短串联重复序列(short tandem repeat,STR)已广泛用于法医学亲子鉴定和个体识别中,但STR的突变可能会影响其结果的解释。在大多数类似研究中,由于忽略“隐性”突变现象,STR的突变率被低估。鉴于此,为获得更加准确的STR实际突变率,本研...短串联重复序列(short tandem repeat,STR)已广泛用于法医学亲子鉴定和个体识别中,但STR的突变可能会影响其结果的解释。在大多数类似研究中,由于忽略“隐性”突变现象,STR的突变率被低估。鉴于此,为获得更加准确的STR实际突变率,本研究使用Slooten与Ricciardi提出的有限突变模型和大规模数据,对28,313例(78,739个体)中国北京汉族已确认亲生关系的亲子鉴定案的20个常染色体STR基因座(D3S1358、D1S1656、D13S317、Penta E、D16S539、D18S51、D2S1338、CSF1PO、Penta D、TH01、vWA、D21S11、D6S1043、D7S820、D5S818、TPOX、D8S1179、D12S391、D19S433和FGA;由于有限突变模型中未包含D6S1043的矫正参数,因此本文实际计算其余19个STR基因座的突变率)进行了调查。结果发现,所有基因座均存在突变现象,总计发生1665个突变事件,包括1614个一步突变,34个两步突变,8个三步突变和9个非整步突变。基因座特异性的平均实际突变率在三联体中为0.00007700(TPOX)~0.00459050(FGA),在二联体中为0.00000000(TPOX)~0.00344850(FGA)。此外,本研究还分析了表面和实际突变率、三联体和二联体突变率、父源和母源的突变率之间的关系。研究表明,实际突变率多大于表面突变率,而且μ1^(*)/μ2^(*)(表面突变率)的比值通常也大于μ1/μ2(实际突变率)(μ1^(*),μ1;μ2^(*),μ2分别是一步和两步的突变率),即更多的“隐性”突变被释放出来。而且父源和母源的三联体和二联体的突变率也有存在差异。随后,将这些突变率数据与已发表的中国其他汉族人口的相关研究进行比较,展现出了STR突变率的时间与区域差异。由于样本量大,本研究中还报告了一些少见的突变事件,例如同卵双胞胎突变和“假四步突变”等。综上所述,本研究通过大量数据获得了接近真实的STR突变率的估计值,不仅可为中国法医DNA数据库和群体遗传学数据库提供重要的基础数据,也对开展法医学个体识别、亲权鉴定和遗传学研究具有重要的意义。展开更多
Identification of the function of all genes in the mammalian genome is critical in understanding basic mechanisms of biology.However,the diploidy of mammalian somatic cells has greatly hindered efforts to elucidate th...Identification of the function of all genes in the mammalian genome is critical in understanding basic mechanisms of biology.However,the diploidy of mammalian somatic cells has greatly hindered efforts to elucidate the gene function in numerous biological processes by mutagenesis-based genetic approaches.Recently,mouse haploid embryonic stem(haES)cells have been successfully isolated from parthenogenetic and androgenetic embryos,providing an ideal tool for genetic analyses.In these studies,mouse haES cells have already shown that they could be used in cell-based forward or reverse genetic screenings and in generating gene-targeting via homologous recombination.In particular,haES cells from androgenetic embryos can be employed as novel,renewable form of fertilization agent for yielding live-born mice via injection into oocytes,thus showing the possibility that genetic analysis can be extended from cellular level to organism level.展开更多
Dear Editor,CRISPR-Cas9 mediated seamless genome editing can be achieved by incorporating donor DNA into the CRISPR-Cas9 target loci via homology-directed repair(HDR),albeit with relative low efficiency due to the ine...Dear Editor,CRISPR-Cas9 mediated seamless genome editing can be achieved by incorporating donor DNA into the CRISPR-Cas9 target loci via homology-directed repair(HDR),albeit with relative low efficiency due to the inefficient delivery of exogenous DNA(Cox et al.,2015;Gao,2021).Retrons are bacterial phage-defense related operons composed of a specialized reverse transcriptase(RT)and a relevant non-coding RNA(ncRNA)which can be partially reverse tran-scribed by RT initiating at a conserved guanosine(G)residue to produce a multicopy single-stranded DNA(msDNA)(Yee et al.,1984;Millman et al.,2020).After being reverse transcribed,the msDNA is usually covalently teth-ered to the ncRNA through the 2',5'-phosphodiesterbond between the priming G in ncRNA and 5'end of msDNA(Dhundale et al.,1987).The reverse transcription process,of which the specialized RT recognizes the unique secondary structure of retron ncRNA,is highly specific(Hsu et al.,1989).Additionally,desired msDNA can be generated in vivo by replacing the dispensable region of retron ncRNA with desired sequences(Mirochnitchenko et al.,1994;Simon et al.,2019).Therefore,retrons are promising biological sources for in vivo generation of DNA donors for HDR-me-diated precise genome editing.展开更多
