桃ERF转录因子家族生物信息学分析及 芽萌发相关基因筛选

以中油四号油桃(Prunus persica var. nectarina)为研究对象, 利用MEGA 6.0、MEME、GSDS和DNAMAN 6.0等软件对桃ERF家族数据进行生物信息学分析, 鉴定得到102个ERF转录因子家族基因, 并通过构建系统进化树将这102个基因分为10个子家族(I-X)。基因结构分析表明, 有81个基因不含内含子, 20个基因含有1个内含子, 有1个基因与其它成员差异较大, 含有5个内含子。保守元件分析表明, ERF家族包含20个保守元件, 其中Motif 1、Motif 2和Motif 4都属于AP2/ERF结构域, 同一个保守元件主要出现在同一个子家族中, 并且大部分保守元件的功能未知。VIII子家族基因的荧光定量PCR分析表明, 在桃叶芽处于不同的发育状态时, PpeERF068的表达量存在较大差异, 光照培养箱中培养的桃芽在萌发过程中各时期表达量变化趋势进一步表明该基因可能与叶芽萌发有关, 将其命名为PpeEBB1。该研究为进一步揭示PpeEBB1的分子机制奠定了基础, 并为桃树的栽培管理和熟期调控了提供理论指导。     

Impacts of fish aggregation devices on size structures of skipjack tuna Katsuwonus pelamis

Tuna purse seine fisheries target fish aggregated in schools, including free schools that are formed naturally based on fish biology and aggregations associated with natural and/or artificial drifting objects. Using data collected from skipjack tuna (Katsuwonus pelamis) fisheries, we evaluated differences in size structures between drifting-floating-object-associated schools and unassociated schools. We developed a generalized linear model to remove impacts of environmental variables on skipjack size composition. This study indicates that the drifting-floating-object-associated schools tended to have significantly wider size ranges than the unassociated schools. This suggests that unassociated schools were likely formed based on similarity in sizes among individuals within a school while drifting-floating-object-associated schools were probably composed of individuals of large size ranges and their formation was not based on the “size selection” rule. We concluded that the unassociated schools and the drifting-floating-object-associated schools were formed through different mechanisms, and drifting floating objects could aggregate unassociated schools of different size structures. Thus, a large scale of deployment of man-made floating objects might disrupt the spatial aggregation pattern of fish that otherwise tended to school based on their sizes in the absence of floating objects.     

Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis

The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.     

Development of a fluorescent probe hydrolysis-insulated isothermal PCR for rapid and sensitive on-site detection of African swine fever virus

Highlights
1. A probe-based insulated isothermal PCR (iiPCR) assay was developed for rapid and onsite detection of ASFV.
2. The developed iiPCR showed similar sensitivity and specificity with OIE recommended real-time PCR.
3. Blood samples could be directly applied as PCR template in iiPCR without DNA extraction.     

Characterization of the androgen-dependent 22Kdalton glycoprotein from rat ventral prostate

Oxidation by molecular oxygen converted the 22Kdalton glycoprotein from rat ventral prostate into a 34K species and this reaction could be reversed by thiol reducing reagent. Measurement of the level of the 22Kdalton glycoprotein in prostatic cytosol by the radial immunodiffusion technique showed that changes in the 22Kdalton glycoprotein concentration in response to androgen withdrawal and replacement were slow in comparison to androgen regulated levels of mRNA coding for the protein. (3) Charcoal absorption steroid binding assays of the 22Kdalton glycoprotein revealed that the protein did not bind testosterone, estradiol, progesterone or corticosterone. These results indicate that the 22Kdalton glycoprotein is metabolically stable, not steroid-binding, and exists as an oligomer through disulfide crosslinking.     

