Mitochondrial DNA (mtDNA) and non-recombining Y chromosome (NRY) are inherited uni-parentally from mother to daughter or from father to son respectively. Their polymorphism has initially been studied throughout popula...Mitochondrial DNA (mtDNA) and non-recombining Y chromosome (NRY) are inherited uni-parentally from mother to daughter or from father to son respectively. Their polymorphism has initially been studied throughout populations of the world to demonstrate the "Out of Africa" hypothesis. Here, to correlate the distribution of nasopharyngeal carcinoma (NPC) in different populations of insular Asia, we analyze the mtDNA information (lineages) obtained from genotyping of the hyper variable region (HVS I & II) among 1400 individuals from island Southeast Asia (ISEA), Taiwan and Fujian and supplemented with the analysis of relevant coding region polymorphisms. Lineages that best represented a clade (a branch of the genetic tree) in the phylogeny were further analyzed using complete genomic mtDNA sequencing. Finally, these complete mtDNA sequences were used to construct a most parsimonious tree which now constitutes the most up-to-date mtDNA dataset available on ISEA and Taiwan. This analysis has exposed new insights of the evolutionary history of insular Asia and has strong implications in assessing possible correlations with linguistic, archaeology, demography and the NPC distribution in populations within these regions. To obtain a more objective and balanced genetic point of view, slowly evolving biallelic Y single nucleotide polymorphism (Y-SNP) was also analyzed. As in the first step above, the technique was first applied to determine affinities (macro analysis) between populations of insular Asia. Secondly, sixteen Y short tandem repeats (Y-STR) were used as they allow deeper insight (micro analysis) into the relationship between individuals of a same region. Together, mtDNA and NRY allowed a better definition of the relational, demographic, cultural and genetic components that constitute the make up of the present day peoples of ISEA. Outstanding findings were obtained on the routes of migration that occurred along with the spread of NPC during the settlement of insular Asia. The results of this analysis will be disc展开更多
The assembly of exogenous artificial architectures inside cells can regulate a series of biological events,which heavily relies on the development of spatiotemporally controlled molecular assembly systems.We herein re...The assembly of exogenous artificial architectures inside cells can regulate a series of biological events,which heavily relies on the development of spatiotemporally controlled molecular assembly systems.We herein report a designer deoxyribonucleic acid(DNA)nanostructure that enables light-mediated spatiotemporally dynamic assembly in living cells and consequently achieves efficient regulation of cell autophagy.The DNA nanostructure was constructed from i-motif moiety-containing branched DNA,photocleavable bond-containing linker,and tumor cell-targeting aptamer.After cellular uptake mediated by aptamers,under the spatiotemporal control of both UV light and late endosomal/lysosomal acidic environments,disassembly/reassembly of DNA nanostructure occurred via two rationally designed routes,generating microsized DNA assembly.As a result,autophagy was significantly enhanced with the increase of DNA assembly size.The enhanced autophagy showed an impact on related biological effects.Our system is expected to be a powerful tool for the regulation of intracellular events and cellular behaviors.展开更多
This study focuses on bioinformatics search for new regulatory structures in the non-coding DNA, located around the patterns of gene expression levels changed significantly in response to oxidative stress. Hypothesize...This study focuses on bioinformatics search for new regulatory structures in the non-coding DNA, located around the patterns of gene expression levels changed significantly in response to oxidative stress. Hypothesized that all of the genes increase the expression in response to oxidative stress may have the same motifs in non-coding DNA. To search for motifs created an integrated collection database of transcription binding sites - JASPAR, TRANSFAC, Hocomoco TF Homo sapiens, Uniprobe TF Mus musculus. Two types of regulatory regions: the promoter region and the sequence with the capture of potential cis-regulatory modules. In the regulatory regions of genes increase the expression in response to oxidative stress, in contrast to the gene expression level did not change, families of transcription factors identified SOX (1-30) and HX (A, B, C, D).展开更多