Dear Editor,Recent studies show that induced pluripotent stem cells(iPSCs)generated through ectopic expression of transcription factors retain an epigenetic memory of their original somatic cells(Kim et al.,2010;Polo ...Dear Editor,Recent studies show that induced pluripotent stem cells(iPSCs)generated through ectopic expression of transcription factors retain an epigenetic memory of their original somatic cells(Kim et al.,2010;Polo et al.,2010)or aberrant silencing of a single imprinted gene cluster(Liu et al.,2010;Stadtfeld et al.,2010),which affects their developmental and differentiation potentials.展开更多
Background:In forensic investigations,accurate estimation of the postmortem interval(PMI)is an important task,but also an ongoing challenge.Especially in cases where the cadaver has been specially treated,for example,...Background:In forensic investigations,accurate estimation of the postmortem interval(PMI)is an important task,but also an ongoing challenge.Especially in cases where the cadaver has been specially treated,for example,by boiling,the determination of PMI becomes extremely difficult.Previous studies have shown that the succession of the microbial community after decomposition of the cadaver can be used to infer PMI.However,the feasibility of determining the PMI of boiled cadavers has not yet been demonstrated.Aims and Objectives:The main objective of this study was to test whether we can infer PMI of boiled cadavers based on the succession of microbial communities.Materials and Methods:SD rats were killed by cervical dislocation.Subsequently,the rat cadavers were divided into the case(boiled cadavers)and control(unboiled cadavers)groups.Rectal samples were collected from the rats for 45 days and at nine time points.High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community in the rectum.Results:The results showed that the composition and relative abundance of bacterial communities at the phylum level were significantly different between the case and control groups.The alpha diversity of the microbial community showed a decreasing trend with the decomposition process.Principal coordinate analysis showed that the case and control groups had obvious patterns along the succession of microbial communities.The rectal microbial communities showed a significant linear trend in the time course of decomposition.A random forest model was used to infer PMI.The goodness-of-fit(R2)of the model was 68.00%and 84.00%,and the mean absolute errors were 2.05 and 1.48 days within 45 days of decomposition for the case and control groups,respectively.Conclusions:Our results suggest that microbial community succession could be a potential method to infer PMI of boiled cadavers.展开更多
文摘短串联重复序列(short tandem repeat,STR)已广泛用于法医学亲子鉴定和个体识别中,但STR的突变可能会影响其结果的解释。在大多数类似研究中,由于忽略“隐性”突变现象,STR的突变率被低估。鉴于此,为获得更加准确的STR实际突变率,本研究使用Slooten与Ricciardi提出的有限突变模型和大规模数据,对28,313例(78,739个体)中国北京汉族已确认亲生关系的亲子鉴定案的20个常染色体STR基因座(D3S1358、D1S1656、D13S317、Penta E、D16S539、D18S51、D2S1338、CSF1PO、Penta D、TH01、vWA、D21S11、D6S1043、D7S820、D5S818、TPOX、D8S1179、D12S391、D19S433和FGA;由于有限突变模型中未包含D6S1043的矫正参数,因此本文实际计算其余19个STR基因座的突变率)进行了调查。结果发现,所有基因座均存在突变现象,总计发生1665个突变事件,包括1614个一步突变,34个两步突变,8个三步突变和9个非整步突变。基因座特异性的平均实际突变率在三联体中为0.00007700(TPOX)~0.00459050(FGA),在二联体中为0.00000000(TPOX)~0.00344850(FGA)。此外,本研究还分析了表面和实际突变率、三联体和二联体突变率、父源和母源的突变率之间的关系。研究表明,实际突变率多大于表面突变率,而且μ1^(*)/μ2^(*)(表面突变率)的比值通常也大于μ1/μ2(实际突变率)(μ1^(*),μ1;μ2^(*),μ2分别是一步和两步的突变率),即更多的“隐性”突变被释放出来。而且父源和母源的三联体和二联体的突变率也有存在差异。随后,将这些突变率数据与已发表的中国其他汉族人口的相关研究进行比较,展现出了STR突变率的时间与区域差异。由于样本量大,本研究中还报告了一些少见的突变事件,例如同卵双胞胎突变和“假四步突变”等。综上所述,本研究通过大量数据获得了接近真实的STR突变率的估计值,不仅可为中国法医DNA数据库和群体遗传学数据库提供重要的基础数据,也对开展法医学个体识别、亲权鉴定和遗传学研究具有重要的意义。
基金supported by grants from the Ministry of Science and Technology of China(No.2009CB941101 to J.L.)the "Strategic Priority Research Program" of the Chinese Academy of Sciences(No.XDA01010403 to J.L.).
