分类: 生物学 >> 植物学 >> 植物生理学 提交时间: 2016-05-03
摘要: The whitefly (Bemisia tabaci) causes tremendous damage to cotton production worldwide. However, very limited information is available about how plants perceive and defend themselves from this destructive pest. In this study, the tran WRKY40 and copper transport protein are hub genes that may regulate cotton defenses to whitefly infestation. Silencing GhMPK3 by virus-induced gene silencing (VIGS) resulted in suppression of the MPK-WRKY-JA and ET pathways and lead to enhanced whitefly susceptibility, suggesting that the candidate insect resistant genes identified in this RNA-Seq analysis are credible and offer significant utility. Taken together, this study provides comprehensive insights into the cotton defense system to whitefly infestation and has identified several candidate genes for control of phloem-feeding pests.
分类: 生物学 >> 植物学 >> 植物生物化学、植物生物物理学 提交时间: 2016-05-03
摘要: Starch is the major component in maize kernels, providing a stable carbohydrate source for humans and livestock as well as raw material for the biofuel industry. Increasing maize kernel starch content will help meet industry demands and has the potential to increase overall yields. We developed a pair of maize near-isogenic lines (NILs) with different alleles for a starch quantitative trait locus on chromosome 3 (qHS3), resulting in different kernel starch content. To investigate the candidate genes for qHS3 and elucidate their effects on starch metabolism, RNA-Seq was performed for the developing kernels of the NILs at 14 and 21 d after pollination (DAP). Analysis of genomic and transcriptomic data identified 76 genes with nonsynonymous single nucleotide polymorphisms and 384 differentially expressed genes (DEGs) in the introgressed fragment, including a hexokinase gene, ZmHXK3a, which catalyzes the conversion of glucose to glucose-6-phosphate and may play a key role in starch metabolism. The expression pattern of all DEGs in starch metabolism shows that altered expression of the candidate genes for qHS3 promoted starch synthesis, with positive consequences for kernel starch content. These results expand the current understanding of starch biosynthesis and accumulation in maize kernels and provide potential candidate genes to increase starch content.
分类: 生物学 >> 植物学 >> 植物生物化学、植物生物物理学 提交时间: 2016-05-03
摘要: The role of plant tyrosyl-DNA phosphodiesterase 1 in genome stability is studied using a Medicago truncatula MtTdp1-depleted line. Lack of MtTdp1 results in a 39% reduction of methylated cytosines as compared to control. RNA-Seq analyses revealed that 11 DNA transposons and 22 retrotransposons were differentially expressed in the Tdp1-2a line. Among them all, DNA transposons (MuDR, hAT, DNA3-11_Mad) and seven retrotransposons (LTR (Long Terminal Repeat)/Gipsy, LTR/Copia, LTR and NonLTR/L1) were down-regulated, while the 15 retrotransposons were up-regulated. Results suggest that the occurrence of stress-responsive cis-elements as well as changes in the methylation pattern at the LTR promoters might be responsible for the enhanced retrotransposon transcription.
分类: 医学、药学 >> 临床医学 提交时间: 2023-10-24 合作期刊: 《中国全科医学》
摘要: 背景 近年来,转录组测序技术在肝癌领域的大量应用为肝癌的基因组和生物学研究提供了帮助,对近二十年 RNA-seq 应用于肝癌研究的文献进行总结分析,有助于让研究者全面了解该领域的研究热点与最新进展,为后续研究提供参考。目的 通过文献计量学分析对 RNA-seq 在肝癌治疗、诊断、发生机制等各方面研究的应用情况进行整体评价,以揭示全球 RNA-seq 应用于肝癌领域研究热点的分布情况,进而推测未来该领域的发展趋势。方法 检索 2001-01-01 至 2022-12-31 期间 Web of Science 数据库收录的 RNA-seq 应用于肝癌研究领域的英文文献,运用Microsoft Excel 2016 软件对文献进行发文量分析,运用 CiteSpace 软件进行作者、国家、机构、关键词的可视化分析,使用发文量、中心性、聚类模块值和平均轮廓值等指标对可视化结果进行评价。结果 在数据库中共检索到 RNA-seq应用于肝癌研究领域的文献 1397 篇,分析结果显示,该领域的核心作者群已经形成;中国发文量最多,但研究深度略有欠缺,美国发文量仅次于中国,但中心性最高,为 0.44;高发文量的机构大多分布在中国,影响力较大的机构大多分布在美国;关键词分析显示领域的研究热点为肝癌发生发展相关的分子机制、基因表达及其分子标志物。结论 肝癌发生发展的分子机制、疾病的的生物标志物和治疗靶点是该领域目前的研究热点,临床精准医疗可能成为未来的重点研究方向。
分类: 生物学 >> 植物学 >> 植物细胞学与植物遗传学、植物形态学 提交时间: 2016-05-03
摘要: Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high-throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker-assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
分类: 生物学 >> 生物物理学 提交时间: 2016-05-15
摘要: PTEN is a tumour suppressor frequently mutated in many types of cancers. Here we show that targeted disruption of PTEN leads to neoplastic transformation of human neural stem cells (NSCs), but not mesenchymal stem cells. PTEN-deficient NSCs display neoplasm-associated metabolic and gene expression profiles and generate intracranial tumours in immunodeficientmice. PTEN is localized to the nucleus in NSCs, binds to the PAX7 promoter through association with cAMP responsive element binding protein 1 (CREB)/CREB binding protein (CBP) and inhibits PAX7 transcription. PTEN deficiency leads to the upregulation of PAX7, which in turn promotes oncogenic transformation of NSCs and instates 'aggressiveness' in human glioblastoma stem cells. In a large clinical database, we find increased PAX7 levels in PTEN-deficient glioblastoma. Furthermore, we identify that mitomycin C selectively triggers apoptosis in NSCs with PTEN deficiency. Together, we uncover a potential mechanism of how PTEN safeguards NSCs, and establish a cellular platform to identify factors involved in NSC transformation, potentially permitting personalized treatment of glioblastoma.