Emergence,evolution, and vaccine production approaches of SARS-CoV-2 virus: Benefits of getting vaccinated and common questions

The emergence of coronavirus disease 2019 (COVID-19) pandemic in Wuhan city, China at the end of 2019 made it urgent to identify the origin of the causal pathogen and its molecular evolution, to appropriately design an effective vaccine. This study analyzes the evolutionary background of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or SARS-2) in accordance with its close relative SARS-CoV (SARS-1), which was emerged in 2002. A comparative genomic and proteomic study was conducted on SARS-2, SARS-1, and Middle East respiratory syndrome coronavirus (MERS), which was emerged in 2012. In silico analysis inferred the genetic variability among the tested viruses. The SARS-1 genome harbored 11 genes encoding 12 proteins, while SARS-2 genome contained only 10 genes encoding for 10 proteins. MERS genome contained 11 genes encoding 11 proteins. The analysis also revealed a slight variation in the whole genome size of SARS-2 comparing to its siblings resulting from sequential insertions and deletions (indels) throughout the viral genome particularly ORF1AB, spike, ORF10 and ORF8. The effective indels were observed in the gene encoding the spike protein that is responsible for viral attachment to the angiotensin-converting enzyme 2 (ACE2) cell receptor and initiating infection. These indels are responsible for the newly emerging COVID-19 variants αCoV, βCoV, γCoV and δCoV. Nowadays, few effective COVID-19 vaccines developed based on spike (S) glycoprotein were approved and become available worldwide. Currently available vaccines can relatively prevent the spread of COVID-19 and suppress the disease. The traditional (killed or attenuated virus vaccine and antibody-based vaccine) and innovated vaccine production technologies (RNA- and DNA-based vaccines and viral vectors) are summarized in this review. We finally highlight the most common questions related to COVID-19 disease and the benefits of getting vaccinated.     

人外周型苯二氮卓受体及其突变受体cDNA克隆和序列分析

用ＲＴ－ＰＣＲ方法扩增并克隆了三种人外周型苯二氮卓受体ＰＢＲｃＤＮＡ,测序表明,４４２ｂｐ片段与文献报道相比缺失８４ｂｐ编码序列,其转录水平高于正常ＰＢＲ．该序列编码一个与ＰＢＲ结构相关但缺失了２８个氨基酸残基的突变受体蛋白．这一异常转录本可能是通过选择性剪接方式转录产生并只存在于中国人肝癌ＢＥＬ７４０２细胞系,表明ＰＢＲ基因表达具有细胞特异性和异质性．突变受体的发现为研究ＰＢＲ的结构和功能提供了理想的分子和细胞模型     

MIC-A polymorphism in Japanese and a MIC-A-MIC-B null haplotype

 A polymorphic gene, MIC-A, is one of the MIC family of genes which is composed of a group of homologous genes interspersed in the class III and class I regions of the major histocompatibility complex. MIC-A is located 46 kilobases (kb) centromeric of HLA-B, and is preferentially expressed in the epithelial cells and intestinal mucosa. Recently, MIC-A and the closely related MIC-B were reported as the molecules that conferred specificity in the recognition by the V_δ1γδT cells. In the present study, polymorphic exons 2, 3, and 4 of the MIC-A gene were analyzed using the polymerase chain reaction-single-strand conformation polymorphism method. The number of patterns found in exons 2, 3, and 4 were 5, 6, and 4, respectively, in 114 healthy Japanese subjects. Eight MIC-A alleles were observed in Japanese individuals, among which one, tentatively named MIC-AMW, has not previously been reported. There was a strong linkage disequilibrium between MIC-A and HLA-B loci: each MIC-A allele showed strong association with a particular HLA-B group. In contrast, B*3901 showed association with multiple MIC-A alleles. Furthermore, the existence of a MIC-A-MIC-B null haplotype, which is associated with HLA-B*4801, was identified. In this haplotype, a large-scale deletion (of approximately 100 kb) including the entire MIC-A gene was indicated and the MIC-B gene possessed a stop codon. Received: 12 November 1998 / Revised: 18 January 1999     

Regulation of Gene Expression in Higher Plants

The study on regulation of gene expression in higher plants has attracted attention of many scientists and is also one of the major scientific research areas in modern biological studies. With advancement of the technology of genetic engineering, more and more details of gene regulation are revealed and it has been found that regulatory zones of most genes are located at the 5' upstream promoter regions. Now,the study on regulation of gene expression is mainly focused on light regulated genes, tissue specific genes, environmental stress induced genes, bormone-induced genes and so on. This article gives a more or less comprehensive review on the several aspects mentioned above.     