逆转录病毒的活动和多种疾病的发生密切相关,其可通过整合自身基因组到宿主基因组中进行大量有害扩增.与此同时,宿主细胞可根据逆转录病毒的整合位置来启动相关通路抑制其活动.因此整合位点的选择是决定逆转录病毒和宿主命运的关键步骤...逆转录病毒的活动和多种疾病的发生密切相关,其可通过整合自身基因组到宿主基因组中进行大量有害扩增.与此同时,宿主细胞可根据逆转录病毒的整合位置来启动相关通路抑制其活动.因此整合位点的选择是决定逆转录病毒和宿主命运的关键步骤.尽管国际上已有报道称逆转录病毒在宿主基因组上整合并不随机,并发现了跨逆转录病毒种属的不同DNA基序偏好性,但是这些不足以解释一些基序偏好较弱的逆转录病毒如何获得整合特异性.DNA结构特征,如DNA形状被提出可以影响DNA结合蛋白与DNA结合的亲和力,但DNA形状对不同逆转录病毒整合的影响机制尚不清楚.本研究通过构建QRIS(quantify the retrovirus integration specificity)机器学习框架,定量评估了DNA形状对逆转录病毒整合位点的影响.通过系统地研究跨越四个种属的六种逆转录病毒,本研究发现,DNA形状可以独立地或与DNA基序协同调控逆转录病毒的整合.基于此,可将六种逆转录病毒分为三类:“强兼性偏好型”“弱兼性偏好型”和“强形状偏好型”逆转录病毒.此外本研究发现,即使没有特定偏好的DNA基序,“强形状偏好型”逆转录病毒也可以通过DNA形状获得整合特异性.本文基于机器学习对于大规模逆转录病毒插入位点特性的研究,揭示了DNA结构特征在逆转录病毒致病位点选择中的重要作用.该发现在临床方面为治疗逆转录病毒的策略提供了新靶点和新思路,在应用方面有助于更精确地设计慢病毒载体用于基因编辑和基因治疗.此外,本文建立的机器学习框架也为其他种类病毒的整合特异性研究提供了新方法和新视角.展开更多
Chemokines are cytokines that can promote the activation and migration of immune cells,and increase the recognition of antigen by antigen-presenting cells(APC).Previous studies showed that a DNA vaccine can induce hum...Chemokines are cytokines that can promote the activation and migration of immune cells,and increase the recognition of antigen by antigen-presenting cells(APC).Previous studies showed that a DNA vaccine can induce humoral and cellular immune responses of flounder after immunization.To explore the improvement of chemokines on the efficiency of OmpK vaccine,two bicistronic DNA candidate vaccines were constructed and the immune responses they induced in the flounder were investigated by reverse transcription polymerase chain reaction(RT-PCR),indirect immunofl uorescent assay(IFA),H&E staining,fl ow cytometry(FCM),and quantifi cational real-time polymerase chain reaction(qRT-PCR).pBudCE4.1 plasmid as an expression vector,bicistronic DNA vaccines encoding OmpK gene and CC-motif ligand 4 gene(p-OmpK-CCL4),or Ompk gene and CC-motif ligand 19 gene(p-OmpK-CCL19)were successfully constructed.The results showed that two bicistronic DNA vaccines expressed Ompk protein of Vibrio anguillarum and CCL4/CCL19 proteins of fl ounder both in vitro and in vivo.After immunization,a large number of leucocytes in muscle were recruited at the injection site in treatment groups.The constructed vaccines induced signifi cant increases in CD4-1^(+) and CD4-2^(+) T lymphocytes,and sIgM^(+) B lymphocytes in peripheral blood,spleen,and head kidney.The percentage of T lymphocytes peaked on the 14^(th) post-vaccination day whereas that of B lymphocytes peaked in the 6^(th) post-vaccination week.Moreover,the expression profi les of 10 immune-related genes increased in muscles around the injection site,spleen,and head kidney.After the challenge,p-OmpK-CCL4 and p-OmpK-CCL19 conferred a relative percentage survival(RPS)of 74.1%and 63.3%,respectively,higher than p-OmpK alone(40.8%).In conclusion,both CCL4 and CCL19 can improve the protection of p-OmpK via evoking local immune response and then humoral and cellular immunity.CCL4 and CCL19 will be potential molecular adjuvants for use in DNA vaccines.展开更多
BACKGROUND Xia–Gibbs syndrome(XGS,OMIM:615829),caused by mutations within the ATHook DNA-binding motif-containing protein 1(AHDC1)gene(OMIM:615790),located on the short arm of chromosome 1 within the cytogenetic band...BACKGROUND Xia–Gibbs syndrome(XGS,OMIM:615829),caused by mutations within the ATHook DNA-binding motif-containing protein 1(AHDC1)gene(OMIM:615790),located on the short arm of chromosome 1 within the cytogenetic band 1p36.11,contains five noncoding 5 exons,a single 4.9-kb coding exon,and a noncoding 3 exon.CASE SUMMARY In this case report,we diagnosed and treated a 6-mo-old girl with XGS.The primary clinical symptoms included global developmental delay,hypotonia,and mild dysmorphic features.Using high-throughput whole-exosome sequencing to sequence the patient and her parents,and the results showed a novel frameshift mutation of c.1155dupG(p.Arg386Alafs*3)in the AHDC1 gene.The paternal gene was wild type.CONCLUSION This report extends the mutation spectrum of the AHDC1 gene to provide the diagnostic basis for genetic counseling in families with XGS.展开更多
