Intricate environment-modulated genetic networks control isoflavone accumulation in soybean seeds

<p>Abstract</p> <p>Background</p> <p>Soybean (<it>Glycine max </it>[L] Merr.) seed isoflavones have long been considered a desirable trait to target in selection programs for their contribution to human health and plant defense systems. However, attempts to modify seed isoflavone contents have not always produced the expected results because their genetic basis is polygenic and complex. Undoubtedly, the extreme variability that seed isoflavones display over environments has obscured our understanding of the genetics involved.</p> <p>Results</p> <p>In this study, a mapping population of RILs with three replicates was analyzed in four different environments (two locations over two years). We found a total of thirty-five main-effect genomic regions and many epistatic interactions controlling genistein, daidzein, glycitein and total isoflavone accumulation in seeds. The use of distinct environments permitted detection of a great number of environment-modulated and minor-effect QTL. Our findings suggest that isoflavone seed concentration is controlled by a complex network of multiple minor-effect loci interconnected by a dense epistatic map of interactions. The magnitude and significance of the effects of many of the nodes and connections in the network varied depending on the environmental conditions. In an attempt to unravel the genetic architecture underlying the traits studied, we searched on a genome-wide scale for genomic regions homologous to the most important identified isoflavone biosynthetic genes. We identified putative candidate genes for several of the main-effect and epistatic QTL and for QTL reported by other groups.</p> <p>Conclusions</p> <p>To better understand the underlying genetics of isoflavone accumulation, we performed a large scale analysis to identify genomic regions associated with isoflavone concentrations. We not only identified a number of such regions, but also found that they can interact with one another and with the environment to form a complex adaptable network controlling seed isoflavone levels. We also found putative candidate genes in several regions and overall we advanced the knowledge of the genetics underlying isoflavone synthesis.</p

Maternal Fish Consumption, Hair Mercury, and Infant Cognition in a U.S. Cohort

Fish and other seafood may contain organic mercury but also beneficial nutrients such as n-3 polyunsaturated fatty acids. We endeavored to study whether maternal fish consumption during pregnancy harms or benefits fetal brain development. We examined associations of maternal fish intake during pregnancy and maternal hair mercury at delivery with infant cognition among 135 mother–infant pairs in Project Viva, a prospective U.S. pregnancy and child cohort study. We assessed infant cognition by the percent novelty preference on visual recognition memory (VRM) testing at 6 months of age. Mothers consumed an average of 1.2 fish servings per week during the second trimester. Mean maternal hair mercury was 0.55 ppm, with 10% of samples > 1.2 ppm. Mean VRM score was 59.8 (range, 10.9–92.5). After adjusting for participant characteristics using linear regression, higher fish intake was associated with higher infant cognition. This association strengthened after adjustment for hair mercury level: For each additional weekly fish serving, offspring VRM score was 4.0 points higher [95% confidence interval (CI), 1.3 to 6.7]. However, an increase of 1 ppm in mercury was associated with a decrement in VRM score of 7.5 (95% CI, –13.7 to –1.2) points. VRM scores were highest among infants of women who consumed > 2 weekly fish servings but had mercury levels ≤1.2 ppm. Higher fish consumption in pregnancy was associated with better infant cognition, but higher mercury levels were associated with lower cognition. Women should continue to eat fish during pregnancy but choose varieties with lower mercury contamination

Exploring the Developmental Overnutrition Hypothesis Using Parental–Offspring Associations and FTO as an Instrumental Variable

Using parental-offspring associations and theFTO gene as an instrumental variable for maternal adiposity, Debbie Lawlor and colleagues found that greater maternal BMI during offspring development does not appear to have a marked effect on offspring fat mass at age 9-11

