Asian rice comprises two major subspecies:Xian(X)and Geng(G),and the diverged resistance genes(R)have provided a foundation for breeding improved cultivars to control rice blast disease.After conducting two-phase alle...Asian rice comprises two major subspecies:Xian(X)and Geng(G),and the diverged resistance genes(R)have provided a foundation for breeding improved cultivars to control rice blast disease.After conducting two-phase allele mining using six updated FNP marker systems,the functional haplotypes at Pit,Pib,and Pi63 strictly diverged into the X-populations and were defined as X-R loci,while those at Pi54,Pi37,and Pi36 into the G-populations as G-R loci.The genic diversity at the three X-R loci(16 alleles)was twofold higher than that at the three G-R loci(8 alleles),and the allelic diversity in the Southern region(21 alleles)was nearly double that in the Northeastern region(11 alleles).Both observations reflect a significant difference in genetic diversity between X-and G-populations,and indicate that the effective R-genes mainly originated from X-subspecies.Based on the allelic structures characterized by a set of 10 parameters,8 and 16 alleles were respectively recognized as favorable and promising ones for the regional breeding programs.The genotypic structures of the two regional populations were almost different,indicating that the diverged alleles have been further assembled into two series of regional genotypes through long-term breeding programs,despite the presence of one-third of region-common alleles.The genotypic diversity in the Southern region(55 genotypes)was nearly twice as high as that in the Northeastern region(28),which perfectly reflects the aforementioned differences in both genic and allelic diversities.After analyzing the genotypic structures using a set of 13 parameters,4 and 23 genotypes,respectively,can be recommended as the favorable and promising ones for the regional breeding programs.The case study serves as a concrete sample of how to identify the favorable and promising alleles and genotypes,and beneficial parents based their comprehensive population structures for gene-designed breeding.展开更多
Salt stress is a critical factor affecting the growth and yield of rice.Egypt,the largest rice producer in North Africa and the Middle East,is facing contrasting challenges related to salinity in its agroecosystems.In...Salt stress is a critical factor affecting the growth and yield of rice.Egypt,the largest rice producer in North Africa and the Middle East,is facing contrasting challenges related to salinity in its agroecosystems.In this study,we compared the salt-induced responses among three rice varieties:Giza 176(Egyptian variety),Kaituodao(Chinese variety),and Pokkali(Sri Lanka variety,used as control)under normal and saline stress(100 mmol/L NaCl)conditions at two seedling stages through RNA-seq expression analysis.Giza 176 displayed a salt tolerance score of 7 on the SES(Standard Evaluation Score).Its transcriptome showed dynamic changes,with the number of upregulated genes increasing from 180 to 735,and downregulated genes increasing from 918 to 2930 from the one-week to two-week stress stages,with activated pathways in ion transport,reactive oxygen species(ROS)scavenging,and protein biosynthesis.展开更多
Acute respiratory tract infections(ARTIs)are among the leading causes of morbidity and mortality in children worldwide.Human adenovirus(HAdV)infections are estimated to account for at least 5%of pediatric ARTIs.The ci...Acute respiratory tract infections(ARTIs)are among the leading causes of morbidity and mortality in children worldwide.Human adenovirus(HAdV)infections are estimated to account for at least 5%of pediatric ARTIs.The circulated genotypes of HAdV and the correlation between genotype and clinical manifestations in Wuhan,China,before and after the complete relaxation of nonpharmaceutical interventions against severe acute respiratory syndrome coronavirus 2,remain unknown.Here,101 HAdV strains were isolated from throat swab samples collected from hospitalized children with ARTIs who tested positive for HAdV nucleic acid.Of these,sixty-six strains from 2022 to twenty-three strains from 2023 were successfully genotyped and subjected to phylogenetic analysis based on the hexon,penton base,and fiber genes.Six genotypes,B3,C1,C2,C5,C104,and C108 were identified.HAdV-B3(84.85%)was the most prevalent type in 2022,while HAdV-C(86.96%),including C1,C2,C108,and C104,was the most prevalent in 2023.These strains were phylogenetically related to strains from Japan,China,and the United States in recent years.When comparing clinical characteristics,pediatric patients infected with B3,C1,C2,C5,C104,or C108 exhibited similar clinical manifestations,primarily fever and cough,but varying interleukin(IL)-10 levels.In conclusion,from June 2022 to September 2023,the circulated genotypes of HAdV in Wuhan included B3,C1,C2,C108,C5,and C104.The endemic pattern of HAdV in Wuhan,China,shifted from species B as the dominant type in 2022 to species C in 2023.展开更多
Background:In 2021,the American College of Medical Genetics and Genomics(ACMG)recommended reporting actionable genotypes in 73 genes associated with diseases for which preventive or therapeutic measures are available....Background:In 2021,the American College of Medical Genetics and Genomics(ACMG)recommended reporting actionable genotypes in 73 genes associated with diseases for which preventive or therapeutic measures are available.Evaluations of the association of actionable genotypes in these genes with life span are currently lacking.Methods:We assessed the prevalence of coding and splice variants in genes on the ACMG Secondary Findings,version 3.0(ACMG SF v3.0),list in the genomes of 57,933 Icelanders.We assigned pathogenicity to all reviewed variants using reported evidence in the ClinVar database,the frequency of variants,and their associations with disease to create a manually curated set of actionable genotypes(variants).We assessed the relationship between these genotypes and life span and further examined the specific causes of death among carriers.展开更多
Background: The incidence of cervical cancer is high in Bangladesh and there is a high prevalence of preinvasive lower genital tract disease among women of reproductive age. Persistent high-risk Human Papilloma Virus ...Background: The incidence of cervical cancer is high in Bangladesh and there is a high prevalence of preinvasive lower genital tract disease among women of reproductive age. Persistent high-risk Human Papilloma Virus (HPV) infection is the main underlying cause of cervical cancer and its precursor, cervical intraepithelial neoplasia (CIN). Objective: The aim of the study was to identify the subtypes of high-risk HPV infection among women with the colposcopic diagnosis of cervical intraepithelial neoplasia in Bangladesh. Methods: This cross-sectional observational study was conducted in the colposcopy clinic of Dhaka Medical College Hospital over a six-month period. A total of 100 participants were enrolled. Married women, between 30 - 60 years of age with colposcopically diagnosed cervical intra epithelial neoplasia were enrolled. Women with chronic illness, pregnancy, and women unable to consent were excluded from this study. After counselling, colposcopically directed punch biopsies were taken from each CIN case concurrently with high-risk HPV testing by polymerase chain reaction (PCR). Results: The mean age of the patients was 38.69 (SD ±7.76) years. CIN 1 was diagnosed in 57% of participants, while 24% had CIN II and 19% had CIN III lesions. High-risk HPV was present in 52 patients. HPV 16 was the most common identified in 28 (53.84%) and HPV 18 was the second most common with 20 (38.46%) either singly or in combination with other high-risk subtypes. The other HPV strains, HPV 31, 33, 35, 52, 56 and 58, were also detected either as mono or co-infections. Out of the 52 HPV positive cases, 29 (55.8%) had mono infection and 23 (44.2%) had co-infection with several subtypes. The highest incidence (50%) of oncogenic HPV infections was present among women aged 35 - 45 years. Risk factors associated with HPV positive cases were high parity (P 0.05), early age at marriage (P = 0.754) and early age of first child. Conclusion: This study identified a high prevalence of HPV 16 and 18 genotypes. HPV vaccination with the current 9-valent HPV vaccine, which contains HPV types 6, 11, 16, 18, 31, 33, 45, 52, and 58. Will be an effective public health measure to eradicate cervical cancer in Bangladesh.展开更多