Transcription factor SPI is a protcin present in mammalian cells that binds to GC box promoter clements of Gene and selectively activates mRNA synthesis. The gene contains functional recognition sites. It contains thr...Transcription factor SPI is a protcin present in mammalian cells that binds to GC box promoter clements of Gene and selectively activates mRNA synthesis. The gene contains functional recognition sites. It contains three continuous zinc finger motifs, which are believed being mctalloprotein structures that interact with DNA. We synthesized the second zine finger fragment of SP1 (SP1-ZF2) and its mutant (SP1-ZF2 / HT. E20→H. R23→T), we also synthesized the Cys-Cys loop (ZF6) and the His-His loop (ZF5) of SPI and linked the twoloops together using a β-turn structure to obtain a finger mimic analogue (ZF-15) by stepwise solid-phase technique. Atomic absorption studies show that SP 1-ZF2 and SP1-ZF2 / HT bind zinc cquimolarly, but ZF-15 docs not bind Zn anyway. The CD experiments demonstrate a significant change in secondary structure in the prescnce or absence of Zn to SP1-ZF2 and SP1-ZF2/ HT, but there is no change about ZF-15. Gcl-retardation clectrophoresis assays indicate that SP1-ZF2 binds to DNA sequence specifically in the presence of Zn, but SP1-ZF2 / HT docs not bind as SP 1-ZF2 did. We observed that a single zine finger like SP1-ZF2 is able to bind DNA sequence specifically.展开更多
Mammalian AlkB homologue 2(ALKBH2)is the primary housekeeping DNA demethylase,effectively repairing endogenously formed methylated lesions in double-stranded DNA.Our previous studies demonstrated that a hydrophobicβ-...Mammalian AlkB homologue 2(ALKBH2)is the primary housekeeping DNA demethylase,effectively repairing endogenously formed methylated lesions in double-stranded DNA.Our previous studies demonstrated that a hydrophobicβ-hairpin motif of ALKBH2 could play crucial roles in base-pair stability interrogation and damaged base flipping.Using chemical cross-linking strategy,we obtained two crystal structures of human ALKBH2 mutant bound to duplex DNA.The structural analysis suggests that theβ-hairpin motif is flexible in conformation and is likely to slide along the DNA duplex in local regions to search for damaged base.This study provides a new mechanistic insight into DNA damage detection by ALKBH2.展开更多
文摘Mitochondrial DNA (mtDNA) and non-recombining Y chromosome (NRY) are inherited uni-parentally from mother to daughter or from father to son respectively. Their polymorphism has initially been studied throughout populations of the world to demonstrate the "Out of Africa" hypothesis. Here, to correlate the distribution of nasopharyngeal carcinoma (NPC) in different populations of insular Asia, we analyze the mtDNA information (lineages) obtained from genotyping of the hyper variable region (HVS I & II) among 1400 individuals from island Southeast Asia (ISEA), Taiwan and Fujian and supplemented with the analysis of relevant coding region polymorphisms. Lineages that best represented a clade (a branch of the genetic tree) in the phylogeny were further analyzed using complete genomic mtDNA sequencing. Finally, these complete mtDNA sequences were used to construct a most parsimonious tree which now constitutes the most up-to-date mtDNA dataset available on ISEA and Taiwan. This analysis has exposed new insights of the evolutionary history of insular Asia and has strong implications in assessing possible correlations with linguistic, archaeology, demography and the NPC distribution in populations within these regions. To obtain a more objective and balanced genetic point of view, slowly evolving biallelic Y single nucleotide polymorphism (Y-SNP) was also analyzed. As in the first step above, the technique was first applied to determine affinities (macro analysis) between populations of insular Asia. Secondly, sixteen Y short tandem repeats (Y-STR) were used as they allow deeper insight (micro analysis) into the relationship between individuals of a same region. Together, mtDNA and NRY allowed a better definition of the relational, demographic, cultural and genetic components that constitute the make up of the present day peoples of ISEA. Outstanding findings were obtained on the routes of migration that occurred along with the spread of NPC during the settlement of insular Asia. The results of this analysis will be disc
基金supported by the National Natural Science Foundation of China(grant nos.22225505,22322407,and 22174097)D.Y.thanks Fudan University Ruiqing Education Funding.
