Objective This study aimed to explore the association of single nucleotide polymorphisms(SNP)in the matrix metalloproteinase 2(MMP-2)signaling pathway and the risk of vascular senescence(VS).Methods In this cross-sect...Objective This study aimed to explore the association of single nucleotide polymorphisms(SNP)in the matrix metalloproteinase 2(MMP-2)signaling pathway and the risk of vascular senescence(VS).Methods In this cross-sectional study,between May and November 2022,peripheral venous blood of151 VS patients(case group)and 233 volunteers(control group)were collected.Fourteen SNPs were identified in five genes encoding the components of the MMP-2 signaling pathway,assessed through carotid-femoral pulse wave velocity(cf PWV),and analyzed using multivariate logistic regression.The multigene influence on the risk of VS was assessed using multifactor dimensionality reduction(MDR)and generalized multifactor dimensionality regression(GMDR)modeling.Results Within the multivariate logistic regression models,four SNPs were screened to have significant associations with VS:chemokine(C-C motif)ligand 2(CCL2)rs4586,MMP2 rs14070,MMP2rs7201,and MMP2 rs1053605.Carriers of the T/C genotype of MMP2 rs14070 had a 2.17-fold increased risk of developing VS compared with those of the C/C genotype,and those of the T/T genotype had a19.375-fold increased risk.CCL2 rs4586 and MMP-2 rs14070 exhibited the most significant interactions.Conclusion CCL2 rs4586,MMP-2 rs14070,MMP-2 rs7201,and MMP-2 rs1053605 polymorphisms were significantly associated with the risk of VS.展开更多
The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy...The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga Pyropia yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria)inheritance in P.yezoensis,the wild type RZ(maternal strain)was crossed with the red mutant HT(paternal strain)and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT)were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP)loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.展开更多
Background: A deletion of 32 bp in the nucleotide sequence of CCR5 gene results in a defective CCR5 which confers protection from HIV infection in the homozygous state, while reducing the rate of disease progression t...Background: A deletion of 32 bp in the nucleotide sequence of CCR5 gene results in a defective CCR5 which confers protection from HIV infection in the homozygous state, while reducing the rate of disease progression to AIDS and death in the heterozygous state. The status of the CCR5Δ32 gene has not been reported in Nigeria. Aim: This study was aimed at analyzing single nucleotide polymorphism of CCR5 gene among the Ijaws resident in Yenagoa, Nigeria. Methods: 100 subjects (75 HIV negative and 25 HIV positive control) were recruited for this study. The CCR5 genes were amplified by 2 Stage PCR reaction using GeneAmp 9700 PCR system utilizing specific primers that would flank 32 bp deletion, followed by agarose gel electrophoresis, DNA sequencing of 20 subjects was done followed by phylogenetic and polymorphism analysis. Results: The results showed that 75 (100%) of the HIV negative subjects had 189 base pair in their CCR5 gene. Nucleotide of the 20 (100%) of the sequenced samples were conservatively same and no SNP was observed. Conclusion: This study documented no SNPs in CCR5 gene of the study population hence;the study population has no protection from HIV infection.展开更多
Stemphylium leaf spot, caused by Stemphylium botryosum f. sp. spinacia, is an important fungal disease of spinach (Spinacia oleracea L.). The aim of this study was to conduct association analysis to identify single nu...Stemphylium leaf spot, caused by Stemphylium botryosum f. sp. spinacia, is an important fungal disease of spinach (Spinacia oleracea L.). The aim of this study was to conduct association analysis to identify single nucleotide polymorphism (SNP) markers associated with Stemphylium leaf spot resistance in spinach. A total of 273 spinach genotypes, including 265 accessions from the USDA spinach germplasm collection and eight commercial cultivars, were used in this study. Phenotyping for Stemphylium leaf spot resistance was evaluated in greenhouse;genotyping was conducted using genotyping by sequencing (GBS) with 787 SNPs;and single marker regression, general linear model, and mixed linear model were used for association analysis of Stemphylium leaf spot. Spinach genotypes showed a skewed distribution for Stemphylium leaf spot resistance, with a range from 0.2% to 23.5% disease severity, suggesting that Stemphylium leaf spot resistance in spinach is a complex, quantitative trait. Association analysis indicated that eight SNP markers, AYZV02052595_115, AYZV02052595_122, AYZV02057770_10404, AYZV02129827_205, AYZV0-2152692_182, AYZV02180153_337, AYZV02225889_197, and AYZV02258563_213 were strongly associated with Stemphylium leaf spot resistance, with a Log of the Odds (LOD) of 2.5 or above. The SNP markers may provide a tool to select for Stemphylium leaf spot resistance in spinach breeding programs through marker-assisted selection (MAS).展开更多
Wenchengia alternifolia(Lamiaceae),the sole species of the genus Wenchengia is extremely rare and is currently listed as Critically Endangered(CR) on the IUCN Red List. The species had long been considered endemic to ...Wenchengia alternifolia(Lamiaceae),the sole species of the genus Wenchengia is extremely rare and is currently listed as Critically Endangered(CR) on the IUCN Red List. The species had long been considered endemic to Hainan Island,China and was once believed to be extinct until a small remnant population was rediscovered at the type locality in 2010.Four more populations were later found on Hainan and in Vietnam.In order to develop genomic resources for further studies on population genetics and conservation biology of this rare species,we identified infraspecific molecular markers in the present study,using genome skimming data of five individuals collected from two populations on Hainan Island and three populations in Vietnam respectively.The length of plastome of the five individuals varied from 152,961 bp to 150,204 bp,and exhibited a typical angiosperm quadripartite structure.Six plastid hotspot regions with the Pi> 0.01(trnH-psbA,psbA-trnK,rpl22,ndhE,ndhG-ndhI rps15-ycf1),and 1621 polymorphic gSSRs,as well as 1657 candidate SNPs in 237 variant nuclear genes were identified,thereby providing important information for further genetic studies.展开更多
