中国4个少数民族中SDF1多态性研究

研究与HIV 1感染相关的基质细胞衍生因子 (SDF1)等位基因突变频率和多态性在中国 4个少数民族的分布特征。应用PCR/ RFLP等方法检测回族 (5 7例 )、鄂伦春族 (71例 )、蒙古族 (30例 )及锡伯族 (2 6例 )共 184个个体中SDF1 -3’A基因突变频率。结果得出中国 4个民族中SDF1- 3’A基因的基因频率分别为 :蒙古族为 38 3%,锡伯族为 2 3 .1%,回族为 2 0 .2 %,鄂伦春族为 10 .6 %。中国 4个少数民族中SDF1- 3’A等位基因频率存在较大的差异 (χ2 =37 .82 6 ,P<0.01) , 提示这 4 个民族的遗传结构存在着一定的差异。 本研究 为评估中国不同民族对 HIV-1 的易感性及艾滋病的流行病学研究提供了基本数据。     

scHiCTools: A computational toolbox for analyzing single-cell Hi-C data

Single-cell Hi-C (scHi-C) sequencing technologies allow us to investigate three-dimensional chromatin organization at the single-cell level. However, we still need computational tools to deal with the sparsity of the contact maps from single cells and embed single cells in a lower-dimensional Euclidean space. This embedding helps us understand relationships between the cells in different dimensions, such as cell-cycle dynamics and cell differentiation. We present an open-source computational toolbox, scHiCTools, for analyzing single-cell Hi-C data comprehensively and efficiently. The toolbox provides two methods for screening single cells, three common methods for smoothing scHi-C data, three efficient methods for calculating the pairwise similarity of cells, three methods for embedding single cells, three methods for clustering cells, and a build-in function to visualize the cells embedding in a two-dimensional or three-dimensional plot. scHiCTools, written in Python3, is compatible with different platforms, including Linux, macOS, and Windows.     

TM7SF1 (GPR137B): a novel lysosome integral membrane protein

In the previous proteomic study of human placenta, transmembrane 7 superfamily member 1 (TM7SF1) was found enriched in lysosome compartments. TM7SF1 encodes a 399-amino acid protein with a calculated molecular mass of 45 kDa. Bioinformatic analysis of its amino acid sequence showed that it is a multipass transmembrane protein containing a potential dileucine-based lysosomal targeting signal and four putative N-glycosylation sites. By percoll-gradient centrifugation and further subfraction ways, the lysosomal solute and membrane compartments were isolated respectively. Immunoblotting analysis indicated that TM7SF1 was co-fractioned with lysosome associated membrane protein 2 (LAMP2), which was only detected in lysosomal membrane compartments whereas not detected in the solute compartments. Using specific anti-TM7SF1 antibody and double-immunofluorescence with lysosome membrane protein LAMP1 and Lyso-Tracker Red, the colocalisations of endogenous TM7SF1 with lysosome and late endosome markers were demonstrated. All of this indicated that TM7SF1 is an integral lysosome membrane protein. Rat ortholog of TM7SF1 was found to be strongly expressed in heart, liver, kidney and brain while not or low detected in other tissues. In summary, TM7SF1 was a lysosomal integral membrane protein that shows tissue-specific expression. As a G-protein-coupled receptor in lysosome membrane, TM7SF1 was predicted function as signal transduction across lysosome membrane.     

吉林珲春自然保护区东北虎和东北豹及其有蹄类猎物的多度与分布

珲春国家级自然保护区是东北虎(Panthera tigris altaica)、东北豹(Panthera pardus orientalis)等濒危物种在中国的核心分布区。为了探究该区域野生动物的多度水平和空间分布, 了解人类干扰情况, 我们运用相对多度指数(relative abundance index, RAI)分析了2013年4-6月设置于此的83个红外相机位点的监测数据。红外相机的总捕获天数6,060 d, 共捕获10科18种野生哺乳动物, 其中鼬科4种, 猫科动物3种, 犬科、鹿科和松鼠科各2种, 猪科、熊科、麝科、猬科和兔科各1种。研究期间共拍摄到东北虎11只个体, 东北豹13只个体。从相对多度指数来看, 东北虎的相对多度(0.84)远高于东北豹(0.48), 它们的有蹄类猎物中梅花鹿(Cervus nippon)的相对多度最高(2.18), 其次为狍(Capreolus pygargus)(1.53)和野猪(Sus scrofa)(0.92)。人类活动和放牧的相对多度水平(分别为40.64和2.76)显著高于野生动物。在空间分布上, 东北虎和梅花鹿主要在保护区的核心区分布, 且与保护区社区共管区的多度水平差异显著, 而东北豹在不同功能区之间的分布差异不显著, 狍在保护区北部的多度水平较高, 但各功能区之间差异不显著, 野猪在社区共管区的多度水平显著高于核心区。可见, 核心区频繁的人类活动和放牧活动对野生动物的保护产生了影响, 未来应加强关于人类干扰对虎、豹种群及其有蹄类猎物的影响评估。     

