Poly-G for tumor matched samples chronicles the evolution of human colorectal cancer / 中华肿瘤杂志

Objective: To analyze poly-guanine (poly-G) genotypes and construct the phylogenetic tree of colorectal cancer (CRC) and provide an efficient and convenient method for the study of intra-tumor heterogeneity and tumor metastasis pathway. Methods: The clinicopathological information of patients with primary colorectal cancer resection with regional lymph node metastases were retrospectively collected in the Department of General Surgery, General Hospital of Tianjin Medical University from January 2017 to December 2017. The paraffin sections of the paired tumor samples were performed consecutively, and multi-region microdissection was performed after histogene staining. The phenol-chloroform extraction and ethanol precipitation scheme was used to obtain DNA, and Poly-G multiplex PCR amplification and capillary electrophoresis detection were performed. The correlation between Poly-G mutation frequency and clinicopathological parameters was analyzed. Based on the difference of Poly-G genotypes between paired samples, the distance matrix was calculated, and the phylogenetic tree was constructed to clarify the tumor metastasis pathway. Results: A total of 237 paired samples were collected from 20 patients including 134 primary lesions, 66 lymph node metastases, 37 normal tissues, and Poly-G mutation was detected in 20 patients (100%). The mutation frequency of Poly-G in low and undifferentiated patients was (74.10±23.11)%, higher than that in high and medium differentiated patients [(31.36±12.04)%, P<0.001]. In microsatellite instability patients, the mutation frequency of Poly-G was (68.19±24.80)%, which was higher than that in microsatellite stable patients [(32.40±14.90)%, P=0.003]. The Poly-G mutation frequency was not correlated with age, gender, and pathological staging (all P>0.05). Based on Poly-G genotype difference of the paired samples, the phylogenetic trees of 20 patients were constructed, showing the evolution process of the tumor, especially the subclonal origins of lymph node metastasis. Conclusion: Poly-G mutations accumulate in the occurrence and development of CRC, and can be used as genetic markers to generate reliable maps of intratumor heterogeneity in large numbers of patients with minimal time and cost expenditure.

Identification and phylogenetic analysis of two clinical isolates of Chryseobacterium / 中华微生物学和免疫学杂志

Objective:To analyze the biological characteristics, phylogenic features and clinical significance of SQ219 and SQ220 isolated from clinical sputum and midstream urine specimens.Methods:The culture and biochemical characteristics of the two strains were observed. VITEK2 System, drug sensitivity testing and MALDI-TOF mass spectrometry were used for bacterial identification. Phylogenetic analysis based on 16S rRNA and core genome was performed. The average nucleotide identity (ANI) based on whole genome sequences was calculated.Results:SQ219 and SQ220 were Gram-stain-negative, aerobic, catalase- and oxidase-positive, and non-motile bacteria. Their optimum growth was observed in NaCl-free medium at 30℃ and pH7. Flexirubin-type pigments were produced by SQ220 on Colombia blood agar, but not by SQ219. Both SQ219 and SQ220 were resistant to aztreonam, amikacin, tobramycin and colistin, which was consistent with the drug resistance phenotype of genus Chryseobacterium. The genome sequences of SQ219 and SQ220 were 5.08 Mb and 4.80 Mb in length, and the G+ C contents were 36.72% and 36.36%, respectively. Both strains carried β-lactam resistance gene ( blaCGA). 16S rRNA phylogenetic analysis showed that SQ219 and SQ220 were closely related to Chryseobacterium gambrini DSM18014 T with the similarities of 98.93% and 98.36%, respectively. Core genome phylogenetic analysis revealed that SQ219 and SQ220 were highly homologous to Chryseobacterium gambrini DSM18014 T. However, the ANI values between the two strains and Chryseobacterium gambrini DSM18014 T were 92.49% and 93.27%, respectively, below the threshold for prokaryotic species identification. Conclusions:Based on the phenotypic and phylogenetic data, SQ219 and SQ220 represent a novel species of the genus Chryseobacterium. This study would help promote the understanding of the evolution of Chrysobacterium and provide reference for the identification of new species of Chrysobacterium.