SIRF: Synergistic Image Reconstruction Framework

The combination of positron emission tomography (PET) with magnetic resonance (MR) imaging opens the way to more accurate diagnosis and improved patient management. At present, the data acquired by PET-MR scanners are essentially processed separately, but the opportunity to improve accuracy of the tomographic reconstruction via synergy of the two imaging techniques is an active area of research. In this paper, we present Release 2.1.0 of the CCP-PETMR Synergistic Image Reconstruction Framework (SIRF) software suite, providing an open-source software platform for efficient implementation and validation of novel reconstruction algorithms. SIRF provides user-friendly Python and MATLAB interfaces built on top of C++ libraries. SIRF uses advanced PET and MR reconstruction software packages and tools. Currently, for PET this is Software for Tomographic Image Reconstruction (STIR); for MR, Gadgetron and ISMRMRD; and for image registration tools, NiftyReg. The software aims to be capable of reconstructing images from acquired scanner data, whilst being simple enough to be used for educational purposes. The most recent version of the software can be downloaded from http://www.ccppetmr.ac.uk/downloads and https://github.com/CCPPETMR/. Program summary: Program Title: Synergistic Image Reconstruction Framework (SIRF) Program Files DOI: http://dx.doi.org/10.17632/s45f5jh55j.1 Licensing provisions: GPLv3 and Apache-2.0 Programming languages: C++, C, Python, MATLAB Nature of problem: In current practice, data acquired by PET-MR scanners are processed separately. Methods for improving the accuracy of the tomographic reconstruction using the synergy of the two imaging techniques are actively being investigated by the PET-MR research and development community, however, practical application is heavily reliant on software. Open-source software available to the PET-MR community – such as the PET package (STIR) (Thielemans et al., 2012) and the MR package Gadgetron (Hansen and Sørensen, 2013) – provide a basis for new synergistic PET-MR software. However, these two software packages are independent and have very different software architectures. They are mostly written in C++ but many researchers in the PET-MR community are more familiar with script-style languages, such as Python and MATLAB, which enable rapid prototyping of novel reconstruction algorithms. In the current situation it is difficult for researchers to exploit any synergy between PET and MR data. Furthermore, techniques from one field cannot easily be applied in the other. Solution method: In SIRF, the bulk of computation is performed by available advanced open-source reconstruction and registration software (currently STIR, Gadgetron and NiftyReg) that can use multithreading and GPUs. The SIRF C++ code provides a thin layer on top of these existing libraries. The SIRF layer has unified data-containers and access mechanisms. This C++ layer provides the basis for a simple and intuitive Python and MATLAB interface, enabling users to quickly develop and test their reconstruction algorithms using these scripting languages only. At the same time, advanced users proficient in C++ can directly utilise wider SIRF functionality via the SIRF C++ libraries that we provide

SIRF: Synergistic Image Reconstruction Framework

The combination of positron emission tomography (PET) with magnetic resonance (MR) imaging opens the way to more accurate diagnosis and improved patient management. At present, the data acquired by PET-MR scanners are essentially processed separately, but the opportunity to improve accuracy of the tomographic reconstruction via synergy of the two imaging techniques is an active area of research. In this paper, we present Release 2.1.0 of the CCP-PETMR Synergistic Image Reconstruction Framework (SIRF) software suite, providing an open-source software platform for efficient implementation and validation of novel reconstruction algorithms. SIRF provides user-friendly Python and MATLAB interfaces built on top of C++ libraries. SIRF uses advanced PET and MR reconstruction software packages and tools. Currently, for PET this is Software for Tomographic Image Reconstruction (STIR); for MR, Gadgetron and ISMRMRD; and for image registration tools, NiftyReg. The software aims to be capable of reconstructing images from acquired scanner data, whilst being simple enough to be used for educational purposes

