Association Mapping for Important Agronomic Traits in Core Collection of Rice (Oryza sativa L.) with SSR Markers

Mining elite genes within rice landraces is of importance for the improvement of cultivated rice. An association mapping for 12 agronomic traits was carried out using a core collection of rice consisting of 150 landraces (Panel 1) with 274 simple sequence repeat (SSR) markers, and the mapping results were further verified using a Chinese national rice micro-core collection (Panel 2) and a collection from a global molecular breeding program (Panel 3). Our results showed that (1) 76 significant (P<0.05) trait-marker associations were detected using mixed linear model (MLM) within Panel 1 in two years, among which 32% were identical with previously mapped QTLs, and 11 significant associations had >10% explained ratio of genetic variation; (2) A total of seven aforementioned trait-marker associations were verified within Panel 2 and 3 when using a general linear model (GLM) and 55 SSR markers of the 76 significant trait-marker associations. However, no significant trait-marker association was found to be identical within three panels when using the MLM model; (3) several desirable alleles of the loci which showed significant trait-marker associations were identified. The research provided important information for further mining these elite genes within rice landraces and using them for rice breeding.     

Ultrasound-Assisted Extraction of Arabinogalactan and Dihydroquercetin Simultaneously from Larix gmelinii as a Pretreatment for Pulping and Papermaking

An ultrasound-assisted extraction (UAE) method using ethanol was applied for extracting arabinogalactan (AG) and dihydroquercetin (DHQ) simultaneously from larch wood, as a pretreatment for pulping and papermaking. The extraction parameters were optimized by a Box-Behnken experimental design with the yields of AG and DHQ as the response values. Under optimum conditions (three extractions, each using 40% ethanol, for 50 min, 200 W ultrasound power and 1∶18 solid-liquid ratio), the yields of AG and DHQ were 183.4 and 36.76 mg/g, respectively. After UAE pretreated, the wood chips were used for Kraft pulping (KP) and high boiling solvent pulping (HBSP). The pulping yield after pretreatment was higher than that of untreated (the pulping yields of untreated HBSP and KP were 42.37% and 39.60%, and the pulping yields of HBSP and KP after UAE-pretreated were 44.23% and 41.50% respectively), as indicated by a lower kappa number (77.91 and 27.30 for untreated HBSP and KP; 77.01 and 26.83 for UAE-pretreated HBSP and KP). Furthermore, the characteristics of paper produced from pretreated wood chips were superior to those from the untreated chips: the basis weight was lower (85.67 and 82.48 g·cm⁻² for paper from untreated KP and HBSP; 79.94 and 80.25 g·cm⁻² for paper from UAE-pretreated KP and HBSP), and the tensile strengths, tearing strengths, bursting strengths, and folding strengths were higher than these of paper after UAE-pretreated, respectively.     

巴西橡胶树转录中介体HbMed25基因克隆与表达分析

转录中介体(mediator,Med)中的Med25基因在植物的组织发育、器官发生、胁迫响应以及调控茉莉酸(JA)信号途径等方面起重要调控作用。该文在巴西橡胶树基因组序列中找到了橡胶树Med25基因的序列,通过RT-qPCR和RACE技术克隆HbMed25基因的全长序列并进行生物信息学预测分析结果显示,HbMed25基因包含2 655 bp的开放阅读框,编码884个氨基酸,蛋白分子量为95 kD,理论等电点为8.68,疏水性蛋白,亚细胞定位最可能为细胞核。Real-time PCR分析结果显示,HbMed25基因在树皮中表达量最高,在植物激素JA处理的形成层和胶乳材料中HbMed25基因在处理早期(1 h和2～4 h)上调表达,受割胶处理HbMed25基因在处理早期上调表达且对高产的橡胶树品系(CATAS 8-79和CATAS 7-33-97)的割胶处理响应更明显。综上结果认为,HbMed25基因极大可能参与了JA信号途径的调控,对阐明JA诱导橡胶树次生乳管分化的分子调控机制具有促进作用。     

Surface salt bridges contribute to the extreme thermal stability of an FN3-like domain from a thermophilic bacterium