The roles of autophagy in development and stress responses in Arabidopsis thaliana

Autophagy is a dynamic process that involves the recycling process of the degradation of intracellular materials. Over the past decade, our molecular and physiological understanding of plant autophagy has greatly been increased. Most essential autophagic machineries are conserved from yeast to plants. The roles that autophagy-related genes (ATGs) family play in the lifecycle of the Arabidopsis are proved to be similar to that in mammal. Autophagy is activated during certain stages of development, senescence or in response to starvation, or environmental stress in Arabidopsis. In the progression of autophagy, ATGs act as central signaling regulators and could develop sophisticated mechanisms to survive when plants are suffering unfavorable environments. It will facilitate further understanding of the molecular mechanisms of autophagy in plant. In this review, we will discuss recent advances in our understanding of autophagy in Arabidopsis, areas of controversy, and highlight potential future directions in autophagy research.     

The combined use of photoaffinity labeling and surface plasmon resonance‐based technology identifies multiple salicylic acid‐binding proteins

Salicylic acid (SA) is a small phenolic molecule that not only is the active ingredient in the multi‐functional drug aspirin, but also serves as a plant hormone that affects diverse processes during growth, development, responses to abiotic stresses and disease resistance. Although a number of SA‐binding proteins (SABPs) have been identified, the underlying mechanisms of action of SA remain largely unknown. Efforts to identify additional SA targets, and thereby elucidate the complex SA signaling network in plants, have been hindered by the lack of effective approaches. Here, we report two sensitive approaches that utilize SA analogs in conjunction with either a photoaffinity labeling technique or surface plasmon resonance‐based technology to identify and evaluate candidate SABPs from Arabidopsis. Using these approaches, multiple proteins, including the E2 subunit of α‐ketoglutarate dehydrogenase and the glutathione S‐transferases GSTF2, GSTF8, GSTF10 and GSTF11, were identified as SABPs. Their association with SA was further substantiated by the ability of SA to inhibit their enzymatic activity. The photoaffinity labeling and surface plasmon resonance‐based approaches appear to be more sensitive than the traditional approach for identifying plant SABPs using size‐exclusion chromatography with radiolabeled SA, as these proteins exhibited little to no SA‐binding activity in such an assay. The development of these approaches therefore complements conventional techniques and helps dissect the SA signaling network in plants, and may also help elucidate the mechanisms through which SA acts as a multi‐functional drug in mammalian systems.     

Natural variation in the promoter of OsHMA3 contributes to differential grain cadmium accumulation between Indica and Japonica rice

Rice is a major source of cadmium(Cd) intake for Asian people. Indica rice usually accumulates more Cd in shoots and grains than Japonica rice. However, underlying genetic bases for differential Cd accumulation between Indica and Japonica rice are still unknown. In this study, we cloned a quantitative trait locus(QTL) grain Cd concentration on chromosome 7(GCC7) responsible for differential grain Cd accumulation between two rice varieties by performing QTL analysis and map-based cloning. We found that the two GCC7 alleles, GCC7~(PA64s) and GCC7~(93-11), had different promoter activity of OsHMA3,leading to different OsHMA3 expression and different shoot and grain Cd concentrations. By analyzing the distribution of different haplotypes of GCC7 among diverse rice accessions, we discovered that the high and low Cd accumulation alleles, namely GCC7~(93-11) and GCC7~(PA64s), were preferentially distributed in Indica and Japonica rice,respectively. We further showed that the GCC7~(PA64s)allele can be used to replace the GCC7~(93-11) allele in the super cultivar 93-11 to reduce grain Cd concentration without adverse effect on agronomic traits. Our results thus reveal that the QTL GCC7 with sequence variation in the OsHMA3 promoter is an important determinant controlling differential grain Cd accumulation between Indica and Japonica rice.