore not inconsistent with the presence of supermassive black holes at their centers.Comment: 15 pages, 7 figures (1 color). Accepted for publication in Ap

Clinical and Mucosal Immune Correlates of HIV-1 Semen Levels in Antiretroviral-Naive Men.

Background. This study was done to characterize parameters associated with semen human immunodeficiency virus (HIV)-1 ribonucleic acid (RNA) viral load (VL) variability in HIV-infected, therapy-naive men. Methods. Paired blood and semen samples were collected from 30 HIV-infected, therapy-naive men who have sex with men, and 13 participants were observed longitudinally for up to 1 year. Human immunodeficiency virus RNA, bacterial load by 16S RNA, herpesvirus (Epstein-Barr virus and cytomegalovirus [CMV]) shedding, and semen cytokines/chemokines were quantified, and semen T-cell subsets were assessed by multiparameter flow cytometry. Results. Semen HIV RNA was detected at 93% of visits, with \u3e50% of men shedding high levels of virus (defined as \u3e5000 copies/mL). In the baseline cross-sectional analysis, an increased semen HIV VL correlated with local CMV reactivation, the semen bacterial load, and semen inflammatory cytokines, particularly interleukin (IL)-8. T cells in semen were more activated than blood, and there was an increased frequency of Th17 cells and γδ-T-cells. Subsequent prospective analysis demonstrated striking interindividual variability in HIV and CMV shedding patterns, and only semen IL-8 levels and the blood VL were independently associated with semen HIV levels. Conclusions. Several clinical and immune parameters were associated with increased HIV semen levels in antiretroviral therapy-naive men, with induction of local proinflammatory cytokines potentially acting as a common pathway

Crop wild relatives as germplasm resource for cultivar improvement in mint (Mentha L.)

Mentha is a strongly scented herb of the Lamiaceae (formerly Labiatae) and includes about 30 species and hybrid species that are distributed or introduced throughout the globe. These fragrant plants have been selected throughout millennia for use by humans as herbs, spices, and pharmaceutical needs. The distilling of essential oils from mint began in Japan and England but has become a significant industrial product for the US, China, India, and other countries. The US Department of Agriculture (USDA), Agricultural Research Service, National Clonal Germplasm Repository (NCGR) maintains a mint genebank in Corvallis, Oregon. This facility preserves and distributes about 450 clones representing 34 taxa, hybrid species, advanced breeder selections, and F1 hybrids. Mint crop wild relatives are included in this unique resource. The majority of mint accessions and hybrids in this collection were initially donated in the 1970s by the A.M. Todd Company, located in Kalamazoo, Michigan. Other representatives of diverse mint taxa and crop wild relatives have since been obtained from collaborators in Australia, New Zealand, Europe, and Vietnam. These mints have been evaluated for cytology, oil components, verticillium wilt resistance, and key morphological characters. Pressed voucher specimens have been prepared for morphological identity verification. An initial set of microsatellite markers has been developed to determine clonal identity and assess genetic diversity. Plant breeders at private and public institutions are using molecular analysis to determine identity and diversity of the USDA mint collection. Evaluation and characterization includes essential oil content, disease resistance, male sterility, and other traits for potential breeding use. These accessions can be a source for parental genes for enhancement efforts to produce hybrids, or for breeding new cultivars for agricultural production. Propagules of Mentha are available for distribution to international researchers as stem cuttings, rhizome cuttings, or seed, which can be requested through the GRIN-Global database of the US National Plant Germplasm System, subject to international treaty and quarantine regulations

Systemic perturbations of the kynurenine pathway precede progression to dementia independently of amyloid-β

Increasing evidence suggests that kynurenine pathway (KP) dyshomeostasis may promote disease progression in dementia. Studies in Alzheimer\u27s disease (AD) patients confirm KP dyshomeostasis in plasma and cerebrospinal fluid (CSF) which correlates with amyloid-β and tau pathology. Herein, we performed the first comprehensive study assessing baseline levels of KP metabolites in participants enrolling in the Australian Imaging Biomarkers Flagship Study of Aging. Our purpose was to test the hypothesis that changes in KP metabolites may be biomarkers of dementia processes that are largely silent. We used a cross-sectional analytical approach to assess non-progressors (N = 73); cognitively normal (CN) or mild cognitive impairment (MCI) participants at baseline and throughout the study, and progressors (N = 166); CN or MCI at baseline but progressing to either MCI or AD during the study. Significant KP changes in progressors included increased 3-hydroxyanthranilic acid (3-HAA) and 3-hydroxyanthranilic acid/anthranilic acid (3-HAA/AA) ratio, the latter having the largest effect on the odds of an individual being a progressor (OR 35.3; 95% CI between 14 and 104). 3-HAA levels were hence surprisingly bi-phasic, high in progressors but low in non-progressors or participants who had already transitioned to MCI or dementia. This is a new, unexpected and interesting result, as most studies of the KP in neurodegenerative disease show reduced 3-HAA/AA ratio after diagnosis. The neuroprotective metabolite picolinic acid was also significantly decreased while the neurotoxic metabolite 3-hydroxykynurenine increased in progressors. These results were significant even after adjustment for confounders. Considering the magnitude of the OR to predict change in cognition, it is important that these findings are replicated in other populations. Independent validation of our findings may confirm the utility of 3-HAA/AA ratio to predict change in cognition leading to dementia in clinical settings

