High-throughput phenotyping-based quantitative trait loci mapping reveals the genetic architecture of the salt stress tolerance of Brassica napus.

Salt stress is a major limiting factor that severely affects the survival and growth of crops. It is important to understand the salt stress tolerance ability of Brassica napus and explore the underlying related genetic resources. We used a high-throughput phenotyping platform to quantify 2111 image-based traits (i-traits) of a natural population under three different salt stress conditions and an intervarietal substitution line (ISL) population under nine different stress conditions to monitor and evaluate the salt stress tolerance of B. napus over time. We finally identified 928 high-quality i-traits associated with the salt stress tolerance of B. napus. Moreover, we mapped the salt stress-related loci in the natural population via a genome-wide association study and performed a linkage analysis associated with the ISL population, respectively. These results revealed 234 candidate genes associated with salt stress response, and two novel candidate genes, BnCKX5 and BnERF3, were experimentally verified to regulate the salt stress tolerance of B. napus. This study demonstrates the feasibility of using high-throughput phenotyping-based quantitative trait loci mapping to accurately and comprehensively quantify i-traits associated with B. napus. The mapped loci could be used for genomics-assisted breeding to genetically improve the salt stress tolerance of B. napus.

Fe-Doped CoS2 Nanoarrays: Efficient Electrocatalytic Nitrate Reduction to Ammonia under Ambient Conditions.

The electrocatalytic nitrate reduction reaction (NO3 - RR) enables the reduction of nitrate to ammonium ions under ambient conditions. It was considered as an alternative reaction for the production of ammonia (NH3 ) in recent years. In this paper, we report that the Fe doping CoS2 nanoarrays can effectively catalyze the formation of NH3 from nitrate (NO3 - ) under ambient conditions. This is mainly due to the increase of the NO3 - reaction active site by Fe doping and the porous nanostructure of the catalyst, which greatly improves the catalytic activity. Specifically, at -0.9 V vs. RHE, the NH3 yield rate (RNH3 ) of Fe-CoS2 /CC is 17.8×10-2  mmol h-1 cm-2 with Faraday Efficiency (FE) of 88.93 %. Besides, such catalyst shows good durability and catalytic stability, which provides the possibility for the future application of electrocatalytic NH3 production.

CRISPR-Cas systems are present predominantly on chromosome and its relationship with MEGs in Vibrio species.

Bacteria have developed diverse strategies to counteract virus predation, one of which is the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR associated (Cas) proteins immune defense system. In this study, the structure and function of the CRISPR-Cas system in 120 Vibrio strains were analyzed by bioinformatics methods, as well as the correlation between CRISPR and mobile genetic elements (MEGs). Only 61 Vibrio strains contained one or more CRISPR structures, and finally 102 CRISPRs were identified. The typical repeat size was 28 bp, and the total length of CRISPRs is nearly 60 bp, which was the most stable length of CRISPR in Vibrio strains. The types of CRISPR-Cas present in 61 strains were I-C, I-E, I-F, II-B, III-B, III-D and the rare type IV systems. Through principal component analysis, we found that Cas gene was most closely related to CRISPR. In addition, phages and plasmids were also highly correlated, showing negative correlation with CRISPR-Cas system. CRISPR-Cas predominantly present on chromosome within Vibrio while rarely in plasmids. Comparing the structural characteristics of plasmids containing CRISPR and without CRISPR, we found plasmid pMBL287 with CRISPR contained a bacteriophage f237, with more MGES, suggesting the diversity was greater. In addition, the same mobile genetic elements IS256 and ISL3 were found in the upstream and downstream of CRISPR. This study provides the prevalence, diversity and phylogenetic distribution of CRISPR-Cas in Vibrio, revealing which type of CRISPR-Cas system is predominant, and the factors affecting its function, as well as its relationship with mobile genetic elements.

Droplet impact on pillar-arrayed non-wetting surfaces.