This study uses differential scanning calorimetry, X-ray crystallography, and molecular dynamics simulations to investigate the structural basis for the high thermal stability (melting temperature 97.5°C) of a FN3-like protein domain from thermophilic bacteria Thermoanaerobacter tengcongensis (FN3tt). FN3tt adopts a typical FN3 fold with a three-stranded beta sheet packing against a four-stranded beta sheet. We identified three solvent exposed arginine residues (R23, R25, and R72), which stabilize the protein through salt bridge interactions with glutamic acid residues on adjacent strands. Alanine mutation of the three arginine residues reduced melting temperature by up to 22°C. Crystal structures of the wild type (WT) and a thermally destabilized (?Tm ?19.7°C) triple mutant (R23L/R25T/R72I) were found to be nearly identical, suggesting that the destabilization is due to interactions of the arginine residues. Molecular dynamics simulations showed that the salt bridge interactions in the WT were stable and provided a dynamical explanation for the cooperativity observed between R23 and R25 based on calorimetry measurements. In addition, folding free energy changes computed using free energy perturbation molecular dynamics simulations showed high correlation with melting temperature changes. This work is another example of surface salt bridges contributing to the enhanced thermal stability of thermophilic proteins. The molecular dynamics simulation methods employed in this study may be broadly useful for in silico surface charge engineering of proteins.     

Screening of microRNA and mRNA related to secondary hair follicle morphogenesis and development and functional analysis in cashmere goats

Functional & Integrative Genomics - microRNA (miRNA) is a type of endogenous short-chain non-coding RNA with regulatory function found in eukaryotes, which is involved in the regulation of a...     

CCL19 and CXCL13 synergistically regulate interaction between B cell acute lymphocytic leukemia CD23+CD5+ B Cells and CD8+ T cells

Interacting with T cells, cytokine-producing B cells play a critical protective role in autoimmune diseases. However, the interaction between malignant B and T cells remains to be fully elucidated. In a previous study, we have reported that ligation of CCL19-CCR7 and CXCL13-CXCR5 activates paternally expressed gene 10 (PEG10), resulting in an enhancement of apoptotic resistance in B-cell acute lymphocytic leukemia (B-ALL) CD23+CD5+ B cells. Here, we report that B-ALL CD23+CD5+ B cells produce IL-10 at high level, which can be further elevated by costimulation with CCL19 and CXCL13. CCL19/CXCL13-activated B-ALL CD23+CD5+ B cells, in turn, increase IL-10 expression in syngeneic CD8+ T cells in a B cell-derived IL-10-dependent manner and requiring a cell-cell contact. IL-10 secreted from B-ALL CD23+CD5+ B cells in vitro impairs tumor-specific CTL responses of syngeneic CD8+ T cells. The impairment of cytotoxicity of syngeneic CD8+ T cells is escalated by means of CCL19/CXCL13-induced up-regulation of IL-10 from B-ALL CD23+CD5+ B cells. Moreover, using a short hairpin RNA to knockdown PEG10, we provide direct evidence that increased expression of PEG10 in B-ALL CD23+CD5+ B cells is involved in malignant B-T cell interaction, contributing to the up-regulation of IL-10 expression, as well as to the impairment of cytotoxicity of syngeneic CD8+ T cells. Thus, malignant B-ALL CD23+CD5+ B cells play an immunoregulatory role in controlling different inflammatory cytokine expressions. IL-10 may be one of the critical cellular factors conferring B-ALL CD23+CD5+ B cells to escape from host immune surveillance.     

基于萤火虫荧光素酶报告基因检测凋亡的系统构建及鉴定

为构建一个能够快速检测凋亡的含荧光素酶报告基因 (Fluc) 的真核表达质粒,采用PCR的方法将Caspase-3的识别基序Asp-Glu-Val-Asp (DEVD) 四个氨基酸引入至Fluc基因的C端和N端之间;同时选取Asp-Glu-Val-Gly (DEVG) 四个氨基酸作为阴性对照。随后重组片段分别克隆至分离型内含肽的N端和C端之间,并命名为pFluc-DEVD和pFluc-DEVG。将该表达质粒与海肾荧光素酶报告质粒 (RLUC) 同时转染至HeLa细胞,通过双荧光素酶报告基因和Western blotting实验检测细胞凋亡水平。双荧光素酶报告基因系统实验结果显示,当发生凋亡时,pFluc-DEVD质粒组表达的萤火虫荧光素酶的含量高出pFluc-DEVG质粒组约3倍。Western blotting检测结果显示,转染pFluc-DEVD质粒的细胞在凋亡药物刺激后,Fluc活化的蛋白显著增多,且Caspase-3 的活化程度与Fluc的表达呈正相关,并有显著的统计学差异。以上结果表明,pFluc-DEVD真核表达质粒表达的萤火虫荧光素酶蛋白能被细胞内的Caspase-3酶裂解,且该质粒能够精确地反映出细胞的凋亡水平,为后续进行凋亡定量检测提供了一个可借鉴的方法。     

1H NMR-Based Metabolomics Investigation of Copper-Laden Rat: A Model of Wilson’s Disease

Background and Purpose

Wilson’s disease (WD), also known as hepatoleticular degeneration (HLD), is a rare autosomal recessive genetic disorder of copper metabolism, which causes copper to accumulate in body tissues. In this study, rats fed with copper-laden diet are used to render the clinical manifestations of WD, and their copper toxicity-induced organ lesions are studied. To investigate metabolic behaviors of ‘decoppering’ process, penicillamine (PA) was used for treating copper-laden rats as this chelating agent could eliminate excess copper through the urine. To date, there has been limited metabolomics study on WD, while metabolic impacts of copper accumulation and PA administration have yet to be established.