Objective In this study,mannan-binding lectin-associated serine protease 2(MASP2)gene variant was evaluated to assess the risk of radiation pneumonitis(RP)in patients with pulmonary malignancies.Methods A total of 169...Objective In this study,mannan-binding lectin-associated serine protease 2(MASP2)gene variant was evaluated to assess the risk of radiation pneumonitis(RP)in patients with pulmonary malignancies.Methods A total of 169 lung cancer patients with radiotherapy were included in our prospective study(NCT02490319)and genotyped using the Sanger sequencing method.Multivariate Cox hazards analysis and multiple testing were applied to estimate the hazard ratio(HR)and 95%confidence intervals(CIs)of all factors possibly associated with RP risk.Results Patients with mean lung disease≥15 Gy and V20≥24%had higher risk of RP≥grade 2 compared with their counterparts(HR=1.888,95%CI:1.186-3.004,P=0.007;HR=2.126,95%CI:1.338-3.378,P=0.001,respectively).Importantly,CC+CA genotype of MASP2:rs12711521 was strongly associated with an increased occurrence of RP≥grade 2(HR=1.949,95%CI:1.278-2.971,P=0.002).Conclusion MASP2:rs12711521 was found to be significantly associated with RP≥grade 2 in our cohort and may thus be one of the important predictors of severe RP before radiotherapy,if further validated in larger population.展开更多
Coloration is an important phenotypic trait for multiple adaptive functions.It is interesting to fi nd white-eye(AW)and orange-eye(AO)phenotypes in the shrimp Alvinocaris longirostris inhabiting the deep-sea cold seep...Coloration is an important phenotypic trait for multiple adaptive functions.It is interesting to fi nd white-eye(AW)and orange-eye(AO)phenotypes in the shrimp Alvinocaris longirostris inhabiting the deep-sea cold seep and hydrothermal vent areas of the northwestern Pacifi c.By comparative transcriptome analyses,1491 diff erentially expressed genes(DEGs)were identified between AW and AO.Among them,many DEGs were associated with immunity,antioxidation,and detoxifi cation.Two signifi cant enzyme encoding genes,xanthine dehydrogenase,and tryptophan oxidase involved in pigment biosynthesis pathways were up-regulated in AW and AO,respectively,which might be related to the diff erences of white and orange eye phenotypes.Moreover,single nucleotide polymorphism(SNP)calling detected that genotypes of 28 SNP distributing in 14 unigenes were completely diff erent between AW and AO.Particularly,there were three and two non-synonymous mutations in immune genes crustin Pm5 and antimicrobial peptide,respectively.Results indicate that the diff erence in eye color is probably resulted from immune response to variable micro-environmental stressors encountered in the dispersal process of the shrimps,such as symbiotic microbes,pathogens,and toxic substances,and might be genetically fi xed at last.The suggested pathway preliminarily explained the formation mechanism of diff erent eye phenotypes in Alvinocaridid shrimps,providing a basis for further study on adaptive evolution of eyes in deep-sea chemosynthetic faunas.展开更多
Cancer-related genes harbored in the loss regions containing a high frequency of hepatocellular carcinoma(HCC)were selected.Related information was gathered and the coding single nucleotide polymorphism(cSNP)sequenc-e...Cancer-related genes harbored in the loss regions containing a high frequency of hepatocellular carcinoma(HCC)were selected.Related information was gathered and the coding single nucleotide polymorphism(cSNP)sequenc-es were obtained from the single nucleotide polymorphism(SNP)database.The appropriate primers and oligonucleotide probes were then designed in accordance with the SNP sites,and subsequently,the gene chips for detecting SNPs were constructed.Genomic DNA was extracted from blood sam-ples of healthy controls and from patients with HBV infec-tion.The sequences,including the SNPs,were amplified via polymerase chain reaction(PCR)and labeled using digoxi-genin deoxyuridine tri-phosphate(Dig-dUTP).The labeled products were then hybridized with the SNP chips.Results confirmed that the differences in allele frequencies of three SNPs EGFL3(rs947345),Caspase9(rs2308950),and E2F2(rs3218171)were distinct between HBV-infected patients and controls,suggesting that these SNPs ocuring in high frequency in HBV-infected individuals may be associated with susceptibility to HCC.展开更多
Genetic linkage maps are valuable tools in evolutionary biology;however, their availability for wild populations is extremely limited. Fundulus heteroclitus (Atlantic killifish) is a non-migratory estuarine fish that ...Genetic linkage maps are valuable tools in evolutionary biology;however, their availability for wild populations is extremely limited. Fundulus heteroclitus (Atlantic killifish) is a non-migratory estuarine fish that exhibits high allelic and phenotypic diversity partitioned among subpopulations that reside in disparate environmental conditions. An ideal candidate model organism for studying gene-environment interactions, the molecular toolbox for F. heteroclitus is limited. We identified hundreds of novel microsatellites which, when combined with existing microsatellites and single nucleotide polymorphisms (SNPs), were used to construct the first genetic linkage map for this species. By integrating independent linkage maps from three genetic crosses, we developed a consensus map containing 24 linkage groups, consistent with the number of chromosomes reported for this species. These linkage groups span 2300 centimorgans (cM) of recombinant genomic space, intermediate in size relative to the current linkage maps for the teleosts, medaka and zebrafish. Comparisons between fish genomes support a high degree of synteny between the consensus F. heteroclitus linkage map and the medaka and (to a lesser extent) zebrafish physical genome assemblies.展开更多
Melatonin receptor 1B(MT2,encoded by the MTNR1B gene),a high-affinity receptor for melatonin,is associated with glucose homeostasis including glucose uptake and transport.The rs10830963 variant in the MTNR1B gene is l...Melatonin receptor 1B(MT2,encoded by the MTNR1B gene),a high-affinity receptor for melatonin,is associated with glucose homeostasis including glucose uptake and transport.The rs10830963 variant in the MTNR1B gene is linked to glucose metabolism disorders including gestational diabetes mellitus(GDM);however,the relationship between MT2-mediated melatonin signaling and a high birth weight of GDM infants from maternal glucose abnormality remains poorly understood.This article aims to investigate the relationship between rs10830963 variants and GDM development,as well as the effects of MT2 receptor on glucose uptake and transport in trophoblasts.TaqMan-MGB(minor groove binder)probe quantitative realtime polymerase chain reaction(qPCR)assays were used for rs10930963 genotyping.MT2 expression in the placenta of GDM and normal pregnant