Genetic diversity analysis of forty-three insertion/deletion loci for forensic individual identification in Han Chinese from Beijing based on a novel panel / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Due to the virtues of no stutter peaks, low rates of mutation, and short amplicon sizes, insertion/deletion (InDel) polymorphism is an indispensable tool for analyzing degraded DNA samples from crime scenes for human identifications (Wang et al., 2021). Herein, a self-developed panel of 43 InDel loci constructed previously by our group was utilized to evaluate the genetic diversities and explore the genetic background of the Han Chinese from Beijing (HCB) including 301 random healthy individuals. The lengths of amplicons at 43 InDel loci in this panel ranged from 87 to 199 bp, which indicated that the panel could be used as an effective tool to utilize highly degraded DNA samples for human identity testing. The loci in this panel were validated and performed well for forensic degraded DNA samples (Jin et al., 2021). The combined discrimination power (PD) and combined probability of exclusion (PE) values in this panel indicated that the 43 InDel loci could be used as the candidate markers in personal identification and parentage testing of HCB. In addition, population genetic relationships between the HCB and 26 reference populations from five continents based on 19 overlapped InDel loci were displayed by constructing a phylogenetic tree, principal component analysis (PCA), and population genetic structure analysis. The results illustrated that the HCB had closer genetic relationships with the Han populations from Chinese different regions.

Risk analysis on duo paternity tests / 中国法医学杂志

Objective To discuss the risk in duo paternity testing. Methods 22 fictitious duo families formed by 22 pairs of unrelated individuals having one or zero inconsistent locus were selected after detected by GoldeneyeTM 20A Kit. The 22 fictitious duo families were further tested with STRtyper-10G kit and/or AGCU 21+1 STR kit until there were more than 3 inconsistent loci and the cumulative paternity index(CPI) value was less than 0.0001. According to the three excluding rules, ① number of inconsistent loci>3; ② CPI ≤ 0.0001; ③ accord with both ① and ② , using multiple STR systems, such as 19 STR loci, 26 STR loci, 39 STR loci and 46 STR loci to test and discuss whether there is difference among the excluding result of unrelated individual. Results Among those 22 fictitious duo families, using three excluding rules, None was excluded by 19 STR loci, and all was excluded by 39 STR loci. Conclusion Duo paternity tests may get a wrong result using only 19 loci system. To reduce the error risk 39 STR-loci systems would be suggested.

Therapeutic effect of early exercise rehabilitation in patients with acute myocardial infarction / 心血管康复医学杂志

Objective:To explore the effect of early exercise rehabilitation in patients with acute myocardial infarction (AMI).Methods:A total of 64 AMI patients with stable vital signs were randomly divided into early exercise reha-bilitation group (n=32)and routine rehabilitation group (n=32)according to number table method.Early exercise rehabilitation group received early exercise rehabilitation guidance by rehabilitation therapists on first day after on-set,while routine rehabilitation group received exercise rehabilitation guidance by rehabilitation therapists of same qualification after one-week absolute bed rest.Besides,the two groups received same therapy and nursing.Incidence of major adverse cardiovascular events (MACE:re-infarction,death,severe arrhythmias,angina pectoris after in-farction and heart failure),hospitalization days and condktion of life self-care ability were observed,compared and analyzed between two groups.Results:Before discharge,there were no significant difference in MACE incidence rate (40.63% vs.43.75%)and percentages of patients with life self-care ability (100% vs.96.88%)between early exercise rehabilitation group and routine rehabilitation group,P >0.05,but length of hospital stay in early rehabili-tation group [(9.23±1.45)d]was significantly shorter than that of routine rehabilitation group [(15.03±2.53) d],P <0.01. Conclusion:Early exercise rehabilitation training can shorten length of hospital stay and is safe in pa-tients with acute myocardial infarction.

Gene identification and expression analysis of 86,136 Expressed Sequence Tags (EST) from the rice genome / 基因组蛋白质组与生物信息学报·英文版

Expressed Sequence Tag (EST) analysis has pioneered genome-wide gene discovery and expression profiling. In order to establish a gene expression index in the rice cultivar indica, we sequenced and analyzed 86,136 ESTs from nine rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars. We assembled these ESTs into 13,232 contigs and leave 8,976 singletons. Overall, 7,497 sequences were found similar to existing sequences in GenBank and 14,711 are novel. These sequences are classified by molecular function, biological process and pathways according to the Gene Ontology. We compared our sequenced ESTs with the publicly available 95,000 ESTs from japonica, and found little sequence variation, despite the large difference between genome sequences. We then assembled the combined 173,000 rice ESTs for further analysis. Using the pooled ESTs, we compared gene expression in metabolism pathway between rice and Arabidopsis according to KEGG. We further profiled gene expression patterns in different tissues, developmental stages, and in a conditional sterile mutant, after checking the libraries are comparable by means of sequence coverage. We also identified some possible library specific genes and a number of enzymes and transcription factors that contribute to rice development.