蚕豆叶片小叶脉不同发育时期ATP酶和酸性磷酸酶的细胞化学超微结构定位

运用CF输导方法确定正在进行库源转换的叶片。采用铅沉淀法对蚕豆(Vicia faba)幼嫩叶片、库源转换叶的库区和源区的小叶脉组织细胞进行了ATP酶和酸性磷酸酶的细胞化学定位。结果显示, 在蚕豆幼嫩叶片的小叶脉中, 传递细胞质膜和细胞壁上存在大量的ATP酶和酸性磷酸酶的标记产物。在库源转换叶库区传递细胞和筛分子质膜上ATP酶和酸性磷酸酶的标记较弱。在库源转换叶的源区传递细胞和筛分子质膜存在较强的ATP酶和酸性磷酸酶的活性反应产物。在小叶脉分化中的木质部分子存在较强的ATP酶和酸性磷酸酶的活性标记, 在分化成熟的木质部分子酶的标记显著减弱。实验结果表明, 依据不同的发育阶段, ATP酶和酸性磷酸酶的含量在蚕豆小叶脉的不同细胞中呈动态变化。据此, 对ATP酶和酸性磷酸酶在蚕豆小叶脉细胞分化和质外体装载中的作用进行了讨论。     

盐胁迫下大豆根组织定量PCR分析中内参基因的选择

实时荧光定量PCR已广泛用于基因表达的分析, 适当的内参基因选择是获得准确分析结果的关键。在大豆(Glycine max)分子生物学研究中, 逆境响应基因和microRNA (miRNA)表达的内参辅助检测基因均有哪些目前尚不清楚。该研究选用不同盐梯度和时间点组合处理的大豆根组织为材料, 对已报道的其它条件下表达相对稳定的内参基因(ACT、ACT2/7、CYP2、ELF1A、ELF1B、F-Box、TUA和UBC2)以及miRNA内参基因(U6、miR1515a、miR1520c、miR1520d、miR171a和miR171b)的表达情况进行了全面检测; 并采用Δ-Ct、Bestkeeper、NormFinder和Genorm四种方法对检测结果进行了综合分析, 发现ELF1B和CYP2适合作为大豆根系盐胁迫响应基因研究的内参基因, miR1515a和U6适合作为盐胁迫下大豆根组织miRNA研究的内参。上述研究结果为大豆盐胁迫响应基因和miRNA表达及其进一步的功能研究奠定了基础。     

内皮素—1预处理大鼠心脏Gaq／11和Gia蛋白含量的变化

The present study was undertaken to explore the mechanism of G protein-mediated signal transduction pathway during endothelin-1 (ET-1) pre-treatment and ischemic preconditioning (IP). Rats were divided into four groups: ET-1, IP, ischaemia-reperfusion (IR) and control groups. ET-1 pre-treatment model was prepared by administrating 0.5 nmol/(L.kg) ET-1 into rat left ventricle, whereas IP model was prepared by ligating the left coronary artery for 5 min followed by 30 min reperfusion. All the animals were subjected to 60 min regional ischaemia and 30 min reperfusion alternately and then parameters of ventricular arrhythmia and expression of cardiac Galphaq/11 and Gialpha2 were measured. The results showed that the scores of ventricular arrhythmia decreased significantly in both ET-1 and IP treated groups as compared with IR group. In comparison with control group, Galphaq/11 increased by 77.8% (P<0.05) and 110.6% (P<0.01) in IP and ET-1 group respectively. Gialpha2 showed no significant difference in IP group, while it decreased by 31.0% (P<0.01) in ET-1 group. In conclusion, activation of G alphaq/11 may be related to the protecting mechanism of ET-1 pre-treatment and IP, whereas Gialpha2 may only play a role in ET-1 pre-treatment.     

珍珠黄杨叶片的蛋白质提取方法探讨

蛋白质样品制备是双向电泳的核心.为了找到一种适合提取珍珠黄杨叶片蛋白质的方法,本文以该树种扦插苗的叶片为材料,用TCA-丙酮沉淀法、Tris-饱和酚法和2-D Clean-up Kit提取蛋白质,并进行双向凝胶电泳,采用银染法进行检测.结果表明,TCA-丙酮沉淀法得到的样品图谱背景模糊、拖尾;Tris-饱和酚法得到的样品图谱清晰,蛋白点饱满,无纵向或横向拖尾,但有蛋白点丢失;2-D Clean-Up Kit提取的蛋白质样品得到了较好双向电泳图谱.