women was detected by immunofluorescence,western blot,and qPCR.The relationship between MT2 and glucose transporters(GLUTs)or peroxisome proliferator-activated receptorγ(PPARγ)was established by western blot,and glucose consumption of trophoblasts was measured by a glucose assay kit.The results showed that the genotype and allele frequencies of rs10830963 were significantly different between GDM and normal pregnant women(P<0.05).The fasting,1-h and 2-h plasma glucose levels of G-allele carriers were significantly higher than those of C-allele carriers(P<0.05).Besides,the protein and messenger RNA(mRNA)expression of MT2 in the placenta of GDM was significantly higher than that of normal pregnant women(P<0.05).Melatonin could stimulate glucose uptake and GLUT4 and PPARγprotein expression in trophoblasts,which could be attenuated by MT2 receptor knockdown.In conclusion,the rs10830963 variant was associated with an increased risk of GDM.The MT2 receptor is essential for melatonin to raise glucose uptake and transport,which may be mediated by PPARγ.展开更多
The study was conducted to explore the mechanisms of sex differences in the response to chronic hepatitis B(CHB)in terms of DNA methylation,SNP genotype,and gene expression.Genomic DNA was isolated from peripheral blo...The study was conducted to explore the mechanisms of sex differences in the response to chronic hepatitis B(CHB)in terms of DNA methylation,SNP genotype,and gene expression.Genomic DNA was isolated from peripheral blood mononuclear cells(PBMCs)of CHB patients and healthy controls and evaluated using the Human Methylation 450 K Assay.The DNA methylation level at hg37 chromosome(CHR)X:7810800 was further validated using pyrosequencing.SNP genotypes,VCX mRNA expression of PBMCs,and plasma VCX protein concentration were further examined using SNaPshot,RT-qPCR,and Western blot,respectively.Results showed that a total of 5529 CpG loci were differentially methylated between male and female CHB patients.DNA methylation level and CC+CT frequency at CHR X:7810800,VCX mRNA expression of PBMCs,and plasma VCX protein concentration were higher in female than in male CHB patients.The CHR X:7810800 locus was hypermethylated in CHB patients with CC+CT genotypes in comparison with those with the TT genotype.In cases of CC-f CT genotypes,VCX mRNA expression was negatively correlated with the DNA methylation level.CHB patients with higher levels of HBV DNA,AST,and GGT or higher GPRI scores exhibited lower VCX expression.In conclusion,SNPs and DNA methylation at the CHR X:7810800 locus cooperatively regulate VCX expression in CHB.The upregulated VCX expression in female CHB patients might represent a mechanism of protection from more severe liver dysfunction and extensive fibrosis,as observed in male CHB patients.展开更多
The custom-designed single nucleotide polymorphism(SNP)panel amplified 231 autosomal SNPs in one PCR reaction and subsequently sequenced with massively parallel sequencing(MPS)technology and Ion Torrent personal genom...The custom-designed single nucleotide polymorphism(SNP)panel amplified 231 autosomal SNPs in one PCR reaction and subsequently sequenced with massively parallel sequencing(MPS)technology and Ion Torrent personal genome machine(PGM).SNPs were chosen from SNPforID,IISNP,HapMap,dbSNP,and related published literatures.Full concordance was obtained between available MPS calling and Sanger sequencing with 9947A and 9948 controls.Ten SNPs(rs4606077,rs334355,rs430046,rs2920816,rs4530059,rs1478829,rs1498553,rs7141285,rs12714757 and rs2189011)with low coverage or heterozygote imbalance should be optimized or excluded from the panel.Sequence data had sufficiently high coverage and gave reliable SNP calling for the remaining 221 loci with the custom MPS-SNP panel.A default DNA input amount of 10 ng per reaction was recommended by Ampliseq technology but sensitivity testing revealed positive results from as little as 1 ng input DNA.Mixture testing with this panel is possible through analysis of the F MAR(frequency of major allele reads)values at most loci with enough high coverage depth and low level of sequencing noise.These results indicate the potential advantage of the custom MPS-SNP assays and Ion Torrent PGM platform for forensic study.展开更多
The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecula...The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 populations.These populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried out.This included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population size.It also included assessment of linkage disequilibrium and construction of phylogenetic trees.Using multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each breed.An overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous breeds.Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding.In general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.展开更多
Starch is the predominant compound in bulb scales,and previous studies have shown that bulblet development is closely associated with starch enrichment.However,how starch synthesis affects bulbification at the molecul...Starch is the predominant compound in bulb scales,and previous studies have shown that bulblet development is closely associated with starch enrichment.However,how starch synthesis affects bulbification at the molecular level is unclear.In this study,we demonstrate that Lilium brownii var.giganteum,a wild lily with a giant bulb in nature,and L.brownii,the native species,have different starch levels and characteristics according to cytological and ultra-structural observations.We cloned the complete sequence of three key gene-encoding enzymes(LbgAGPS,LbgGBSS,and LbgSSⅢ)during starch synthesis by rapid amplification of 5’and 3’complementary DNA(cDNA)ends(RACE)technology.Bioinformatics analysis revealed that the proteins deduced by these genes contain the canonical conserved domains.Constructed phylogenetic trees confirmed the evolutionary relationships with proteins from other species,including monocotyledons and dicotyledons.The transcript levels of various tissues and time course samples obtained during bulblet development uncovered relatively high expression levels in bulblets and gradual increase expression accompanying bulblet growth.Moreover,a set of single nucleotide polymorphisms(SNPs)was discovered in the AGPS genes of four lily genotypes,and a purifying selection fashion was predicted according to the non-synonymous/synonymous(Ka/Ks)values.Taken together,our results suggested that key starch-synthesizing genes might play important roles in bulblet development and lead to distinctive phenotypes in bulblet size.展开更多