Molecular epidemiological characteristics of human rhinovirus in adults with upper respiratory tract infection in Nanjing / 中华微生物学和免疫学杂志

Objective:To analyze the clinical and epidemiological features of human rhinovirus (HRV) infection in adult patients with upper respiratory tract infection (URTI) in Nanjing.Methods:Epidemiological data of adult patients with URTI in Nanjing from October 2021 to September 2022 were collected. Clinical specimens were collected and subjected to quantitative reverse transcription polymerase chain reaction (qRT-PCR) for the detection of 14 common respiratory viruses. The VP4/VP2 genes in HRV-positive samples were amplified and sequenced. Then a phylogenetic tree was constructed.Results:A total of 399 pharyngeal swabs were collected from patients with URTI. The overall positive rate of respiratory viruses was 28.07% (112/399) with HRV accounting for most at 9.52% (38/399). Thirty-seven VP4/VP2 sequences were successfully obtained from the 38 HRV-positive specimens. Three genotypes involving 25 serotypes were identified with 13 strains belonging to HRV-A, 14 belonging to HRV-B, and 10 belonging to HRV-C. The three genotypes of HRV showed alternate prevalence or co-prevalence.Conclusions:HRV was the main pathogen causing URTI in adult patients in Nanjing from October 2021 to September 2022, and three genotypes of HRV-A, B and C were prevalent alternatively or together.

Isolation, Identification and Evaluation of the Plant Growth Promoting Activities of Endophytic Stenotrophomonas maltophilia to Stimulate Growth of Clover Plants under Salt Stress

Two endophytic bacterial isolates were obtained from root nodules of clover plants grown in salt affected clay soil of Egypt. The isolates were closely linked to Stenotrophomonas maltophilia strains IPR-Pv696 and 262XG2 based on the sequencing and phylogenetic analysis of 16S rRNA genes, and deposited in GenBank with accession numbers OM980221.1 (AM1) and OM980223.1 (AM2) respectively. The isolates were evaluated for their potential to promote plant growth. The results revealed that the two isolates of S. maltophilia strains (IPR-Pv696 and 262XG2) respectively exhibited production for indole-3- acetic acid (30.26 & 31.15 µg/ml), exopolysaccharides (13.57 & 13.68 g/l), nitrogen fixation activity and they solubilize the phosphate (278 & 208 mg/l) and potassium (33.5 & 32.9 µg/ml). In a field trial, these two isolates increased clover plant growth, chlorophyll, carbohydrates content and nutrients uptake while lowering proline levels. Hence this highlights its application to be exploited as biofertilizer by leading to sustainable agriculture. This could be a promising inoculant for many other crops.

Molecular epidemiological characteristics of human rhinovirus in patients with upper respiratory tract infection in Qingdao in the winter of 2020 / 中华微生物学和免疫学杂志

Objective:To analyze the epidemiological characteristics and genotypes of human rhinovirus (HRV) in patients with upper respiratory tract infection in Qingdao in the winter of 2020.Methods:Throat swab samples were collected from 101 patients with upper respiratory tract infection in Qingdao from November 2020 to January 2021. Quantitative PCR was used to detect 15 common respiratory viruses in the samples. HRV-positive samples were further analyzed with RT-PCR to amplify and sequence HRV VP4/VP2 gene. A phylogenetic tree was constructed based on the sequencing results and homology analysis was conducted.Results:Six common respiratory viruses were detected in the 101 patients. Thirty-four cases (34/101, 33.66%) were single pathogen infection and two cases were multiple infection (2/101, 1.98%). The positive rate of HRV was the highest (21.78%, 22/101). Twenty HRV VP4/VP2 sequences were successfully amplified. Phylogenetic analysis showed that there were 16 strains of HRV-A subtype and four strains of HRV-C subtype and 14 serotypes were involved.Conclusions:HRV was one of the leading viral pathogens causing upper respiratory tract infection in Qingdao in the winter of 2020 and the predominant subtype was HRV-A.

Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 - May 2021 / 生物医学与环境科学（英文）

Objective@#The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been engendering enormous hazards to the world. We obtained the complete genome sequences of SARS-CoV-2 from imported cases admitted to the Guangzhou Eighth People's Hospital, which was appointed by the Guangdong provincial government to treat coronavirus disease 2019 (COVID-19). The SARS-CoV-2 diversity was analyzed, and the mutation characteristics, time, and regional trend of variant emergence were evaluated.@*Methods@#In total, 177 throat swab samples were obtained from COVID-19 patients (from October 2020 to May 2021). High-throughput sequencing technology was used to detect the viral sequences of patients infected with SARS-CoV-2. Phylogenetic and molecular evolutionary analyses were used to evaluate the mutation characteristics and the time and regional trends of variants.@*Results@#We observed that the imported cases mainly occurred after January 2021, peaking in May 2021, with the highest proportion observed from cases originating from the United States. The main lineages were found in Europe, Africa, and North America, and B.1.1.7 and B.1.351 were the two major sublineages. Sublineage B.1.618 was the Asian lineage (Indian) found in this study, and B.1.1.228 was not included in the lineage list of the Pangolin web. A reasonably high homology was observed among all samples. The total frequency of mutations showed that the open reading frame 1a (ORF1a) protein had the highest mutation density at the nucleotide level, and the D614G mutation in the spike protein was the commonest at the amino acid level. Most importantly, we identified some amino acid mutations in positions S, ORF7b, and ORF9b, and they have neither been reported on the Global Initiative of Sharing All Influenza Data nor published in PubMed among all missense mutations.@*Conclusion@#These results suggested the diversity of lineages and sublineages and the high homology at the amino acid level among imported cases infected with SARS-CoV-2 in Guangdong Province, China.

Pathogen identification and genotyping of two cluster outbreaks of herpangina in children in Dapeng New District， Shenzhen / 上海预防医学

ObjectiveTo determine the pathogenic characteristics and genotype of two outbreaks of herpangina in children in Dapeng New District， Shenzhen， in May 2021. MethodsA total of five throat swabs from children in the two outbreaks of herpangina were collected and examined for common enteroviruses by real-time PCR. The VP1 region was further amplified by nested RT-PCR. The CLUSTAL W program in MEGA7 software was used to conduct the alignment and reconstruct a phylogenetic tree. ResultsThe pathogen causing the 2 cluster outbreaks of herpangina was coxsackievirus A4 （CVA4）. The sequences of CVA4 VP1 genes revealed that a nucleotide identity of 92% between the strains in the two outbreaks. The three CVA4 strains isolated in kindergarten A had the closest phylogenetic relationship with that isolated in Shenzhen in 2018（MN840533）， with the nucleotide identity of 98.11%. The two strains in kindergarten B had the closest phylogenetic relationship with CVA4 strain isolated in Sichuan in 2018（MW178763）， with the nucleotide identity of 97.88%. The phylogenetic tree showed that all five CVA4 strains in this study belonged to the C2 genotype. ConclusionThe C2 genotype of CVA4 is the causative agent in both outbreaks of herpangina.

Application of SifaInDel 45plex System in the Han and Mongolian Populations / 法医学杂志

