Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding

The gene content of plants varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will modify the genomic landscape, though the nature of these modifications is only understood for specific genes or on a more general level (e.g., by a loss of genetic diversity). Here we have assembled and analyzed a soybean (Glycine spp.) pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genomewide changes in gene and allele frequency during domestication and breeding. We identified 3,765 genes that are absent from the Lee reference genome assembly and assessed the presence/absence of all genes across this population. In addition to a loss of genetic diversity, we found a significant reduction in the average number of protein-coding genes per individual during domestication and subsequent breeding, though with some genes and allelic variants increasing in frequency associated with selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in this important oilseed crop

Simple model of adsorption on external surface of carbon nanotubes: a new analytical approach basing on molecular simulation data

Nitrogen adsorption on carbon nanotubes is wide- ly studied because nitrogen adsorption isotherm measurement is a standard method applied for porosity characterization. A further reason is that carbon nanotubes are potential adsorbents for separation of nitrogen from oxygen in air. The study presented here describes the results of GCMC simulations of nitrogen (three site model) adsorption on single and multi walled closed nanotubes. The results obtained are described by a new adsorption isotherm model proposed in this study. The model can be treated as the tube analogue of the GAB isotherm taking into account the lateral adsorbate-adsorbate interactions. We show that the model describes the simulated data satisfactorily. Next this new approach is applied for a description of experimental data measured on different commercially available (and characterized using HRTEM) carbon nanotubes. We show that generally a quite good fit is observed and therefore it is suggested that the observed mechanism of adsorption in the studied materials is mainly determined by adsorption on tubes separated at large distances, so the tubes behave almost independently

A Model for the Development of the Rhizobial and Arbuscular Mycorrhizal Symbioses in Legumes and Its Use to Understand the Roles of Ethylene in the Establishment of these two Symbioses

We propose a model depicting the development of nodulation and arbuscular mycorrhizae. Both processes are dissected into many steps, using Pisum sativum L. nodulation mutants as a guideline. For nodulation, we distinguish two main developmental programs, one epidermal and one cortical. Whereas Nod factors alone affect the cortical program, bacteria are required to trigger the epidermal events. We propose that the two programs of the rhizobial symbiosis evolved separately and that, over time, they came to function together. The distinction between these two programs does not exist for arbuscular mycorrhizae development despite events occurring in both root tissues. Mutations that affect both symbioses are restricted to the epidermal program. We propose here sites of action and potential roles for ethylene during the formation of the two symbioses with a specific hypothesis for nodule organogenesis. Assuming the epidermis does not make ethylene, the microsymbionts probably first encounter a regulatory level of ethylene at the epidermis–outermost cortical cell layer interface. Depending on the hormone concentrations there, infection will either progress or be blocked. In the former case, ethylene affects the cortex cytoskeleton, allowing reorganization that facilitates infection; in the latter case, ethylene acts on several enzymes that interfere with infection thread growth, causing it to abort. Throughout this review, the difficulty of generalizing the roles of ethylene is emphasized and numerous examples are given to demonstrate the diversity that exists in plants

The potential benefits of on-farm mitigation scenarios for reducing multiple pollutant loadings in prioritised agri-environment areas across England

The authors gratefully acknowledge the funding provided by the Department for Environment, Food and Rural Affairs (Defra) via project LM0304

Perustilaselvitys direktiivilaitosten ympäristölupaharkinnassa ja pilaantuneen ympäristön puhdistamista koskevassa sääntelyssä