[Objective] To study the effects of Zinc on the yield,nitrogen/phosphorus/potassium/Zinc uptake and distribution of different genotypes of maize.[Method] Using two different genotypes of maize as materials,the effects...[Objective] To study the effects of Zinc on the yield,nitrogen/phosphorus/potassium/Zinc uptake and distribution of different genotypes of maize.[Method] Using two different genotypes of maize as materials,the effects of Zn on the yield,N/P/K /Zn uptake and distribution of different genotypes of maize were studied by pot cultivation.[Result] Appropriate Zn supply could improve the grain number per kernel.The Zn content in different organs of maize showed little difference under low Zn treatment （Zn0,Zn1）.With the increase of Zn supply,Zn content in leaf,stem and sheath rapidly increased,but the increasing amplitude of Zn content in the kernel and bract were less.The excessive Zn in maize was mainly translocated in lower organs to reduce the damage of them to plants.Different Zn supply levels had less effects on the absorption and translocation of N,P and K in low-Zn insensitive variety Mudan 9.While the absorption and translation of N,P,K in low Zn sensitive variety （Sidan 19） was more easily influenced by the amount of Zn supplied.[Conclusion] Appropriate Zn supply could enhance the maize yield and utilization rate of N and K,and reduce the absorption and utilization of P.展开更多
The levels of endogenous plant hormones regulate floret development and degeneration, and thus grain set in flower crops. This study was undertaken to characterize the changes of endogenous hormone levels during flor...The levels of endogenous plant hormones regulate floret development and degeneration, and thus grain set in flower crops. This study was undertaken to characterize the changes of endogenous hormone levels during floret development in three wheat ( Triticum aestivum L.) genotypes: “97J1' with the highest grain set and fertile florets per spike, “H8679' with the lowest grain set and fertile florets per spike, and a medium, “YM158'. The results showed that the peak level of ABA appeared between stamen and pistil differentiation and antherlobe formation of floret development, and the timing delayed with the size of spike (earliest in “H8679” and latest in “97J1”). From antherlobe formation to meiosis, the levels of ABA and GA 1+3 decreased sharply in the ears of “97J1”, while in the ears of “H8679” there was only a slight decrease in ABA, and even an increase in GA 1+3 . The ratio of isopentenyladenosine (iPA)/ABA and IAA/ABA in the ears of “97J1” increased sharply from antherlobe formation to meiosis, but changed only slightly in the ears of “H8679”. At antherlobe formation, IAA and GA 1+3 levels were higher in the ears of “97J1”, but lower in the ears of “H8679” than in the leaves. At meiosis, ABA, GA 1+3 and IAA levels in the “97J1” ears were much lower than in the leaves, but similar in “H8679”. These results indicated that the sharp decreases of ABA and GA 1+3 in ears from antherlobe formation to meiosis and the lowest maintenance at meiosis may be favorable for development of fertile florets and enhancement of grain set in wheat.展开更多
[Objective]This study was to screen out suitable genotypes and basic medium for the culture of maize mature embryos.[Method]Using mature embryos of nine maize genotypes as explants,the effects of genotypes and basic m...[Objective]This study was to screen out suitable genotypes and basic medium for the culture of maize mature embryos.[Method]Using mature embryos of nine maize genotypes as explants,the effects of genotypes and basic medium on callus induction and subculture were investigated.[Result]The genotypes performed better in callus induction and subculture were found in turn 853-35,853-209,Dan 34 and 81162.MS medium is better than N6 medium in the callus induction from maize embryos,while N6 medium is more suitable for callus subculture.[Conclusion]Our study further improved the tissue culture system in maize with mature embryos as explants.展开更多
[Objective] This study aimed to investigate differences in phosphorus effi-ciency between two-rowed barley and multiple-rowed barley and differences in phos-phorus efficiency among various agronomic traits, and to exp...[Objective] This study aimed to investigate differences in phosphorus effi-ciency between two-rowed barley and multiple-rowed barley and differences in phos-phorus efficiency among various agronomic traits, and to explore the relationship be-tween agronomic traits and row type with phosphorus efficiency. [Method] Under available phosphorus mass fractions of 1.32 and 36.6 mg/kg, 172 barley varieties, including 79 two-rowed foreign barley, 22 multiple-rowed foreign barley, 58 two-rowed Chinese barley and 13 multiple-rowed Chinese barley, were selected to com-pare differences in phosphorus efficiency-related agronomic traits. Plant height, spike length, number of unfil ed grains, number of unfil ed grains, main panicle weight, to-tal panicle weight, total stem weight, weight of aerial part and heading stage were surveyed for statistical analysis. [Result] The results showed that, various agronomic traits were larger under fertilization condition than under non-fertilization condition ex-cept number of unfil ed grains and heading stage. Plant high, spike length, weight of aerial part and heading stage varied greatly under non-fertilization condition; number of fil ed grains, number of unfil ed grains and total stem weight varied greatly under fertilization condition. In two-rowed barley, plant height and number of fil ed grains of Chinese varieties were higher than those of foreign varieties, while other agronomic traits such as spike length, number of unfil ed grains, main panicle weight, total panicle weight, total stem weight, weight of aerial part and heading stage of foreign varieties were higher than those of Chinese varieties. Spike length and weight of aerial part in multiple-rowed and two-rowed foreign barley were higher than those in Chinese barley. In multiple-rowed barley, plant height, number of unfil ed grains, total panicle weight and total stem weight of foreign varieties were higher under non-fer-tilization condition and lower under fertilization condition compared with those of Chi-nese varieties; number of fil ed grains, main panicle weight and heading stage of foreign varieties were lower under non-fertilization condition and higher under fertil-ization condition compared with those of Chinese varieties. [Conclusion] Heading stage, number of fil ed grains, number of unfil ed grains and total stem weight are more sensitive to phosphorus efficiency. Multiple-rowed barley is more sensitive to phosphorus efficiency than two-rowed barley.展开更多
With 12 Vicia faba L. varieties of different genotypes as the research ma- terials, the contents of 9 kinds of quality factors of protein, fat, free amino acid as well as beneficial mineral elements were analyzed with...With 12 Vicia faba L. varieties of different genotypes as the research ma- terials, the contents of 9 kinds of quality factors of protein, fat, free amino acid as well as beneficial mineral elements were analyzed with the aim to provide the nec- essary theoretical basis for the selection of new varieties of high quality faba beans. The results showed that in the faba beans of different genotypes, the protein content ranged from 27.9% to 31.2%, fat content of 1.2-1.4%, tannin content of 4 700-5 280 mg/kg, iron content of 47.45-67.15 mgJkg, calcium content of 571.30-1 397.22 mg/kg, zinc content of 47.34-66.10 mg/kg, potassium content of 1.09-1.38%, and selenium content ranged from 0.031 mg/kg to 0.064 mg/kg. There were significant differences in the contents of different free amino acids between different genotypes, and the total free amino acid content was between 1.062% and 0.915%.展开更多
[Objective] This study was conducted to select wheat varieties with high P use efficiency. [Method] A field experiment was carried out with 112 wheat germplasm varieties as experiment materials under normal （NP） and...[Objective] This study was conducted to select wheat varieties with high P use efficiency. [Method] A field experiment was carried out with 112 wheat germplasm varieties as experiment materials under normal （NP） and low phosphorus （LP） conditions, and with Jimai 22 as control, genotypes with high P use efficiency and excellent yield traits were selected. [Result] Compared with NP treatment, 8 wheat yield-related traits, spike number per plant, thousand-grain weight plant height, spike length, fertile spikelet number per spike, grain number per spike, grain weight per plant and above-land weight per plant, and 3 P content traits, grain, straw and above-land P contents per plant decreased significantly under LP condition （P〈〈 0.05）, while 3 P utilization efficiency traits, grain, straw and aboveground P utilization efficiencies increased obviously, indicating that low P stress would greatly reduce yield and P content of wheat at adult stage, but would remarkably improve P utilization efficiency. Correlation analysis showed that plant height, fertile spikelet number per spike and grain weight per plant and straw and above-land P concentrations were in significant positive correlation with 3 P content traits, grain, straw and above-land P contents per plant, and in significant negative correlation with 2 Putilization efficiency traits, straw and above-land P utilization efficiencies （P〈0.01）, and could serve as indexes for preliminary rapid evaluation of P use efficiency. Under NP treatment, 17 genotypes with high P use efficiency were selected, and among them, Hanxuan H28, 2010 Pin 4891 and Zhoumai 28 showed grain weights per plant higher than Jimai 22 by 36.07%, 31.96% and 37.44%, respectively, and above-land P utilization efficiency higher than Jimai 22 by 49.34%, 49.42% and 33.05%, respectively; and under LP treatment, 10 genotypes with high P use efficiency were selected, and among them, Henong 826 showed grain weight per plant and above-land P utilization efficiency higher than Jimai 22 by 37.60% and 20.42%, respectively. Furthermore, Hanxuan H23, Hanxuan H28 and Xumai 856 were identified as genotypes with high P use efficiency under both NP and LP treatments. [Conclusion] This study provides good parent materials for breeding of varieties with high P use efficiency.展开更多
Aims: To assess the frequency and the main HPV genotypes circulating among a group of women attending at a third level Hospital in Mexico City. Methods: A cross-sectional and descriptive study was performed in a group...Aims: To assess the frequency and the main HPV genotypes circulating among a group of women attending at a third level Hospital in Mexico City. Methods: A cross-sectional and descriptive study was performed in a group of 143 female outpatients of the Gynecology and Obstetrics Service at the National Institute of Perinatology of Mexico. Cervical swabs were taken from participants and subjected to simultaneous detection/genotyping of HPV by Linear Array Genotyping Test (Roche Molecular Systems). Mann-Whitney U, median and/or Square Chi tests were used to compare socio-demographical features between HPV-infected and uninfected women. Results: A total of 66 women (46.2%) had HPV infection. Overall, 112 genotypes were detected either as single infections (45.5%) or multiple genotype infections (54.5%). The cumulated frequency of multiple infections with high-/low- and high-/high-risk HPV genotypes was 63.9 %. The most frequent high-risk genotypes were HPV52 HPV58 and HPV51, whereas the most frequent low-risk genotypes were HPV6, HPV53 and HPV84. Infected women were significantly younger and have less stable partner relationships than uninfected women (p < 0.05). Conclusion: A relevant frequency of mixed infections with high- and low-risk HPV genotypes, other than those considered most prevalent worldwide, was observed. Most circulating high-risk genotypes among the women of this study are not covered by commercial vaccine formulations.展开更多
Changes in the efficiency of the primary light energy conversion, fluorescence quenching parameters and contents of photosynthetic pigments were compared between two wheat ( Triticum aestivum L.) genotypes in respo...Changes in the efficiency of the primary light energy conversion, fluorescence quenching parameters and contents of photosynthetic pigments were compared between two wheat ( Triticum aestivum L.) genotypes in response to high light stress. The contents of chlorophyll and carotenoid in “Jing_411' were slightly higher than those in “Xiaoyan_54'. Under high light stress, photoinhibition as indicated by a sustained decrease in PSⅡ photochemical efficiency was more pronounced in “Jing_411' than in “Xiaoyan_54'. The content of ascorbate and the activity of the deepoxidase were higher in “Xiaoyan_54' than in “Jing_411'. The genotypic difference in resistance to photoinhibition is related to the capacity to dissipate the excess energy nonradiatively.展开更多
Objective:To examine the multiplication efficiency Japanese encephalitis virus(JEV)genotype Ⅰ(G Ⅰ) and genotype Ⅲ(GⅢ) of different cell lines which originated from human,porcine,mosquitoes in order to prove mechan...Objective:To examine the multiplication efficiency Japanese encephalitis virus(JEV)genotype Ⅰ(G Ⅰ) and genotype Ⅲ(GⅢ) of different cell lines which originated from human,porcine,mosquitoes in order to prove mechanism of JEV G Ⅰ replacement JEV GⅢ since it emerging in nature recent decades.Methods:The mixture of Gi and GⅢ JEV isolates was inoculated on human rhabdomyosarcoma(RD).pig kidney epithelial(PS) and Aedes albopictus C6/36 clone(C6/36) which originated from human,porcine and mosquitoes,respectively.Plaque assays were performed to calculate virus titer and real-time RT-PCR with GⅠand GⅢspecific primer sets to quantify the number of GⅠ and GUI RNA copies.Results:The highest virus titer reached at the 3rd day of post infection when G Ⅰand GⅢ mixture was inoculated on RD and PS and that of C636 was at the 4^(th)day.JEVs were amplified and maintained by C6/36 cells after 10 passages whereas that by RD and PS only limited within 8 and 6 passages,respectively.GⅠ strain amplified and maintained more efficiently on C6/36 and PS but not RD.whereas GⅢ strain amplified and maintained more efficiently on RD.Conclusions:There is a correlation between the multiplication efficiency of GⅠ and GⅢ JEV strains when these two genotype strains co-infected on different cell lines with the predominance of GⅠstrains in C6/36 and PS and the limited detection of G 1 strains in RD cells proving a possible mechanism of shift JEV genotypes in nature recent decades since GⅠ emerging.展开更多