OBJECTIVES@#To investigate the genetic polymorphism of InDel loci in SifalnDel 45plex system in the Han population in Jiangsu Province and the Mongolian population in Inner Mongolia, and to evaluate the effectiveness of the system in forensic medicine.@*METHODS@#SifaInDel 45plex system was used for genotyping in blood samples of 398 unrelated individuals from the above two populations, and allele frequencies and population genetic parameters of the two populations were calculated respectively. Eight intercontinental populations in the gnomAD database were used as reference populations. The genetic distances between the two studied populations and eight reference populations were calculated based on the allele frequencies of 27 autosomal-InDels (A-InDels). The phylogenetic trees and multidimensional scaling (MDS) analysis diagrams were constructed accordingly.@*RESULTS@#Among two studied populations, the 27 A-InDels and 16 X-InDels showed no linkage disequilibrium between each other and the allele frequency distributions were in Hardy-Weinberg equilibrium. The CDP of the 27 A-InDels in two studied populations were all higher than 0.999 999 999 9, and the CPEtrio were all less than 0.999 9. The CDP of the 16 X-InDels in Han in Jiangsu and Mongolian in Inner Mongolia female and male samples were 0.999 997 962, 0.999 998 389, and 0.999 818 940, 0.999 856 063, respectively. The CMECtrio were all less than 0.999 9. The results of population genetics showed that the Jiangsu Han nationality, Inner Mongolia Mongolian nationality and East Asian population clustered into one branch, showing closer genetic relationship. The other 7 intercontinental populations clustered into another group. And the above 3 populations displayed distant genetic relationships with the other 7 intercontinental populations.@*CONCLUSIONS@#The InDels in the SifaInDel 45plex system have good genetic polymorphism in the two studied populations, which can be used for forensic individual identification or as an effective complement for paternity identification, and to distinguish different intercontinental populations.

Genetic Polymorphism of 16 X-STR Loci in Xinjiang Uygur Population / 法医学杂志

OBJECTIVES@#To study the genetic polymorphism and population genetic parameters of 16 X-STR loci in Xinjiang Uygur population.@*METHODS@#The Goldeneye® DNA identification system 17X was used to amplify 16 X-STR loci in 502 unrelated individuals (251 females and 251 males). The amplified products were detected by 3130xl genetic analyzer. Allele frequencies and population genetic parameters were analyzed statistically. The genetic distances between Uygur and other 8 populations were calculated. Multidimensional scaling and phylogenetic tree were constructed based on genetic distance.@*RESULTS@#In the 16 X-STR loci, a total of 67 alleles were detected in 502 Xinjiang Uygur unrelated individuals. The allele frequencies ranged from 0.001 3 to 0.572 4. PIC ranged from 0.568 8 to 0.855 3. The cumulative discrimination power in females and males were 0.999 999 999 999 999 and 0.999 999 999 743 071, respectively. The cumulative mean paternity exclusion chance in trios and in duos were 0.999 999 997 791 859 and 0.999 998 989 000 730, respectively. The genetic distance between Uygur population and Kazakh population was closer, and the genetic distance between Uygur and Han population was farther.@*CONCLUSIONS@#The 16 X-STR loci are highly polymorphic and suitable for identification in Uygur population, which can provide a powerful supplement for the study of individual identification, paternity identification and population genetics.

Morphological study and molecular epidemiology of Anisakis larvae in mackerel fish

Objective: To examine and study the morphology, epidemiology, and molecular phylogeny of Anisakis larvae in blue mackerel [Scomber australasicus (Cuvier, 1832)] and Indian mackerel [Rastrelliger kanagurta (Cuvier, 1816)] using light microscope, scanning electron microscope, molecular phylogeny, and species delimitation methods for confirmation and investigation of Anisakis species and their evolutionary relationship. Methods: A total of 90 fish (45 per species) were purchased from a department store in Chiang Mai, Thailand. Anisakis samples were investigated for morphological characteristics using light and scanning electron microscopes. Molecular phylogeny and species delimitation methods based on the cox2 gene were performed. Results: The prevalence, mean intensity (Mean±SEM), and mean abundance of Anisakis larvae (Mean±SEM) in blue mackerel were 77.78%, 6.74±1.320, and 5.24±1.107, respectively, and in Indian mackerel, these values were 13.33%, 2.50±0.764, and 0.33±0.159, respectively. Scanning electron microscopy showed the detail of morphological characteristics and provided the different shapes of mucron and excretory pores in Anisakis larvae congruent with the phylogenetic tree. The species tree was congruent with the phylogenetic tree. Conclusions: The prevalence, mean intensity, and mean abundance of Anisakis larvae were higher in blue mackerel. To the best of our knowledge, this is the first time that Anisakis pegreffii was found in blue mackerel in Thailand. The phylogenetic tree also supported the morphological data of Anisakis larvae. However, species delimitation based on cox2 revealed 1-3 possible cryptic species in this genus. Anisakis spp. contamination of fish products is unpleasant and a health concern considering human infection with larvae (anisakiasis) arises.