Tutkielman aiheena on teollisuuspäästödirektiiviin perustuva perustilaselvitys, joka on Suomessa pantu täytäntöön ympäristönsuojelulain kokonaisuudistuksen yhteydessä. Perustilaselvityksellä tarkoitetaan ympäristön tilainventaariota, jolla selvitetään direktiivilaitosten toimintaan liittyvien merkityksellisten vaarallisten aineiden maaperälle ja pohjavedelle aiheuttama muutos. Euroopan komission mukaan perustilaselvitys on työkalu, jonka avulla pilaantuneen ympäristön ennallistamisen tavoitetaso voidaan teollisen toiminnan päätyttyä määrittää. Tutkielman tavoitteena on selvittää perustilaselvityssääntelyn aiheuttama oikeustilan muutos sekä arvioida selvityksen soveltuvuutta suomalaiseen ympäristölupaharkintaan ja pilaantuneita alueita koskevaan sääntelyyn. Tutkielmassa on lyhyesti esitelty muissa jäsenvaltioissa valittuja toimeenpanoratkaisuja ja arvioitu Suomessa valitun implementointiratkaisun onnistumista suhteessa sääntelyn tavoitteisiin. Aineistona on teollisuuspäästödirektiivin ja ympäristönsuojelulakia koskevan hallituksen esityksen lisäksi käytetty perustilaselvitystä koskevia komission ja ympäristöministeriön ohjeita ja soveltuvissa määrin oikeuskirjallisuutta, joka pääsääntöisesti on peräisin ajalta ennen ympäristönsuojelulain voimaantuloa 1.9.2014. Kirjallisuuden on katsottu olevan käyttökelpoista, koska pilaantuneen ympäristön puhdistamista koskeva sääntely on ympäristönsuojelulain kokonaisuudistuksessa säilytetty pääosin ennallaan. Tutkielma on luonteeltaan lainopillinen, ongelmakeskeinen esitys, joka sijoittuu tutkimuskysymystensä, metodologiansa ja tavoitteidensa johdosta ympäristöoikeuden alalle. Tutkielman perusteella voidaan todeta, että perustilaselvityssääntely ei täysin sovellu suomalaisen ympäristön pilaantumista koskevaan sääntely-ympäristöön. Perustilaselvityksen laatimista koskeva sääntely ja ohjeistus on toteutettu teollisuuspäästödirektiivin tavoitteiden mukaisesti, mutta sääntely on tulkinnanvaraista. Perustilan palauttamista koskeva sääntely on perustilasääntelyn ongelmakohta eikä toiminnan lopettamisvaiheeseen liittyvästä menettelystä sen perusteella synny selkeää kuvaa. Perustilaselvityksen laatiminen voi olla vaikea tehtävä, koska toiminnanharjoittajilta edellytetään vaarallisten aineiden maaperälle ja pohjavedelle mahdollisesti aiheuttaman pilaantumisriskin syvällistä arviointia. Selvityksen mahdolliset hyödyt liittyvät sen ympäristönsuojelullisiin vaikutuksiin. Toiminnanharjoittajien selvilläolovelvollisuus korostuu ja perustilaselvitysten avulla saadaan ajantasaista tietoa maaperän ja pohjaveden tilasta. Tietojen avulla ennaltaehkäisymenetelmiä ja parempia tekniikoita voidaan edelleen kehittää. Maaperän ja pohjaveden laatuinventaariona perustilaselvityksen laatiminen tukee alueiden ennallistamista niiden yksilölliset tarpeet huomioivalla tavalla. Selvitys tarjoaa lupaharkinnassa käytettäväksi aikaisempaa kattavamman ympäristön tilaa koskevan aineiston

A precise measurement of the magnetic field in the corona of the black hole binary V404 Cygni

Observations of binary stars containing an accreting black hole or neutron star often show x-ray emission extending to high energies (>10 kilo­–electron volts), which is ascribed to an accretion disk corona of energetic particles akin to those seen in the solar corona. Despite their ubiquity, the physical conditions in accretion disk coronae remain poorly constrained. Using simultaneous infrared, optical, x-ray, and radio observations of the Galactic black hole system V404 Cygni, showing a rapid synchrotron cooling event in its 2015 outburst, we present a precise 461 ± 12 gauss magnetic field measurement in the corona. This measurement is substantially lower than previous estimates for such systems, providing constraints on physical models of accretion physics in black hole and neutron star binary systems. This article has a correction. Please see: http://science.sciencemag.org/content/360/6386/eaat927

AD51B in Familial Breast Cancer

Common variation on 14q24.1, close to RAD51B, has been associated with breast cancer: rs999737 and rs2588809 with the risk of female breast cancer and rs1314913 with the risk of male breast cancer. The aim of this study was to investigate the role of RAD51B variants in breast cancer predisposition, particularly in the context of familial breast cancer in Finland. We sequenced the coding region of RAD51B in 168 Finnish breast cancer patients from the Helsinki region for identification of possible recurrent founder mutations. In addition, we studied the known rs999737, rs2588809, and rs1314913 SNPs and RAD51B haplotypes in 44,791 breast cancer cases and 43,583 controls from 40 studies participating in the Breast Cancer Association Consortium (BCAC) that were genotyped on a custom chip (iCOGS). We identified one putatively pathogenic missense mutation c.541C>T among the Finnish cancer patients and subsequently genotyped the mutation in additional breast cancer cases (n = 5259) and population controls (n = 3586) from Finland and Belarus. No significant association with breast cancer risk was seen in the meta-analysis of the Finnish datasets or in the large BCAC dataset. The association with previously identified risk variants rs999737, rs2588809, and rs1314913 was replicated among all breast cancer cases and also among familial cases in the BCAC dataset. The most significant association was observed for the haplotype carrying the risk-alleles of all the three SNPs both among all cases (odds ratio (OR): 1.15, 95% confidence interval (CI): 1.11–1.19, P = 8.88 x 10−16) and among familial cases (OR: 1.24, 95% CI: 1.16–1.32, P = 6.19 x 10−11), compared to the haplotype with the respective protective alleles. Our results suggest that loss-of-function mutations in RAD51B are rare, but common variation at the RAD51B region is significantly associated with familial breast cancer risk

A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers

Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P < 10−8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD, SP11 and EIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease