Uncovering the dispersion history, adaptive evolution and selection of wheat in China

Wheat was introduced to China approximately 4500 years ago, where it adapted over a span of time to various environments in agro-ecological growing zones. We investigated 717 Chinese and 14 Iranian/Turkish geographically diverse, locally adapted wheat landraces with 27,933 DArTseq (for 717 landraces) and 312,831 Wheat660K (for a subset of 285 landraces) markers. This study highlights the adaptive evolutionary history of wheat cultivation in China. Environmental stresses and independent selection efforts have resulted in considerable genome-wide divergence at the population level in Chinese wheat landraces. In total, 148 regions of the wheat genome show signs of selection in at least one geographic area. Our data show adaptive events across geographic areas, from the xeric northwest to the mesic south, along and among homoeologous chromosomes, with fewer variations in the D genome than in the A and B genomes. Multiple variations in interdependent functional genes, such as regulatory and metabolic genes controlling germination and flowering time were characterized, showing clear allelic frequency changes corresponding to the dispersion of wheat in China. Population structure and selection data reveal that Chinese wheat spread from the northwestern Caspian Sea region to south China, adapting during its agricultural trajectory to increasingly mesic and warm climatic areas

Genome-Wide Association Study for Adult-Plant Resistance to Stripe Rust in Chinese Wheat Landraces (Triticum aestivum L.) From the Yellow and Huai River Valleys

Stripe rust (also known as yellow rust), caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is a common and serious fungal disease of wheat (Triticum aestivum L.) worldwide. To identify effective stripe rust resistance loci, a genome-wide association study was performed using 152 wheat landraces from the Yellow and Huai River Valleys in China based on Diversity Arrays Technology and simple sequence repeat markers. Phenotypic evaluation of the degree of resistance to stripe rust at the adult-plant stage under field conditions was carried out in five environments. In total, 19 accessions displayed stable, high degrees of resistance to stripe rust development when exposed to mixed races of Pst at the adult-plant stage in multi-environment field assessments. A marker–trait association analysis indicated that 51 loci were significantly associated with adult-plant resistance to stripe rust. These loci included 40 quantitative trait loci (QTL) regions for adult-plant resistance. Twenty identified resistance QTL were linked closely to previously reported yellow rust resistance genes or QTL regions, which were distributed across chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6B, 7A, 7B, and 7D. Six multi-trait QTL were detected on chromosomes 1B, 1D, 2B, 3A, 3B, and 7D. Twenty QTL were mapped to chromosomes 1D, 2A, 2D, 4B, 5B, 6A, 6B, 6D, 7A, 7B, and 7D, distant from previously identified yellow rust resistance genes. Consequently, these QTL are potentially novel loci for stripe rust resistance. Among the 20 potentially novel QTL, five (QDS.sicau-2A, QIT.sicau-4B, QDS.sicau-4B.2, QDS.sicau-6A.3, and QYr.sicau-7D) were associated with field responses at the adult-plant stage in at least two environments, and may have large effects on stripe rust resistance. The novel effective QTL for adult-plant resistance to stripe rust will improve understanding of the genetic mechanisms that control the spread of stripe rust, and will aid in the molecular marker-assisted selection-based breeding of wheat for stripe rust resistance

Developments in the QM/MM Approach to Modelling Polar Molecules and Applications to HIV-1 Protease

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Accounting for non-optimal interactions in molecular recognition: A study of ion-π complexes using a QM/MM model with a dipole-polarisable MM region

For a quantitative understanding of molecular structure, interaction and dynamics, accurate modelling of the energetics of both near-equilibrium and less optimal contacts is important. In this work, we explore the potential energy surfaces of representative ion-π complexes. We examine the performance of a semi-empirical QM/MM approach and the corresponding QM/MMpol model, where inducible point dipoles are additionally employed in the MM region. The predicted potential energy surfaces of cation-benzene complexes are improved by inclusion of explicit MM polarisation of the π-molecule. For cation-formamide complexes, inducible dipoles appreciably improve energetic estimates at geometries forming non-optimal interactions. Energetic component analysis suggests that the implicit MM polarisation of the fixed charge QM/MM model mirrors the behaviour of the QM/MMpol dipole model for the energetics of near-equilibrium conformations. However, for complexes at less optimal orientations, the QM/MM model exhibits higher errors than the QM/MMpol approach, being unable to capture orientation-dependent variations in polarisation energy. © the Owner Societies 2011

United polarizable multipole water model for molecular mechanics simulation

We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3-5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water