Materials and Methods

A combination of ¹HNMR spectroscopy and multivariate statistical analysis was applied to examine the metabolic profiles of the urine and blood serum samples collected from the copper-laden rat model of WD with PA treatment.

Results

Copper accumulation in the copper-laden rats is associated with increased lactate, creatinine, valine and leucine, as well as decreased levels of glucose and taurine in the blood serum. There were also significant changes in p-hydroxyphenylacetate (p-HPA), creatinine, alpha-ketoglutarate (α-KG), dimethylamine, N-acetylglutamate (NAG), N-acetylglycoprotein (NAC) in the urine of these rats. Notably, the changes in p-HPA, glucose, lactate, taurine, valine, leucine, and NAG were found reversed following PA treatment. Nevertheless, there were no changes for dimethylamine, α-KG, and NAC as a result of the treatment. Compared with the controls, the concentrations of hippurate, formate, alanine, and lactate were changed when PA was applied and this is probably due to its side effect. A tool named SMPDB (Small Molecule Pathway Database) is introduced to identify the metabolic pathway influenced by the copper-laden diet.

Conclusion

The study has shown the potential application of NMR-based metabolomic analysis in providing further insights into the molecular mechanism underlying disorder due to WD.     

Stormwater Runoff Pollutant Loading Distributions and Their Correlation with Rainfall and Catchment Characteristics in a Rapidly Industrialized City

Fast urbanization and industrialization in developing countries result in significant stormwater runoff pollution, due to drastic changes in land-use, from rural to urban. A three-year study on the stormwater runoff pollutant loading distributions of industrial, parking lot and mixed commercial and residential catchments was conducted in the Tongsha reservoir watershed of Dongguan city, a typical, rapidly industrialized urban area in China. This study presents the changes in concentration during rainfall events, event mean concentrations (EMCs) and event pollution loads per unit area (EPLs). The first flush criterion, namely the mass first flush ratio (MFFn), was used to identify the first flush effects. The impacts of rainfall and catchment characterization on EMCs and pollutant loads percentage transported by the first 40% of runoff volume (FF₄₀) were evaluated. The results indicated that the pollutant wash-off process of runoff during the rainfall events has significant temporal and spatial variations. The mean rainfall intensity (I), the impervious rate (IMR) and max 5-min intensity (I_max5) are the critical parameters of EMCs, while I_max5, antecedent dry days (ADD) and rainfall depth (R_D) are the critical parameters of FF₄₀. Intercepting the first 40% of runoff volume can remove 55% of TSS load, 53% of COD load, 58% of TN load, and 61% of TP load, respectively, according to all the storm events. These results may be helpful in mitigating stormwater runoff pollution for many other urban areas in developing countries.     

石山苣苔属的潜在适生区特征及其环境驱动变量

石山苣苔属(Petrocodon Hance)是著名的观赏花卉之一，但气候动荡和人类活动的强烈干扰，使其绝大部分被评估为极危(CR),至少也是易危(VU)以上。为重建末次间冰期以来石山苣苔属潜在适生区的时空变化，探讨适生区对环境变化的响应关系，为石山苣苔属的起源、地理分化研究和中国特有种质资源保护、园林开发利用提供理论指导，该研究结合120个分布记录和17个环境变量，应用优化的MaxEnt模型和地理信息技术(ArcGIS)对石山苣苔属在中国及中南半岛的适生区及其分布格局进行模拟，并基于逐步多元线性回归分析、冗余分析和蒙特卡洛检验评估影响石山苣苔属当前地理分布的主导变量。结果表明：(1)优化的MaxEnt模型的预测精度高，AUC值大于0.96;石山苣苔属当前适生区从中国西南部连续分布至越南北部，零散分布于中国中部和南部、块状分布于缅甸北部，其中以中国云贵高原南部为最佳适生区。(2)制约石山苣苔属当前地理分布的主导环境变量为最干月降雨量(bio14)、最热季度平均降雨量(bio18)、最湿季降雨量(bio16)、温度变化方差(bio4)、最冷月最低温度(bio6)、海拔(alt)。(3)在...