Since the introduction of intracytoplasmic sperm injection （ICSI） using single sperm isolated from testicular tissue in men with obstructive and non-obstructive azoospermia, or using ejaculated sperm in those with p...Since the introduction of intracytoplasmic sperm injection （ICSI） using single sperm isolated from testicular tissue in men with obstructive and non-obstructive azoospermia, or using ejaculated sperm in those with poor semen quality, there have been concerns that this might have adverse effects on the offspring compared to conventional in vitrofertilisation （IVF） and natural conceptions. ICSI is done for reasons other than male factor infertility, and on the whole has not been shown to have any more negative effects than those seen with IVF. There have however, been very few studies of ICSI with a focus on, or large enough numbers to examine, the specific outcomes associated with male factor infertility. From the limited information available in relation to the source of the sperm and aetiology of infertility in the presence of ICSI, there appears to be no increased risk of congenital malformations. There is, however, a small increase in both de novoand inherited chromosome abnormalities. In terms of growth and neurodevelopment, there are very few studies, and so far, no adverse outcomes have been found in young children whose fathers have a sperm defect. The origin of the sperm used in ICSI does not have a major influence on the early life outcomes for the offspring, but transgenerational and epigenetic effects remain unknown. When the male factor infertility is known or thought to be due to a Y-chromosome deletion, this information should be given to the young male offspring at a time that will ensure his own reproductive health and plans are optimized.展开更多
AIM: To evaluate the relationship between glutathione S-transferase M1(GSTM1) polymorphism and susceptibility to esophageal cancer(EC).METHODS: A comprehensive search of the United States National Library of Medicine ...AIM: To evaluate the relationship between glutathione S-transferase M1(GSTM1) polymorphism and susceptibility to esophageal cancer(EC).METHODS: A comprehensive search of the United States National Library of Medicine Pub Med database and the Elsevier, Springer, and China National Knowledge Infrastructure databases for all relevant studies was conducted using combinations of the following terms: "glutathione S-transferase M1", "GSTM1", "polymorphism", and "EC"(until November 1, 2014). The statistical analysis was performed using the SAS software(v.9.1.3; SAS Institute, Cary, NC, United States) and the Review Manager software(v.5.0; Oxford, England); crude odds ratios(ORs) with 95% confidence intervals(CIs) were used to assess the association between the GSTM1 null genotype and the risk of EC.RESULTS: A total of 37 studies involving 2236 EC cases and 3243 controls were included in this metaanalysis. We observed that the GSTM1 null genotype was a significant risk factor for EC in most populations(OR = 1.33, 95%CI: 1.12-1.57, P_(heterogeneity) < 0.000001, and I2 = 77.0%), particularly in the Asian population(OR = 1.53, 95%CI: 1.26-1.86, P_(heterogeneity)< 0.000001, and I2 = 77.0%), but not in the Caucasian population(OR = 1.02, 95%CI: 0.87-1.19, P_(heterogeneity) = 0.97, and I2 = 0%).CONCLUSION: The GSTM1 null polymorphism may be associated with an increased risk for EC in Asian but not Caucasian populations.展开更多
The antibody repertoire of Bos taurus is characterized by a subset of variable heavy(VH)chain regions with ultralong third complementarity determining regions(CDR3)which,compared to other species,can provide a potent ...The antibody repertoire of Bos taurus is characterized by a subset of variable heavy(VH)chain regions with ultralong third complementarity determining regions(CDR3)which,compared to other species,can provide a potent response to challenging antigens like HIV env.These unusual CDR3 can range to over seventy highly diverse amino acids in length and form uniqueβ-ribbon‘stalk’and disulfide bonded‘knob’structures,far from the typical antigen binding site.The genetic components and processes for forming these unusual cattle antibody VH CDR3 are not well understood.Here we analyze sequences of Bos taurus antibody VH domains and find that the subset with ultralong CDR3 exclusively uses a single variable gene,IGHV1-7(VHBUL)rearranged to the longest diversity gene,IGHD8-2.An eight nucleotide duplication at the 3′end of IGHV1-7 encodes a longer V-region producing an extended Fβ-strand that contributes to the stalk in a rearranged CDR3.A low amino acid variability was observed in CDR1 and CDR2,suggesting that antigen binding for this subset most likely only depends on the CDR3.Importantly a novel,potentially AID mediated,deletional diversification mechanism of the B.taurus VH ultralong CDR3 knob was discovered,in which interior codons of the IGHD8-2 region are removed while maintaining integral structural components of the knob and descending strand of the stalk in place.These deletions serve to further diversify cysteine positions,and thus disulfide bonded loops.Hence,both germline and somatic genetic factors and processes appear to be involved in diversification of this structurally unusual cattle VH ultralong CDR3 repertoire.展开更多
BACKGROUND Laron syndrome(LS)is an autosomal recessive hereditary condition affecting only 1/1000000 births.The cause is associated with mutations in the growth hormone(GH)receptor(GHR),leading to GH insensitivity.LS ...BACKGROUND Laron syndrome(LS)is an autosomal recessive hereditary condition affecting only 1/1000000 births.The cause is associated with mutations in the growth hormone(GH)receptor(GHR),leading to GH insensitivity.LS patients typically present with severe growth retardation,obesity,and abnormal sexual maturation.Currently,LS diagnosis is performed post-delivery.Therefore,we assessed the efficiency of Pre-implantation Genetic Testing(PGT)coupled with monoplex-polymerase chain reaction(PCR)technology for detecting this monogenic disease in embryos from a couple confirmed as LS heterozygous carriers CASE SUMMARY The couple LS-carriers were confirmed by the presence of a first child born with LS.The couple underwent a standard in vitro fertilization(IVF)protocol.DNA was collected from trophectoderm cells from day 5 embryos.Whole genome amplification(WGA)was performed using a Sureplex DNA Amplification System and analyzed by PCR,targeting the deletion of the exons 5 and 6 in the GHR gene as well as PGT by Next-generation Sequencing(Illumina).Eleven embryos were collected and analyzed.27.3%were the wild type for GHR,45.5%were heterozygotes,and 18.2%homozygous mutants.One embryo yielded no results.Three 2-embryos transfers were performed;2 normal homozygous and four heterozygous carriers were selected for transfer.The first two transfers were unsuccessful,whereas the final transfer with two heterozygous embryos resulted in clinical pregnancy.The genomic composition of the fetus was verified,applying the same techniques using amniocytes,extracted after 21 wk of the ongoing pregnancy.The fetus was confirmed as GHR deletion in exon 5-6,carrier.A non-affected baby was born.CONCLUSION Here,we present a case demonstrating that using WGA as a template in addition to PCR targeting specific gene regions,exons 5 and 6 on the GHR gene,could identify LS carrier embryos.This provides evidence that WGA and PCR serve as an excellent tool to detect this specific monogenic disease in IVF embryos,thus allowing selection of candidate embr展开更多
A dataset of 103 SARS-CoV isolates （101 human patients and 2 palm civets） was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide...A dataset of 103 SARS-CoV isolates （101 human patients and 2 palm civets） was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations （SNVs） and insertions and deletions, with respect to a “profile”, were determined and discussed （“profile” being a sequence containing the most represented letter per position）. Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid （a.a.） property changes. Similar analysis was performed for the spike （S） protein in all the isolates （55 of them being predicted for the first time）. The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes： TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.展开更多
Insertion and deletion(indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evol...Insertion and deletion(indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evolution. However, genetic and evolutionary mechanisms of indels remain elusive. We establish a comparative genome-transcriptome-alignment approach for a large-scale identification of indels in Monopterus population. Over 2000 indels in 1738 indel genes, including 1-21 bp deletions and 1-15 bp insertions, were detected. Each indel gene had ～1.1 deletions/insertions, and 2-4 alleles in population. Frequencies of deletions were prominently higher than those of insertions on both genome and population levels. Most of the indels led to in frame mutations with multiples of three and majorly occurred in non-domain regions, indicating functional constraint or tolerance of the indels. All indel genes showed higher expression levels than non-indel genes during sex reversal. Slide window analysis of global expression levels in gonads showed a significant positive correlation with indel density in the genome. Moreover, indel genes were evolutionarily conserved and evolved slowly compared to nonindel genes. Notably, population genetic structure of indels revealed divergent evolution of Monopterus population, as bottleneck effect of biogeographic isolation by Taiwan Strait, China.展开更多
BACKGROUND Antiviral treatment of patients with chronic hepatitis B(CHB)in the grey zone of treatment comands risk management in order to optimize the health outcome.In this sense,the identification of HBV mutants rel...BACKGROUND Antiviral treatment of patients with chronic hepatitis B(CHB)in the grey zone of treatment comands risk management in order to optimize the health outcome.In this sense,the identification of HBV mutants related with an increased risk of hepatocellular carcinoma(HCC)could be useful to identify subpopulations with potential indication of antiviral treatment.AIM To analyze the prevalence/persistence of hepatitis B virus(HBV)preS and basal core promoter(BCP)/precore/core variants associated to HCC development in CHB patients in the grey zone.METHODS Work was designed as a longitudinal retrospective study,including 106 plasma samples from 31 patients with CHB in the grey zone of treatment:Hepatitis B e antigen negative,HBV-DNA levels between 12-20000 IU/mL,normal or discordant transaminase levels during follow up and mild/moderate necroinflammatory activity in liver biopsy or Fibroscan(up to 9.5 kPa).Serum HBVDNA was tested using the Abbott Real Time HBV Assay and the BCP/precore/core and the hepatitis B surface antigen(HBsAg)coding regions were analyzed in positive samples by PCR/bulk-sequencing to identify the HCCrelated HBV mutants.RESULTS High-risk HCC related mutants were detected in 24(77%)patients:19(61%)in the BCP/precore/core,and 7(23%)in the HBsAg coding region(2 preS1 and 5 preS2 deletions).The prevalence of preS deletions was genotype-dependent:3/5(60%)patients with preS2 deletions and 1/2 with preS1 deletions were infected with the HBV-E genotype.Since HBV-E was the most prevalent in sub-Saharan patients,a correlation between preS deletions and ethnicity was also found:6/8(75%)sub-Saharan vs 1/19(5%)Caucasian patients had preS deletions(P=0.00016).Remarkably,this correlation was maintained in those patients infected with HBV-A,a minor genotype in sub-Saharan patients:2/2 patients infected with HBV-A from West Africa vs 0/6 of Caucasian origin had preS deletions.The HCC related variants were the major strains and persisted over time(up to 48 mo).Patients with preS deletions had a significant hig展开更多
Background: Analysis of Philadelphia (Ph) chromosome, a hallmark of chronic myeloid leukemia (CML) plays an important role in disease monitoring of the targeted drug Imatinib. Apart from Ph, genomic imbalances such as...Background: Analysis of Philadelphia (Ph) chromosome, a hallmark of chronic myeloid leukemia (CML) plays an important role in disease monitoring of the targeted drug Imatinib. Apart from Ph, genomic imbalances such as additional chromosomal abnormalities (ACAs) of major route occur during transformation of the disease and show negative impact on prognosis. Objective: The present study was carried out to investigate frequencies of ACAs, genomic deletions, complex Ph variants and their prognostic influences in a large cohort of newly diagnosed CML-CP (chronic phase) and CML-AP/BP (accelerated/blast phase). Material & Methods: Retrospective, single institutional study on 1367 cases of CML-CP and 82 cases of CML-AP/BP between 2009 and 2015, using conventional cytogenetics along with fluorescence in situ hybridization. Results: Of the 1367 patients in CML-CP, 1041 patients who completed 12 - 18 months of Imatinib therapy showed complete cytogenetic remission (CCyR) rates of 76% and 82% at 12 and 18 months respectively. Imatinib induced 81% and 33% CCyR in CML-AP and CML-BP respectively. Frequencies of ACAs in CML-CP, AP and BP were 2%, 27% and 67% respectively. Patients in chronic and AP/BP phase with ACAs showed resistance to Imatinib (p < 0.0005). The incidence of genomic deletions and complex Ph variants was 21% and 6.3% respectively with no comparable difference of cytogenetic response to Imatinib (p p < 0.210 respectively). In a cohort of 112 patients in CCyR, development of new clonal abnormalities, more frequently trisomy 8 was detected in Ph negative clone. Conclusion: Our data demonstrated that Imatinib as a frontline therapy had significantly improved management of CML. However, ACAs play an important role in resistance to Imatinib, both in chronic and acute phase, which may limit sole ABL targeted therapy.展开更多
作为中国第一本无机化学教材,《化学鉴原》对晚清翻译、传播化学知识产生了重要作用。文章通过对《化学鉴原》(1871)及其底本《韦而司化学原理及化学应用》(Wells’s Principles and Applications of Chemistry)的对比研究,发现《化学...作为中国第一本无机化学教材,《化学鉴原》对晚清翻译、传播化学知识产生了重要作用。文章通过对《化学鉴原》(1871)及其底本《韦而司化学原理及化学应用》(Wells’s Principles and Applications of Chemistry)的对比研究,发现《化学鉴原》在翻译过程中对底本进行了结构调整与内容增删,使译本更为适应国人的需要,有利于知识的传播,同时也使译本在知识之间的逻辑关系及化学理论方面略显不足。展开更多
Abstract Objectives To investigate the tissue specificity of reactive oxygen species (ROS) damage to mitochondrial DNA (mtDNA) and to determine whether cochlear mtDNA is a sensitive target for ROS damage. Methods 10...Abstract Objectives To investigate the tissue specificity of reactive oxygen species (ROS) damage to mitochondrial DNA (mtDNA) and to determine whether cochlear mtDNA is a sensitive target for ROS damage. Methods 10 Cu/ZnSOD gene (Cu/Zn superoxide dismutase gene, Sod1) knockout mice and 16 wild-type mice were analyzed by nested polymerase chain reaction (PCR).Results Three deletions were detected in various tissues of Sod1 knockout mice. MtDNA3867bp and mtDNA3726bp deletions were the most visible, and mtDNA4236bp deletion was barely detected in these tissues. There were obvious differences in the ratio of deleted mtDNA/total mtDNA in different tissue. Deleted mtDNA was most abundant in the liver and kidney and less in cochlea, heart and brain. The lowest was in spleen and skin. The ratio in various tissues was 3-20 times in Sod1 knockout mice over wild-type mice. In cochlea, the ratio was about 15. Conclusions Without the protection of Sod1, ROS can lead to mtDNA deletions in various tissues with significant tissue specificity. Cochlear mtDNA is a sensitive target for ROS damage.展开更多
