Differential effects of dietary supplements on metabolomic profile of smokers versus non-smokers.

BackgroundCigarette smoking is well-known to associate with accelerated skin aging as well as cardiovascular disease and lung cancer, in large part due to oxidative stress. Because metabolites are downstream of genetic variation, as well as transcriptional changes and post-translational modifications of proteins, they are the most proximal reporters of disease states or reversal of disease states.MethodsIn this study, we explore the potential effects of commonly available oral supplements (containing antioxidants, vitamins and omega-3 fatty acids) on the metabolomes of smokers (n = 11) compared to non-smokers (n = 17). At baseline and after 12 weeks of supplementation, metabolomic analysis was performed on serum by liquid and gas chromatography with mass spectroscopy (LC-MS and GC-MS). Furthermore, clinical parameters of skin aging, including cutometry as assessed by three dermatologist raters blinded to subjects' age and smoking status, were measured.ResultsLong-chain fatty acids, including palmitate and oleate, decreased in smokers by 0.76-fold (P = 0.0045) and 0.72-fold (P = 0.0112), respectively. These changes were not observed in non-smokers. Furthermore, age and smoking status showed increased glow (P = 0.004) and a decrease in fine wrinkling (P = 0.038). Cutometry showed an increase in skin elasticity in smokers (P = 0.049) but not in non-smokers. Complexion analysis software (VISIA) revealed decreases in the number of ultraviolet spots (P = 0.031), and cutometry showed increased elasticity (P = 0.05) in smokers but not non-smokers.ConclusionsAdditional future work may shed light on the specific mechanisms by which long-chain fatty acids can lead to increased glow, improved elasticity measures and decreased fine wrinkling in smokers' skin. Our study provides a novel, medicine-focused application of available metabolomic technology to identify changes in sera of human subjects with oxidative stress, and suggests that oral supplementation (in particular, commonly available antioxidants, vitamins and omega-3 fatty acids) affects these individuals in a way that is unique (compared to non-smokers) on a broad level

Archeological Testing and Data Recovery at 41ZV202, Zavala County, Texas

At the request of the Texas Department of Transportation, Environmental Affairs Division (TxDOT-ENV), the Center for Archaeological Research (CAR) of The University of Texas at San Antonio (UTSA) conducted archeological significance testing at 41ZV202, a prehistoric site located in northwestern Zavala County, in March of 2003. The work, conducted under Texas Antiquities Permit No. 3071 issued to Dr. Steven A. Tomka, was done in anticipation of the potential widening by TxDOT of FM 481. While materials dating to the Archaic were also present, the testing demonstrated the presence of significant Late Prehistoric (Austin Interval) deposits with good integrity within a portion of the TxDOT right-of-way (ROW). As TxDOT construction could not avoid these deposits, and as both the Texas Historical Commission (THC) and TxDOT concurred with CAR’s recommendations that the deposits were eligible for listing on the National Register of Historic Places (NRHP) under criterion d of 36CFR 60.4, data recovery investigations were initiated. CAR began that work in July and August of 2003. The testing permit was amended to include the data recovery efforts. Dr. Russell Greaves served as project archeologist for both the testing and data recovery effort at 41ZV202. The testing and data recovery work consisted of the excavation of a 53-m-long Gradall trench, exposing and profiling a 75-m-long road cut, and the hand excavation of 52 1 x 1 meter units that removed approximately 34.6 m3 of soil. Testing identified two large, dark stained areas designated Features 4 and 5, an associated hearth (Feature 7), and a small cluster of FCR (Feature 6). Just over 1,000 chipped stone items were recovered, including several Scallorn points, one reworked dart point, several bifaces, and two flake tools. Eleven AMS radiocarbon dates were submitted from deposits, with eight clustering around 1000 BP. Data recovery efforts defined FCR features 8 through 13. In addition, 24 arrow points, several dart points, a variety of unifacial and bifacial tools, a small number of cores, roughly 6,000 pieces of debitage, and a variety of burned sandstone, were recovered. We also collected small quantities of bone and mussel shell along with about 14,350 gastropod shells, and a variety of soil samples. Finally, all calcium carbonate nodules were retained from the screens. Following the completion of data recovery efforts, the CAR was directed by TxDOT to develop a research design for the analysis of the material from 41ZV202. TxDOT and THC accepted that research design in November of 2004, at which time the CAR began analysis and report production. Unfortunately, by 2005 project archeologist Russell Greaves had left the CAR. At that point, CAR assistant director Dr. Raymond Mauldin took over the project. The analysis of the 41ZV202 Late Prehistoric data outlined in this report is conducted in the context of a large-scale, theoretically driven model of adaptation for hunters and gatherers loosely based on aspects of Optimal Foraging Theory. In addition to 41ZV202, the approach relies on comparative data sets from Late Archaic and other Late Prehistoric sites from South and South-Central Texas to investigate shifts in subsistence, technology, and mobility across this broad region. At this time, discard decisions have not been made. However, all artifacts and associated samples collected and retained during this project, along with all project-associated documentation, are to be permanently curated at the CAR according to Texas Historical Commission guidelines