Droplet impact on pillar-arrayed polydimethylsiloxane (PDMS) surfaces with different solid fractions was studied. The lower and upper limits of Weber number, We, for complete rebound of impacting droplets decreased with decreasing solid fractions. Gaps were visible during the spreading and retraction processes of bouncing droplets on the surface with a solid fraction of 0.06 while no gaps were observed during the retraction process when We was greater than its upper limit, indicating that there existed a transition from the Cassie-Baxter wetting state to the Wenzel wetting state. Therefore, a novel model accounting for the penetration of a liquid into the cavities between the pillars was developed to predict the upper limit of the impact velocity of bouncing droplets. At high We, partial rebound was observed for surfaces with solid fractions of 0.50 and 0.20 while a sticky state was observed for the surface with a solid fraction of 0.06. Moreover, surface roughness has a great influence on the contact time of bouncing droplets. Besides, the maximum spreading parameter was found to follow a scaling law of We1/4.

[Electroencephalogram Feature Selection Based on Correlation Coefficient Analysis].

In order to improve the accuracy of classification with small amount of motor imagery training data on the development of brain-computer interface (BCD systems, we proposed an analyzing method to automatically select the characteristic parameters based on correlation coefficient analysis. Throughout the five sample data of dataset IV a from 2005 BCI Competition, we utilized short-time Fourier transform (STFT) and correlation coefficient calculation to reduce the number of primitive electroencephalogram dimension, then introduced feature extraction based on common spatial pattern (CSP) and classified by linear discriminant analysis (LDA). Simulation results showed that the average rate of classification accuracy could be improved by using correlation coefficient feature selection method than those without using this algorithm. Comparing with support vector machine (SVM) optimization features algorithm, the correlation coefficient analysis can lead better selection parameters to improve the accuracy of classification.

Characterization and comparative genomics analysis of RepA_N multi-resistance plasmids carrying optrA from Enterococcus faecalis.

Introduction: This research aimed to investigate the antibiotic resistance of Enterococcus faecalis from swine farms in Zhejiang Province and the prevalence and transmission mechanism of oxazolidone resistance gene optrA. Method: A total of 226 Enterococcus faecalis were isolated and their resistance to 14 antibiotics was detected by broth microdilution. The resistance genes were detected by PCR. Results: The antibiotic resistance rate of 226 isolates to nearly 57% (8/14) of commonly used antibiotics was higher than 50%. The resistance rate of tiamulin was highest (98.23%), that of tilmicosin, erythromycin, tetracycline and florfenicol was higher than 80%, and that of oxazolidone antibiotic linezolid was 38.49%. The overall antibiotics resistance in Hangzhou, Quzhou and Jinhua was more serious than that in the coastal cities of Ningbo and Wenzhou. The result of PCR showed that optrA was the main oxazolidinone and phenicols resistance gene, with a detection rate of 71.68%, and optrA often coexisted with fexA in the isolates. Through multi-locus sequence typing, conjugation transfer, and replicon typing experiments, it was found that the horizontal transmission mediated by RepA_N plasmid was the main mechanism of optrA resistance gene transmission in E. faecalis from Zhejiang Province. Two conjugative multi-resistance plasmids carrying optrA, RepA_N plasmid pHZ318-optrA from Hangzhou and Rep3 plasmid from Ningbo, were sequenced and analyzed. pHZ318-optrA contain two multidrug resistance regions (MDR), which contributed to the MDR profile of the strains. optrA and fexA resistance genes coexisted in IS1216E-fexA-optrA-ferr-erm(A)-IS1216E complex transposon, and there was a partial sequence of Tn554 transposon downstream. However, pNB304-optrA only contain optrA, fexA and an insertion sequence ISVlu1. The presence of mobile genetic elements at the boundaries can possibly facilitate transfer among Enterococcus through inter-replicon gene transfer. Discussion: This study can provide theoretical basis for ensuring the quality and safety of food of animal origin, and provide scientific guidance for slowing down the development of multi-antibiotic resistant Enterococcus.

Genome-Wide Association Studies of Salt-Alkali Tolerance at Seedling and Mature Stages in Brassica napus.

Most plants are sensitive to salt-alkali stress, and the degree of tolerance to salt-alkali stress varies from different species and varieties. In order to explore the salt-alkali stress adaptability of Brassica napus, we collected the phenotypic data of 505 B. napus accessions at seedling and mature stages under control, low and high salt-alkali soil stress conditions in Inner Mongolia of China. Six resistant and 5 sensitive materials, respectively, have been identified both in Inner Mongolia and Xinjiang Uygur Autonomous Region of China. Genome-wide association studies (GWAS) for 15 absolute values and 10 tolerance coefficients (TCs) of growth and agronomic traits were applied to investigate the genetic basis of salt-alkali tolerance of B. napus. We finally mapped 9 significant QTLs related to salt-alkali stress response and predicted 20 candidate genes related to salt-alkali stress tolerance. Some important candidate genes, including BnABA4, BnBBX14, BnVTI12, BnPYL8, and BnCRR1, were identified by combining sequence variation annotation and expression differences. The identified valuable loci and germplasms could be useful for breeding salt-alkali-tolerant B.napus varieties. This study laid a foundation for understanding molecular mechanism of salt-alkali stress adaptation and provides rich genetic resources for the large-scale production of B. napus on salt-alkali land in the future.

Characterization and Comparative Genomics Analysis of lncFII Multi-Resistance Plasmids Carrying bla CTX - M and Type1 Integrons From Escherichia coli.

This research aimed to investigate the presence and transferability of the extended-spectrum ß-lactamase resistance genes to identify the genetic context of multi-drug resistant (MDR) loci in two Escherichia coli plasmids from livestock and poultry breeding environment. MICs were determined by broth microdilution. A total of 137 E. coli resistant to extended-spectrum ß-lactam antibiotics were screened for the presence of the ESBL genes by PCR. Only two E. coli out of 206 strains produced carbapenemases, including strain 11011 that produced enzyme A, and strain 417957 that produced enzyme B. The genes were bla KPC and bla NDM , respectively. The plasmids containing bla CTX - M were conjugatable, and the plasmids containing carbapenem resistance gene were not conjugatable. Six extended-spectrum ß-lactamase resistance genes were detected in this research, including bla TEM, bla CTX - M, bla SHV, bla OAX - 1, bla KPC, and bla NDM , and the detection rates were 94.89% (130/137), 92.7% (127/137), 24.81% (34/137), 20.43% (28/137), 0.72% (1/137), and 0.72% (1/137), respectively. Two conjugative lncFII multi-resistance plasmids carrying bla CTX - M, p11011-fosA and p417957-CTXM, were sequenced and analyzed. Both conjugative plasmids were larger than 100 kb and contained three accessory modules, including MDR region. The MDR region of the two plasmids contained many antibiotic resistance genes, including bla CTX - M, mph (A), dfrA17, aadA5, sul1, etc. After transfer, both the transconjugants displayed elevated MICs of the respective antimicrobial agents. A large number of resistance genes clusters in specific regions may contribute to the MDR profile of the strains. The presence of mobile genetic elements at the boundaries can possibly facilitate transfer among Enterobacteriaceae through inter-replicon gene transfer. Our study provides beta-lactam resistance profile of bacteria, reveals the prevalence of ß-lactamase resistance genes in livestock and poultry breeding environment in Zhejiang Province, and enriches the research on IncFII plasmids containing bla CTX - M.

Genome-Wide Association Studies of Salt Tolerance at Seed Germination and Seedling Stages in Brassica napus.

Most crops are sensitive to salt stress, but their degree of susceptibility varies among species and cultivars. In order to understand the salt stress adaptability of Brassica napus to salt stress, we collected the phenotypic data of 505 B. napus accessions at the germination stage under 150 or 215 mM sodium chloride (NaCl) and at the seedling stage under 215 mM NaCl. Genome-wide association studies (GWAS) of 16 salt tolerance coefficients (STCs) were applied to investigate the genetic basis of salt stress tolerance of B. napus. In this study, we mapped 31 salts stress-related QTLs and identified 177 and 228 candidate genes related to salt stress tolerance were detected at germination and seedling stages, respectively. Overexpression of two candidate genes, BnCKX5 and BnERF3 overexpression, were found to increase the sensitivity to salt and mannitol stresses at the germination stage. This study demonstrated that it is a feasible method to dissect the genetic basis of salt stress tolerance at germination and seedling stages in B. napus by GWAS, which provides valuable loci for improving the salt stress tolerance of B. napus. Moreover, these candidate genes are rich genetic resources for the following exploration of molecular mechanisms in adaptation to salt stress in B. napus.

The Clustered Regularly Interspaced Short Palindromic Repeats-Associated System and Its Relationship With Mobile Genetic Elements in Klebsiella.

Microorganisms have developed many strategies in the process of long-term defense against external attacks, one of which is the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) bacterial immunological system. In this study, the whole genome of 300 strains of Klebsiella was collected, the CRISPR-Cas system in the strains was statistically analyzed, and the types and structures of CRISPR system in Klebsiella were explored, as well as the correlation between CRISPR and mobile genetic elements (MGEs). Through principal component analysis (PCA), we found that Cas gene, plasmids, integron, IS1, IS609, and enzymes of DNA metabolism were closely related to CRISPR-Cas. Compared the structural characteristics of plasmids, the DinG family helicases, Cas6, Csf2, and IS5 were observed near the CRISPR loci in plasmid, which is also confirmed by the results of PCA that they may be important factors affecting the plasmid with CRISPR.

A Comparative Study of Cavitation Characteristics of Nano-fluid and Deionized Water in Micro-channels.

Hydrodynamic cavitation has been widely applied in micro-fluidic systems. Cavitating flow characteristics are closely related to the fluid properties. In this paper, the cavitation characteristics of Cu nano-fluid in micro-channels were numerically investigated and compared with those of the deionized (DI) water. The mathematical model was verified by comparing the numerical results with the experiment observation. The curved orifice (R = 0.3 mm) was found to have the highest efficiencies of cavitation for both fluids. With the increase of inlet pressure, cavitating jet lengths of the two fluids significantly increased. While, the cavitating jet length of the nano-fluid was shorter than that of the DI water at the same inlet pressure. The cavitation inception number of the DI water and nano-fluid were approximately 0.061 and 0.039, respectively. The results indicate that the nano-particles played negative effects on the cavitation inception. In addition, with the decrease of outlet pressure, the cavitation strength gradually increased and the mass flow rate remained nearly unchanged at the same time.

Anchoring Au(111) on a Bismuth Sulfide Nanorod: Boosting the Artificial Electrocatalytic Nitrogen Reduction Reaction under Ambient Conditions.

Electrocatalytic nitrogen reduction reaction (NRR), as a green and sustainable method for ammonia synthesis, has become one of the candidates to substitute industrial Haber-Bosch ammonia synthesis in the near future. In this work, gold nanoparticles (Au NPs) were successfully anchored on bismuth sulfide nanorods (Bi2S3 NRs), which acted as highly efficient electrocatalytic NRR catalysts. The N-philic nature of Bi and the unique mutual coordination of Au-S-Bi can greatly promote the nitrogen adsorption and form the intermediate product N2H*, achieving a boosted improvement in the NRR activity through a continuous hydrogenation reaction. Definitely, the as-synthesized Au(111)@Bi2S3 nanorod catalyst exhibits an excellent NH3 generation rate of 45.57 µg h-1 mgcat.-1 with a faradic efficiency of 3.10% at -0.8 V vs reversible hydrogen electrode. High stability and reproducibility are also demonstrated throughout the electrocatalytic NRR process. Density functional theory calculations were performed to further understand the NRR catalytic mechanism on the Au(111)@Bi2S3 nanorods catalyst.