Global climate change and acquired resistance to insecticides are threats to world food security.Drosophila suzukii,a devastating invasive pest in many parts of the world,causes substantial economic losses to fruit pr...Global climate change and acquired resistance to insecticides are threats to world food security.Drosophila suzukii,a devastating invasive pest in many parts of the world,causes substantial economic losses to fruit production industries,forcing farmers to apply broad-spectrum insecticides frequently,This could lead to the development of insecticide resistance.We determined the Lethal Concentration 50 (median lethal concen- tration,LC50)values of zeta-cypermethrin,spinosad,and malathion insecticides against D.suzukii colonies established from Clarke and Pierce county Georgia,United States. The LC50 values were 3 fold higher in the Pierce county population for all insecticide treatments.We then used RNA sequencing to analyze the responses of Pierce and Clarke population flies surviving a LC50 treatment of the 3 insecticides.We identified a high num- ber of differentially expressed genes that are likely involved in detoxification and reduced cuticular penetration,especially in the Pierce population,with extensive overlap in differ- entially expressed genes between the 3 insecticide treatments.Finally,we predicted fewer nonsynonymous single nucleotide variants having deleterious effects on protein function among detoxification,insecticide target,and cuticular protein encoding genes in Pierce flies.Thus a combination of increased gene expression and fewer deleterious single nu- cleotide variants highlights molecular mechanisms underlying the higher LC50 values for Pierce population flies.展开更多
Phenylketonuria(PKU)is an autosomal recessive metabolic disorder caused by deficiency of phenylalanine hydroxylase(PAH).The major molecular defects causing PKU are missense mutations of PAH gene.Large deletions of exo...Phenylketonuria(PKU)is an autosomal recessive metabolic disorder caused by deficiency of phenylalanine hydroxylase(PAH).The major molecular defects causing PKU are missense mutations of PAH gene.Large deletions of exon 5(EX5del955 and EX5del4232ins)were first reported by the Czech study and were later found also in the Polish,Slovak,Slovenian and Italian PKU-patients.These observations demonstrate the existence of a common subset of this mutation predominantly among Central European populations of Slavic descent.That is why we suggest that EX5del1955 and EX5del4232ins268 mutations might be frequent causes of PKU in Ukrainian patients.EX5del955 and EX5del4232ins268 mutations were analyzed in 106 unrelated PKU patients negative for PAH gene mutations on one or both alleles from our previous analysis.The simultaneous detection of EX5del4232ins268 and EX5del955 mutations was performed by PCR amplification of mutant alleles.EX5del955 mutation was not detected in the Ukrainian patients.This relative alleles frequency of EX5del4232ins268 mutation in the Ukrainian PKU population was determined as 1,66%.Our findings can be the one more evidence of Central European Slavic origin of EX5del4232ins268 mutation,suggested previously.This finding is important for the improvement of DNA diagnosis necessary for the management of PKU patients from Ukraine.展开更多
Allergic asthma is a diverse chronic respiratory disease characterized by the inflammation of the lower airway disease affecting many people around the world with rising morbidity and mortality.Association between ast...Allergic asthma is a diverse chronic respiratory disease characterized by the inflammation of the lower airway disease affecting many people around the world with rising morbidity and mortality.Association between asthma and certain demographic features was studied in relation to genotype from 244 allergic individuals of local population.Skin prick test was used to confirm asthma.Genetic polymorphism in Glutathione-S-transferases(GSTs)was studied using multiplex PCR based method and IgE level by ELISA.Pollen and dust were the major causative aeroallergens(26%),which were associated to higher IgE levels(P<0.05).Smoking was found to be significantly associated with asthma in only males(P Z 0.004).A low prevalence of null genotype of both GSTM1 and GSTT1 genes was observed in the patients(4.34%)compared to control group(14%).No association of combined GSTM1 and GSTT1 null genotype was found with the asthma in local population.GSTM1t and GSTTgenotype had higher risk(OR Z 1.3681,P Z 0.001)for development of asthma.There was a significant association of asthma with combined genotype of GSTM1t and GSTTwhen data was analyzed on gender basis in males(P Z 0.006)and highly significant in age range of 26e40 years(P Z 0.001).Combined GSTMt and GSTTgenotype was found to be risk factor for asthma in addition to family history in male patients.However a data with large patient size and different ethnic distribution may reveal the exact etiology.展开更多
Copy number variants (CNVs) are pieces of genomic DNA of 1000 base pairs or longer which occur in a given genome at a different frequency than in a reference genome. Their importance as a source for phenotypic variabi...Copy number variants (CNVs) are pieces of genomic DNA of 1000 base pairs or longer which occur in a given genome at a different frequency than in a reference genome. Their importance as a source for phenotypic variability has been recognized only in the last couple of years. Chromosomal deletions can be seen as a special case of CNVs where stretches of DNA are missing in certain lines when compared to the reference genome of the mouse line C57BL/6, for example. Based upon more than 8 million single nucleotide polymorphisms (SNPs) in the fifteen inbred mouse lines which were determined in a whole genome chip based resequencing project by Perlegen Sciences, we detected 20166 such long chromosomal deletions. They cover altogether between 4.4 million and 8.8 million base pairs, depending on the mouse line. Thus, their extent is comparable to that of SNPs. The chromosomal deletions were found by searching for clusters of missing values in the genotyping data by applying bioinformatics and biostatistical methods. In contrast to isolated missing values, clusters are likely the consequence of missing DNA probe rather than of a failed hybridization or deficient oligos. We analyzed these deletion sites in various ways. Twenty-two percent of these deletion sites overlap with exons; they could therefore affect a gene's functioning. The corresponding genes seem to exist in alternative forms, a phenomenon that reminds of the alternative forms of mRNA generated during gene splicing. We furthermore detected statistically significant association between hundreds of deletion sites and fat weight at the age of eight weeks.展开更多