Patient and public involvement in pragmatic trials : online survey of corresponding authors of published trials

Acknowledgements The authors acknowledge Dr. Paxton Montgomery Moon, Alison Howie, Hayden Nix and Dr. Merrick Zwarenstein for their contributions to the data extraction. They also thank Drs. Bruno Giraudeau and Agnes Caille (University of Tours), Dr. Laura Hanson (University of North Carolina School of Medicine) and Dr. Jill Harrison (Brown University) for assistance with pilot testing of the survey questionnaire. Funding: This work was supported by the Canadian Institutes of Health Research through the Project Grant competition (competitive, peer-reviewed), award number PJT-153045, and the National Institute of Aging ( NIA) of the National Institutes of Health under Award Number U54AG063546, which funds NIA Imbedded Pragmatic Alzheimer’s Disease and Related Dementias Clinical Trials Collaboratory ( NIA IMPACT Collaboratory). The funders had no role in the study design; in the collection, analysis and interpretation of data; in the writing of the report; and in the decision to submit the article for publication.Peer reviewedPublisher PD

Myocardial Perfusion Reserve but not fibrosis predicts outcomes in initially asymptomatic patients with moderate to severe aortic stenosis : the PRognostic Importance of MIcrovascular Dysfunction in AS study- PRIMID AS

Peer reviewedPublisher PD

A new class of Cu/ZnO catalysts derived from zincian georgeite precursors prepared by co-precipitation

Zincian georgeite, an amorphous copper-zinc hydroxycarbonate, has been prepared by co-precipitation using acetate salts and ammonium carbonate. Incorporation of zinc into the georgeite phase and mild ageing conditions inhibits crystallisation into zincian malachite or aurichalcite. This zincian georgeite precursor was used to prepare a Cu/ZnO catalyst, which exhibits a superior performance to a zincian malachite derived catalyst for methanol synthesis and the low temperature water-gas shift (LTS) reaction. Furthermore, the enhanced LTS activity and stability in comparison to that of a commercial Cu/ZnO/Al2O3 catalyst, indicates that the addition of alumina as a stabiliser may not be required for the zincian georgeite derived Cu/ZnO catalyst. The enhanced performance is partly attributed to the exclusion of alkali metals from the synthesis procedure, which are known to act as catalyst poisons. The effect of residual sodium on the microstructural properties of the catalyst precursor was investigated further with preparations using sodium carbonate

Preparation of a highly active ternary Cu-Zn-Al oxide methanol synthesis catalyst by supercritical CO2 anti-solvent precipitation

Methanol synthesis using Cu/ZnO/Al2O3 catalysts is a well-established industrial process. Catalyst development is always an important factor and this has resulted in the current fully optimised commercial catalyst that is prepared by co-precipitation via hydroxycarbonate precursors. Recently, the synthesis of a CuZn hydroxycarbonate precursor, analogous to the rare mineral georgeite, was reported to produce a high activity methanol synthesis catalyst. Here we report the addition of Al 3+ , the third component found in industrial catalysts, to the zincian georgeite-derived catalyst prepared using a supercritical CO 2 anti-solvent precipitation methodology. The co-addition of an AlO(OH) sol to the Cu/Zn precursor solution was found to not disrupt the formation of the CuZn georgeite phase, while providing efficient mixing of the Al 3+ within the material. The catalyst derived from the CuZn georgeite precursor phase doped with Al 3+ showed a high level of methanol synthesis productivity, which was comparable to that of the binary CuZn georgeite derived catalyst. This material also exhibited enhanced stability during an accelerated ageing test compared to the non-Al doped zincian georgeite material. Performance was benchmarked against an industrially relevant Cu/ZnO/Al2O3 standard catalyst