简介：AbstractSingle-nucleotide polymorphisms (SNPs) are the third generation of genetic markers, having been refined from the first generation of restriction fragment length polymorphisms and the second generation of microsatellite polymorphisms. SNPs represent a focal point of current studies of Staphylococcus aureus. On one hand, this review aims to summarize common methodologies for detecting SNPs. These methods have typically included DNA genome sequencing methods and PCR-based detection methods. Alternative methods, such as mass spectrometry, denaturing high-performance liquid chromatography, SNaPshot, and SNP array have also been employed for SNP analysis. On the other hand, we enumerate a series of applications of SNP analysis in investigations of Staphylococcus aureus. SNP analysis can be applied to investigate epidemiological outbreaks and transmission of Staphylococcus aureus infections, the transmission and evolution of antimicrobial resistance genes in Staphylococcus aureus isolates, interactions of Staphylococcus aureus with other bacteria, and the links between Staphylococcus aureus in humans and livestock.

简介：Tamiflu(Oseltamivirphosphate)seemstobeadouble-edgedswordtosomeinAsia.Whileitiscountedonagainstinfluenzaandafearedavianinfluenzapandemic[1],thedrugisalsoassociatedwithsideeffects,rangingfromneu-ropsychiatric,gastrointestinal,tohyperthenniaandskinproblems.AccordingtoadocumentfromUSFoodandDrugAdministrationin2005[2],1184casesofsideeffectshavebeenreported.Interestingly69outofthe75pediatriccaseswerefromJapan,includingtwoteensuicides.Thesituationseemedtohavemadeagloomierturnrecently.ItwasreportedinFebruary,2007thattwoJapaneseteenagersjumpedfromapartmentbuildingsaftertakingTamifluanddied,bringingthetotalnumberofdeathsaftertakingTamiftuinJapanto54[3,4].Althoughnodirectcausalrelationshiphadbeenes-tablishedyet,theJapanHealthMinistrywarneddoctorsaboutgivingthedrugtoteenagers.Incomparison,relativelyfewcasesofseveresideeffectswerereportedfromAmericaandEuropeancountries[5].Whatiswrongwiththispicture?Ithasconcernedandbewilderedmany.Thepagesinthisissue[6]offeronefascinatinghypothesisthattriestoexplainthemysteryusinganintegratedapproachcombiningstructuralbioinformaticanalysisandenzymeassays.

简介：AbstractBackground:Recent studies identifying methylenetetrahydrofolate reductase (MTHFR) polymorphisms associated with breast cancer (BC), ovarian cancer (OC), cervical cancer, and endometrial cancer (EC) have reported conflicting results and been underpowered. To clarify the correlation between MTHFR mutations and these common female malignancies, we conducted a comprehensive meta-analysis incorporating all eligible publications.Methods:Relevant reports published before January 20, 2020, were retrieved from PubMed, Embase, the Cochrane Library, and the China National Knowledge Infrastructure databases. The odds ratio and 95% confidence interval summaries for the MTHFR 677C/T and 1298A/C polymorphisms in BC, OC, cervical cancer, and EC were estimated.Results:A total of 171 studies comprising 56,675 cancer cases and 67,559 controls were included. The results showed a markedly elevated risk of cancer susceptibility related to MTHFR 677C/T based on all genetic models. Similarly, we identified a significant correlation between 1298A/C mutation and cancer risk based on overall comparisons among all models, except the heterozygous model. Moreover, subgroup analysis by cancer type revealed a significantly increased risk of BC associated with 677C/T in the five models and of cervical cancer associated with 1298A/C in some models. Based on ethnicity, significant associations were observed between Asian, African, and mixed populations for 677C/T and the Asian population for 1298A/C. With regard to the sample type used for analysis, we detected a positive association between using blood as the DNA source and cancer risk for 677C/T in all genetic models and for 1298A/C in some genetic models. Further stratification of the results revealed that a notably increased risk was associated with the use of polymerase chain reaction-restriction fragment-length polymorphism or TaqMan as the genotyping method, as well as with the use of population-or hospital-based groups as the controls for 677C/T and 1298A/C, respectively.Conclusion:This meta-analysis suggests that MTHFR 677C/T and 1298A/C polymorphisms correlate with the risk of common gynecological cancers, with these findings potentially applicable for overall comparisons of related data.