The rapid progress and plummeting costs of human-genome sequencing enable the availability of large amount of personal biomedical information,leading to one of the most important concerns—genomic data privacy.Since p...The rapid progress and plummeting costs of human-genome sequencing enable the availability of large amount of personal biomedical information,leading to one of the most important concerns—genomic data privacy.Since personal biomedical data are highly correlated with relatives,with the increasing availability of genomes and personal traits online(i.e.,leakage unwittingly,or after their releasing intentionally to genetic service platforms),kin-genomic data privacy is threatened.We propose new inference attacks to predict unknown Single Nucleotide Polymorphisms(SNPs)and human traits of individuals in a familial genomic dataset based on probabilistic graphical models and belief propagation.With this method,the adversary can predict the unobserved genomes or traits of targeted individuals in a family genomic dataset where some individuals’genomes and traits are observed,relying on SNP-trait association from Genome-Wide Association Study(GWAS),Mendel’s Laws,and statistical relations between SNPs.Existing genome inferences have relatively high computational complexity with the input of tens of millions of SNPs and human traits.Then,we propose an approach to publish genomic data with differential privacy guarantee.After finding an approximate distribution of the input genomic dataset relying on Bayesian networks,a noisy distribution is obtained after injecting noise into the approximate distribution.Finally,synthetic genomic dataset is sampled and it is proved that any query on synthetic dataset satisfies differential privacy guarantee.展开更多
Massively parallel sequencing(MPS)offers a useful alternative to capillary electrophoresis(CE)based analysis of human identification markers in forensic genetics.By sequencing short tandem repeats(STRs)instead of dete...Massively parallel sequencing(MPS)offers a useful alternative to capillary electrophoresis(CE)based analysis of human identification markers in forensic genetics.By sequencing short tandem repeats(STRs)instead of determining the fragment lengths by CE,the sequence variation within the repeat region and the flanking regions may be identified.In this study,we typed 264 Uyghur individuals using the MiSeq FGx^(^(TM)) Forensic Genomics System and Primer Mix A of the ForenSeq^(^(TM)) DNA Signature Prep Kit that amplifies 27 autosomal STRs,25 Y-STRs,seven X-STRs,and 94 HID-SNPs.STRinNGS v.1.0 and GATK 3.6 were used to analyse the STR regions and HID-SNPs,respectively.Increased allelic diversity was observed for 33 STRs with the PCR-MPS assay.The largest increases were found in DYS389II and D12S391,where the numbers of sequenced alleles were 3–4 times larger than those of alleles determined by repeat length alone.A relatively large number of flanking region variants(28 SNPs and three InDels)were observed in the Uyghur population.Seventeen of the flanking region SNPs were rare,and 12 of these SNPs had no accession number in dbSNP.The combined mean match probability and typical paternity index based on 26 sequenced autosomal STRs were 3.85E36 and 1.49Eþ16,respectively.This was 10000 times lower and 1000 times higher,respectively,than the same parameters calculated from STR repeat lengths.展开更多
Background and Aims:In Europeans,variants in the hydroxysteroid 17-beta dehydrogenase 13(HSD17B13)gene impact liver histology in metabolic-associated fatty liver disease(MAFLD).The impact of these variants in ethnic C...Background and Aims:In Europeans,variants in the hydroxysteroid 17-beta dehydrogenase 13(HSD17B13)gene impact liver histology in metabolic-associated fatty liver disease(MAFLD).The impact of these variants in ethnic Chinese is unknown.The aim of this study was to investigate the potential associations in Chinese patients.Methods:In total,427 Han Chinese with biopsy-confirmed MAFLD were enrolled.Two single nucleotide polymorphisms in HSD17B13 were genotyped:rs72613567 and rs6531975.Logistic regression was used to test the association between the single nucleotide polymorphisms and liver histology.Results:In our cohort,the minor allele TA of the rs72613567 variant was related to an increased risk of fibrosis[odds ratio(OR):2.93(1.20–7.17),p=0.019 for the additive model;OR:3.32(1.39–7.91),p=0.007 for the recessive model],representing an inverse association as compared to the results from European cohorts.In contrast,we observed a protective effect on fibrosis for the minor A allele carriers of the HSD17B13 rs6531975 variant[OR:0.48(0.24–0.98),p=0.043 for the additive model;OR:0.62(0.40–0.94),p=0.025 for the dominant model].HSD17B13 variants were only associated with fibrosis but no other histological features.Furthermore,HSD17B13 rs6531975 modulated the effect of PNPLA3 rs738409 on hepatic steatosis.Conclusions:HSD17B13 rs72613567 is a risk variant for fibrosis in a Han Chinese MAFLD population but with a different direction for allelic association to that seen in Europeans.These data exemplify the need for studying diverse populations in genetic studies in order to fine map genome-wide association studies signals.展开更多
基金supported by the Construction of Prevention and Treatment System of Geriatric Syndromes Focusing on Disability and Dementia(No.21-1-2-2-zyyd-nsh)。
文摘Objective This study aimed to explore the association of single nucleotide polymorphisms(SNP)in the matrix metalloproteinase 2(MMP-2)signaling pathway and the risk of vascular senescence(VS).Methods In this cross-sectional study,between May and November 2022,peripheral venous blood of151 VS patients(case group)and 233 volunteers(control group)were collected.Fourteen SNPs were identified in five genes encoding the components of the MMP-2 signaling pathway,assessed through carotid-femoral pulse wave velocity(cf PWV),and analyzed using multivariate logistic regression.The multigene influence on the risk of VS was assessed using multifactor dimensionality reduction(MDR)and generalized multifactor dimensionality regression(GMDR)modeling.Results Within the multivariate logistic regression models,four SNPs were screened to have significant associations with VS:chemokine(C-C motif)ligand 2(CCL2)rs4586,MMP2 rs14070,MMP2rs7201,and MMP2 rs1053605.Carriers of the T/C genotype of MMP2 rs14070 had a 2.17-fold increased risk of developing VS compared with those of the C/C genotype,and those of the T/T genotype had a19.375-fold increased risk.CCL2 rs4586 and MMP-2 rs14070 exhibited the most significant interactions.Conclusion CCL2 rs4586,MMP-2 rs14070,MMP-2 rs7201,and MMP-2 rs1053605 polymorphisms were significantly associated with the risk of VS.