Factors Affecting the Detection of Hexavalent Chromium in Cr-Contaminated Soil

The alkali digestion pretreatment method in the United States Environmental Protection Agency (USEPA) Method 3060A could underestimate the content of Cr(VI) in Cr-contaminated soils, especially for soils mixed with chromite ore processing residue (COPR), which leads to a misjudgment of the Cr(VI) level in soils after remediation, causing secondary pollution to the environment. In this study, a new pretreatment method to analyze Cr(VI) concentration in contaminated soils was established. The impacts of soil quality, particle size, alkali digestion time and the rounds of alkali digestion on Cr(VI) detection in contaminated soils was explored and the alkali digestion method was optimized. Compared with USEPA Method 3060A, the alkaline digestion time was prolonged to 6 h and multiple alkali digestion was employed until the amount of Cr(VI) in the last extraction was less than 10% of the total amount of Cr(VI). Because Cr(VI) in COPR is usually embedded in the mineral phase structure, the hydration products were dissolved and Cr(VI) was released gradually during the alkaline digestion process. The amount of Cr(VI) detected showed high correlation coefficients with the percentage of F1 (mild acid-soluble fraction), F2 (reducible fraction) and F4 (residual fraction). The Cr(VI) contents detected by the new alkaline digestion method and USEPA Method 3060A showed significant differences for soil samples mixed with COPR due to their high percentage of residual fraction. This new pretreatment method could quantify more than 90% of Cr(VI) in Cr-contaminated soils, especially those mixed with COPR, which proved to be a promising method for Cr(VI) analysis in soils, before and after remediation

The relationship between the platelet to leukocyte ratio and mechanical thrombectomy outcomes in acute ischemic stroke patients.

BACKGROUND AND PURPOSE: The predictive effect of blood cell ratio on ischemic event has been widely confirmed. Whether PWR and PNR can assess the risk of endovascular treatment (EVT) is largely unclear. This study aimed to investigate the prognostic value of PNR and PWR in acute ischemic stroke patients treated with EVT. METHODS: Poor functional outcome was defined as Modified Rankin Scale (mRS) of 3-6 at 3 months, Symptomatic intracranial hemorrhage (sICH) was diagnosed based on CT scan and classified according to the criterial of Heidelberg Bleeding Classification. Binary logistical regression was used to analyze the relationship of PWR, PNR with functional outcome and symptomatic intracranial hemorrhage (sICH). RESULTS: Patients with good prognosis had higher PNR and PWR value (29 vs. 24, P=0.002) (22 vs. 19, P=0.009), a lower rate of sICH (2.9% vs. 24.9%, P<0.001). In model 1, the lower PNR significantly associated with poor functional outcome (OR, 0.48; 95% CI 0.26-0.88; P=0.018), and sICH (OR, 0.42; 95% CI 0.19-0.91; P=0.028). The lower PWR only significantly associated with poor prognosis (OR, 0.97; 95% CI 0.94-1.00; P=0.038), and had a trend relation with sICH (OR, 0.98; 95% CI 0.94-1.02; P=0.328). In model 2 lower PNR still significantly associated with poor functional outcome (OR, 0.53; 95% CI 0.29-0.99; P=0.047), but showed a trend for predicting sICH (OR, 0.56; 95% CI 0.25-1.25; P=0.158). CONCLUSION: Platelet to leukocyte ratio may be use to assess the risk of functional outcome and sICH in patients with acute anterior circulation occlusion stroke undergoing endovascular treatment in real world China

General Charge Transfer Dipole Model for AMOEBA-Like Force Fields

The development of highly accurate force fields is always an importance aspect in molecular modeling. In this work, we introduce a general damping-based charge transfer dipole (D-CTD) model to describe the charge transfer energy and the corresponding charge flow for H, C, N, O, P, S, F, Cl, and Br elements in common bio-organic systems. Then, two effective schemes to evaluate the charge flow from the corresponding induced dipole moment between the interacting molecules were also proposed and discussed. The potential applicability of the D-CTD model in ion-containing systems was also demonstrated in a series of ion–water complexes including Li+, Na+, K+, Mg2+, Ca2+, Fe2+, Zn2+, Pt2+, F–, Cl–, Br–, and I– ions. In general, the D-CTD model demonstrated good accuracy and good transferability in both charge transfer energy and the corresponding charge flow for a wide range of model systems. By distinguishing the intermolecular charge redistribution (charge transfer) under the influence of an external electric field from the accompanying intramolecular charge redistribution (polarization), the D-CTD model is theoretically consistent with current induced dipole-based polarizable dipole models and hence can be easily implemented and parameterized. Along with our previous work in charge penetration-corrected electrostatics, a bottom-up approach constructed water model was also proposed and demonstrated. The structure-maker and structure-breaker roles of cations and anions were also correctly reproduced using Na+, K+, Cl–, and I– ions in the new water model, respectively. This work demonstrates a cost-effective approach to describe the charge transfer phenomena. The water and ion models also show the feasibility of a modulated development approach for future force fields