AIM:To analyze the hepatitis B virus(HBV) characters in China,as well as the correlation between several HBV mutation and hepatitis symptoms.METHODS:A total of 1148 HBV genome sequences from patients throughout China ...AIM:To analyze the hepatitis B virus(HBV) characters in China,as well as the correlation between several HBV mutation and hepatitis symptoms.METHODS:A total of 1148 HBV genome sequences from patients throughout China were collected via the National Center For Biotechnology Information database(information including:genotype,territory and clinical status).HBV genotypes were classified by a direct reference from the Genbank sequence annotation,phylogenetic tree and online software analysis(http://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi).The phylogenetic tree was constructed based on the neighbor-joining method by MEGA5.0 software.HBV sequences were grouped based on phylogenetic tree and the distance between the groups was calculated by using the computer between group mean distance methods.Seven hundred and twelve HBV sequences with clear annotation of clinical symptoms were selected to analyses the correlation of mutation and clinical symptoms.Characteristics of sequences were analyzed by using DNAStar and BioEdit software packages.The codon usage bias and RNA secondary structures analysis were performed by RNAdraw software.Recombination analysis was performed by using Simplot software.RESULTS:In China,HBV genotype C was the predominant in Northeastern,genotype B was predominant in Central Southern areas,genotype B and C were both dominant in Southwestern areas,and the recombinant genotype C/D was predominant in Northwestern areas.C2 and B2 were identified as the two major sub-genotypes,FJ386674 might be a putative sub-genotype as B10.The basal core promoter double mutation and pre-C mutation showed various significant differences between hepatitis symptoms.In addition to ATG,many other HBV initiation codons also exist.HBV has codon usage bias;the termination codon of X,C and P open reading frames(ORF) were TAA,TAG,and TGA,respectively.The major stop codons of S-ORF were TAA(96.45%) and TGA(83.60%) in B2 and C2 subtype,respectively.CONCLUSION:This study recapitulated the epidemiology of HBV in China,and the information might be meaningful critical for the future prevention and therapy of HBV infections.展开更多
At least 600000 individuals worldwide annually die of hepatitis B virus(HBV)-related diseases,such as chronic hepatitis B(CHB),liver cirrhosis(LC),and hepatocellular carcinoma(HCC).Many viral factors,such as viral loa...At least 600000 individuals worldwide annually die of hepatitis B virus(HBV)-related diseases,such as chronic hepatitis B(CHB),liver cirrhosis(LC),and hepatocellular carcinoma(HCC).Many viral factors,such as viral load,genotype,and specific viral mutations,are known to affect disease progression.HBV reverse transcriptase does not have a proofreading function,therefore,many HBV genotypes,sub-genotypes,mutants,and recombinants emerge.Differences between genotypes in response to antiviral treatment have been determined.To date,10 HBV genotypes,scattered across different geographical regions,have been identified.For example,genotype A has a tendency for chronicity,whereas viral mutations are frequently encountered in genotype C.Both chronicity and mutation frequency are common in genotype D.LC and progression to HCC are more commonly encountered with genotypes C and D than the other genotypes.Pathogenic differences between HBV genotypes explain disease intensity,progression to LC,and HCC.In conclusion,genotype determination in CHB infection is important in estimating disease progression and planning optimal antiviral treatment.展开更多
Helicobacter pylori (H. pylori ) is a major causativebacterium of chronic gastritis, peptic ulcer and mucosaassociated lymphoid tissue lymphoma in humans, and associated with an increased risk of gastric cancer[1 -8]....Helicobacter pylori (H. pylori ) is a major causativebacterium of chronic gastritis, peptic ulcer and mucosaassociated lymphoid tissue lymphoma in humans, and associated with an increased risk of gastric cancer[1 -8]. An important virulant factor of H. pylori is the vacuolating cytotoxin ( VacA ) encoded by vacA that induces cytoplasmic vacuolation in target cells both in vitro and in vivo[9-11]. VacA is produced as a 140 kDa precursor which contains an N-terminal signal peptide and an approximately 33 kDa C-terminal outer membrance exporter. The precursor is cleaved at both N-terminal and C-terminal and secreted into the extracellular milieu as a 95 kDa mature protein. The mature protein futher undergoes specific cleavage to yield 37 kDa and 58 kDa subunits[12-14] Although vacA is present in all H. pylori strains, only about 50% to 60% of strains can induce vacuolation of epithelial cells as assessed by the HeLa cell assay. vacA shows considerable genetic variation in H. pylori isolated from all over the world and contains at least two variable regions. The s region exists as sl or s2 allelic types. Among type sl strains, subtypes sla and slb have been identified. The m region occurs as ml or m2 allelic types. Specific vacA genotype of H. pylori strains are associated with the production of the cytotoxin in vitro, epithelial damage in vivo, and clinical consequences[15-27]. The other virulant factor is the cytotoxin-associated protein (CagA) encoded by the cytotoxin-associated gene (cagA). The cagA gene is present in about 60% to 70% of strains and all of these strains express the cagA. The presence of cagA is also associated with the production of the cytotoxin in vitro, and clinical outcome[24-30]. The aim of this study was (i) to identify vacA genotypes and cagA status of H. pylori isolated from Chinese patients; (ii) to evaluation the relatioship beween vacA genotypes, cagA status and related gastroenterological disorders.展开更多
The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the hig...The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term “recombino-subgenotype”. Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term “immigro-subgenotype” to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment.展开更多
Objective: Precise prevention is more desired for cervical cancer due to the huge population, high prevalence of human papillomavirus(HPV) infection in China and the vision of screen-and-treat strategies in low-and mi...Objective: Precise prevention is more desired for cervical cancer due to the huge population, high prevalence of human papillomavirus(HPV) infection in China and the vision of screen-and-treat strategies in low-and middleincome countries(LMICs). Considerations of combining type-specific prevalence and attribution proportion to high-grade cervical intraepithelial neoplasia are informative to more precise and effective region-specific cervical cancer prevention and control programs. The aim of the current study was to determine the genotype distribution of HPV and attribution to cervical precancerous lesions among women from rural areas in North China.Methods: A total of 9,526 women participated in the cervical cancer screening project in rural China. The samples of women who tested positive for HPV were retested with a polymerase chain reaction(PCR)-based HPV genotyping test. The attribution proportion of specific high-risk human papillomavirus(HR-HPV) types for different grades of cervical lesions was calculated by using the type contribution weighting method.Results: A total of 22.2%(2,112/9,526) of women were HR-HPV positive and HPV52(21.7%) was the most common HR-HPV genotype, followed by HPV58(18.2%), HPV53(18.2%) and HPV16(16.2%). The top three genotypes detected in HR-HPV-positive cervical intraepithelial neoplasia(CIN)1 were HPV16(36.7%), HPV58(20.4%), HPV56(15.3%). Among CIN2+, the most frequent genotypes were HPV16(75.6%), HPV52(17.8%),HPV58(16.7%). HPV16, 56, 58, 53, 52, 59, 68, and 18 combined were attributed to 84.17% of all CIN1 lesions,and HPV16, 58, and 52 combined were attributed to 86.98% of all CIN2+ lesions.Conclusions: The prevalence of HR-HPV infection among women from rural areas in North China was high and HPV16, HPV58, HPV52 had paramount attributable fraction in CIN2+. Type-specific HPV prevalence and attribution proportion to cervical precancerous lesions should be taken into consideration in the development of vaccines and strategy for screening in this population.展开更多
基金funded by grants from the National Key R&D Project(2023YFD1400201-02,2023YFD1400203-02)the National Natural Science Foundation of China(31870137)+1 种基金the National Transgenic Research Project(2015ZX08001-002)the Key R&D Project of Guangdong Province(2022B0202060005).