A novel pathogenic Colletotrichum species for rhizome rot disease of Polygonatum kingianum / 中国中药杂志

Rhizome rot disease is one of the main disease of planted Polygonatum kingianum. In this study, six strains of pathogenic fungus was isolated from P. kingianum samples with rhizome rot disease collected from six counties in Yunnan province. Its pathogenicity was confirmed by inoculation to healthy P. kingianum rhizome according to Koch's postulates. The colonies of the isolated fungi on potato dextrose agar(PDA) were orange with abundant crescentic conidia which were eseptate with a mean size of 19. 3-24. 9 μm×5. 2-5. 9 μm and a L/W ratio of 3. 4-4. 5. There was an oil ball in the center of the conidium. It's easy to see setae on PDA colony.The phylogenetic tree based on ITS, GAPDH, CHS-1, HIS3, ACT, and TUB2 sequences by maximum likelihood(ML) method indicated that the pathogenic fungus for P. kingianum rhizome rot disease was clustered into the clade of Colletotrichum spaethianum species complex, and was close to C. spaethianum. However, there were some differences in morphological and genetic characteristics between the pathogenic fungus and C. spaethianum. Therefore, the pathogenic fungus for rhizome rot disease of P. kingianum was identified as a new Colletotrichum species named C. kingianum. The disease spreads primarily due to the plantation of infected seedlings of P. kingianum. It is necessary to choose healthy seedlings and take rigorous disinfection measures for the disease prevention.

Identification of Chinese medicine sea snake based on cytochrome B (Cytb) / 中国中药杂志

The identification of species primordium has been one of the hot issues in the identification of traditional Chinese medicine. Sea snake is one of the most valuable Chinese medicinal materials in China. In order to understand the origin and varieties of sea snake in the market, we studied the molecular identification of 46 sea snakes by cytochrome B(Cytb). After comparison and manual correction, the sequence length was 582 bp, and the content of A+T(58.9%) was higher than that of G+C(41.1%). There exist 197 variable sites and 179 parsimony-informative sites of the sequence. There are 44 kinds of sequence alignment with consistency equal to 100%, and 2 kinds equal to 96%. A total of 408 Cytb effective sequences were downloaded from GenBank database, with a total of 68 species. Phylogenetic tree of a total of 454 sea snake sequences with the samples in this study were constructed by neighbor-joining trees and Bayesian inference method, respectively, which can identify 42 samples of medicinal materials, while 4 samples can not be identified because of their low node support. The results showed that the species of the sea snake medicine were at least from 2 genera and 5 species, namely, Aipysurus eydouxii, Hydrophis curtus, H. caerulescen, H. curtus, H. ornatus and H. spiralis. This study suggested that the original species of commercial sea snake are very complex and can provide insight into the identification of sea snakes.

Isolation and identification of phosphatolytic bacteria in Paris polyphylla var. yunnanensis / 中国中药杂志