Archeological Testing and Data Recovery at 41ZV202, Zavala County, Texas

At the request of the Texas Department of Transportation, Environmental Affairs Division (TxDOT-ENV), the Center for Archaeological Research (CAR) of The University of Texas at San Antonio (UTSA) conducted archeological significance testing at 41ZV202, a prehistoric site located in northwestern Zavala County, in March of 2003. The work, conducted under Texas Antiquities Permit No. 3071 issued to Dr. Steven A. Tomka, was done in anticipation of the potential widening by TxDOT of FM 481. While materials dating to the Archaic were also present, the testing demonstrated the presence of significant Late Prehistoric (Austin Interval) deposits with good integrity within a portion of the TxDOT right-of-way (ROW). As TxDOT construction could not avoid these deposits, and as both the Texas Historical Commission (THC) and TxDOT concurred with CAR’s recommendations that the deposits were eligible for listing on the National Register of Historic Places (NRHP) under criterion d of 36CFR 60.4, data recovery investigations were initiated. CAR began that work in July and August of 2003. The testing permit was amended to include the data recovery efforts. Dr. Russell Greaves served as project archeologist for both the testing and data recovery effort at 41ZV202. The testing and data recovery work consisted of the excavation of a 53-m-long Gradall trench, exposing and profiling a 75-m-long road cut, and the hand excavation of 52 1 x 1 meter units that removed approximately 34.6 m3 of soil. Testing identified two large, dark stained areas designated Features 4 and 5, an associated hearth (Feature 7), and a small cluster of FCR (Feature 6). Just over 1,000 chipped stone items were recovered, including several Scallorn points, one reworked dart point, several bifaces, and two flake tools. Eleven AMS radiocarbon dates were submitted from deposits, with eight clustering around 1000 BP. Data recovery efforts defined FCR features 8 through 13. In addition, 24 arrow points, several dart points, a variety of unifacial and bifacial tools, a small number of cores, roughly 6,000 pieces of debitage, and a variety of burned sandstone, were recovered. We also collected small quantities of bone and mussel shell along with about 14,350 gastropod shells, and a variety of soil samples. Finally, all calcium carbonate nodules were retained from the screens. Following the completion of data recovery efforts, the CAR was directed by TxDOT to develop a research design for the analysis of the material from 41ZV202. TxDOT and THC accepted that research design in November of 2004, at which time the CAR began analysis and report production. Unfortunately, by 2005 project archeologist Russell Greaves had left the CAR. At that point, CAR assistant director Dr. Raymond Mauldin took over the project. The analysis of the 41ZV202 Late Prehistoric data outlined in this report is conducted in the context of a large-scale, theoretically driven model of adaptation for hunters and gatherers loosely based on aspects of Optimal Foraging Theory. In addition to 41ZV202, the approach relies on comparative data sets from Late Archaic and other Late Prehistoric sites from South and South-Central Texas to investigate shifts in subsistence, technology, and mobility across this broad region. At this time, discard decisions have not been made. However, all artifacts and associated samples collected and retained during this project, along with all project-associated documentation, are to be permanently curated at the CAR according to Texas Historical Commission guidelines

Genome Resources for Climate‐Resilient Cowpea, an Essential Crop for Food Security

Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought‐prone climates, and a primary source of protein in sub‐Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K‐499‐35 include a whole‐genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi‐parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited‐input small‐holder farming and climate stress

Maternal and neonatal data collection systems in low- and middle-income countries: Scoping review protocol