基金Supported by the National Key R&D Program of China(Nos.2018YFD0900106,2018YFC1406700)the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(No.2018SDKJ0302-4)the MOA Modern Agricultural Talents Support Project。
文摘The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga Pyropia yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria)inheritance in P.yezoensis,the wild type RZ(maternal strain)was crossed with the red mutant HT(paternal strain)and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT)were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP)loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.
文摘Background: A deletion of 32 bp in the nucleotide sequence of CCR5 gene results in a defective CCR5 which confers protection from HIV infection in the homozygous state, while reducing the rate of disease progression to AIDS and death in the heterozygous state. The status of the CCR5Δ32 gene has not been reported in Nigeria. Aim: This study was aimed at analyzing single nucleotide polymorphism of CCR5 gene among the Ijaws resident in Yenagoa, Nigeria. Methods: 100 subjects (75 HIV negative and 25 HIV positive control) were recruited for this study. The CCR5 genes were amplified by 2 Stage PCR reaction using GeneAmp 9700 PCR system utilizing specific primers that would flank 32 bp deletion, followed by agarose gel electrophoresis, DNA sequencing of 20 subjects was done followed by phylogenetic and polymorphism analysis. Results: The results showed that 75 (100%) of the HIV negative subjects had 189 base pair in their CCR5 gene. Nucleotide of the 20 (100%) of the sequenced samples were conservatively same and no SNP was observed. Conclusion: This study documented no SNPs in CCR5 gene of the study population hence;the study population has no protection from HIV infection.
文摘Stemphylium leaf spot, caused by Stemphylium botryosum f. sp. spinacia, is an important fungal disease of spinach (Spinacia oleracea L.). The aim of this study was to conduct association analysis to identify single nucleotide polymorphism (SNP) markers associated with Stemphylium leaf spot resistance in spinach. A total of 273 spinach genotypes, including 265 accessions from the USDA spinach germplasm collection and eight commercial cultivars, were used in this study. Phenotyping for Stemphylium leaf spot resistance was evaluated in greenhouse;genotyping was conducted using genotyping by sequencing (GBS) with 787 SNPs;and single marker regression, general linear model, and mixed linear model were used for association analysis of Stemphylium leaf spot. Spinach genotypes showed a skewed distribution for Stemphylium leaf spot resistance, with a range from 0.2% to 23.5% disease severity, suggesting that Stemphylium leaf spot resistance in spinach is a complex, quantitative trait. Association analysis indicated that eight SNP markers, AYZV02052595_115, AYZV02052595_122, AYZV02057770_10404, AYZV02129827_205, AYZV0-2152692_182, AYZV02180153_337, AYZV02225889_197, and AYZV02258563_213 were strongly associated with Stemphylium leaf spot resistance, with a Log of the Odds (LOD) of 2.5 or above. The SNP markers may provide a tool to select for Stemphylium leaf spot resistance in spinach breeding programs through marker-assisted selection (MAS).
基金the National Natural Science Foundation of China(grant number 31970225 and 31900181)the Zhejiang Provincial Natural Science Foundation(grant number LY19C030007)the Open Fund of Shanghai Key Laboratory of Plant Functional Genomics and Resources(PFGR202104).
文摘Wenchengia alternifolia(Lamiaceae),the sole species of the genus Wenchengia is extremely rare and is currently listed as Critically Endangered(CR) on the IUCN Red List. The species had long been considered endemic to Hainan Island,China and was once believed to be extinct until a small remnant population was rediscovered at the type locality in 2010.Four more populations were later found on Hainan and in Vietnam.In order to develop genomic resources for further studies on population genetics and conservation biology of this rare species,we identified infraspecific molecular markers in the present study,using genome skimming data of five individuals collected from two populations on Hainan Island and three populations in Vietnam respectively.The length of plastome of the five individuals varied from 152,961 bp to 150,204 bp,and exhibited a typical angiosperm quadripartite structure.Six plastid hotspot regions with the Pi> 0.01(trnH-psbA,psbA-trnK,rpl22,ndhE,ndhG-ndhI rps15-ycf1),and 1621 polymorphic gSSRs,as well as 1657 candidate SNPs in 237 variant nuclear genes were identified,thereby providing important information for further genetic studies.
