基于焦磷酸测序技术建立基因编辑水稻检测方法

基因编辑技术发展迅速,但对应的检测方法较少。为寻找创建基因编辑作物适用的检测方法,以 PL3 基因编辑水稻编辑位点为靶标,有效设计了焦磷酸测序的扩增引物及测序引物,并进行有效性检测,分别利用Sequence to Analyze等程序以及SNP和AQ两种模式完成了对PL3 基因的定性和定量检测试验,建立了 PL3 基因编辑水稻编辑位点焦磷酸测序检测方法。结果表明,基于焦磷酸测序技术可以通过检测编辑位点从而将基因编辑型水稻与野生型水稻进行区分。与常规的转基因检测方法相比,该检测方法具有较好的准确性、高效性及高灵敏度等优点,在基因编辑型水稻编辑位点定性和定量检测分析方面具有很好的应用前景。     

培养基灭菌方式对细菌分离效率的影响

自然界蕴含大量未/难培养微生物,分离这些微生物对理论研究和资源开发具有重要意义。本研究使用高压灭菌和过滤除菌方式制备培养基,采用稀释涂布方法,从红树林灰泥样品中分离获得123株细菌,通过16S rRNA基因序列分析对其进行鉴定,进而探究培养基灭菌方式对细菌分离效果的影响。结果表明：过滤除菌培养基生长的单菌落数目（339±82）个显著多于高压灭菌培养基生长的单菌落数目（179±65）个;两种培养基分离细菌的群落结构在门、科和属分类水平上总体相似,但优势类群的数目和少数类群存在差异;过滤除菌培养基分离细菌的Shannon Wiener’s指数、均匀度、新种率、基因多样性均高于高压灭菌培养基,而其与近缘模式菌株相似度的平均值和中位数则低于高压灭菌培养基。因此,过滤除菌培养基分离获得细菌的多样性、均匀性和新颖性均高于高压灭菌培养基。本研究首次探究培养基灭菌方式对细菌分离效果的影响,具有更高分离效率的过滤除菌培养基为未/难培养微生物菌株资源获取提供了借鉴。     

A correlation between BCL-2 modifying factor,p53 and livin gene expressions in cancer colon patients

Accumulating evidence has revealed that livin gene and BCL-2 modifying factor (BMF) gene are closely associated with the initiation and progression of colon carcinoma by activating or suppressing multiple malignant processes. Those genes that can detect colon - cancer are a promising approach for cancer screening and diagnosis. This study aimed to evaluate correlation between livin, BMF and p53 genes expression in colon cancer tissues of patients included in the study, and their relationship with clinicopathological features and survival outcome in those patients. In this study, 50 pathologically diagnosed early cancer colon patients included and their tissue biopsy with 50 matched adjacent normal tissue, and 50 adenoma tissue specimens were analyzed for livin gene and BMF gene expressions using real time PCR. The relationship of those genes expressions with clinicopathological features, tumor markers, Time to Progression and overall survival for those patients were correlated in cancer colon group. In this study, there was a significant a reciprocal relationship between over expression of livin gene and down regulation of BMF and p53 genes in colon cancer cells. Livin mRNA was significantly higher, while BMF and p53 mRNA were significantly lower in colorectal cancer tissue compared to benign and normal colon tissue specimens (P < 0.001), however, this finding was absent between colon adenomas and normal mucosa. There was a significant association between up regulation of livin and down regulation of BMF and p53 expressions with more aggressive tumor (advanced TNM stage), rapid progression with metastasis and decreased overall survival in cancer colon patients, hence these genes can serve as significant prognostic markers of poor outcome in colon cancer patients. This work highlights the role of livin, BMF and p53 genes in colorectal tumorigenesis and the applicability of using those genes as a diagnostic and prognostic markers in patients with colon carcinoma and as a good target for cancer colon treatment in the future.     

The landscape and prognostic value of immune characteristics in uterine corpus endometrial cancer

In the present study, we explored the clinical and immunological characteristics of 575 uterine corpus endometrial carcinoma (UCEC) samples obtained from The Cancer Genome Atlas (TCGA) using the ESTIMATE and CIBERSORT algorithms. First, Kaplan–Meier and univariate Cox regression analyses indicated that the immune cell score was a prognostic factor for overall survival (OS) and recurrence-free survival (RFS). Multivariate Cox regression analysis further revealed that the immune cell score was an independent prognostic factor for UCEC patients. Second, we investigated the correlation between the infiltration levels of 22 types of immune cells and the immune score. Survival analysis based on the 22 immune cell types showed that higher levels of regulatory T cell, activated NK cell, and follicular helper T-cell infiltration were associated with longer OS, while higher levels of CD8+ T cell and naive B-cell infiltration were associated with longer RFS. Next, we performed differential expression and prognosis analyses on 1534 immune-related genes and selected five from 14 candidate genes to construct a prognostic prediction model. The area under the receiver-operating characteristic (ROC) curve (AUC) for 3- and 5-year survival were 0.711 and 0.728, respectively. Further validation using a stage I–II subgroup showed similar results, presenting AUC values for 3- and five-year survival of 0.677 and 0.692, respectively. Taken together, the present study provides not only a deeper understanding of the relationship between UCEC and the immune landscape but also guidance for the future development of UCEC immunotherapy.     