Background: Pregnant women and neonates represent one of the most vulnerable groups, especially in low- and middle-income countries (LMICs). A recent analysis reported that most vaccine pharmacovigilance systems in LMICs consist of spontaneous (passive) adverse event reporting. Thus, LMICs need effective active surveillance approaches, such as pregnancy registries. We intend to identify currently active maternal and neonatal data collection systems in LMICs, with the potential to inform active safety electronic surveillance for novel vaccines using standardized definitions. Methods: A scoping review will be conducted based on established methodology. Multiple databases of indexed and grey literature will be searched with a specific focus on existing electronic and paper-electronic systems in LMICs that collect continuous, prospective, and individual-level data from antenatal care, delivery, neonatal care (up to 28 days), and postpartum (up to 42 days) at the facility and community level, at the national and district level, and at large hospitals. Also, experts will be contacted to identify unpublished information on relevant data collection systems. General and specific descriptions of Health Information Systems (HIS) extracted from the different sources will be combined and duplicated HIS will be removed, producing a list of unique statements. We will present a final list of Maternal, Newborn, and Child Health systems considered flexible enough to be updated with necessary improvements to detect, assess and respond to safety concerns during the introduction of vaccines and other maternal health interventions. Selected experts will participate in an in-person consultation meeting to select up to three systems to be further explored in situ. Results and knowledge gaps will be synthesized after expert consultation.Fil: Berrueta, Mabel. Instituto de Efectividad Clínica y Sanitaria; ArgentinaFil: Bardach, Ariel Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Epidemiología y Salud Pública. Instituto de Efectividad Clínica y Sanitaria. Centro de Investigaciones en Epidemiología y Salud Pública; ArgentinaFil: Ciapponi, Agustín. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Epidemiología y Salud Pública. Instituto de Efectividad Clínica y Sanitaria. Centro de Investigaciones en Epidemiología y Salud Pública; ArgentinaFil: Xiong, Xu. University of Tulane; Estados UnidosFil: Stergachis, Andy. University of Washington; Estados UnidosFil: Zaraa, Sabra. University of Washington; Estados UnidosFil: Buekens, Pierre. University of Tulane; Estados UnidosFil: Absalon, Judith. No especifíca;Fil: Anderson, Steve. No especifíca;Fil: Althabe, Fernando. Instituto de Efectividad Clínica y Sanitaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Madhi, Shabir A.. No especifíca;Fil: McClure, Elizabeth. No especifíca;Fil: Munoz, Flor M.. No especifíca;Fil: Mwamwitwa, Kissa W.. No especifíca;Fil: Nakimuli, Annettee. No especifíca;Fil: Clark Nelson, Jennifer. No especifíca;Fil: Noguchi, Lisa. No especifíca;Fil: Panagiotakopoulos, Lakshmi. No especifíca;Fil: Sevene, Esperanca. No especifíca;Fil: Zuber, Patrick. No especifíca;Fil: Belizan, Maria. No especifíca;Fil: Bergel, Eduardo. No especifíca;Fil: Rodriguez Cairoli, Federico. No especifíca;Fil: Castellanos, Fabricio. No especifíca;Fil: Ciganda, Alvaro. No especifíca;Fil: Comande, Daniel. No especifíca;Fil: Pingray, Veronica. No especifíca

A chemical survey of exoplanets with ARIEL

Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. `Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).Peer reviewe

The CANDELS/SHARDS multiwavelength catalog in GOODS-N : photometry, photometric redshifts, stellar masses, emission-line fluxes, and star formation rates

We present a WFC3 F160W (H-band) selected catalog in the CANDELS/GOODS-N field containing photometry from the ultraviolet (UV) to the far-infrared (IR), photometric redshifts, and stellar parameters derived from the analysis of the multiwavelength data. The catalog contains 35,445 sources over the 171 arcmin(2) of the CANDELS F160W mosaic. The 5 sigma detection limits (within an aperture of radius 0 ''.17) of the mosaic range between H = 27.8, 28.2, and 28.7 in the wide, intermediate, and deep regions, which span approximately 50%, 15%, and 35% of the total area. The multiwavelength photometry includes broadband data from the UV (U band from KPNO and LBC), optical (HST/ACS F435W, F606W, F775W, F814W, and F850LP), near-to-mid IR (HST/WFC3 F105W, F125W, F140W, and F160W; Subaru/MOIRCS Ks; CFHT/Megacam K; and Spitzer/IRAC 3.6, 4.5, 5.8, and 8.0 mu m), and far-IR (Spitzer/MIPS 24 mu m, HERSCHEL/PACS 100 and 160 mu m, SPIRE 250, 350 and 500 mu m) observations. In addition, the catalog also includes optical medium-band data (R similar to 50) in 25 consecutive bands, lambda = 500-950 nm, from the SHARDS survey and WFC3 IR spectroscopic observations with the G102 and G141 grisms (R similar to 210 and 130). The use of higher spectral resolution data to estimate photometric redshifts provides very high, and nearly uniform, precision from z = 0-2.5. The comparison to 1485 good-quality spectroscopic redshifts up to z similar to 3 yields Delta z/(1 + z(spec)) = 0.0032 and an outlier fraction of eta = 4.3%. In addition to the multiband photometry, we release value-added catalogs with emission-line fluxes, stellar masses, dust attenuations, UV- and IR-based star formation rates, and rest-frame colors

Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage

The International Stem Cell Initiative analyzed 125 human embryonic stem (ES) cell lines and 11 induced pluripotent stem (iPS) cell lines, from 38 laboratories worldwide, for genetic changes occurring during culture. Most lines were analyzed at an early and late passage. Single-nucleotide polymorphism (SNP) analysis revealed that they included representatives of most major ethnic groups. Most lines remained karyotypically normal, but there was a progressive tendency to acquire changes on prolonged culture, commonly affecting chromosomes 1, 12, 17 and 20. DNA methylation patterns changed haphazardly with no link to time in culture. Structural variants, determined from the SNP arrays, also appeared sporadically. No common variants related to culture were observed on chromosomes 1, 12 and 17, but a minimal amplicon in chromosome 20q11.21, including three genes expressed in human ES cells, ID1, BCL2L1 and HM13, occurred in >20% of the lines. Of these genes, BCL2L1 is a strong candidate for driving culture adaptation of ES cells

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine