Theoretical investigation on the diatomic ligand migration process and ligand binding properties in non‐O2‐binding H‐NOX domain

The Nostoc sp (Ns) H‐NOX (heme‐nitric oxide or OXygen‐binding) domain shares 35% sequence identity with soluble guanylate cyclase (sGC) and exhibits similar ligand binding property with the sGC. Previously, our molecular dynamic (MD) simulation work identified that there exists a Y‐shaped tunnel system hosted in the Ns H‐NOX interior, which servers for ligand migration. The tunnels were then confirmed by Winter et al. [PNAS 2011;108(43):E 881–889] recently using x‐ray crystallography with xenon pressured conditions. In this work, to further investigate how the protein matrix of Ns H‐NOX modulates the ligand migration process and how the distal residue composition affects the ligand binding prosperities, the free energy profiles for nitric oxide (NO), carbon monooxide (CO), and O₂ migration are explored using the steered MDs simulation and the ligand binding energies are calculated using QM/MM schemes. The potential of mean force profiles suggest that the longer branch of the tunnel would be the most favorable route for NO migration and a second NO trapping site other than the distal heme pocket along this route in the Ns H‐NOX was identified. On the contrary, CO and O₂ would prefer to diffuse via the shorter branch of the tunnel. The QM/MM (quantum mechanics/molecular mechanics) calculations suggest that the hydrophobic distal pocket of Ns H‐NOX would provide an approximately vacuum environment and the ligand discrimination would be determined by the intrinsic binding properties of the diatomic gas ligand to the heme group. Proteins 2013; 81:1363–1376. © 2013 Wiley Periodicals, Inc.     

饲养林麝的种群特征和幼麝的存活研究

对饲养在上海崇明岛东平林场的林麝种群特征以及1998～2000 年间该种群所出生的74 只幼麝存活情况进行分析研究。结果表明: 该林麝种群中能繁殖的个体占51.1 % , 种群数量逐渐增长。种群存活率曲线呈C 型,说明林麝的死亡主要发生在幼麝时期。从不同年龄段性比变化来看, 初生幼麝的性比接近1∶1 , 由于雌幼麝比雄幼麝具有更高的存活率( P < 0.05) , 进入亚成体以后雄性比例逐渐下降, 显示幼麝时期存在偏雄性死亡。早出生幼麝的存活率明显高于晚出生幼麝( P < 0.05) 。引起幼麝死亡的主要原因是疾病(45. 9 %) 。     

Overexpression of a Triticum aestivum Calreticulin gene (TaCRT1) Improves Salinity Tolerance in Tobacco

Calreticulin (CRT) is a highly conserved and abundant multifunctional protein that is encoded by a small gene family and is often associated with abiotic/biotic stress responses in plants. However, the roles played by this protein in salt stress responses in wheat (Triticum aestivum) remain obscure. In this study, three TaCRT genes were identified in wheat and named TaCRT1, TaCRT2 and TaCRT3-1 based on their sequence characteristics and their high homology to other known CRT genes. Quantitative real-time PCR expression data revealed that these three genes exhibit different expression patterns in different tissues and are strongly induced under salt stress in wheat. The calcium-binding properties of the purified recombinant TaCRT1 protein were determined using a PIPES/Arsenazo III analysis. TaCRT1 gene overexpression in Nicotiana tabacum decreased salt stress damage in transgenic tobacco plants. Physiological measurements indicated that transgenic tobacco plants showed higher activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) than non-transgenic tobacco under normal growth conditions. Interestingly, overexpression of the entire TaCRT1 gene or of partial TaCRT1 segments resulted in significantly higher tolerance to salt stress in transgenic plants compared with their WT counterparts, thus revealing the essential role of the C-domain of TaCRT1 in countering salt stress in plants.     

暹罗芽孢杆菌高产γ-聚谷氨酸的发酵条件优化

【背景】γ-聚谷氨酸（poly-γ-glutamic acid,γ-PGA）产生菌多为枯草芽孢杆菌（Bacillus subtilis）、解淀粉芽孢杆菌（Bacillus amyloliquefaciens）、地衣芽孢杆菌（Bacillus licheniformis）等,而暹罗芽孢杆菌（Bacillus siamensis）相关研究较少。【目的】研究暹罗芽孢杆菌产γ-PGA的液体发酵条件。【方法】以自行分离的暹罗芽孢杆菌CAU83为出发菌株进行液体发酵,通过单因素试验和正交试验法研究了碳氮源、前体物质、发酵温度及pH对菌株生产γ-PGA的影响。【结果】经摇瓶优化,γ-PGA的最适碳源、氮源和前体物质分别为乳糖30g/L、酵母提取物5g/L和L-谷氨酸钠60 g/L,最适培养条件为发酵温度37℃和pH 7.0,γ-PGA产量由8.4 g/L提升至30.1 g/L,比优化前提高了260%。经分批补料发酵,60 h时γ-PGA产量最高为59.5 g/L,比摇瓶提高了98%,产率为0.99 g/（L·h）。所产γ-PGA分子量为3.8×10⁶ Da,聚合度较高。【结论】...     

cTrans: generating polypeptide databases from cDNA sequences

cTrans is a comprehensive utility used to generate polypeptide databases from cDNA sequences. The goal is achieved through integrating four main functions, including retrieving sequences of species of interest from the downloaded packages from dbEST of GenBank, format conversion, checking and deleting vector and adaptor contamination, and translating the cDNA sequences in all six frames and selecting specific translations for database construction in a user-defined length threshold. In addition, this utility is also applicable to cDNA sequences produced by users themselves.     