基金Supported by grants from the National Natural Science Foundation of China(No.81773360,81700145).
文摘Objective In this study,mannan-binding lectin-associated serine protease 2(MASP2)gene variant was evaluated to assess the risk of radiation pneumonitis(RP)in patients with pulmonary malignancies.Methods A total of 169 lung cancer patients with radiotherapy were included in our prospective study(NCT02490319)and genotyped using the Sanger sequencing method.Multivariate Cox hazards analysis and multiple testing were applied to estimate the hazard ratio(HR)and 95%confidence intervals(CIs)of all factors possibly associated with RP risk.Results Patients with mean lung disease≥15 Gy and V20≥24%had higher risk of RP≥grade 2 compared with their counterparts(HR=1.888,95%CI:1.186-3.004,P=0.007;HR=2.126,95%CI:1.338-3.378,P=0.001,respectively).Importantly,CC+CA genotype of MASP2:rs12711521 was strongly associated with an increased occurrence of RP≥grade 2(HR=1.949,95%CI:1.278-2.971,P=0.002).Conclusion MASP2:rs12711521 was found to be significantly associated with RP≥grade 2 in our cohort and may thus be one of the important predictors of severe RP before radiotherapy,if further validated in larger population.
基金Supported by the National Key R&D Program of China(No.2018YFC0310802)the National Natural Science Foundation of China(No.31872215)+2 种基金the Senior User Project of R/V Kexue(No.KEXUE2019GZ02)the Strategic Priority Research Program of the Chinese Academy of Sciences(CAS)(No.XDA22050302)the Key Research Program of Frontier Sciences,CAS(No.QYZDB-SSW-DQC036)。
文摘Coloration is an important phenotypic trait for multiple adaptive functions.It is interesting to fi nd white-eye(AW)and orange-eye(AO)phenotypes in the shrimp Alvinocaris longirostris inhabiting the deep-sea cold seep and hydrothermal vent areas of the northwestern Pacifi c.By comparative transcriptome analyses,1491 diff erentially expressed genes(DEGs)were identified between AW and AO.Among them,many DEGs were associated with immunity,antioxidation,and detoxifi cation.Two signifi cant enzyme encoding genes,xanthine dehydrogenase,and tryptophan oxidase involved in pigment biosynthesis pathways were up-regulated in AW and AO,respectively,which might be related to the diff erences of white and orange eye phenotypes.Moreover,single nucleotide polymorphism(SNP)calling detected that genotypes of 28 SNP distributing in 14 unigenes were completely diff erent between AW and AO.Particularly,there were three and two non-synonymous mutations in immune genes crustin Pm5 and antimicrobial peptide,respectively.Results indicate that the diff erence in eye color is probably resulted from immune response to variable micro-environmental stressors encountered in the dispersal process of the shrimps,such as symbiotic microbes,pathogens,and toxic substances,and might be genetically fi xed at last.The suggested pathway preliminarily explained the formation mechanism of diff erent eye phenotypes in Alvinocaridid shrimps,providing a basis for further study on adaptive evolution of eyes in deep-sea chemosynthetic faunas.
文摘Cancer-related genes harbored in the loss regions containing a high frequency of hepatocellular carcinoma(HCC)were selected.Related information was gathered and the coding single nucleotide polymorphism(cSNP)sequenc-es were obtained from the single nucleotide polymorphism(SNP)database.The appropriate primers and oligonucleotide probes were then designed in accordance with the SNP sites,and subsequently,the gene chips for detecting SNPs were constructed.Genomic DNA was extracted from blood sam-ples of healthy controls and from patients with HBV infec-tion.The sequences,including the SNPs,were amplified via polymerase chain reaction(PCR)and labeled using digoxi-genin deoxyuridine tri-phosphate(Dig-dUTP).The labeled products were then hybridized with the SNP chips.Results confirmed that the differences in allele frequencies of three SNPs EGFL3(rs947345),Caspase9(rs2308950),and E2F2(rs3218171)were distinct between HBV-infected patients and controls,suggesting that these SNPs ocuring in high frequency in HBV-infected individuals may be associated with susceptibility to HCC.
文摘Genetic linkage maps are valuable tools in evolutionary biology;however, their availability for wild populations is extremely limited. Fundulus heteroclitus (Atlantic killifish) is a non-migratory estuarine fish that exhibits high allelic and phenotypic diversity partitioned among subpopulations that reside in disparate environmental conditions. An ideal candidate model organism for studying gene-environment interactions, the molecular toolbox for F. heteroclitus is limited. We identified hundreds of novel microsatellites which, when combined with existing microsatellites and single nucleotide polymorphisms (SNPs), were used to construct the first genetic linkage map for this species. By integrating independent linkage maps from three genetic crosses, we developed a consensus map containing 24 linkage groups, consistent with the number of chromosomes reported for this species. These linkage groups span 2300 centimorgans (cM) of recombinant genomic space, intermediate in size relative to the current linkage maps for the teleosts, medaka and zebrafish. Comparisons between fish genomes support a high degree of synteny between the consensus F. heteroclitus linkage map and the medaka and (to a lesser extent) zebrafish physical genome assemblies.