Single-stranded conformation polymorphism (SSCP)-driven indirect sequencing in detection of short deletion

To seek for novel rare and/or sporadic mutations within genomic neighborhood of common −344 C>T (rs2427827) FCER1A proximal promoter polymorphism, which by its prevalence could have masked the presence of less frequent genetic variants in our previous single-stranded conformational polymorphism (SSCP) mutational search study, SSCP screening was repeated using primers fixing −344 C>T variant. The genomic region surrounding −344 C>T polymorphism was confirmed to be fairly conservative and only a single sporadic mutation (present in 1 out of 196 chromosomes), a 6-bp deletion −262 to 257 del CTAGAC, was found. From the methodological point of view, we demonstrated a successful detection of a short-length polymorphism using SSCP screening in a population, in which the same genomic region contained frequent single-nucleotide polymorphic variant. In conjunction with subsequent cloning of aberrantly migrating PCR products and SSCP-driven indirect sequencing of the clones, this method offers a superior (to direct sequencing of PCR products) detection of rare mutations. The cost-effective method applied by us enables a reliable characterization of infrequent (thus present only in heterozygotic form) short-length variance of the sequence which are difficult to interpret by direct sequencing.     

Analysis of eighteen deletion breakpoints in the parkin gene

Parkin mutations are responsible for the pathogenesis of autosomal-recessive juvenile parkinsonism (AR-JP). On initial screening of Japanese patients with AR-JP, we had found that approximately half of the parkin mutations are deletions occurring between exons 2 and 5, forming a deletion hot spot. In this study, we investigated the deletion breakpoints of the parkin mutations in 22 families with AR-JP and examined the possible association between these deletion events and meiotic recombinations. We identified 18 deletion breakpoints at the DNA nucleotide sequence level. Almost all these deletions were different, indicating that the deletion hot spot was generated by recurrent but independent events. We found no association between the deletions and specific DNA elements. Recent copy number variation (CNV) data from various ethnic groups showed that the deletion hot spot is overlapped by a highly polymorphic CNV region, indicating that the recurrent deletion mutation or CNV is observable worldwide. By comparing Marshfield and deCODE linkage maps, we found that the parkin deletion hot spot may be associated with a meiotic recombination hot spot, although such association was not found on comparison with recent high-resolution genetic maps generated from the International HapMap project. Here, we discuss the possible mechanisms for deletion hot spot formation and its effects on human genomes.     

水稻新基因OsRwp34在大肠杆菌中表达的毒害作用

在水稻高温诱导cDNA文库中克隆了一个新的水稻基因O sRwp34,同源性分析表明O sRwp34是一典型的孤儿基因。为了研究O sRwp34的功能,构建了O sRwp34的表达载体pET-28(a)OsRwp34,并转化大肠杆菌菌株BL21(DE3),用IPTG诱导并定时从培养液中取样以检测OD600值和用平板记数法测定活菌数,结果发现在诱导30 m in后宿主菌开始大量死亡,表明O sRwp34的表达产物使宿主菌死亡。随后构建了1个N末端缺失15个氨基酸残基和2个C末端分别缺失12和47个氨基酸残基的O sRwp34缺失体,IPTG诱导后都没有出现毒性作用,推测N和C末端氨基酸残基的同时存在是OsRwp34的毒性作用所必须的。其详细机理有待进一步研究。     

Sinorhizobium fredii WGF03胞外多糖分泌相关基因exoD功能初探

从费氏中华根瘤菌WGF03的基因组中克隆出与胞外多糖分泌密切相关的基因exoD,研究该基因对胞外多糖合成、菌株共生结瘤能力和固氮效率的影响。利用自杀性质粒pK18mobsacB,通过同源双交换法构建exoD基因的缺失突变体ΔexoD。实验发现:与野生菌株相比,突变株在YMA培养基平板上胞外多糖产量明显减少、运动能力也有所减弱;在NaCl浓度小于350 mmol/L范围内,菌体均能维持稳定生长;接种于大豆幼苗后,产生的根瘤数量较多,但个体小、形状不一,且固氮酶活也显著下降。研究结果说明exoD基因参与S.fredii WGF03胞外多糖的合成并影响菌株共生结瘤能力和固氮效率。     

Extended physical maps and a consensus physical map of the homoeologous group-6 chromosomes of wheat (Triticum aestivum L. em Thell.)

Extended physical maps of chromosomes 6A, 6B and 6D of common wheat (Triticum aestivum L. em Thell., 2n=6x=42, AABBDD) were constructed with 107 DNA clones and 45 homoeologous group-6 deletion lines. Two-hundred and ten RFLP loci were mapped, including three orthologous loci with each of 34 clones, two orthologous loci with each of 31 clones, one locus with 40 clones, two paralogous loci with one clone, and four loci, including three orthologs and one paralog, with one clone. Fifty five, 74 and 81 loci were mapped in 6A, 6B and 6D, respectively. The linear orders of the mapped orthologous loci in 6A, 6B and 6D appear to be identical and 65 loci were placed on a group-6 consensus physical map. Comparison of the consensus physical map with eight linkage maps of homoeologous group-6 chromosomes from six Triticeaespecies disclosed that the linear orders of the loci on the maps are largely, if not entirely, conserved. The relative distributions of loci on the physical and linkage maps differ markedly, however. On most of the linkage maps, the loci are either distributed relatively evenly or clustered around the centromere. In contrast, approximately 90% of the loci on the three physical maps are located either in the distal one-half or the distal two-thirds of the six chromosome arms and most of the loci are clustered in two or three segments in each chromosome. Received: 19 April 1999 / Accepted: 28 July 1999