文摘Since the introduction of intracytoplasmic sperm injection （ICSI） using single sperm isolated from testicular tissue in men with obstructive and non-obstructive azoospermia, or using ejaculated sperm in those with poor semen quality, there have been concerns that this might have adverse effects on the offspring compared to conventional in vitrofertilisation （IVF） and natural conceptions. ICSI is done for reasons other than male factor infertility, and on the whole has not been shown to have any more negative effects than those seen with IVF. There have however, been very few studies of ICSI with a focus on, or large enough numbers to examine, the specific outcomes associated with male factor infertility. From the limited information available in relation to the source of the sperm and aetiology of infertility in the presence of ICSI, there appears to be no increased risk of congenital malformations. There is, however, a small increase in both de novoand inherited chromosome abnormalities. In terms of growth and neurodevelopment, there are very few studies, and so far, no adverse outcomes have been found in young children whose fathers have a sperm defect. The origin of the sperm used in ICSI does not have a major influence on the early life outcomes for the offspring, but transgenerational and epigenetic effects remain unknown. When the male factor infertility is known or thought to be due to a Y-chromosome deletion, this information should be given to the young male offspring at a time that will ensure his own reproductive health and plans are optimized.
基金Supported by Science and Technology Project of The Health Department of Henan ProvinceChinaNo.510102050432
文摘AIM: To evaluate the relationship between glutathione S-transferase M1(GSTM1) polymorphism and susceptibility to esophageal cancer(EC).METHODS: A comprehensive search of the United States National Library of Medicine Pub Med database and the Elsevier, Springer, and China National Knowledge Infrastructure databases for all relevant studies was conducted using combinations of the following terms: "glutathione S-transferase M1", "GSTM1", "polymorphism", and "EC"(until November 1, 2014). The statistical analysis was performed using the SAS software(v.9.1.3; SAS Institute, Cary, NC, United States) and the Review Manager software(v.5.0; Oxford, England); crude odds ratios(ORs) with 95% confidence intervals(CIs) were used to assess the association between the GSTM1 null genotype and the risk of EC.RESULTS: A total of 37 studies involving 2236 EC cases and 3243 controls were included in this metaanalysis. We observed that the GSTM1 null genotype was a significant risk factor for EC in most populations(OR = 1.33, 95%CI: 1.12-1.57, P_(heterogeneity) < 0.000001, and I2 = 77.0%), particularly in the Asian population(OR = 1.53, 95%CI: 1.26-1.86, P_(heterogeneity)< 0.000001, and I2 = 77.0%), but not in the Caucasian population(OR = 1.02, 95%CI: 0.87-1.19, P_(heterogeneity) = 0.97, and I2 = 0%).CONCLUSION: The GSTM1 null polymorphism may be associated with an increased risk for EC in Asian but not Caucasian populations.
基金This work was supported by NIH grant R01 GM105826-01 to VVSR21 AI120791 to VVS,WM and MFC+2 种基金NSF grant#IOS1257829 to MFCAT is supported by Scripps Genomic Medicine,an NIH-NCATS Clinical and Translational Science Award(CTSA5 UL1 RR025774).
文摘The antibody repertoire of Bos taurus is characterized by a subset of variable heavy(VH)chain regions with ultralong third complementarity determining regions(CDR3)which,compared to other species,can provide a potent response to challenging antigens like HIV env.These unusual CDR3 can range to over seventy highly diverse amino acids in length and form uniqueβ-ribbon‘stalk’and disulfide bonded‘knob’structures,far from the typical antigen binding site.The genetic components and processes for forming these unusual cattle antibody VH CDR3 are not well understood.Here we analyze sequences of Bos taurus antibody VH domains and find that the subset with ultralong CDR3 exclusively uses a single variable gene,IGHV1-7(VHBUL)rearranged to the longest diversity gene,IGHD8-2.An eight nucleotide duplication at the 3′end of IGHV1-7 encodes a longer V-region producing an extended Fβ-strand that contributes to the stalk in a rearranged CDR3.A low amino acid variability was observed in CDR1 and CDR2,suggesting that antigen binding for this subset most likely only depends on the CDR3.Importantly a novel,potentially AID mediated,deletional diversification mechanism of the B.taurus VH ultralong CDR3 knob was discovered,in which interior codons of the IGHD8-2 region are removed while maintaining integral structural components of the knob and descending strand of the stalk in place.These deletions serve to further diversify cysteine positions,and thus disulfide bonded loops.Hence,both germline and somatic genetic factors and processes appear to be involved in diversification of this structurally unusual cattle VH ultralong CDR3 repertoire.