简介：Folliclestimulatinghormoneβ(FSHβ)ofJapaneseflounder(Paralichthysolivaceus)playsakeyroleintheregulationofgonadaldevelopment.ThisstudyaimedtoinvestigatemoleculargeneticcharacteristicsoftheFSHβgeneandelucidatetheeffectsofsinglenucleotidepolymorphisms(SNPs)ofFSHβonreproductivetraitsinJapaneseflounder.Weusedpolymerasechainreactionsingle-strandconformationpolymorphism(PCR-SSCP)andsequencingoftheFSHβgenein60individuals.WeidentifiedonlyanSNP(T/C)inthecodingregionofexon3ofFSHβ.TheSNP(T/C)didnotleadtoaminoacidchangesattheposition340bpofFSHβgene.StatisticalanalysisshowedthattheSNPwassignificantlyassociatedwithtestosterone(T)levelandgonadosomaticindex(GSI)(P<0.05).IndividualswithgenotypeTCoftheSNPhadsignificantlyhigherserumTlevelsandGSI(P<0.05)thanthatofgenotypeCC.Therefore,FSHβgenecouldbeausefulmolecularmarkerinselectionforprominentreproductivetraitinJapaneseFlounder.

简介：AbstractObjective:To evaluate the effect of preimplantation genetic testing for aneuploidy (PGT-A) in infertile patients with recurrent pregnancy loss (RPL).Methods:A prospective randomized clinical trial was performed in a university-affiliated fertility center in Shanghai, China. Patients in the PGT-A group underwent blastocyst biopsy followed by single-nucleotide polymorphism microarray-based PGT-A and single euploid blastocyst transfer, whereas patients in the control group underwent routine in vitro fertilization/ICSI procedures and frozen embryo transfer of 1-2 embryos selected according to morphological standards.Results:Two hundred and seven infertile patients with RPL were included in this study and randomly assigned to either the control or the PGT-A group. Baseline variables and cycle characteristics were comparable between the two groups. The results showed that PGT-A significantly improved the ongoing pregnancy rate (55.34% vs. 29.81%) as well as the live birth rate (48.54% vs. 27.88%) and significantly reduced the miscarriage rate (0.00% vs. 14.42%) on a per-patient analysis. A significant increase in cumulative ongoing pregnancy rates over time was observed in the PGT-A group. Subgroup analysis showed that the significant benefit diminished for patients who attempted ≥2 PGT-A cycles.Conclusions:PGT-A significantly improved the ongoing pregnancy and live birth rate, while reduced miscarriage rate in infertile RPL patients. However, the significance diminished in patients attempting ≥2 cycles; thus, further studies are warranted to explore the most cost-effective number of attempts in these patients to avoid overuse.

简介：为单个核苷酸多型性(SNP)的当前的方法分析消费aretime并且复杂。我们为快速的SNP分析在一步舞的开发瞄准了即时fluorescencemutant-allele-specific扩大(MASA)方法。方法是二种技术的婚姻:为目标脱氧核糖核酸和双stranded的MASA教材DNA选择的荧光染料，格林·西布尔I.Genotypes根据thewild类型的不同阀值周期被分开，变异的primers.K地岬oncogene被用作一个目标验证不同遗传型能清楚地是，这试金区别的试验性的结果显示出的themethod.The的可行性。即时荧光MASA方法将由于它的简洁和低费用为快、可靠的SNP分析有一个庞大的潜力。