Rcs双组分调节系统对细菌环境应答的分子调控研究进展

荚膜异多糖酸合成调节(Regulator of Capsule Synthesis,Rcs)系统是存在于许多肠杆菌科细菌中非典型的双组分调节系统,由3种核心蛋白(跨膜感应激酶RcsC、跨膜蛋白RcsD和响应调节剂RcsB)及多种辅助蛋白共同构成。Rcs系统能整合环境信号、调节基因表达并改变细菌的生理行为。近年来,对细菌Rcs系统环境应答机制的探索成为一个新的研究热点。本文重点综述Rcs系统上游信号的感知与传导、Rcs系统调节的下游靶基因及其生命现象,以期能增进对细菌Rcs系统的认识,同时为细菌的安全控制、感染预防和治疗新方案的开发提供参考。     

解淀粉芽孢杆菌生防菌BS-3全基因组测序及生物信息分析

【背景】解淀粉芽孢杆菌BS-3是从健康橡胶树树根中分离获得的一株对真菌具有较强抗菌活性的内生细菌,有作为生物农药的潜力。【目的】解析菌株BS-3的基因组序列信息,以深入研究该菌株防病促生机制及挖掘次级代谢产物基因资源。【方法】采用第二代BGISEQ与第三代Pac Bio平台相结合的测序技术,对生防菌BS-3进行全基因组测序,并对测序数据进行基因组组装、基因预测与功能注释、共线性分析及次级代谢产物合成基因簇预测等。【结果】BS-3全基因组大小为3 870 130 bp,平均GC含量为46.88%,共编码4 161个基因;含有92个t RNA基因、28个r RNA、10个sRNA;含有122个串联重复序列、98个小卫星DNA、2个微卫星。在COG、GO、KEGG、NR和Swiss-Prot数据库分别注释到基因2 875、2 620、1 885、4 040和3 328个。同时,预测到BS-3中有10个次级代谢产物合成基因簇,编码表面活性素、丰原素、多烯类、儿茶酚型嗜铁素等抑菌物质。基因组测序数据提交至NCBI获得GenBank登录号为CP060384。【结论】为基因组层面上解析菌株BS-3具有良好防病效果的内在原因提供基础数据,为深入了解解淀粉芽孢杆菌次级代谢合成途径提供参考信息,对菌株BS-3后续相关研究具有重要意义。     

气囊在细菌中的生理功能、生物合成及应用研究进展

气囊是在水生细菌中广泛存在的一种具有刚性中空蛋白结构的特殊细胞器,不仅为水生细菌提供浮力,还对其在不利环境或应激条件下的生存至关重要。近期研究发现在其他非水生细菌如沙雷氏菌和链霉菌中也存在气囊结构,而且表现出不同的生理功能。来源于不同种属细菌的气囊生物合成基因簇具有各自鲜明的特征,其生物合成和调控机制也有所不同。本综述将介绍和总结不同细菌中气囊的基本生理功能和生物合成及调控机制,以及气囊的生物技术应用,并对气囊在链霉菌中的生物合成研究以及人工重组气囊的潜在应用进行展望。     

Sex identification of morphologically-undifferentiated Siberian sturgeon with statistical analysis of gene expression patterns

The purpose of this study was to detail a simple strategy for sexing morphologically-undifferentiated fish using statistical analysis of gene expression patterns characterized by quantitative PCR. This approach is especially relevant for species without known genomic sex markers. The method was developed for early identification of female Siberian sturgeon as part of a genomics study. That study documented activation of the enzyme 17ß-hydroxy-steroid-dehydrogenase (hsd17b1) in future ovarian tissue at 3 months of age, concurrent with a small forkhead box L2 (foxl2) peak and emerging cytochrome P450, family 19, subfamily A (cyp19a1) expression. Major cyp19a1 and foxl2 peaks occurred in presumptive female gonads at 5–6 months. This pattern suggested a genetic relay mediating estrogen production throughout differentiation, possibly to maintain gonadal femininity. Genes involved in stem cell proliferation (lim homeobox 2 (lhx2)) and somatic-germ cell interaction maintenance (iroquois homeobox 5 (irx5) and iroquois homeobox 3 (irx3)) were also expressed during molecular differentiation, at 5–6 months. The roles of lhx2, irx3, and irx5 in fish sex differentiation should be confirmed using other methodologies. These results indicate that estrogens are crucial for ovarian differentiation in basal non-teleost fish, consistent with well-established patterns in teleosts, with hsd17b1 as one of the earliest biomarkers of gonadal development.     

赤水河外来鱼类尖头(鱥)和董氏须鳅的引种溯源及生态适应性分析

历史上,赤水河流域干流及支流的鱼类物种组成中未曾出现过尖头 （Rhynchocypris oxycephalus）和董氏须鳅（Barbatula toni）。但是,近年来在赤水河支流白沙河的鱼类资源调查中发现了这两个物种的分布,其来源及未来的生存可能性受到关注。本研究比较了尖头 赤水河野外种群与养殖种群形态上的差异;基于线粒体Cyt b基因序列,分析了赤水河流域尖头 和董氏须鳅的来源,并通过生态位模型分析了这两种鱼在赤水河流域的生态适应性。形态数据结果表明,尖头 在赤水河的野外种群与养殖种群的个体大小存在显著差异,养殖种群的体长、尾柄长、尾柄高3个形态数据均高于野外种群。分子系统发育分析结果显示,尖头 赤水河流域野外种群及养殖种群与辽宁杨运种群聚为一支,董氏须鳅则与来自内蒙古、辽宁和河北的种群聚为一支。生态位模型分析表明,赤水河支流白沙河具有尖头 的中度适生区,其适生性概率为0.620;而董氏须鳅在该区域的适生性概率较低,仅为0.025,这可能与该物种已有分布数据较少有关。采样中发现白沙河实际采样点的水温较低,与北方分布点的水温接近,推测该区域仍具备尖头 和董氏须鳅生存的条件。综上所述,赤水河流域的尖头 和董氏须鳅均为来自东北地区的外来种,且能适应赤水河的生态环境。这与现场访问结果一致,未来需要加强种群监测以防成为外来入侵种。