文摘BACKGROUND Laron syndrome(LS)is an autosomal recessive hereditary condition affecting only 1/1000000 births.The cause is associated with mutations in the growth hormone(GH)receptor(GHR),leading to GH insensitivity.LS patients typically present with severe growth retardation,obesity,and abnormal sexual maturation.Currently,LS diagnosis is performed post-delivery.Therefore,we assessed the efficiency of Pre-implantation Genetic Testing(PGT)coupled with monoplex-polymerase chain reaction(PCR)technology for detecting this monogenic disease in embryos from a couple confirmed as LS heterozygous carriers CASE SUMMARY The couple LS-carriers were confirmed by the presence of a first child born with LS.The couple underwent a standard in vitro fertilization(IVF)protocol.DNA was collected from trophectoderm cells from day 5 embryos.Whole genome amplification(WGA)was performed using a Sureplex DNA Amplification System and analyzed by PCR,targeting the deletion of the exons 5 and 6 in the GHR gene as well as PGT by Next-generation Sequencing(Illumina).Eleven embryos were collected and analyzed.27.3%were the wild type for GHR,45.5%were heterozygotes,and 18.2%homozygous mutants.One embryo yielded no results.Three 2-embryos transfers were performed;2 normal homozygous and four heterozygous carriers were selected for transfer.The first two transfers were unsuccessful,whereas the final transfer with two heterozygous embryos resulted in clinical pregnancy.The genomic composition of the fetus was verified,applying the same techniques using amniocytes,extracted after 21 wk of the ongoing pregnancy.The fetus was confirmed as GHR deletion in exon 5-6,carrier.A non-affected baby was born.CONCLUSION Here,we present a case demonstrating that using WGA as a template in addition to PCR targeting specific gene regions,exons 5 and 6 on the GHR gene,could identify LS carrier embryos.This provides evidence that WGA and PCR serve as an excellent tool to detect this specific monogenic disease in IVF embryos,thus allowing selection of candidate embr
基金This work was supported by the Ministry of Science and Technology,Republic of Serbia,Project No.1858
文摘A dataset of 103 SARS-CoV isolates （101 human patients and 2 palm civets） was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations （SNVs） and insertions and deletions, with respect to a “profile”, were determined and discussed （“profile” being a sequence containing the most represented letter per position）. Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid （a.a.） property changes. Similar analysis was performed for the spike （S） protein in all the isolates （55 of them being predicted for the first time）. The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes： TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.
基金supported by the National Natural Science Foundation of China (31571280 and 31771370)National Key Technologies R&D Program and Hubei Province Science and Technology project
文摘Insertion and deletion(indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evolution. However, genetic and evolutionary mechanisms of indels remain elusive. We establish a comparative genome-transcriptome-alignment approach for a large-scale identification of indels in Monopterus population. Over 2000 indels in 1738 indel genes, including 1-21 bp deletions and 1-15 bp insertions, were detected. Each indel gene had ～1.1 deletions/insertions, and 2-4 alleles in population. Frequencies of deletions were prominently higher than those of insertions on both genome and population levels. Most of the indels led to in frame mutations with multiples of three and majorly occurred in non-domain regions, indicating functional constraint or tolerance of the indels. All indel genes showed higher expression levels than non-indel genes during sex reversal. Slide window analysis of global expression levels in gonads showed a significant positive correlation with indel density in the genome. Moreover, indel genes were evolutionarily conserved and evolved slowly compared to nonindel genes. Notably, population genetic structure of indels revealed divergent evolution of Monopterus population, as bottleneck effect of biogeographic isolation by Taiwan Strait, China.