The wild resources of Paris polyphylla var. yunnanensis, a secondary endangered medicinal plant, are severely scarce. Introduction and cultivation can alleviate market demand. To screen phosphatolytic bacteria in the rhizosphere soil of P. polyphylla var. yunnanensis and provide data support for the development of high-efficiency microbial fertilizer, in this study, the dilution plate coating method was used to isolate and screen the phosphorus solubilizing bacteria with the ability of mineralizing organic phosphorus from the rhizosphere soil of wild and transplanted varieties of P. polyphylla var. yunnanensis in 10 different locations in Yunnan, Sichuan and Guizhou. After separation and purification, the phosphatolytic capacity was analyzed by qualitative and quantitative analysis. Combined with physiological and biochemical experiments, the strains were identified using 16 S rDNA sequencing analysis. Forty one strains were selected from the rhizosphere soil of P. polyphylla var. yunnanensis from 10 different habitats. Among them, 21 strains were obtained from the rhizosphere soil of the wild variety P. polyphylla var. yunnanensis and 20 strains were obtained from the rhizosphere soil of the transplanted variety. And significance analysis found that 41 organophosphate solubilizing strains had significant differences in their ability to solubilize phosphorus. The amount of phosphate solubilizing was 0.08-67.61 mg·L~(-1), the pH value was between 4.27 and 6.82. The phosphatolytic amount of strain Y3-5 was 67.61 mg·L~(-1), and the phosphorus increase amount was 57.57 mg·L~(-1). All 41 strains were identified as Gram-positive Bacillus. Combining physiological characteristic and phylogenetic trees, Bacillus mobilis Y3-5 was finally selected as the candidate rhizosphere phosphatolytic bacteria of P. polyphylla var. yunnanensis. The distribution of phosphorus solubilizing bacteria in the rhizosphere soil of P. polyphylla var. yunnanensis was different, and there were significant diffe-rences in phosphorus solubility. Organophosphate-dissolving strain Y3-5 is expected to be a candidate strain of P. polyphylla var. yunnanensis microbial fertilizer.

Molecular analysis of the first dengue fever case in Dapeng New District of Shenzhen City / 上海预防医学

Objective:To analyze the first suspected dengue fever case in Dapeng New District by characterizing the virus and exploring its origin. Methods:Dengue virus nucleic acid in blood sample was identified by real-time fluorescent RT-PCR. The E gene of dengue virus was amplified and sequenced. Homology and phylogenetic tree of this dengue virus were compared with the isolates from other regions. Results:Nucleic acid of dengue virus type 1 was detected in the serum sample from the suspected dengue fever patient. Phylogenetic tree showed that the homology based on nucleotide sequence of E gene of DP-DGR19001 was very similar with the isolates of MG894965/TW/CHN/2016 （99.87%）， LC428079/VNM/2017（99.80%）， MG894867/TW/CHN/2015 （99.60%） and MN512242/GX/CHN/2014 （99.46%）. The deduced amino acid sequence of 5 isolates was 100% identical. The patient had traveled to high-incidence country Cambodia in 14 days before infection. Conclusions:The first suspected dengue fever case in Dapeng New District is caused by dengue virus type 1. The case is an imported dengue fever .

Chloroplast Genomic Analysis of Pyrrosia assimilis / 中国实验方剂学杂志

Objective::The complete chloroplast genome of Pyrrosia assimilis was sequenced, its sequence characteristics was analyzed and herbgenomics of P. assimilis was discussed. Method::Its complete chloroplast genome sequence was determined through high-throughput sequencing technology, and its structural characteristics and phylogenetic relationships were analyzed by bioinformatics. Result::The chloroplast genome of P. assimilis was a circular double-chain structure with a total length of 154 964 bp, and the total content of guanine and cytosine (GC) was 41.2%. A total of 131 genes were annotated, including 88 protein-coding genes, 35 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. A total of 43 dispersed repetitive sequences and 56 simple sequence repeats (SSRs) were detected. The frequency of codon encoding leucine was the highest, while the number of codon encoding tryptophan was the lowest. Five highly divergent regions (psbA, rrn16, petA-psbJ, ndhC-trnM, and psbM-petN) were screened, phylogenetic analysis showed that P. assimilis was closely related to P. bonii. Conclusion::Comparative analysis of the complete chloroplast genome of P. assimilis reveals that non-coding regions exhibited a higher divergence than the coding regions, the large single copy region (LSC) and small single copy region (SSC) are more divergent than the reverse repeat region (IR), the selected five highly variable regions can be used as specific DNA barcodes for identification of Pyrrosia species. Study on the chloroplast genome of P. assimilis can provide a reference for the molecular identification, genetic transformation, expression of resistance protein and secondary metabolism pathway analysis of other Pyrrosia medicinal plants.