简介：这份报告描述了能够基于调停toehold的海滨排水量反应(toehold-SDR)和microbead俘获技术的联合在正常温度检测单个核苷酸多型性的一个免费酶、方便、便宜的genotyping生物传感器。生物传感器由一根记者探针和一根俘获探针形成的pre-hybridized海滨组成。面对一个变异的序列，没有调停toehold的海滨排水量，记者探查不能被免除pre-hybridized海滨。Microbeads俘获荧光灯通过biotin-streptavidin相互作用的pre-hybridized海滨microbeads给出重要荧光信号，当在答案没有荧光时。面对一个匹配的目标，然而，海滨排水量有效地被开始，记者探查被免除pre-hybridized海滨。在增加microbeads以后，解决方案生产明亮的荧光，当时microbeads没有明显的信号。遗传型根据答案的荧光紧张方便地被识别。方法提供简单、便宜的策略检测点变化。而且，这个生物传感器在1-40 的范围显示出线性关系；nmol/L和活动范围0.3 的察觉限制；nmol/L。

简介：AbstractObjective:Isolated hereditary hypotrichosis is caused by mutations in as many as 11 different genes. The conventional mutation detection strategy consists of sequencing of individual candidate genes separately, a time consuming and costly approach. In this study, we perform genome-wide single nucleotide polymorphism (SNP) array to identify candidate genes of hereditary hypotrichosis.Methods:A consanguineous family with two patients with hereditary hypotrichosis was enrolled, and autozygosity mapping by genome-wide SNP array was utilized to identify candidate genes.Results:Autozygosity mapping delineated runs of homozygosity, and alignment of the 11 genes identified the hairless (HR) gene as the candidate gene. Nucleotide sequencing revealed a novel homozygous mutation c.381delT, p.Ser127ArgfsTer40.Conclusion:This study illustrates how autozygosity mapping by a high-density SNP array streamlines mutation detection in heritable skin diseases.

简介：Encodingsinpolymorphismwithfiniteproducttypesareconsidered.TheseencodingsaregivenintermsofI-algebras.Theyhavethpropertythatthegroundtermsarepreciselytheclosednormaltermsoftheencodedtypes.Theproofofawell-knownresultistransplantedtothesettinganditisshownwhyweakrecursionisadmissible.Thepaperalsoshowshowtocarryoutthedualencodingsusingtheexistentialquantifier.

简介：TherRNAgeneticlocusisfoundinallprokaryoticorganisms,andishighlyconservative,althoughitsrelativelystablevariationsarefoundfrequentlyindifferentbacteria.Theutilityofthislocusasataxonomicandphylogenetictoolhasbeenreportedwidely.Thisstudy,aimedat16SrRNAgene(16SrDNA)andwiththehelpofbiomolecularmethods,attemptedtoachievethegoalofrapididentificationofcommonpathogensInthisstudy,333clinicalisolatedpathogenicbacteriawerecollected。TwopairsofprimerswerechosenandlabeledwithdifferentfluorescentdyesandthenusedtoamplifythegenomicDNAextractedfrombacteria.ThePCRproductswerethendetectedbycapillaryelectrophoresis-singlestrandconformationpolymorphism(CE-SSCP).Inordertopursuehigherresolutionandpeak-separationeffect,ahighefficientseparatingmedium,linerpolyacrylamidedel(LPA),wasputtouseinthisstudy.Finally,everybacteriacolonygenerateddistinctpatternsfromeachother,whichwereeasilytobeusedforidentification.TheseresultsindicatedthatPCR-CE-SSCPwasarapididentificationmethodforbacterialidentification,withtheaspectsofhighefficiencyandhighprecision.Comparedwithtraditionalmethod,thistechnologyisofgreatutilityforclinicaluseespeciallyforitshighsensitivity.