Uncovering the MIR emission of quiescent galaxies with JWSTJWST

We present a study of the mid-IR (MIR) emission of quiescent galaxies (QGs) beyond the local universe. Using deep $JWST$ imaging in the SMACS-0723 cluster field we identify a mass limited ($M_{*} >10^{9}$M$_{\odot}$) sample of intermediate redshift QGs ($0.2<z<0.7$) and perform modeling of their rest-frame UV to MIR photometry. We find that QGs exhibit a range of MIR spectra that are composed of a stellar continuum and a dust component that is 1-2 orders of magnitude fainter to that of star-forming galaxies. The observed scatter in the MIR spectra, especially at $\lambda_{\rm rest} > 5 \mu$m, can be attributed to different dust continuum levels and/or the presence of Polycyclic Aromatic Hydrocarbons (PAHs) features. The latter would indicate enhanced 11.3- and 12.7 $\mu$m PAHs strengths with respect to those at 6.2- and 7.7$\mu$m, consistent with the observed spectra of local ellipticals and indicative of soft radiation fields. Finally, we augment the average UV-to-MIR spectrum of the population with cold dust and gas emission in the far-IR/mm and construct a panchromatic UV-to-radio SED that can serve as a template for the future exploration of the interstellar medium of $z>0$ QGs with ALMA and $JWST$.Comment: The panchromatic QG SED has been made publicly available at http://www.georgiosmagdis.com/softwar

A Search for Jet Handedness in Hadronic Z0Z^0 Decays

We have searched for signatures of polarization in hadronic jets from $Z^0 \to q \bar{q}$ decays using the ``jet handedness'' method. The polar angle asymmetry induced by the high SLC electron-beam polarization was used to separate quark jets from antiquark jets, expected to be left- and right-polarized, respectively. We find no evidence for jet handedness in our global sample or in a sample of light quark jets and we set upper limits at the 95% C.L. of 0.063 and 0.099 respectively on the magnitude of the analyzing power of the method proposed by Efremov {\it et al.}Comment: Revtex, 8 pages, 2 figure

Analytical approaches for the evaluation of data deficient simulated leachable compounds in ENDS products: a case study

Leachable investigations are routinely undertaken across a range of sectors (e.g., pharmaceuticals, medical devices, etc.) to determine whether chemicals from a container closure system transfer into a product under normal conditions of use. For Electronic Nicotine Delivery Systems (ENDS) the container closure system includes all materials in contact with the e-liquid that is aerosolized and subsequently inhaled by the user. Currently, there is no guidance for conducting leachable studies for ENDS products, however, there are relevant guidance documents for orally inhaled drug products that can be applied to an ENDS container closure system. We present a case study of the analytical investigation of two leachable compounds identified in simulated leachable studies using aged JUULpods filled with unflavored e-liquid (PG/VG/nicotine/benzoic acid). Both compounds had limited toxicological information and were considered data deficient. A qualitative analysis of the aerosol collected from aged commercial JUULpods (Virginia Tobacco and Menthol), using a similar analytical method (LC-MS/MS) used in the simulated leachable studies, showed no trace or detectable levels of either leachable compound. Therefore, this qualitative analysis did not provide semi-quantitative values for the data-deficient leachable compounds necessary to support toxicological risk assessment. Further, no commercial authentic standards or reasonable synthetic route were available due to the molecular size and structural complexity of the compounds. Instead, method limits were established using an alternative approach to standard ICH guidelines. The experimentally determined method limit of quantitation, using spiked samples of simulated leachable e-liquid, provided conservative semi-quantitative values for each data deficient leachable compound in the aerosol that enabled a transfer efficiency from e-liquid to aerosol to be estimated. The transfer efficiency of each leachable compound was experimentally determined to be less than 2% based on the limit of quantitation, which then could be used to define a relevant exposure limit for the toxicological risk assessment. This work details a novel analytical approach for determining the transfer efficiency of data deficient leachable compounds from ENDS container closure systems into the ENDS aerosol to support toxicological health risk assessments

Screening for Syphilis Infection in Nonpregnant Adults and Adolescents: US Preventive Services Task Force Recommendation Statement