基金This work was supported by the Health Commission of Hubei Province Scientific Research Project(No.WJ2021M129)the National Key Research and Development Program of China(No.2021YFC2701502)。
文摘Melatonin receptor 1B(MT2,encoded by the MTNR1B gene),a high-affinity receptor for melatonin,is associated with glucose homeostasis including glucose uptake and transport.The rs10830963 variant in the MTNR1B gene is linked to glucose metabolism disorders including gestational diabetes mellitus(GDM);however,the relationship between MT2-mediated melatonin signaling and a high birth weight of GDM infants from maternal glucose abnormality remains poorly understood.This article aims to investigate the relationship between rs10830963 variants and GDM development,as well as the effects of MT2 receptor on glucose uptake and transport in trophoblasts.TaqMan-MGB(minor groove binder)probe quantitative realtime polymerase chain reaction(qPCR)assays were used for rs10930963 genotyping.MT2 expression in the placenta of GDM and normal pregnant women was detected by immunofluorescence,western blot,and qPCR.The relationship between MT2 and glucose transporters(GLUTs)or peroxisome proliferator-activated receptorγ(PPARγ)was established by western blot,and glucose consumption of trophoblasts was measured by a glucose assay kit.The results showed that the genotype and allele frequencies of rs10830963 were significantly different between GDM and normal pregnant women(P<0.05).The fasting,1-h and 2-h plasma glucose levels of G-allele carriers were significantly higher than those of C-allele carriers(P<0.05).Besides,the protein and messenger RNA(mRNA)expression of MT2 in the placenta of GDM was significantly higher than that of normal pregnant women(P<0.05).Melatonin could stimulate glucose uptake and GLUT4 and PPARγprotein expression in trophoblasts,which could be attenuated by MT2 receptor knockdown.In conclusion,the rs10830963 variant was associated with an increased risk of GDM.The MT2 receptor is essential for melatonin to raise glucose uptake and transport,which may be mediated by PPARγ.
基金supported by the Key Program of National Natural Science Foundation of China (81330084)the E-institutes of Shanghai Municipal Education Commission (No E03008)+1 种基金supported by the National Science and Technology Major Project of China (2012ZX10005001-004)supported by the Science and Technology Commission of Shanghai Municipality (19YF1449900)
文摘The study was conducted to explore the mechanisms of sex differences in the response to chronic hepatitis B(CHB)in terms of DNA methylation,SNP genotype,and gene expression.Genomic DNA was isolated from peripheral blood mononuclear cells(PBMCs)of CHB patients and healthy controls and evaluated using the Human Methylation 450 K Assay.The DNA methylation level at hg37 chromosome(CHR)X:7810800 was further validated using pyrosequencing.SNP genotypes,VCX mRNA expression of PBMCs,and plasma VCX protein concentration were further examined using SNaPshot,RT-qPCR,and Western blot,respectively.Results showed that a total of 5529 CpG loci were differentially methylated between male and female CHB patients.DNA methylation level and CC+CT frequency at CHR X:7810800,VCX mRNA expression of PBMCs,and plasma VCX protein concentration were higher in female than in male CHB patients.The CHR X:7810800 locus was hypermethylated in CHB patients with CC+CT genotypes in comparison with those with the TT genotype.In cases of CC-f CT genotypes,VCX mRNA expression was negatively correlated with the DNA methylation level.CHB patients with higher levels of HBV DNA,AST,and GGT or higher GPRI scores exhibited lower VCX expression.In conclusion,SNPs and DNA methylation at the CHR X:7810800 locus cooperatively regulate VCX expression in CHB.The upregulated VCX expression in female CHB patients might represent a mechanism of protection from more severe liver dysfunction and extensive fibrosis,as observed in male CHB patients.
基金supported by grants from the National Natu-ral Science Foundation of China[grant number 81330073],[grant number 81302620]the Ministry of Science and Technology of China[grant number 2016YFC0800703]the Science and Technology Commission of Shanghai Municipality[grant number 14DZ2270800].
文摘The custom-designed single nucleotide polymorphism(SNP)panel amplified 231 autosomal SNPs in one PCR reaction and subsequently sequenced with massively parallel sequencing(MPS)technology and Ion Torrent personal genome machine(PGM).SNPs were chosen from SNPforID,IISNP,HapMap,dbSNP,and related published literatures.Full concordance was obtained between available MPS calling and Sanger sequencing with 9947A and 9948 controls.Ten SNPs(rs4606077,rs334355,rs430046,rs2920816,rs4530059,rs1478829,rs1498553,rs7141285,rs12714757 and rs2189011)with low coverage or heterozygote imbalance should be optimized or excluded from the panel.Sequence data had sufficiently high coverage and gave reliable SNP calling for the remaining 221 loci with the custom MPS-SNP panel.A default DNA input amount of 10 ng per reaction was recommended by Ampliseq technology but sensitivity testing revealed positive results from as little as 1 ng input DNA.Mixture testing with this panel is possible through analysis of the F MAR(frequency of major allele reads)values at most loci with enough high coverage depth and low level of sequencing noise.These results indicate the potential advantage of the custom MPS-SNP assays and Ion Torrent PGM platform for forensic study.
基金supported by the Ministry of Science and Higher Education of the Russian Federation(No.075-152021-1037,Internal No.15.BRK.21.0001)。
文摘The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 populations.These populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried out.This included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population size.It also included assessment of linkage disequilibrium and construction of phylogenetic trees.Using multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each breed.An overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous breeds.Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding.In general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.