A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in South China / 基因组蛋白质组与生物信息学报·英文版

We report a complete genomic sequence of rare isolates (minor genotype) of the SARS-CoV from SARS patients in Guangdong, China, where the first few cases emerged. The most striking discovery from the isolate is an extra 29-nucleotide sequence located at the nucleotide positions between 27,863 and 27,864 (referred to the complete sequence of BJ01) within an overlapped region composed of BGI-PUP5 (BGI-postulated uncharacterized protein 5) and BGI-PUP6 upstream of the N (nucleocapsid) protein. The discovery of this minor genotype, GD-Ins29, suggests a significant genetic event and differentiates it from the previously reported genotype, the dominant form among all sequenced SARS-CoV isolates. A 17-nt segment of this extra sequence is identical to a segment of the same size in two human mRNA sequences that may interfere with viral replication and transcription in the cytosol of the infected cells. It provides a new avenue for the exploration of the virus-host interaction in viral evolution, host pathogenesis, and vaccine development.

The structural characterization and antigenicity of the S protein of SARS-CoV / 基因组蛋白质组与生物信息学报·英文版

The corona-like spikes or peplomers on the surface of the virion under electronic microscope are the most striking features of coronaviruses. The S (spike) protein is the largest structural protein, with 1,255 amino acids, in the viral genome. Its structure can be divided into three regions: a long N-terminal region in the exterior, a characteristic transmembrane (TM) region, and a short C-terminus in the interior of a virion. We detected fifteen substitutions of nucleotides by comparisons with the seventeen published SARS-CoV genome sequences, eight (53.3%) of which are non-synonymous mutations leading to amino acid alternations with predicted physiochemical changes. The possible antigenic determinants of the S protein are predicted, and the result is confirmed by ELISA (enzyme-linked immunosorbent assay) with synthesized peptides. Another profound finding is that three disulfide bonds are defined at the C-terminus with the N-terminus of the E (envelope) protein, based on the typical sequence and positions, thus establishing the structural connection with these two important structural proteins, if confirmed. Phylogenetic analysis reveals several conserved regions that might be potent drug targets.

Polymorphism profile of nine short tandem repeat Loci in the Han chinese / 基因组蛋白质组与生物信息学报·英文版

Nine short tandem repeat (STR) markers (D3S1358, VWA, FGA, THO1, TPOX, CSFIPO, D5S818, D13S317, and D7S820) and a sex-identification marker (Amelogenin locus) were amplified with multiplex PCR and were genotyped with a four-color fluorescence method in samples from 174 unrelated Han individuals in North China. The allele frequencies, genotype frequencies, heterozygosity, probability of discrimination powers, probability of paternity exclusion and Hardy-Weinberg equilibrium expectations were determined. The results demonstrated that the genotypes at all these STR loci in Han population conform to Hardy-Weinberg equilibrium expectations. The combined discrimination power (DP) was 1.05 x 10(-10) within nine STR loci analyzed and the probability of paternity exclusion (EPP) was 0.9998. The results indicate that these nine STR loci and the Amelogenin locus are useful markers for human identification, paternity and maternity testing and sex determination in forensic sciences.

Gene expression profiling in porcine fetal thymus / 基因组蛋白质组与生物信息学报·英文版

To obtain an initial overview of gene diversity and expression pattern in porcine thymus, 11,712 ESTs (Expressed Sequence Tags) from 100-day-old porcine thymus (FTY) were sequenced and 7,071 cleaned ESTs were used for gene expression analysis. Clustered by the PHRAP program, 959 contigs and 3,074 singlets were obtained. Blast search showed that 806 contigs and 1,669 singlets (totally 5,442 ESTs) had homologues in GenBank and 1,629 ESTs were novel. According to the Gene Ontology classification, 36.99% ESTs were cataloged into the gene expression group, indicating that although the functional gene (18.78% in defense group) of thymus is expressed in a certain degree, the 100-day-old porcine thymus still exists in a developmental stage. Comparative analysis showed that the gene expression pattern of the 100-day-old porcine thymus is similar to that of the human infant thymus.

Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04) / 基因组蛋白质组与生物信息学报·英文版

Beijing has been one of the epicenters attacked most severely by the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) since the first patient was diagnosed in one of the city's hospitals. We now report complete genome sequences of the BJ Group, including four isolates (Isolates BJ01, BJ02, BJ03, and BJ04) of the SARS-CoV. It is remarkable that all members of the BJ Group share a common haplotype, consisting of seven loci that differentiate the group from other isolates published to date. Among 42 substitutions uniquely identified from the BJ group, 32 are non-synonymous changes at the amino acid level. Rooted phylogenetic trees, proposed on the basis of haplotypes and other sequence variations of SARS-CoV isolates from Canada, USA, Singapore, and China, gave rise to different paradigms but positioned the BJ Group, together with the newly discovered GD01 (GD-Ins29) in the same clade, followed by the H-U Group (from Hong Kong to USA) and the H-T Group (from Hong Kong to Toronto), leaving the SP Group (Singapore) more distant. This result appears to suggest a possible transmission path from Guangdong to Beijing/Hong Kong, then to other countries and regions.