文摘Identification of the function of all genes in the mammalian genome is critical in understanding basic mechanisms of biology.However,the diploidy of mammalian somatic cells has greatly hindered efforts to elucidate the gene function in numerous biological processes by mutagenesis-based genetic approaches.Recently,mouse haploid embryonic stem(haES)cells have been successfully isolated from parthenogenetic and androgenetic embryos,providing an ideal tool for genetic analyses.In these studies,mouse haES cells have already shown that they could be used in cell-based forward or reverse genetic screenings and in generating gene-targeting via homologous recombination.In particular,haES cells from androgenetic embryos can be employed as novel,renewable form of fertilization agent for yielding live-born mice via injection into oocytes,thus showing the possibility that genetic analysis can be extended from cellular level to organism level.
文摘Dear Editor,CRISPR-Cas9 mediated seamless genome editing can be achieved by incorporating donor DNA into the CRISPR-Cas9 target loci via homology-directed repair(HDR),albeit with relative low efficiency due to the inefficient delivery of exogenous DNA(Cox et al.,2015;Gao,2021).Retrons are bacterial phage-defense related operons composed of a specialized reverse transcriptase(RT)and a relevant non-coding RNA(ncRNA)which can be partially reverse tran-scribed by RT initiating at a conserved guanosine(G)residue to produce a multicopy single-stranded DNA(msDNA)(Yee et al.,1984;Millman et al.,2020).After being reverse transcribed,the msDNA is usually covalently teth-ered to the ncRNA through the 2',5'-phosphodiesterbond between the priming G in ncRNA and 5'end of msDNA(Dhundale et al.,1987).The reverse transcription process,of which the specialized RT recognizes the unique secondary structure of retron ncRNA,is highly specific(Hsu et al.,1989).Additionally,desired msDNA can be generated in vivo by replacing the dispensable region of retron ncRNA with desired sequences(Mirochnitchenko et al.,1994;Simon et al.,2019).Therefore,retrons are promising biological sources for in vivo generation of DNA donors for HDR-me-diated precise genome editing.
基金supported in part by grants from the Chinese Academy of Sciences(KSCX2-YW-R-110,KSCX2-YW-R-229,XDA01010403 to J.L.,KSCX1-YW-02,KJCX2-YW-M15 to J.W.)the Ministry of Science and Technology(2007CB947101,2009CB941101 to J.L.,2006CB503900,2010CB912102 to J.W.)+1 种基金the National Natural Science Foundation of China(30871430 to J.L.,30821065 to J.W.)the Shanghai Municipal Commission for Science and Technology(07DZ22919,08DJ1400502,09PJ1410900 to J.L.,07dz05907 to J.W.).
文摘Dear Editor,Recent studies show that induced pluripotent stem cells(iPSCs)generated through ectopic expression of transcription factors retain an epigenetic memory of their original somatic cells(Kim et al.,2010;Polo et al.,2010)or aberrant silencing of a single imprinted gene cluster(Liu et al.,2010;Stadtfeld et al.,2010),which affects their developmental and differentiation potentials.
基金supported by the National Natural Science Foundation of China(82030058,82101977,82130056).
文摘Background:In forensic investigations,accurate estimation of the postmortem interval(PMI)is an important task,but also an ongoing challenge.Especially in cases where the cadaver has been specially treated,for example,by boiling,the determination of PMI becomes extremely difficult.Previous studies have shown that the succession of the microbial community after decomposition of the cadaver can be used to infer PMI.However,the feasibility of determining the PMI of boiled cadavers has not yet been demonstrated.Aims and Objectives:The main objective of this study was to test whether we can infer PMI of boiled cadavers based on the succession of microbial communities.Materials and Methods:SD rats were killed by cervical dislocation.Subsequently,the rat cadavers were divided into the case(boiled cadavers)and control(unboiled cadavers)groups.Rectal samples were collected from the rats for 45 days and at nine time points.High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community in the rectum.Results:The results showed that the composition and relative abundance of bacterial communities at the phylum level were significantly different between the case and control groups.The alpha diversity of the microbial community showed a decreasing trend with the decomposition process.Principal coordinate analysis showed that the case and control groups had obvious patterns along the succession of microbial communities.The rectal microbial communities showed a significant linear trend in the time course of decomposition.A random forest model was used to infer PMI.The goodness-of-fit(R2)of the model was 68.00%and 84.00%,and the mean absolute errors were 2.05 and 1.48 days within 45 days of decomposition for the case and control groups,respectively.Conclusions:Our results suggest that microbial community succession could be a potential method to infer PMI of boiled cadavers.