Screening and identification of fibrinolytic enzyme-producing microbes in fermentation process of Sojae Semen Praeparatum / 中草药

Objective: To screen and identify the dominant strains which produce fibrinolytic enzyme during the processing of Sojae Semen Praeparatum (SSP, Dandouchi in Chinese). Methods: SSP was prepared according to the Chinese Pharmacopoeia (2020 edition), and samples were taken at different time points during the fermenting process of SSP.The casein plate method and fibrin plate method were used to screen the fibrinolytic enzyme-producing microorganisms in samples at different time points. The fibrinolytic enzyme-producing microorganisms were inoculated in the designated liquid medium to obtain single strain fermentation broth, and fibrin plate method was used to measure the fibrinolytic activity of the fermentation broth. The DNA sequences of fibrinolytic enzyme-producing bacteria and fungi were amplified using 16S rDNA and 18S rDNA universal primer by PCR respectively.The amplified products were sequenced, and the sequencing results were identified through NCBI homology comparison. Molecular biological identification was done by phylogenetic tree constructed by MEGA 4.1 software. Results: Three types of fibrinolytic enzyme-producing bacteria were screened out and identified in this study. They were Bacillus subtilis, Stenotrophomonas maltophilia and Micrococcus, respectively. The result of fibrin plate method showed that the fermentation broth of S. maltophilia had the highest fibrinolytic activity, reaching 527.49 IU/mL. Conclusion: There are fibrinolytic enzyme-producing dominant microorganisms existing in the fermenting process of SSP and the thrombolytic effect of SSP is worthy of further study. This study lays the foundation for revealing the formation mechanism of fibrinolytic enzyme in the fermentation process of SSP.

Identification of hepatitis C virus genotypes in volunteer blood donors from blood transfusion center of Tuban, Indonesia

@#Aims: The most common transmission route of hepatitis C virus (HCV) is via blood transfusion. Therefore, the screening of HCV is necessary to be performed regularly for all the volunteer blood donors. The prevalence of HCV subtypes varies in different geographical areas. The aim of this study is to identify the HCV genotypes of the HCV-RNA positive samples and performed serological and molecular characterization of HCV among blood donors from Blood Transfusion Center of Tuban, East Java, Indonesia collected during the year of 2015. Methodology and results: All blood donor samples were screened by enzyme-linked immunosorbent assay (ELISA) for anti-HCV. Reverse Transcription - Polymerase Chain Reaction (RT-PCR) was performed to detect the HCV-RNA. Subsequently, the HCV-RNA positive samples were genotyped using direct sequencing followed by subtype/genotype and phylogenetic analysis. Of the 500 blood samples, 7 were positive for anti-HCV antibody (1.4%) and 6 out of 7 (85.71%) were determined to be HCV-RNA positive. Among HCV-RNA carriers, genotyping showed genotypes 1 was the most prevalent. HCV subtypes 1a and 1b were detected in total of 4 out of 6 individuals (66.67%), two individuals for each. HCV subtypes 2a and genotype 1 were the least frequent among blood donors (each counted for 16.67%). Conclusion, significance and impact for study: The prevalence of HCV found in this study is considerably low. The identification of genotypes 1a and 1b as major HCV genotypes circulating in blood donors in the Tuban city of East Java. This result may contribute in a better medical management towards HCV carriers.

Deciphering species relationships and evolution in Chenopodium through sequence variations in nuclear internal transcribed spacer region and amplified fragment-length polymorphism in nuclear DNA

Evaluation of sequence variations in the internal transcribed spacer (ITS) region of 19 accessions, comprising of 11 accessions of Chenopodium quinoa, eight accessions of Chenopodium album and 165 retrieved sequences of different species of Chenopodium belonging to subfamily Chenopodioideae revealed a higher intraspecific genetic diversity in Himalayan C. album than that in C. quinoa. ITS and amplified fragment-length profiles of the accessions suggest the existence of accessions of Himalayan C. album as heteromorphs of the same species rather than a heterogenous assemblage of taxa. While the evolutionary relationship reconstructed from variations in 184 sequences of ITS region from species belonging to Chenopodiaceae, Amaranthaceae, Polygonaceae and Nelumbonaceae established a paraphyletic evolution of family Chenopodiaceae, it also revealed a monophyletic evolution of Chenopodieae I. The reconstruction also established five independent lineages of the subfamily Chenopodioideae with C. album as a sister clade of C. quinoa within the tribe Chenopodieae I. The results also indicate a much younger age for Himalayan chenopods (C. album) than the reported crown age of Chenopodieae I.