基金Supported by Análisis genético y epigenético del VHB en pacientes portadores asintomáticos.Implicaciones en la decisión terapéutica funded in the 1~(st) Edition of the Gilead Fellowship Program,No.GLD13/00046 and Modificaciones de los niveles de expresión génica mediada por mutantes naturales de la región PreS del virus de la hepatitis B,y asociación con genes implicados en el desarrollo de hepatocarcinoma Efecto del tratamiento antiviral
文摘BACKGROUND Antiviral treatment of patients with chronic hepatitis B(CHB)in the grey zone of treatment comands risk management in order to optimize the health outcome.In this sense,the identification of HBV mutants related with an increased risk of hepatocellular carcinoma(HCC)could be useful to identify subpopulations with potential indication of antiviral treatment.AIM To analyze the prevalence/persistence of hepatitis B virus(HBV)preS and basal core promoter(BCP)/precore/core variants associated to HCC development in CHB patients in the grey zone.METHODS Work was designed as a longitudinal retrospective study,including 106 plasma samples from 31 patients with CHB in the grey zone of treatment:Hepatitis B e antigen negative,HBV-DNA levels between 12-20000 IU/mL,normal or discordant transaminase levels during follow up and mild/moderate necroinflammatory activity in liver biopsy or Fibroscan(up to 9.5 kPa).Serum HBVDNA was tested using the Abbott Real Time HBV Assay and the BCP/precore/core and the hepatitis B surface antigen(HBsAg)coding regions were analyzed in positive samples by PCR/bulk-sequencing to identify the HCCrelated HBV mutants.RESULTS High-risk HCC related mutants were detected in 24(77%)patients:19(61%)in the BCP/precore/core,and 7(23%)in the HBsAg coding region(2 preS1 and 5 preS2 deletions).The prevalence of preS deletions was genotype-dependent:3/5(60%)patients with preS2 deletions and 1/2 with preS1 deletions were infected with the HBV-E genotype.Since HBV-E was the most prevalent in sub-Saharan patients,a correlation between preS deletions and ethnicity was also found:6/8(75%)sub-Saharan vs 1/19(5%)Caucasian patients had preS deletions(P=0.00016).Remarkably,this correlation was maintained in those patients infected with HBV-A,a minor genotype in sub-Saharan patients:2/2 patients infected with HBV-A from West Africa vs 0/6 of Caucasian origin had preS deletions.The HCC related variants were the major strains and persisted over time(up to 48 mo).Patients with preS deletions had a significant hig
文摘Background: Analysis of Philadelphia (Ph) chromosome, a hallmark of chronic myeloid leukemia (CML) plays an important role in disease monitoring of the targeted drug Imatinib. Apart from Ph, genomic imbalances such as additional chromosomal abnormalities (ACAs) of major route occur during transformation of the disease and show negative impact on prognosis. Objective: The present study was carried out to investigate frequencies of ACAs, genomic deletions, complex Ph variants and their prognostic influences in a large cohort of newly diagnosed CML-CP (chronic phase) and CML-AP/BP (accelerated/blast phase). Material & Methods: Retrospective, single institutional study on 1367 cases of CML-CP and 82 cases of CML-AP/BP between 2009 and 2015, using conventional cytogenetics along with fluorescence in situ hybridization. Results: Of the 1367 patients in CML-CP, 1041 patients who completed 12 - 18 months of Imatinib therapy showed complete cytogenetic remission (CCyR) rates of 76% and 82% at 12 and 18 months respectively. Imatinib induced 81% and 33% CCyR in CML-AP and CML-BP respectively. Frequencies of ACAs in CML-CP, AP and BP were 2%, 27% and 67% respectively. Patients in chronic and AP/BP phase with ACAs showed resistance to Imatinib (p < 0.0005). The incidence of genomic deletions and complex Ph variants was 21% and 6.3% respectively with no comparable difference of cytogenetic response to Imatinib (p p < 0.210 respectively). In a cohort of 112 patients in CCyR, development of new clonal abnormalities, more frequently trisomy 8 was detected in Ph negative clone. Conclusion: Our data demonstrated that Imatinib as a frontline therapy had significantly improved management of CML. However, ACAs play an important role in resistance to Imatinib, both in chronic and acute phase, which may limit sole ABL targeted therapy.
文摘作为中国第一本无机化学教材,《化学鉴原》对晚清翻译、传播化学知识产生了重要作用。文章通过对《化学鉴原》(1871)及其底本《韦而司化学原理及化学应用》(Wells’s Principles and Applications of Chemistry)的对比研究,发现《化学鉴原》在翻译过程中对底本进行了结构调整与内容增删,使译本更为适应国人的需要,有利于知识的传播,同时也使译本在知识之间的逻辑关系及化学理论方面略显不足。
基金NationalOutstandingYouthSciencesFoundation (No 3972 5 0 2 6)andPostdoctoralSciencesFoundationofChina (No 2 0 0 0 2 3)
文摘Abstract Objectives To investigate the tissue specificity of reactive oxygen species (ROS) damage to mitochondrial DNA (mtDNA) and to determine whether cochlear mtDNA is a sensitive target for ROS damage. Methods 10 Cu/ZnSOD gene (Cu/Zn superoxide dismutase gene, Sod1) knockout mice and 16 wild-type mice were analyzed by nested polymerase chain reaction (PCR).Results Three deletions were detected in various tissues of Sod1 knockout mice. MtDNA3867bp and mtDNA3726bp deletions were the most visible, and mtDNA4236bp deletion was barely detected in these tissues. There were obvious differences in the ratio of deleted mtDNA/total mtDNA in different tissue. Deleted mtDNA was most abundant in the liver and kidney and less in cochlea, heart and brain. The lowest was in spleen and skin. The ratio in various tissues was 3-20 times in Sod1 knockout mice over wild-type mice. In cochlea, the ratio was about 15. Conclusions Without the protection of Sod1, ROS can lead to mtDNA deletions in various tissues with significant tissue specificity. Cochlear mtDNA is a sensitive target for ROS damage.