文摘Asian rice comprises two major subspecies:Xian(X)and Geng(G),and the diverged resistance genes(R)have provided a foundation for breeding improved cultivars to control rice blast disease.After conducting two-phase allele mining using six updated FNP marker systems,the functional haplotypes at Pit,Pib,and Pi63 strictly diverged into the X-populations and were defined as X-R loci,while those at Pi54,Pi37,and Pi36 into the G-populations as G-R loci.The genic diversity at the three X-R loci(16 alleles)was twofold higher than that at the three G-R loci(8 alleles),and the allelic diversity in the Southern region(21 alleles)was nearly double that in the Northeastern region(11 alleles).Both observations reflect a significant difference in genetic diversity between X-and G-populations,and indicate that the effective R-genes mainly originated from X-subspecies.Based on the allelic structures characterized by a set of 10 parameters,8 and 16 alleles were respectively recognized as favorable and promising ones for the regional breeding programs.The genotypic structures of the two regional populations were almost different,indicating that the diverged alleles have been further assembled into two series of regional genotypes through long-term breeding programs,despite the presence of one-third of region-common alleles.The genotypic diversity in the Southern region(55 genotypes)was nearly twice as high as that in the Northeastern region(28),which perfectly reflects the aforementioned differences in both genic and allelic diversities.After analyzing the genotypic structures using a set of 13 parameters,4 and 23 genotypes,respectively,can be recommended as the favorable and promising ones for the regional breeding programs.The case study serves as a concrete sample of how to identify the favorable and promising alleles and genotypes,and beneficial parents based their comprehensive population structures for gene-designed breeding.
基金funded by the National Key R&D Program of China(Grant No.2022YFE0139400)the Egyptian-Chinese Research Fund,and Science,Technology&Innovation Funding Authority Egypt(Grant No.46512)the National Natural Science Foundation of China(Grant No.261143470).
文摘Salt stress is a critical factor affecting the growth and yield of rice.Egypt,the largest rice producer in North Africa and the Middle East,is facing contrasting challenges related to salinity in its agroecosystems.In this study,we compared the salt-induced responses among three rice varieties:Giza 176(Egyptian variety),Kaituodao(Chinese variety),and Pokkali(Sri Lanka variety,used as control)under normal and saline stress(100 mmol/L NaCl)conditions at two seedling stages through RNA-seq expression analysis.Giza 176 displayed a salt tolerance score of 7 on the SES(Standard Evaluation Score).Its transcriptome showed dynamic changes,with the number of upregulated genes increasing from 180 to 735,and downregulated genes increasing from 918 to 2930 from the one-week to two-week stress stages,with activated pathways in ion transport,reactive oxygen species(ROS)scavenging,and protein biosynthesis.
基金supported by the projects of National Virus Resource Center(NVRC-PY-03,E1YZ020501)Natural Science Foundation of Hubei Province(2022CFB564)+4 种基金Foundation of Hubei Provincial Health Commission(WJ2023M108)National Basic Science Data Sharing Platform(no.2018ZX10101004)National Basic Science Data Sharing Service Platform(no.NBSDC-DB-13)the International Cooperation Base of Hubei Province for Infection and Immunitysupported by Outstanding Medical Young Scholars of Hubei Province and Wuhan Young and Middle-aged Medical Backbone Talent Program.
文摘Acute respiratory tract infections(ARTIs)are among the leading causes of morbidity and mortality in children worldwide.Human adenovirus(HAdV)infections are estimated to account for at least 5%of pediatric ARTIs.The circulated genotypes of HAdV and the correlation between genotype and clinical manifestations in Wuhan,China,before and after the complete relaxation of nonpharmaceutical interventions against severe acute respiratory syndrome coronavirus 2,remain unknown.Here,101 HAdV strains were isolated from throat swab samples collected from hospitalized children with ARTIs who tested positive for HAdV nucleic acid.Of these,sixty-six strains from 2022 to twenty-three strains from 2023 were successfully genotyped and subjected to phylogenetic analysis based on the hexon,penton base,and fiber genes.Six genotypes,B3,C1,C2,C5,C104,and C108 were identified.HAdV-B3(84.85%)was the most prevalent type in 2022,while HAdV-C(86.96%),including C1,C2,C108,and C104,was the most prevalent in 2023.These strains were phylogenetically related to strains from Japan,China,and the United States in recent years.When comparing clinical characteristics,pediatric patients infected with B3,C1,C2,C5,C104,or C108 exhibited similar clinical manifestations,primarily fever and cough,but varying interleukin(IL)-10 levels.In conclusion,from June 2022 to September 2023,the circulated genotypes of HAdV in Wuhan included B3,C1,C2,C108,C5,and C104.The endemic pattern of HAdV in Wuhan,China,shifted from species B as the dominant type in 2022 to species C in 2023.
文摘Background:In 2021,the American College of Medical Genetics and Genomics(ACMG)recommended reporting actionable genotypes in 73 genes associated with diseases for which preventive or therapeutic measures are available.Evaluations of the association of actionable genotypes in these genes with life span are currently lacking.Methods:We assessed the prevalence of coding and splice variants in genes on the ACMG Secondary Findings,version 3.0(ACMG SF v3.0),list in the genomes of 57,933 Icelanders.We assigned pathogenicity to all reviewed variants using reported evidence in the ClinVar database,the frequency of variants,and their associations with disease to create a manually curated set of actionable genotypes(variants).We assessed the relationship between these genotypes and life span and further examined the specific causes of death among carriers.
