High-quality genome assembly of Huazhan and Tianfeng,the parents of an elite rice hybrid Tian-you-hua-zhan

High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding. Tian-you-hua-zhan has been a leading hybrid in China over the past decade. Here, de novo genome assembly strategy optimization for the rice indica lines Huazhan (HZ) and Tianfeng (TF), including sequencing platforms, assembly pipelines and sequence depth, was carried out. The PacBio and Nanopore platforms for long-read sequencing were utilized, with the Canu, wtdbg2, SMARTdenovo, Flye, Canu-wtdbg2, Canu-SMARTdenovo and Canu-Flye assemblers. The combination of PacBio and Canu was optimal, considering the contig N50 length, contig number, assembled genome size and polishing process. The assembled contigs were scaffolded with Hi-C data, resulting in two “golden quality” rice reference genomes, and evaluated using the scaffold N50, BUSCO, and LTR assembly index. Furthermore, 42,625 and 41,815 non-transposable element genes were annotated for HZ and TF, respectively. Based on our assembly of HZ and TF, as well as Zhenshan97, Minghui63, Shuhui498 and 9311, comprehensive variations were identified using Nipponbare as a reference. The de novo assembly strategy for rice we optimized and the “golden quality” rice genomes we produced for HZ and TF will benefit rice genomics and breeding research, especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.

     

Visualization of the uptake of high-density lipoprotein by rat aortic endothelial cells and smooth muscle cells in vitro

High-density lipoproteins (HDL) were conjugated to Fluorescein 1,1-dioctadecyl 3,3,3,3-tetramethylindocarbocyanine perchlorate (DiI) or colloidal gold for the investigation of ultrastructural aspects of binding and uptake of HDL by cholesterol-loaded cultured endothelial and smooth muscle cells from rat aorta. When cells were incubated for 2h at 4°C, HDL–DiI and HDL–gold conjugates were seen only on the cell surface. When cells were returned to incubation at 37°C for 5min, HDL–DiI appeared in the cytoplasm and colocalized with the fluorescent cholesteryl ester tag BODIPY-FL-C₁₂. HDL–gold conjugates appeared in the plasmalemmal invaginations and plasmalemmal vesicles. After incubation for 15min, most of the HDL–gold conjugates reappeared on the cell surface. After incubation for 30min, only a few conjugates were observed and they localized in lysosomal-like bodies. Quantitative data indicated that when the cholesterol-loaded cells were incubated at 4°C for 2h, the numbers of HDL–gold associated in clusters on the endothelial cell surface was 1.18 clusters/m. When cells were returned to incubation at 37°C for 5min, this value decreased to 0.7, increased again to 1.13 at 15min, and decreased to 0.29 at 30min. The numbers of clusters in the plasmalemmal invaginations were 0.06 clusters/m at 4°C for 2h, increased to 0.34 at 37°C for 5min and decreased gradually to 0.19 and 0.04 at 15 and 30min, respectively. The incidence of clusters in the plasmalemmal vesicles per non-nuclear cytoplasm was 0.01 clusters/m² at 4°C for 2h, increased significantly to 1.08 at 37°C for 5min, and decreased to 0.43 and 0.14 at 15 and 30min, respectively. This work supports that the plasmalemmal invaginations and plasmalemmal vesicles are linked to the HDL uptake in cholesterol-loaded aortic endothelial cells and smooth muscle cells.     

微波杀菌过程中大肠杆菌与金黄色葡萄球菌细胞膜通透性的改变

对细胞膜通透性变化的研究是认识微波杀菌机理的途径之一。用荧光探针检测微波处理后细胞内Ca2 浓度的变化,可以精确地表征细胞膜通透性的改变。选用二乙酸荧光素(FDA)和Fluo-3/AM两种荧光染料,对大肠杆菌(Escherichiacoli)和金黄色葡萄球菌(Staphylococcus aureus)经微波处理后的酯酶活性及细胞膜通透性进行研究,结果表明大肠杆菌与金黄色葡萄球菌的胞内非特异性酯酶(NSE)活性及细胞膜通透性的变化情形有所不同。在50℃、55℃、60℃和65℃微波处理条件下,大肠杆菌细胞膜通透性分别增加了20.7%、28.1%、74.8%、89.8%,而金黄色葡萄球的增加不显著,分别比对照组提高了4.1%、6.0%、21.9%和19.7%。细胞膜通透性的改变与微生物致死率有一定的相关性,也可能是微波杀菌非热效应的表现之一。     

nisZ启动子结构与功能的研究

应用βGlucuronidase基因(gusA)作为报告基因,通过定点突变方法分别缺失nisZ编码区上游两个启动子结构(promoter1和promoter2)中的一个,发现只有靠近编码区的promoter2是nisZ启动子诱导表达所必需。将promoter2中10区及其上游的一个碱基突变为乳酸菌中典型的组成型启动子的10区结构,该改变使nisZ启动子诱导功能下降;将promoter2的10区和35区的间隔区由20个碱基缺失突变为17个碱基,则nisZ启动子失去诱导功能。据此认为该间隔区的结构与nisZ启动子的诱导表达密切相关。     

