单细胞转录组测序技术在细胞分类中的应用

多细胞有机体的细胞类型多且复杂,细胞间普遍存在异质性。目前,单细胞转录组测序(single-cell RNA sequencing,scRNA-seq)技术是一项新兴的研究单个细胞转录水平的技术,其从数千个平行的细胞中生成转录谱,揭示个体细胞基因组的差异性表达,反映细胞间的异质性,从而鉴定出不同细胞类型,形成组织或器官的细胞图谱,在生物和临床医学等领域发挥重要作用。该文在对scRNA-seq测序平台进行阐述和比较的基础上,着重介绍其在神经系统和免疫系统细胞类型探索中的应用,并且总结scRNA-seq与空间转录组技术相结合的研究成果。     

Assessment and Refinement of Sample Preparation Methods for Deep and Quantitative Plant Proteome Profiling

A major challenge in the field of proteomics is obtaining high‐quality peptides for comprehensive proteome profiling by LC–MS. Here, evaluation and modification of a range of sample preparation methods using photosynthetically active Arabidopsis leaf tissue are done. It was found that inclusion of filter‐aided sample preparation (FASP) based on filter digestion improves all protein extraction methods tested. Ultimately, a detergent‐free urea‐FASP approach that enables deep and robust quantification of leaf and root proteomes is shown. For example, from 4‐day‐old leaf tissue, up to 11 690 proteins were profiled from a single sample replicate. This method should be broadly applicable to researchers working with difficult to process plant samples.     

表油菜素内酯对拟南芥细胞分化的影响

研究了表油菜素内酯（ｅｐｉ－ＢＲ）对拟南芥细胞体外分化的影响．表明ｅｐｉ－ＢＲ不仅能促进愈伤组织的增殖,而且还能有效地诱导愈伤组织转绿,继而分化绿芽和长成小植株,其诱导频率高达７０％以上。电镜观察表明,ｅｐｉ－ＢＲ诱导的转绿细胞中的叶绿体发育正常。     

利用激光扫描共聚焦显微镜研究植物细胞发育形态学变化

通过激光扫描共聚焦显微镜,利用不同种类(波长)的激光研究植物细胞发育形态学变化。结果表明,利用紫外激光(351 nm)扫描可以清楚地观察到拟南芥叶片表皮细胞的形态及其变化,在已分化的叶片表皮上可观察到包括“铺垫”表皮细胞(epidermal pavement cells)、气孔保卫细胞(guard cell)、气孔伴胞(subsidiarycells)、表皮毛细胞(trichomes)和表皮毛的足细胞(socket cells)等多种形态不同的细胞种类;利用蓝光激光(488nm)辅助曙红浅染,可清晰地显示出拟南芥根生长区内部的各种原始细胞,包括静止区(quiescent center)细胞、皮层/内皮层原始细胞(cortex/endodermal initial cell)、表皮/根冠原始细胞(epidermal/root cap initial cell)和中柱/根冠原始细胞(columella/root cap initial cell)等。利用双光子激光(800 nm)连续扫描30 s可以诱发叶绿体产生自发荧光,并可观察到叶绿体在叶肉细胞中的运动轨迹。结果说明激光扫描共聚焦显微镜在植物细胞形态及发育研究上具有独特的功能。     

小鼠正常黑素细胞和小鼠B16黑素瘤细胞的环状RNAs表达谱

黑素瘤是一种多发于皮肤的恶性肿瘤,因其侵袭性强,预后差等特点一直是科研人员关注的热点。环状RNAs(circRNAs)是一种新型内源性非编码RNA,广泛参与动物生长发育、细胞分化和信号转导等生理过程,但circRNAs在黑素瘤细胞内的分子机制尚未被充分解析。本研究以小鼠(C57BL/6J)正常黑素细胞及B16黑素瘤细胞为研究对象,采用二代测序技术分析两种细胞间circRNAs表达特性。测序结果显示,小鼠正常黑素细胞和黑素瘤细胞中共有851个circRNAs,其中195个差异表达circRNAs(DECs)。GO及KEGG数据库注释发现,DECs的来源基因主要参与细胞周期(cell cycle)、紧密结合(tight junction)、Rap1信号通路(Rap1 signaling pathway)、TGF-beta信号通路(TGF-beta signaling pathway)等与细胞增殖、迁移相关的信号通路;探究发现,黑素瘤细胞中显著性高表达的circE2F5(circ-3:14578602|14606309)通过上调E2F5的表达促进黑素瘤细胞增殖。circRNA靶基因预测发现,...     

Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing

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环境激素DBP对拟南芥试管形态发生的影响

报道了酞酸酯类化合物DBP对拟南芥试管形态发生的影响。利用不同浓度的DBF处理拟南芥茎段外植体,切片观察拟南芥茎段试管形态发生过程中脱分化、分化及再分化的变化情况。结果发现：拟南芥茎段外植体在对照组培养基上生长良好,首先是愈伤组织产生,而后愈伤组织块增大,颜色呈淡绿色,生长旺盛,并有分化出芽现象;添加0．01mg／L、0．1mg／L和1．0mg／LDBP,茎段愈伤组织诱导率低,且高浓度时愈伤组织出现褐化、活力差的现象;培养12h、24h、2d、3d、7d、14d、21d和28d茎段显微切片结果显示,DBP具有抑制拟南芥试管形态发生的作用,随着DBP浓度的增加呈现剂量抑制效应。     

Phosphorylated Glycans Produced from Nonreducing Mono- and Oligosaccharides by the Action of P2O5 in Dimethyl Sulfoxide,and Their Interactions with Concanavalin A

The action of P₂O₅ in DMSO on methyl α-d-glucopyranoside, sucrose and trehalose afforded nondializable, phosphorylated glycans in 6~34% yields. Polysucrose has a molecular weight of ~9,500. The synthetic glycans consist of carbohydrate (46~59%) and P (11.4~13.1%) and show reducing sugar values (5.0~30.8%). The alkaline hydrolysis of polysucrose was accompanied with a depolymerization and afforded sugar phosphates and oligosaccharides. The periodate oxidation gave formic acid (0.15~0.34 mole) and formaldehyde (0.07~0.17 mole/monosaccharide residue). The methylation study indicated their variously branched structures. 2,3,4,6-Tetra-O-methyl-d-glucose was found in only 0.7 ~3.2% yields, and this is in agreement with their weak precipitation reactions with Con A. It is considered that the glycans are produced from nonreducing mono- and oligosaccharides by dehydration, transglycosidation and esterification with phosphate.     

拟南芥色氨酸与吲哚乙酸生物合成的研究进展

拟南芥色氨酸生物合成途径的研究已逐渐成为植物分子生物学家了解植物基因结构和表达调控最主要的模式系统之一。到目前为止,编码拟南芥色氨酸合成途径的七种酶蛋白的基因已经全部被克隆,并进行了不同程度的分子生物学研究。长期以来,色氨酸一直被认为是植物生长素吲哚乙酸（ＩＡＡ）生物合成（从头合成）的前体物,但近年来人们发现生长素合成的非色氨酸途径可能是其在植物中生物合成的主要途径。植物在不同的发育阶段可能采用不同的方式合成ＩＡＡ。     

Monitoring differential synthesis of RNA in individual cells by capillary electrophoresis

A capillary electrophoresis (CE)-based technique is reported here to monitor differential RNA synthesis in individual Chinese hamster ovary cells at distinct stages of the cell proliferation cycle. Cell synchronization was achieved by the shake-off method, in which mitotic (M) cells were dislodged, and cells at G(1), S, and G(2) phases were harvested 2.5, 10, and 13 h, respectively, after synchronizing the mitotic cells. Thirty-two cells (eight from each phase) were analyzed by injecting each cell into the capillary, lysing it with dilute surfactant, separating the RNA by capillary electrophoresis, and detecting the peaks with laser-induced fluorescence. The results from single cells show that the total amount of RNA increased at each successive stage (from G(1) to M), while the relative synthetic rates of different RNA fractions varied with progression through the cycle. There was a threefold increase in the synthetic rate of total RNA from S to G(2), compared with G(1) to S. In addition, differential accumulation of specific RNA fractions was observed, with the low-molecular-mass fraction exhibiting a much higher synthetic rate from G(2) to M, relative to the rates of the larger ribosomal RNA (rRNA) fractions. Comparison of the large rRNA fractions with one another reveals that at S phase more 28S rRNA was accumulated than 18S rRNA, and at G(1) and M phases, the synthetic rate of 28S rRNA was slowed compared with that of 18S. Minimal sample preparation, combined with the separation power of CE and single-cell detection sensitivity of laser-induced fluorescence, results in a simple method for assessing differential accumulation of RNA from distinct individual cells.     