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简介：DNAcompositiondynamicsacrossgenomesofdiversetaxonomyisamajorsubjectofgenomeanalyses.DNAcompositionchangesarecharacteristicsofbothreplicationandrepairmachineries.Weinvestigated3,611,007singlenucleotidepolymorphisms(SNPs)generatedbycomparingtwosequencedricegenomesfromdistantinbredlines(subspecies),includingthosefrom242,811intronsand45,462protein-codingsequences(CDSs).Neighboring-nucleotideeffects(NNEs)oftheseSNPsarediverse,dependingonstructuralcontent-basedclassifications(genomewide,intronic,andCDS)andsequencecontext-basedcategories(A/C,A/G,A/T,C/G,C/T,andG/Tsubstitutions)oftheanalyzedSNPs.StrongandevidentNNEsandnucleotideproportionbiasessurroundingtheanalyzedSNPswereobservedin1-3bpsequencesonbothsidesofanSNP.Strongbiaseswereobservedaroundneighboringnucleotidesofprotein-codingSNPs,whichexhibitaperiodicityofthreeinnucleotidecontent,constrainedbyacombinedeffectofcodon-relatedrulesandDNArepairmechanisms.Unlikeapreviousfindinginthehumangenome,wefoundnegativecorrelationbetweenGCcontentsofchromosomesandthemagnitudeofcorrespondingbiasofnucleotideCat-1siteandGat+1site.Theseresultswillfurtherourunderstandingofthemutationmechanisminriceaswellasitsevolutionaryimplications.

简介：Objective:Toclone,sequenceandexpresstheprimateβ-chemokineRANTESgenes,hRANTESfromH.sapiensandmRANTESfromM.Mulatta,inordertoexplorethepossibilityofAIDSgenetherapy.Methods:hRANTESandmRANTESwereamplifiedbyreversetranscription-polymerasechainreaction(RT-PCR)fromRNAsextractedfromphytoagglutinin(PHA)-activatedperipheralbloodlymphocytes,hRANTESwascloned,sequencedandexpressedinvitro,andmRANTESwasdirectlysequencedforhomologycomparison.Results:Anexpected276bpfragmentwasobtainedinbothamplifications,andsequencedatademonstratedarelativelyhighhomologyamongdifferentcopiesofhRANTES(97%),andhRANTESwasupto95.6%homologoustomRANTES.WhencomparedwithRANTESfromothermammals,hRANTESgaverisetoahomologyrangingfrom77%to86%.TheclonedhRANTESwasexpressedinvitroandapositivesignalofRANTESwasdetectedbydotblotting.Conclusion:Thefull-lengthofhRANTESsequencewassubmittedtoGenBankandhadbeenreleased.OurmRANTESsequenceisfirstreportedandnotyetappearedinGenBank.ThesuccessfulcloningandexpressionofhRANTESwillprovideabasisforAIDSgenetherapyinthefuture.

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简介：Adatasetof103SARS-CoVisolates(101humanpatientsand2palmcivets)wasinvestigatedondifferentaspectsofgenomepolymorphismandisolateclassification.Thenumberandthedistributionofsinglenucleotidevariations(SNVs)andinsertionsanddeletions,withrespecttoa"profile",weredeterminedanddiscussed("profile"beingasequencecontainingthemostrepresentedletterperposition).Distributionofsubstitutioncategoriespercodonpositions,aswellassynonymousandnon-synonymoussubstitutionsincodingregionsofannotatedisolates,wasdetermined,alongwithaminoacid(a.a.)propertychanges.Similaranalysiswasperformedforthespike(S)proteininalltheisolates(55ofthembeingpredictedforthefirsttime).TheratioKa/KsconfirmedthattheSgenewassubjectedtotheDarwinianselectionduringvirustransmissionfromanimalstohumans.Isolatesfromthedatasetwereclassifiedaccordingtogenomepolymorphismandgenotypes.Genomepolymorphismyieldstotwogroups,onewithasmallnumberofSNVsandanotherwithalargenumberofSNVs,withuptofoursubgroupswithrespecttoinsertionsanddeletions.Weidentifiedthreebasicnine-locusgenotypes:TTTT/TTCGG,CGCC/TTCAT,andTGCC/TTCGT,withfoursubgenotypes.Bothclassificationsproposedareinaccordancewiththenewinsightsintopossibleepidemiologicalspread,bothinspaceandtime.