文摘Background: The incidence of cervical cancer is high in Bangladesh and there is a high prevalence of preinvasive lower genital tract disease among women of reproductive age. Persistent high-risk Human Papilloma Virus (HPV) infection is the main underlying cause of cervical cancer and its precursor, cervical intraepithelial neoplasia (CIN). Objective: The aim of the study was to identify the subtypes of high-risk HPV infection among women with the colposcopic diagnosis of cervical intraepithelial neoplasia in Bangladesh. Methods: This cross-sectional observational study was conducted in the colposcopy clinic of Dhaka Medical College Hospital over a six-month period. A total of 100 participants were enrolled. Married women, between 30 - 60 years of age with colposcopically diagnosed cervical intra epithelial neoplasia were enrolled. Women with chronic illness, pregnancy, and women unable to consent were excluded from this study. After counselling, colposcopically directed punch biopsies were taken from each CIN case concurrently with high-risk HPV testing by polymerase chain reaction (PCR). Results: The mean age of the patients was 38.69 (SD ±7.76) years. CIN 1 was diagnosed in 57% of participants, while 24% had CIN II and 19% had CIN III lesions. High-risk HPV was present in 52 patients. HPV 16 was the most common identified in 28 (53.84%) and HPV 18 was the second most common with 20 (38.46%) either singly or in combination with other high-risk subtypes. The other HPV strains, HPV 31, 33, 35, 52, 56 and 58, were also detected either as mono or co-infections. Out of the 52 HPV positive cases, 29 (55.8%) had mono infection and 23 (44.2%) had co-infection with several subtypes. The highest incidence (50%) of oncogenic HPV infections was present among women aged 35 - 45 years. Risk factors associated with HPV positive cases were high parity (P 0.05), early age at marriage (P = 0.754) and early age of first child. Conclusion: This study identified a high prevalence of HPV 16 and 18 genotypes. HPV vaccination with the current 9-valent HPV vaccine, which contains HPV types 6, 11, 16, 18, 31, 33, 45, 52, and 58. Will be an effective public health measure to eradicate cervical cancer in Bangladesh.
基金Supported by National "11th five-year" Plan Science and Technolo-gy Support Project (2006BAD02A11)"11th five-year plan" of Tackling Key Problems Projects of Heilongjiang Province(GA07B101)~~
文摘[Objective] To study the effects of Zinc on the yield,nitrogen/phosphorus/potassium/Zinc uptake and distribution of different genotypes of maize.[Method] Using two different genotypes of maize as materials,the effects of Zn on the yield,N/P/K /Zn uptake and distribution of different genotypes of maize were studied by pot cultivation.[Result] Appropriate Zn supply could improve the grain number per kernel.The Zn content in different organs of maize showed little difference under low Zn treatment （Zn0,Zn1）.With the increase of Zn supply,Zn content in leaf,stem and sheath rapidly increased,but the increasing amplitude of Zn content in the kernel and bract were less.The excessive Zn in maize was mainly translocated in lower organs to reduce the damage of them to plants.Different Zn supply levels had less effects on the absorption and translocation of N,P and K in low-Zn insensitive variety Mudan 9.While the absorption and translation of N,P,K in low Zn sensitive variety （Sidan 19） was more easily influenced by the amount of Zn supplied.[Conclusion] Appropriate Zn supply could enhance the maize yield and utilization rate of N and K,and reduce the absorption and utilization of P.
文摘The levels of endogenous plant hormones regulate floret development and degeneration, and thus grain set in flower crops. This study was undertaken to characterize the changes of endogenous hormone levels during floret development in three wheat ( Triticum aestivum L.) genotypes: “97J1' with the highest grain set and fertile florets per spike, “H8679' with the lowest grain set and fertile florets per spike, and a medium, “YM158'. The results showed that the peak level of ABA appeared between stamen and pistil differentiation and antherlobe formation of floret development, and the timing delayed with the size of spike (earliest in “H8679” and latest in “97J1”). From antherlobe formation to meiosis, the levels of ABA and GA 1+3 decreased sharply in the ears of “97J1”, while in the ears of “H8679” there was only a slight decrease in ABA, and even an increase in GA 1+3 . The ratio of isopentenyladenosine (iPA)/ABA and IAA/ABA in the ears of “97J1” increased sharply from antherlobe formation to meiosis, but changed only slightly in the ears of “H8679”. At antherlobe formation, IAA and GA 1+3 levels were higher in the ears of “97J1”, but lower in the ears of “H8679” than in the leaves. At meiosis, ABA, GA 1+3 and IAA levels in the “97J1” ears were much lower than in the leaves, but similar in “H8679”. These results indicated that the sharp decreases of ABA and GA 1+3 in ears from antherlobe formation to meiosis and the lowest maintenance at meiosis may be favorable for development of fertile florets and enhancement of grain set in wheat.
基金Supported by National Natural Science Foundation of China(31070224)National Natural Science Foundation of China(30970219)Key Project from Science and Technology Department in Jilin Province(20080203)~~
文摘[Objective]This study was to screen out suitable genotypes and basic medium for the culture of maize mature embryos.[Method]Using mature embryos of nine maize genotypes as explants,the effects of genotypes and basic medium on callus induction and subculture were investigated.[Result]The genotypes performed better in callus induction and subculture were found in turn 853-35,853-209,Dan 34 and 81162.MS medium is better than N6 medium in the callus induction from maize embryos,while N6 medium is more suitable for callus subculture.[Conclusion]Our study further improved the tissue culture system in maize with mature embryos as explants.
基金Supported by China Agriculture Research System(CARS-05)National Natural Science Foundation of China(No.31260326)Personnel Training Plan of Technological Innovation of Yunnan Province(No.2012HB050)~~
文摘[Objective] This study aimed to investigate differences in phosphorus effi-ciency between two-rowed barley and multiple-rowed barley and differences in phos-phorus efficiency among various agronomic traits, and to explore the relationship be-tween agronomic traits and row type with phosphorus efficiency. [Method] Under available phosphorus mass fractions of 1.32 and 36.6 mg/kg, 172 barley varieties, including 79 two-rowed foreign barley, 22 multiple-rowed foreign barley, 58 two-rowed Chinese barley and 13 multiple-rowed Chinese barley, were selected to com-pare differences in phosphorus efficiency-related agronomic traits. Plant height, spike length, number of unfil ed grains, number of unfil ed grains, main panicle weight, to-tal panicle weight, total stem weight, weight of aerial part and heading stage were surveyed for statistical analysis. [Result] The results showed that, various agronomic traits were larger under fertilization condition than under non-fertilization condition ex-cept number of unfil ed grains and heading stage. Plant high, spike length, weight of aerial part and heading stage varied greatly under non-fertilization condition; number of fil ed grains, number of unfil ed grains and total stem weight varied greatly under fertilization condition. In two-rowed barley, plant height and number of fil ed grains of Chinese varieties were higher than those of foreign varieties, while other agronomic traits such as spike length, number of unfil ed grains, main panicle weight, total panicle weight, total stem weight, weight of aerial part and heading stage of foreign varieties were higher than those of Chinese varieties. Spike length and weight of aerial part in multiple-rowed and two-rowed foreign barley were higher than those in Chinese barley. In multiple-rowed barley, plant height, number of unfil ed grains, total panicle weight and total stem weight of foreign varieties were higher under non-fer-tilization condition and lower under fertilization condition compared with those of Chi-nese varieties; number of fil ed grains, main panicle weight and heading stage of foreign varieties were lower under non-fertilization condition and higher under fertil-ization condition compared with those of Chinese varieties. [Conclusion] Heading stage, number of fil ed grains, number of unfil ed grains and total stem weight are more sensitive to phosphorus efficiency. Multiple-rowed barley is more sensitive to phosphorus efficiency than two-rowed barley.