文摘Global climate change and acquired resistance to insecticides are threats to world food security.Drosophila suzukii,a devastating invasive pest in many parts of the world,causes substantial economic losses to fruit production industries,forcing farmers to apply broad-spectrum insecticides frequently,This could lead to the development of insecticide resistance.We determined the Lethal Concentration 50 (median lethal concen- tration,LC50)values of zeta-cypermethrin,spinosad,and malathion insecticides against D.suzukii colonies established from Clarke and Pierce county Georgia,United States. The LC50 values were 3 fold higher in the Pierce county population for all insecticide treatments.We then used RNA sequencing to analyze the responses of Pierce and Clarke population flies surviving a LC50 treatment of the 3 insecticides.We identified a high num- ber of differentially expressed genes that are likely involved in detoxification and reduced cuticular penetration,especially in the Pierce population,with extensive overlap in differ- entially expressed genes between the 3 insecticide treatments.Finally,we predicted fewer nonsynonymous single nucleotide variants having deleterious effects on protein function among detoxification,insecticide target,and cuticular protein encoding genes in Pierce flies.Thus a combination of increased gene expression and fewer deleterious single nu- cleotide variants highlights molecular mechanisms underlying the higher LC50 values for Pierce population flies.
基金We cordially thank all PKU families who participated in this study.This study was supported by a grant from the National Academy of Science of Ukraine(no.0115U003747).
文摘Phenylketonuria(PKU)is an autosomal recessive metabolic disorder caused by deficiency of phenylalanine hydroxylase(PAH).The major molecular defects causing PKU are missense mutations of PAH gene.Large deletions of exon 5(EX5del955 and EX5del4232ins)were first reported by the Czech study and were later found also in the Polish,Slovak,Slovenian and Italian PKU-patients.These observations demonstrate the existence of a common subset of this mutation predominantly among Central European populations of Slavic descent.That is why we suggest that EX5del1955 and EX5del4232ins268 mutations might be frequent causes of PKU in Ukrainian patients.EX5del955 and EX5del4232ins268 mutations were analyzed in 106 unrelated PKU patients negative for PAH gene mutations on one or both alleles from our previous analysis.The simultaneous detection of EX5del4232ins268 and EX5del955 mutations was performed by PCR amplification of mutant alleles.EX5del955 mutation was not detected in the Ukrainian patients.This relative alleles frequency of EX5del4232ins268 mutation in the Ukrainian PKU population was determined as 1,66%.Our findings can be the one more evidence of Central European Slavic origin of EX5del4232ins268 mutation,suggested previously.This finding is important for the improvement of DNA diagnosis necessary for the management of PKU patients from Ukraine.
文摘Allergic asthma is a diverse chronic respiratory disease characterized by the inflammation of the lower airway disease affecting many people around the world with rising morbidity and mortality.Association between asthma and certain demographic features was studied in relation to genotype from 244 allergic individuals of local population.Skin prick test was used to confirm asthma.Genetic polymorphism in Glutathione-S-transferases(GSTs)was studied using multiplex PCR based method and IgE level by ELISA.Pollen and dust were the major causative aeroallergens(26%),which were associated to higher IgE levels(P<0.05).Smoking was found to be significantly associated with asthma in only males(P Z 0.004).A low prevalence of null genotype of both GSTM1 and GSTT1 genes was observed in the patients(4.34%)compared to control group(14%).No association of combined GSTM1 and GSTT1 null genotype was found with the asthma in local population.GSTM1t and GSTTgenotype had higher risk(OR Z 1.3681,P Z 0.001)for development of asthma.There was a significant association of asthma with combined genotype of GSTM1t and GSTTwhen data was analyzed on gender basis in males(P Z 0.006)and highly significant in age range of 26e40 years(P Z 0.001).Combined GSTMt and GSTTgenotype was found to be risk factor for asthma in addition to family history in male patients.However a data with large patient size and different ethnic distribution may reveal the exact etiology.
基金Project supported by the German Ministry of Education and Research (BMBF) through the National Genome Research Network(NGFN) (Nos. 01GS0486 and 01GR0460)the DeutscheForschungsgemeinschaft (DFG) for a Travel Grant to Armin O.Schmitt
文摘Copy number variants (CNVs) are pieces of genomic DNA of 1000 base pairs or longer which occur in a given genome at a different frequency than in a reference genome. Their importance as a source for phenotypic variability has been recognized only in the last couple of years. Chromosomal deletions can be seen as a special case of CNVs where stretches of DNA are missing in certain lines when compared to the reference genome of the mouse line C57BL/6, for example. Based upon more than 8 million single nucleotide polymorphisms (SNPs) in the fifteen inbred mouse lines which were determined in a whole genome chip based resequencing project by Perlegen Sciences, we detected 20166 such long chromosomal deletions. They cover altogether between 4.4 million and 8.8 million base pairs, depending on the mouse line. Thus, their extent is comparable to that of SNPs. The chromosomal deletions were found by searching for clusters of missing values in the genotyping data by applying bioinformatics and biostatistical methods. In contrast to isolated missing values, clusters are likely the consequence of missing DNA probe rather than of a failed hybridization or deficient oligos. We analyzed these deletion sites in various ways. Twenty-two percent of these deletion sites overlap with exons; they could therefore affect a gene's functioning. The corresponding genes seem to exist in alternative forms, a phenomenon that reminds of the alternative forms of mRNA generated during gene splicing. We furthermore detected statistically significant association between hundreds of deletion sites and fat weight at the age of eight weeks.