Chromosomal intervals responsible for tissue culture response of wheat immature embryos

To study the genetic mechanism underlying the tissue culture response (TCR) of immature embryos, callus induction and regeneration were performed in two separate trials using the recombinant inbred line (RIL) derived from a cross of Nanda2419 with Wangshuibai. In the first trial, immature embryos were collected from plants grown in the greenhouse in the winter of 2005; while in the second trial, immature embryos were collected from donor plants grown in the field during the growing season. Through whole genome screening, seven chromosome regions conditioning percent embryos forming embryogenic callus (PEFEC) and one conditioning percent callus pieces regenerating plantlets (PCRP) were detected. These QTLs were distributed on chromosomes of homoeologous groups 2, 3, 5 and 7. Among all, QPefec.nau-3B.2, QPefec.nau-7D, and QPcrp.nau-3A were consistently identified. The relationship of these identified wheat TCR QTLs with those of other cereal crops has been evaluated. PCR markers linked to TCR QTLs would facilitate germplasm identification, marker-assisted evaluation and utilization of these QTLs.     

Genetic dissection of yield-related traits in a recombinant inbred line population created using a key breeding parent in China’s wheat breeding

Understanding the genetics underlying yield formation of wheat is important for increasing wheat yield potential in breeding programs. Nanda2419 was a widely used cultivar for wheat production and breeding in China. In this study, we evaluated yield components and a few yield-related traits of a recombinant inbred line (RIL) population created by crossing Nanda2419 with the indigenous cultivar Wangshuibai in three to four trials at different geographical locations. Negative and positive correlations were found among some of these evaluated traits. Five traits had over 50 % trial-wide broad sense heritability. Using a framework marker map of the genome constructed with this population, quantitative trait loci (QTL) were identified for all traits, and epistatic loci were identified for seven of them. Our results confirmed some of the previously reported QTLs in wheat and identified several new ones, including QSn.nau-6D for effective tillers, QGn.nau-4B.2 for kernel number, QGw.nau-4D for kernel weight, QPh.nau-4B.2 and QPh.nau-4A for plant height, and QFlw.nau-5A.1 for flag leaf width. In the investigated population, Nanda2419 contributed all QTLs associated with higher kernel weight, higher leaf chlorophyll content, and a major QTL associated with wider flag leaf. Seven chromosome regions were related to more than one trait. Four QTL clusters contributed positively to breeding goal-based trait improvement through the Nanda2419 alleles and were detected in trials set in different ecological regions. The findings of this study are relevant to the molecular improvement of wheat yield and to the goal of screening cultivars for better breeding parents.     

C-6 aryl substituted 4-quinolone-3-carboxylic acids as inhibitors of hepatitis C virus

Quinolone-3-carboxylic acid represents a highly privileged chemotype in medicinal chemistry and has been extensively explored as antibiotics and antivirals targeting human immunodeficiency virus (HIV) integrase (IN). Herein we describe the synthesis and anti-hepatitis C virus (HCV) profile of a series of C-6 aryl substituted 4-quinlone-3-carboxylic acid analogues. Significant inhibition was observed with a few analogues at low micromolar range against HCV replicon in cell culture and a reduction in replicon RNA was confirmed through an RT-qPCR assay. Interestingly, evaluation of analogues as inhibitors of NS5B in a biochemical assay yielded only modest inhibitory activities, suggesting that a different mechanism of action could operate in cell culture.     

Genome-wide association and validation of key loci for yield-related traits in wheat founder parent Xiaoyan 6

Xiaoyan 6, one of the most important founder parents in wheat, possesses many superior agronomic traits and has played a crucial role in Chinese wheat breeding programs. In this study, a panel of 66 elite wheat accessions derived from Xiaoyan 6 was planted in four growing seasons; genome-wide association study (GWAS) was performed for six yield-related traits using the wheat 90K genotyping assay. A total of 803 significant marker-trait associations (MTAs) that explained up to 35.0% of the phenotypic variation were detected. Of these, the locus QTkw-5B which contains 19 MTAs for thousand kernel weight (TKW) was consistently detected in three growing seasons and confirmed in a recombinant inbred line (RIL) population by developing simple sequence repeats (SSR) and kompetitive allele-specific PCR (KASP) markers. The locus QPh-3A containing eight repetitive MTAs for plant height (PH) was consistently identified in all the four growing seasons and validated in a RIL population by developing SSR markers. The transmission of Xiaoyan 6 allele indicated that the favorite allele of QPh-3A was strongly selected in breeding programs. Comparing with previous studies, QTkw-5B and QPh-3A should be novel QTL. The locus QFss-2D for fertile spikelet number per spike (FSS) was identified and then validated in three bi-parental populations. This locus controlled various spike-related traits and may be a key spike polymorphic locus. This study could provide insight into dissecting yield-related traits in the breeding population and reliable molecular markers that might be valuable for marker-assisted selection in wheat high-yield breeding programs.