Cryptic population genetic structure: the number of inferred clusters depends on sample size

Clustering methods have been used extensively to unravel cryptic population genetic structure. We investigated the effect of the number of individuals sampled in each location on the resulting number of clusters. Our study was motivated by recent results in Arabidopsis thaliana: studies in which more than one individual was sampled per location apparently have led to a much higher number of clusters than studies where only one individual was sampled in each location, as is generally done in this species. We show, using computer simulations and microsatellite data in A. thaliana, that the number of sampled individuals indeed has a strong impact on the number of resulting clusters. This effect is smaller if the sampled populations have a hierarchical structure. In most cases, sampling 5–10 individuals per population should be enough. The results argue for abandoning the concept of ‘accessions’ in partially selfing organisms.     

Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana

Hybrids often differ in fitness from their parents. They may be superior, translating into hybrid vigour or heterosis, but they may also be markedly inferior, because of hybrid weakness or incompatibility. The underlying genetic causes for the latter can often be traced back to genes that evolve rapidly because of sexual or host–pathogen conflicts. Hybrid weakness may manifest itself only in later generations, in a phenomenon called hybrid breakdown. We have characterized a case of hybrid breakdown among two Arabidopsis thaliana accessions, Shahdara (Sha, Tajikistan) and Lövvik‐5 (Lov‐5, Northern Sweden). In addition to chlorosis, a fraction of the F₂ plants have defects in leaf and embryo development, and reduced photosynthetic efficiency. Hybrid chlorosis is due to two major‐effect loci, of which one, originating from Lov‐5, appears to encode an RNA helicase (AtRH18). To examine the role of the chlorosis allele in the Lövvik area, in addition to eight accessions collected in 2009, we collected another 240 accessions from 15 collections sites, including Lövvik, from Northern Sweden in 2015. Genotyping revealed that Lövvik collection site is separated from the rest. Crosses between 109 accessions from this area and Sha revealed 85 cases of hybrid chlorosis, indicating that the chlorosis‐causing allele is common in this area. These results suggest that hybrid breakdown alleles not only occur at rapidly evolving loci, but also at genes that code for conserved processes.     

Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing

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细胞周期后期促进因子DIG9对植物侧根发生的调控研究

在植物体内,细胞周期对于植物的萌发、生长、开花、结实等各个生长发育阶段具有重要作用。细胞周期正常运转需要依赖一些细胞周期蛋白,但是目前关于细胞周期蛋白调控根发育的分子机制还不清楚。通过筛选模式植物拟南芥的根发育异常突变体,分离鉴定了1个突变体dig9（drought inhibition of lateral root growth）,该突变体表现为主根短、侧根少、发育迟缓、顶端分生组织变小、叶片扭曲、无主茎等表型。通过图位克隆,成功定位并克隆了DIG9基因,该基因编码一个细胞周期蛋白,是有丝分裂后期促进复合体的一个亚基APC8 （anaphase-promoting complex）。通过亚细胞定位发现DIG9定位于细胞核;qRT-PCR检测发现DIG9基因在根中有较高的表达量,进一步通过启动子-GUS报告系统发现DIG9在根尖、侧根和顶端分生组织等细胞分裂旺盛区域表达。外施IAA能恢复dig9突变体的侧根表型但不能恢复根短表型。dig9突变体对干旱及盐胁迫反应不敏感。研究结果表明DIG9基因可能通过影响IAA的产生来调控植物的侧根发育。     

The peptaibol alamethicin induces an rRNA-cleavage-associated death in Arabidopsis thaliana

The plant-metabolic response to amphipathic peptides produced by the soil fungi of the genus Trichoderma remains largely unknown. The present investigation was undertaken to examine the death process in alamethicin-treated Arabidopsis thaliana plantlets. The rapid death triggered by alamethicin (at 50 microM) was shown to be associated with protein-synthesis arrest and with specific cleavage of 18S and 25S ribosomal RNA. The use of an inhibitor of nitric oxide (NO) synthases and of an NO scavenger suggested that rRNA cleavage was suppressed by NO. Experiments conducted with a synthetic alamethicin analogue, in which all alpha-aminoisobutyric acid (Aib) residues have been replaced by leucine moieties, showed that the non-coded residues are essential for the ability of the peptaibol to induce rRNA cleavage in Arabidopsis. Our data indicate that further investigations on the mode of action of alamethicin in planta could be of great interest to study the death-signaling pathway associated with rRNA degradation in plants.