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简介：TodeterminewhetherthepossessionofcertainHLA-DQA1alleleswasassociatedwiththeriskofdevelopingidiopathicdilatedcardiomyopathy(IDC)andtosubstantiatetheroleofanautoimmunologicpathogenesisinIDC.TypetheallelesofHLA-DQA1bypolymerasechainreactionwithsequence-specificprimers(PCR-SSP)techniquein38patientsofidiopathicdilatedcardiomyopathy(7womenand31men),agedfrom17to56yearsoldwithdiagnosisbeingaccordingtoWorldHealthOrganizationcriteria(IDCgroup),in50patientsofend-stageheartfailureofknownetiology(18womenand32men),withagesrangingfrom34to72(HFgroup),andinthecontrolgroupconsistingofpresumably100healthysubjects(39womenand61men)fromthehealthsurvey,agedfrom30to59yearsold.ThefrequencyofHLA-DQA1*0501intheDCMpatientswassignificantlyelevatedthanthatintheHFandthecontrolgroup.MolecularanalysisoftheDQA1genepolymorphismperformedinthethreesubgroupsshowsanincreasedfrequencyofDQA1*0501amongpatientswithlessEF.TheHFgroupcarriesahighfrequencyofHLA-DQA1*0301.AnincreasedfrequencyofDQA1*0201andDQA1*0103wasfoundinthecontrolgroup.HLA-DQA1*0501isanassociatedgeneofidiopathicdilatedcardiomyopathyandthepossessionofDQA1*0301maybeindicativeoftheknownetiologicheartfailure,suggestingthatthemechanismsinvolvedinthepathogenesisofIDCandotherwiseheartfailurearedifferent.ImmunologicabnormalitiesmaybeamajorcontributortothesusceptibilityofdevelopingofIDC.

简介：AbstractThe virulence of influenza viruses is a complex multigenic trait. Previous studies about the virulence determinants of influenza viruses mainly focused on amino acid sites, ignoring the influence of nucleotide mutations. In this study, we collected >200 viral strains from 21 subtypes of influenza A viruses with virulence in mammals and obtained over 100 mammalian virulence-related nucleotide sites across the genome by computational analysis. Fifty of these nucleotide sites only experienced synonymous mutations. Experiments showed that synonymous mutations in three high-scoring nucleotide sites, i.e., PB1–2031, PB1–633, and PB1–720, enhanced the pathogenicity of the influenza A(H1N1) viruses in mice. Besides, machine-learning models with accepted accuracy for predicting mammalian virulence of influenza A viruses were built. Overall, this study highlighted the importance of nucleotide mutations, especially synonymous mutations in viral virulence, and provided rapid methods for evaluating the virulence of influenza A viruses. It could be helpful for early warning of newly emerging influenza A viruses.

简介：Nineshorttandemrepeat(STR)markers(D3S1358,VWA,FGA,THO1,TPOX,CSFIPO,D5S818,D13S317,andD7S820)andasex-identificationmarker(Amel-ogeninlocus)wereamplifiedwithmultiplexPCRandweregenotypedwithafour-colorfluorescencemethodinsamplesfrom174unrelatedHanindividualsinNorthChina.Theallelefrequencies,genotypefrequencies,heterozygosity,prob-abilityofdiscriminationpowers,probabilityofpaternityexclusionandHardy-Weinbergequilibriumexpectationsweredetermined.TheresultsdemonstratedthatthegenotypesatalltheseSTRlociinHanpopulationconformtoHardy-Weinbergequilibriumexpectations.Thecombineddiscriminationpower(DP)was1.05×10-10withinnineSTRlocianalyzedandtheprobabilityofpaternityexclusion(EPP)was0.9998.TheresultsindicatethatthesenineSTRlociandtheAmelo-geninlocusareusefulmarkersforhumanidentification,paternityandmaternitytestingandsexdeterminationinforensicsciences.

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