基金Supported by the China Agriculture Research System(CARS-09)~~
文摘With 12 Vicia faba L. varieties of different genotypes as the research ma- terials, the contents of 9 kinds of quality factors of protein, fat, free amino acid as well as beneficial mineral elements were analyzed with the aim to provide the nec- essary theoretical basis for the selection of new varieties of high quality faba beans. The results showed that in the faba beans of different genotypes, the protein content ranged from 27.9% to 31.2%, fat content of 1.2-1.4%, tannin content of 4 700-5 280 mg/kg, iron content of 47.45-67.15 mgJkg, calcium content of 571.30-1 397.22 mg/kg, zinc content of 47.34-66.10 mg/kg, potassium content of 1.09-1.38%, and selenium content ranged from 0.031 mg/kg to 0.064 mg/kg. There were significant differences in the contents of different free amino acids between different genotypes, and the total free amino acid content was between 1.062% and 0.915%.
基金Supported by Jinan Agricultural Science and Technology Innovation Project(201313,201404)Jinan Science and Technology Planning Project(201401103)~~
文摘[Objective] This study was conducted to select wheat varieties with high P use efficiency. [Method] A field experiment was carried out with 112 wheat germplasm varieties as experiment materials under normal （NP） and low phosphorus （LP） conditions, and with Jimai 22 as control, genotypes with high P use efficiency and excellent yield traits were selected. [Result] Compared with NP treatment, 8 wheat yield-related traits, spike number per plant, thousand-grain weight plant height, spike length, fertile spikelet number per spike, grain number per spike, grain weight per plant and above-land weight per plant, and 3 P content traits, grain, straw and above-land P contents per plant decreased significantly under LP condition （P〈〈 0.05）, while 3 P utilization efficiency traits, grain, straw and aboveground P utilization efficiencies increased obviously, indicating that low P stress would greatly reduce yield and P content of wheat at adult stage, but would remarkably improve P utilization efficiency. Correlation analysis showed that plant height, fertile spikelet number per spike and grain weight per plant and straw and above-land P concentrations were in significant positive correlation with 3 P content traits, grain, straw and above-land P contents per plant, and in significant negative correlation with 2 Putilization efficiency traits, straw and above-land P utilization efficiencies （P〈0.01）, and could serve as indexes for preliminary rapid evaluation of P use efficiency. Under NP treatment, 17 genotypes with high P use efficiency were selected, and among them, Hanxuan H28, 2010 Pin 4891 and Zhoumai 28 showed grain weights per plant higher than Jimai 22 by 36.07%, 31.96% and 37.44%, respectively, and above-land P utilization efficiency higher than Jimai 22 by 49.34%, 49.42% and 33.05%, respectively; and under LP treatment, 10 genotypes with high P use efficiency were selected, and among them, Henong 826 showed grain weight per plant and above-land P utilization efficiency higher than Jimai 22 by 37.60% and 20.42%, respectively. Furthermore, Hanxuan H23, Hanxuan H28 and Xumai 856 were identified as genotypes with high P use efficiency under both NP and LP treatments. [Conclusion] This study provides good parent materials for breeding of varieties with high P use efficiency.
文摘Aims: To assess the frequency and the main HPV genotypes circulating among a group of women attending at a third level Hospital in Mexico City. Methods: A cross-sectional and descriptive study was performed in a group of 143 female outpatients of the Gynecology and Obstetrics Service at the National Institute of Perinatology of Mexico. Cervical swabs were taken from participants and subjected to simultaneous detection/genotyping of HPV by Linear Array Genotyping Test (Roche Molecular Systems). Mann-Whitney U, median and/or Square Chi tests were used to compare socio-demographical features between HPV-infected and uninfected women. Results: A total of 66 women (46.2%) had HPV infection. Overall, 112 genotypes were detected either as single infections (45.5%) or multiple genotype infections (54.5%). The cumulated frequency of multiple infections with high-/low- and high-/high-risk HPV genotypes was 63.9 %. The most frequent high-risk genotypes were HPV52 HPV58 and HPV51, whereas the most frequent low-risk genotypes were HPV6, HPV53 and HPV84. Infected women were significantly younger and have less stable partner relationships than uninfected women (p < 0.05). Conclusion: A relevant frequency of mixed infections with high- and low-risk HPV genotypes, other than those considered most prevalent worldwide, was observed. Most circulating high-risk genotypes among the women of this study are not covered by commercial vaccine formulations.
基金The Chinese State Key Basic Research and Development Plan to KUANGT-Y
文摘Changes in the efficiency of the primary light energy conversion, fluorescence quenching parameters and contents of photosynthetic pigments were compared between two wheat ( Triticum aestivum L.) genotypes in response to high light stress. The contents of chlorophyll and carotenoid in “Jing_411' were slightly higher than those in “Xiaoyan_54'. Under high light stress, photoinhibition as indicated by a sustained decrease in PSⅡ photochemical efficiency was more pronounced in “Jing_411' than in “Xiaoyan_54'. The content of ascorbate and the activity of the deepoxidase were higher in “Xiaoyan_54' than in “Jing_411'. The genotypic difference in resistance to photoinhibition is related to the capacity to dissipate the excess energy nonradiatively.
基金funded by Vietnam National Foundation for ScienceTechnology Development(NAFOSTED)under grant number:106.16-2011.68
文摘Objective:To examine the multiplication efficiency Japanese encephalitis virus(JEV)genotype Ⅰ(G Ⅰ) and genotype Ⅲ(GⅢ) of different cell lines which originated from human,porcine,mosquitoes in order to prove mechanism of JEV G Ⅰ replacement JEV GⅢ since it emerging in nature recent decades.Methods:The mixture of Gi and GⅢ JEV isolates was inoculated on human rhabdomyosarcoma(RD).pig kidney epithelial(PS) and Aedes albopictus C6/36 clone(C6/36) which originated from human,porcine and mosquitoes,respectively.Plaque assays were performed to calculate virus titer and real-time RT-PCR with GⅠand GⅢspecific primer sets to quantify the number of GⅠ and GUI RNA copies.Results:The highest virus titer reached at the 3rd day of post infection when G Ⅰand GⅢ mixture was inoculated on RD and PS and that of C636 was at the 4^(th)day.JEVs were amplified and maintained by C6/36 cells after 10 passages whereas that by RD and PS only limited within 8 and 6 passages,respectively.GⅠ strain amplified and maintained more efficiently on C6/36 and PS but not RD.whereas GⅢ strain amplified and maintained more efficiently on RD.Conclusions:There is a correlation between the multiplication efficiency of GⅠ and GⅢ JEV strains when these two genotype strains co-infected on different cell lines with the predominance of GⅠstrains in C6/36 and PS and the limited detection of G 1 strains in RD cells proving a possible mechanism of shift JEV genotypes in nature recent decades since GⅠ emerging.