Selenium-containing 15-mer peptides with high glutathione peroxidase-like activity

Glutathione peroxidase (GPX) is one of the most crucial antioxidant enzymes in a variety of organisms. Here we described a new strategy for generating a novel GPX mimic by combination of a phage-displayed random 15-mer peptide library followed by computer-aided rational design and chemical mutation. The novel GPX mimic is a homodimer consisting of a 15-mer selenopeptide with an appropriate catalytic center, a specific binding site for substrates, and high catalytic efficiency. Its steady state kinetics was also studied, and the values of k(cat)/K(m)(GSH) and k(cat)/ K(mH(2)O(2)) were found to be similar to that of native GPX and the highest among the existing GPX mimics. Moreover, the novel GPX mimic was confirmed to have a strong antioxidant ability to inhibit lipid peroxidation by measuring the content of malondialdehyde, cell viability, and lactate dehydrogenase activity. Importantly, the novel GPX mimic can penetrate into the cell membrane because of its small molecular size. These characteristics endue the novel mimic with potential perspective for pharmaceutical applications.     

Epitope Tags beside the N-Terminal Cytoplasmic Tail of Human BST-2 Alter Its Intracellular Trafficking and HIV-1 Restriction

BST-2 blocks the particle release of various enveloped viruses including HIV-1, and this antiviral activity is dependent on the topological arrangement of its four structural domains. Several functions of the cytoplasmic tail (CT) of BST-2 have been previously discussed, but the exact role of this domain remains to be clearly defined. In this study, we investigated the impact of truncation and commonly-used tags addition into the CT region of human BST-2 on its intracellular trafficking and signaling as well as its anti-HIV-1 function. The CT-truncated BST-2 exhibited potent inhibition on Vpu-defective HIV-1 and even wild-type HIV-1. However, the N-terminal HA-tagged CT-truncated BST-2 retained little antiviral activity and dramatically differed from its original protein in the cell surface level and intracellular localization. Further, we showed that the replacement of the CT domain with a hydrophobic tag altered BST-2 function possibly by preventing its normal vesicular trafficking. Notably, we demonstrated that a positive charged motif “KRXK” in the conjunctive region between the cytotail and the transmembrane domain which is conserved in primate BST-2 is important for the protein trafficking and the antiviral function. These results suggest that although the CT of BST-2 is not essential for its antiviral activity, the composition of residues in this region may play important roles in its normal trafficking which subsequently affected its function. These observations provide additional implications for the structure-function model of BST-2.     

西南岩溶地区黄荆和檵木叶片结构对其生态环境的响应

应用常规石蜡切片法对生长于桂林毛村岩溶区和非岩溶区的黄荆(Vitex negundo)和檵木(Loropetalumchinense)的解剖特征进行了比较研究,并对两区的黄荆叶片表皮形态进行了扫描电镜观察.结果显示:(1)两地的黄荆叶片背面均有浓密的绒毛,但致密程度有差异,岩溶区黄荆叶片的气孔深藏于绒毛间隙,这种结构可减少水分蒸发,降低因岩溶干旱带来的水分缺失.(2)岩溶区黄荆和檵木的叶片厚度、上下表皮厚度、栅栏组织的厚度以及栅栏组织的致密程度均大于非岩溶区,这些特征有利于减少水分蒸腾.(3)岩溶区黄荆和檵木叶片的维管组织发达程度高于非岩溶区,有利于在蒸腾减小的情况下促进水分运输和营养元素的迁移,说明2种植物叶片结构特征在不同生境区的改变是其长期在岩溶区干旱环境条件下形成的适应性变化.     

植物转基因沉默研究进展

随着转基因技术在植物中的广泛应用,转基因沉默受到越来越多的重视。转基因沉默可发生在转录和转录后两种水平,其基本特征就是依赖于同源的重复序列。转基因的重复拷贝间,转基因与同源的内源基因间及RNA病毒与同源转基因间都会发生基因沉默。可能有不同的机制导致转基因沉默,本文综述了转基因沉默的机理研究及转基因沉默在植物抗病基因工程和植物功能基因组学方面的应用 。