Characteristics of gene sequence changes of hemorrhagic fever with renal syndrome virus in Heilongjiang Province / 中国实用内科杂志

OBJECTIVE: To study the gene sequence characteristics of hantavirus in Heilongjiang Province in order to find out the reasons for the changes of clinical characteristics of hemorrhagic fever with renal syndrome in Heilongjiang Province in recent years.METHODS: Totally 110 rat lung specimens,121 blood specimens from patients diagnosed with mild or atypical HFRS and 100 blood specimens from patients diagnosed with typical HFRS in the First Affiliated Hospital of Harbin Medical University and the Seventh Hospital of Qiqihar City from 2005 to 2015 were collected. The gene sequences were obtained by nucleic acid extraction, RT-NestPCR, and gene sequencing. Explore the possible reasons for the changes in clinical characteristics of HFRS by comparing the obtained sequences with previous strains, homology analysis, building phylogenetic trees of M gene, and finding out the law of nucleotide and amino acid loci changes. RESULTS: TM gene of twenty-six mild or atypical HFRS patients were successfully amplified, including 14 cases of HTN type and 12 cases of SEO type; M gene of twenty-two typical HFRS patients were amplified, including 19 cases of HTN type and 3 cases of SEO type. Compared with the standard strain 76-118, the nucleotide homology of hantavirus from mild or atypical HFRS patients, typical HFRS patients and mice was 74.4%-89.2%, 87.4%-90.3% and 88.1%-88.5%. Comparing hantavirus gene sequence from mice and from patients, the nucleotide homology was 79.7-99.1%. Hljh38 and Hljh39 from patients were significantly different from the other strains. They were the same subtype as Amur virus because they had high homology with Amur strains H5 and H8205(94.9%-97.6%). The deduced amino acids showed some variations compared with the standard strains, but no obvious variation law was observed. CONCLUSION: The reason for the changes of clinical characteristics of hemorrhagic fever with renal syndrome in Heilongjiang province is related to the change of viral type. There are also variations of hantavirus and amino acid, but the relationship between specific variation law and clinical manifestations needs to be further verified.

Determination of Place of Residence Using the Gene Information of Plants Carried by the Human Body / 法医学杂志

Objective To identify the plant species using the DNA sequence of plant pollen from lung tissues of a unidentified body, infer the possible long-term places of residence of the deceased according to the distribution area of the pollen in the lung tissues, therefore narrow the scope of criminal investigation and provide clues for case solving. Methods Lung tissues were extracted from the deceased, total DNA was extracted by the mCTAB method. Gene fragments of the two plant DNA barcodes, matK and rbcL, were acquired using specific primers for amplification, then sequenced. The DNA sequences of target gene fragments were acquired through bioinformatics analysis. The sequences were combined with reference sequence data. Phylogenetic analysis was made to identify the species that the DNA sequences belonged to. The places where the deceased could have lived for a long time were inferred, according to the distribution information of plant species. Results Gene fragments of 32 plant species which belonged to 31 genera of 27 families were in the lung tissues of the deceased. Among them, plants of 9 genera that had certain indicative function were mainly endemic plants from Hainan, Guangdong, Guangxi and Yunnan. These results showed that the deceased may have stayed in these areas for a long time before death. After further investigation, the victim was confirmed to have come from a county in southern Guangxi, which was in accordance with the research results. Conclusion The method of using gene information of plants from lung tissues of human bodies to infer places of residence can assist inference of the places where the deceased could have lived for a long time. The present study may also provide new ideas for locating sources of the corpses in cases with unidentified victims.