基金Supported by National Natural Science Foundation of China,No.81160352grants from the Education Department Foundation of Yunnan Province,No.2012J091+1 种基金Health Bureau of Yunnan Province,No.D-201203(partly)Science and Technology Department of Yunnan Province,No.2013HB084(partly)
文摘AIM:To analyze the hepatitis B virus(HBV) characters in China,as well as the correlation between several HBV mutation and hepatitis symptoms.METHODS:A total of 1148 HBV genome sequences from patients throughout China were collected via the National Center For Biotechnology Information database(information including:genotype,territory and clinical status).HBV genotypes were classified by a direct reference from the Genbank sequence annotation,phylogenetic tree and online software analysis(http://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi).The phylogenetic tree was constructed based on the neighbor-joining method by MEGA5.0 software.HBV sequences were grouped based on phylogenetic tree and the distance between the groups was calculated by using the computer between group mean distance methods.Seven hundred and twelve HBV sequences with clear annotation of clinical symptoms were selected to analyses the correlation of mutation and clinical symptoms.Characteristics of sequences were analyzed by using DNAStar and BioEdit software packages.The codon usage bias and RNA secondary structures analysis were performed by RNAdraw software.Recombination analysis was performed by using Simplot software.RESULTS:In China,HBV genotype C was the predominant in Northeastern,genotype B was predominant in Central Southern areas,genotype B and C were both dominant in Southwestern areas,and the recombinant genotype C/D was predominant in Northwestern areas.C2 and B2 were identified as the two major sub-genotypes,FJ386674 might be a putative sub-genotype as B10.The basal core promoter double mutation and pre-C mutation showed various significant differences between hepatitis symptoms.In addition to ATG,many other HBV initiation codons also exist.HBV has codon usage bias;the termination codon of X,C and P open reading frames(ORF) were TAA,TAG,and TGA,respectively.The major stop codons of S-ORF were TAA(96.45%) and TGA(83.60%) in B2 and C2 subtype,respectively.CONCLUSION:This study recapitulated the epidemiology of HBV in China,and the information might be meaningful critical for the future prevention and therapy of HBV infections.
文摘At least 600000 individuals worldwide annually die of hepatitis B virus(HBV)-related diseases,such as chronic hepatitis B(CHB),liver cirrhosis(LC),and hepatocellular carcinoma(HCC).Many viral factors,such as viral load,genotype,and specific viral mutations,are known to affect disease progression.HBV reverse transcriptase does not have a proofreading function,therefore,many HBV genotypes,sub-genotypes,mutants,and recombinants emerge.Differences between genotypes in response to antiviral treatment have been determined.To date,10 HBV genotypes,scattered across different geographical regions,have been identified.For example,genotype A has a tendency for chronicity,whereas viral mutations are frequently encountered in genotype C.Both chronicity and mutation frequency are common in genotype D.LC and progression to HCC are more commonly encountered with genotypes C and D than the other genotypes.Pathogenic differences between HBV genotypes explain disease intensity,progression to LC,and HCC.In conclusion,genotype determination in CHB infection is important in estimating disease progression and planning optimal antiviral treatment.
基金the National Natural Science Foundation of China,№39670648
文摘Helicobacter pylori (H. pylori ) is a major causativebacterium of chronic gastritis, peptic ulcer and mucosaassociated lymphoid tissue lymphoma in humans, and associated with an increased risk of gastric cancer[1 -8]. An important virulant factor of H. pylori is the vacuolating cytotoxin ( VacA ) encoded by vacA that induces cytoplasmic vacuolation in target cells both in vitro and in vivo[9-11]. VacA is produced as a 140 kDa precursor which contains an N-terminal signal peptide and an approximately 33 kDa C-terminal outer membrance exporter. The precursor is cleaved at both N-terminal and C-terminal and secreted into the extracellular milieu as a 95 kDa mature protein. The mature protein futher undergoes specific cleavage to yield 37 kDa and 58 kDa subunits[12-14] Although vacA is present in all H. pylori strains, only about 50% to 60% of strains can induce vacuolation of epithelial cells as assessed by the HeLa cell assay. vacA shows considerable genetic variation in H. pylori isolated from all over the world and contains at least two variable regions. The s region exists as sl or s2 allelic types. Among type sl strains, subtypes sla and slb have been identified. The m region occurs as ml or m2 allelic types. Specific vacA genotype of H. pylori strains are associated with the production of the cytotoxin in vitro, epithelial damage in vivo, and clinical consequences[15-27]. The other virulant factor is the cytotoxin-associated protein (CagA) encoded by the cytotoxin-associated gene (cagA). The cagA gene is present in about 60% to 70% of strains and all of these strains express the cagA. The presence of cagA is also associated with the production of the cytotoxin in vitro, and clinical outcome[24-30]. The aim of this study was (i) to identify vacA genotypes and cagA status of H. pylori isolated from Chinese patients; (ii) to evaluation the relatioship beween vacA genotypes, cagA status and related gastroenterological disorders.
基金Supported by Mahmoud Reza Pourkarim is supported by a postdoctoral grant from the''Fonds voor Wetenschappelijk Onderzoek Vlaanderen''
文摘The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term “recombino-subgenotype”. Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term “immigro-subgenotype” to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment.
基金supported by the China Medical Board (CMB) (No: 16-255)Chinese Academy of Medical Science Initiative for Innovative Medicine (No: 2017-I2M1-002)
文摘Objective: Precise prevention is more desired for cervical cancer due to the huge population, high prevalence of human papillomavirus(HPV) infection in China and the vision of screen-and-treat strategies in low-and middleincome countries(LMICs). Considerations of combining type-specific prevalence and attribution proportion to high-grade cervical intraepithelial neoplasia are informative to more precise and effective region-specific cervical cancer prevention and control programs. The aim of the current study was to determine the genotype distribution of HPV and attribution to cervical precancerous lesions among women from rural areas in North China.Methods: A total of 9,526 women participated in the cervical cancer screening project in rural China. The samples of women who tested positive for HPV were retested with a polymerase chain reaction(PCR)-based HPV genotyping test. The attribution proportion of specific high-risk human papillomavirus(HR-HPV) types for different grades of cervical lesions was calculated by using the type contribution weighting method.Results: A total of 22.2%(2,112/9,526) of women were HR-HPV positive and HPV52(21.7%) was the most common HR-HPV genotype, followed by HPV58(18.2%), HPV53(18.2%) and HPV16(16.2%). The top three genotypes detected in HR-HPV-positive cervical intraepithelial neoplasia(CIN)1 were HPV16(36.7%), HPV58(20.4%), HPV56(15.3%). Among CIN2+, the most frequent genotypes were HPV16(75.6%), HPV52(17.8%),HPV58(16.7%). HPV16, 56, 58, 53, 52, 59, 68, and 18 combined were attributed to 84.17% of all CIN1 lesions,and HPV16, 58, and 52 combined were attributed to 86.98% of all CIN2+ lesions.Conclusions: The prevalence of HR-HPV infection among women from rural areas in North China was high and HPV16, HPV58, HPV52 had paramount attributable fraction in CIN2+. Type-specific HPV prevalence and attribution proportion to cervical precancerous lesions should be taken into consideration in the development of vaccines and strategy for screening in this population.