基金the National Natural Science Foundation of China(No.31772337)the Lishui Research Fund(No.2020zdhz03)+1 种基金the China Postdoctoral Science Foundation(No.2017M612005)the National Key Research and Development Program of China(No.2018YFD1000401)。
文摘Starch is the predominant compound in bulb scales,and previous studies have shown that bulblet development is closely associated with starch enrichment.However,how starch synthesis affects bulbification at the molecular level is unclear.In this study,we demonstrate that Lilium brownii var.giganteum,a wild lily with a giant bulb in nature,and L.brownii,the native species,have different starch levels and characteristics according to cytological and ultra-structural observations.We cloned the complete sequence of three key gene-encoding enzymes(LbgAGPS,LbgGBSS,and LbgSSⅢ)during starch synthesis by rapid amplification of 5’and 3’complementary DNA(cDNA)ends(RACE)technology.Bioinformatics analysis revealed that the proteins deduced by these genes contain the canonical conserved domains.Constructed phylogenetic trees confirmed the evolutionary relationships with proteins from other species,including monocotyledons and dicotyledons.The transcript levels of various tissues and time course samples obtained during bulblet development uncovered relatively high expression levels in bulblets and gradual increase expression accompanying bulblet growth.Moreover,a set of single nucleotide polymorphisms(SNPs)was discovered in the AGPS genes of four lily genotypes,and a purifying selection fashion was predicted according to the non-synonymous/synonymous(Ka/Ks)values.Taken together,our results suggested that key starch-synthesizing genes might play important roles in bulblet development and lead to distinctive phenotypes in bulblet size.
文摘The rapid progress and plummeting costs of human-genome sequencing enable the availability of large amount of personal biomedical information,leading to one of the most important concerns—genomic data privacy.Since personal biomedical data are highly correlated with relatives,with the increasing availability of genomes and personal traits online(i.e.,leakage unwittingly,or after their releasing intentionally to genetic service platforms),kin-genomic data privacy is threatened.We propose new inference attacks to predict unknown Single Nucleotide Polymorphisms(SNPs)and human traits of individuals in a familial genomic dataset based on probabilistic graphical models and belief propagation.With this method,the adversary can predict the unobserved genomes or traits of targeted individuals in a family genomic dataset where some individuals’genomes and traits are observed,relying on SNP-trait association from Genome-Wide Association Study(GWAS),Mendel’s Laws,and statistical relations between SNPs.Existing genome inferences have relatively high computational complexity with the input of tens of millions of SNPs and human traits.Then,we propose an approach to publish genomic data with differential privacy guarantee.After finding an approximate distribution of the input genomic dataset relying on Bayesian networks,a noisy distribution is obtained after injecting noise into the approximate distribution.Finally,synthetic genomic dataset is sampled and it is proved that any query on synthetic dataset satisfies differential privacy guarantee.
文摘Massively parallel sequencing(MPS)offers a useful alternative to capillary electrophoresis(CE)based analysis of human identification markers in forensic genetics.By sequencing short tandem repeats(STRs)instead of determining the fragment lengths by CE,the sequence variation within the repeat region and the flanking regions may be identified.In this study,we typed 264 Uyghur individuals using the MiSeq FGx^(^(TM)) Forensic Genomics System and Primer Mix A of the ForenSeq^(^(TM)) DNA Signature Prep Kit that amplifies 27 autosomal STRs,25 Y-STRs,seven X-STRs,and 94 HID-SNPs.STRinNGS v.1.0 and GATK 3.6 were used to analyse the STR regions and HID-SNPs,respectively.Increased allelic diversity was observed for 33 STRs with the PCR-MPS assay.The largest increases were found in DYS389II and D12S391,where the numbers of sequenced alleles were 3–4 times larger than those of alleles determined by repeat length alone.A relatively large number of flanking region variants(28 SNPs and three InDels)were observed in the Uyghur population.Seventeen of the flanking region SNPs were rare,and 12 of these SNPs had no accession number in dbSNP.The combined mean match probability and typical paternity index based on 26 sequenced autosomal STRs were 3.85E36 and 1.49Eþ16,respectively.This was 10000 times lower and 1000 times higher,respectively,than the same parameters calculated from STR repeat lengths.
基金This work was supported by grants from the National Natural Science Foundation of China(82070588)High Level Creative Talents from Department of Public Health in Zhejiang Province(S2032102600032)+3 种基金Project of New Century 551 Talent Nurturing in Wenzhou.GT was supported in part by grants from the University School of Medicine of Verona(Verona,Italy)CDB was supported in part by the Southampton NIHR Biomedical Research Centre(ISBRC-20004)UK.ME and JG were supported by the Robert W.Storr Bequest to the Sydney Medical Foundation,University of Sydney(Sydney,Australia)and the National Health and Medical Research Council of Australia(NHMRC)Program(APP1053206,APP1149976)Project(APP1107178 and APP1108422)grants.
文摘Background and Aims:In Europeans,variants in the hydroxysteroid 17-beta dehydrogenase 13(HSD17B13)gene impact liver histology in metabolic-associated fatty liver disease(MAFLD).The impact of these variants in ethnic Chinese is unknown.The aim of this study was to investigate the potential associations in Chinese patients.Methods:In total,427 Han Chinese with biopsy-confirmed MAFLD were enrolled.Two single nucleotide polymorphisms in HSD17B13 were genotyped:rs72613567 and rs6531975.Logistic regression was used to test the association between the single nucleotide polymorphisms and liver histology.Results:In our cohort,the minor allele TA of the rs72613567 variant was related to an increased risk of fibrosis[odds ratio(OR):2.93(1.20–7.17),p=0.019 for the additive model;OR:3.32(1.39–7.91),p=0.007 for the recessive model],representing an inverse association as compared to the results from European cohorts.In contrast,we observed a protective effect on fibrosis for the minor A allele carriers of the HSD17B13 rs6531975 variant[OR:0.48(0.24–0.98),p=0.043 for the additive model;OR:0.62(0.40–0.94),p=0.025 for the dominant model].HSD17B13 variants were only associated with fibrosis but no other histological features.Furthermore,HSD17B13 rs6531975 modulated the effect of PNPLA3 rs738409 on hepatic steatosis.Conclusions:HSD17B13 rs72613567 is a risk variant for fibrosis in a Han Chinese MAFLD population but with a different direction for allelic association to that seen in Europeans.These data exemplify the need for studying diverse populations in genetic studies in order to fine map genome-wide association studies signals.