Clinical Review & Education US Preventive Services Task Force | RECOMMENDATION STATEMENT Screening for Syphilis Infection in Nonpregnant Adults and Adolescents US Preventive Services Task Force Recommendation Statement US Preventive Services Task Force (USPSTF) Editorial page 2281 IMPORTANCE In 2014, 19 999 cases of syphilis were reported in the United States. Left untreated, syphilis can progress to late-stage disease in about 15% of persons who are infected. Late-stage syphilis can lead to development of inflammatory lesions throughout the body, which can lead to cardiovascular or organ dysfunction. Syphilis infection also increases the risk for acquiring or transmitting HIV infection. OBJECTIVE To update the 2004 US Preventive Services Task Force (USPSTF) recommendation on screening for syphilis infection in nonpregnant adults. Screening for syphilis in pregnant women was updated in a separate recommendation statement in 2009 (A recommendation). EVIDENCE REVIEW The USPSTF reviewed the evidence on screening for syphilis infection in asymptomatic, nonpregnant adults and adolescents, including patients coinfected with other sexually transmitted infections (such as HIV). Author Audio Interview at jama.com Related article page 2328 and JAMA Patient Page page 2367 CME Quiz at jamanetworkcme.com and CME Questions page 2342 Related articles at jamadermatology.com, jamaneurology.com, jamapediatrics.com FINDINGS The USPSTF found convincing evidence that screening for syphilis infection in asymptomatic, nonpregnant persons at increased risk for infection provides substantial benefit. Accurate screening tests are available to identify syphilis infection in populations at increased risk. Effective treatment with antibiotics can prevent progression to late-stage disease, with small associated harms, providing an overall substantial health benefit. CONCLUSIONS AND RECOMMENDATION The USPSTF recommends screening for syphilis infection in persons who are at increased risk for infection. (A recommendation) Authors/Group Information: The USPSTF members are listed at the end of the article. JAMA. 2016;315(21):2321-2327. doi:10.1001/jama.2016.5824 Corresponding Author: Kirsten Bibbins-Domingo, PhD, MD, MAS ([email protected]). T he US Preventive Services Task Force (USPSTF) makes recommendations about the effectiveness of specific preventive care services for patients without obvious related signs or symptoms. It bases its recommendations on the evidence of both the benefits and harms of the service and an assessment of the bal- ance. The USPSTF does not consider the costs of providing a ser- vice in this assessment. The USPSTF recognizes that clinical decisions involve more con- siderations than evidence alone. Clinicians should understand the evidence but individualize decision making to the specific patient or situation. Similarly, the USPSTF notes that policy and coverage decisions involve considerations in addition to the evidence of clini- cal benefits and harms. Summary of Recommendation and Evidence The USPSTF recommends screening for syphilis infection in per- sons who are at increased risk for infection. (A recommendation) (Figure 1) jama.com See the Clinical Considerations section later in this article for in- formation on risk factors for infection. Rationale Importance The number of cases of primary and secondary syphilis have been in- creasing since 2000. In 2014, 19 999 cases (6.3 cases per 100 000 persons)ofprimaryandsecondarysyphiliswerereportedintheUnited States. 1 Left untreated, syphilis can progress to late-stage disease in approximately 15% of persons who are infected. 2 Consequences of late-stage syphilis include development of inflammatory lesions throughout the body (eg, aortitis, gummatous lesions, and osteitis), which can lead to cardiovascular or organ dysfunction. Syphilis in- fection of the central nervous system (neurosyphilis) can occur at any stage of disease and can result in blindness, paresis, tabes dor- salis, and dementia. Syphilis infection also increases the risk for ac- quiring or transmitting HIV infection. The USPSTF addresses screening for syphilis in pregnant women in a separate recommendation statement. 3 (Reprinted) JAMA June 7, 2016 Volume 315, Number 21 Copyright 2016 American Medical Association. All rights reserved. Downloaded From: http://jamanetwork.com/ by a University of California - Los Angeles User on 09/21/201