文摘The assembly of exogenous artificial architectures inside cells can regulate a series of biological events,which heavily relies on the development of spatiotemporally controlled molecular assembly systems.We herein report a designer deoxyribonucleic acid(DNA)nanostructure that enables light-mediated spatiotemporally dynamic assembly in living cells and consequently achieves efficient regulation of cell autophagy.The DNA nanostructure was constructed from i-motif moiety-containing branched DNA,photocleavable bond-containing linker,and tumor cell-targeting aptamer.After cellular uptake mediated by aptamers,under the spatiotemporal control of both UV light and late endosomal/lysosomal acidic environments,disassembly/reassembly of DNA nanostructure occurred via two rationally designed routes,generating microsized DNA assembly.As a result,autophagy was significantly enhanced with the increase of DNA assembly size.The enhanced autophagy showed an impact on related biological effects.Our system is expected to be a powerful tool for the regulation of intracellular events and cellular behaviors.
文摘This study focuses on bioinformatics search for new regulatory structures in the non-coding DNA, located around the patterns of gene expression levels changed significantly in response to oxidative stress. Hypothesized that all of the genes increase the expression in response to oxidative stress may have the same motifs in non-coding DNA. To search for motifs created an integrated collection database of transcription binding sites - JASPAR, TRANSFAC, Hocomoco TF Homo sapiens, Uniprobe TF Mus musculus. Two types of regulatory regions: the promoter region and the sequence with the capture of potential cis-regulatory modules. In the regulatory regions of genes increase the expression in response to oxidative stress, in contrast to the gene expression level did not change, families of transcription factors identified SOX (1-30) and HX (A, B, C, D).
文摘逆转录病毒的活动和多种疾病的发生密切相关,其可通过整合自身基因组到宿主基因组中进行大量有害扩增.与此同时,宿主细胞可根据逆转录病毒的整合位置来启动相关通路抑制其活动.因此整合位点的选择是决定逆转录病毒和宿主命运的关键步骤.尽管国际上已有报道称逆转录病毒在宿主基因组上整合并不随机,并发现了跨逆转录病毒种属的不同DNA基序偏好性,但是这些不足以解释一些基序偏好较弱的逆转录病毒如何获得整合特异性.DNA结构特征,如DNA形状被提出可以影响DNA结合蛋白与DNA结合的亲和力,但DNA形状对不同逆转录病毒整合的影响机制尚不清楚.本研究通过构建QRIS(quantify the retrovirus integration specificity)机器学习框架,定量评估了DNA形状对逆转录病毒整合位点的影响.通过系统地研究跨越四个种属的六种逆转录病毒,本研究发现,DNA形状可以独立地或与DNA基序协同调控逆转录病毒的整合.基于此,可将六种逆转录病毒分为三类:“强兼性偏好型”“弱兼性偏好型”和“强形状偏好型”逆转录病毒.此外本研究发现,即使没有特定偏好的DNA基序,“强形状偏好型”逆转录病毒也可以通过DNA形状获得整合特异性.本文基于机器学习对于大规模逆转录病毒插入位点特性的研究,揭示了DNA结构特征在逆转录病毒致病位点选择中的重要作用.该发现在临床方面为治疗逆转录病毒的策略提供了新靶点和新思路,在应用方面有助于更精确地设计慢病毒载体用于基因编辑和基因治疗.此外,本文建立的机器学习框架也为其他种类病毒的整合特异性研究提供了新方法和新视角.
基金Supported by the National Natural Science Foundation of China(Nos.32173005,31730101,31672684)the National Key Research and Development Program of China(No.2018YFD0900503)+5 种基金the Shandong Provincial Natural Science Foundation(No.ZR2020KC025)the Fundamental Research Funds for the Central Universities(No.201822015)the Director Foundation of Functional Laboratory for Marine Fisheries Science and Food Production Processes,Qingdao National Laboratory for Marine Science and Technology(No.2018MFSD-01)the NBRPC(No.2012CB114406)the Key Research and Development Program of Shandong Province(No.2016GNC115001)the Taishan Scholar Program of Shandong Province。
文摘Chemokines are cytokines that can promote the activation and migration of immune cells,and increase the recognition of antigen by antigen-presenting cells(APC).Previous studies showed that a DNA vaccine can induce humoral and cellular immune responses of flounder after immunization.To explore the improvement of chemokines on the efficiency of OmpK vaccine,two bicistronic DNA candidate vaccines were constructed and the immune responses they induced in the flounder were investigated by reverse transcription polymerase chain reaction(RT-PCR),indirect immunofl uorescent assay(IFA),H&E staining,fl ow cytometry(FCM),and quantifi cational real-time polymerase chain reaction(qRT-PCR).pBudCE4.1 plasmid as an expression vector,bicistronic DNA vaccines encoding OmpK gene and CC-motif ligand 4 gene(p-OmpK-CCL4),or Ompk gene and CC-motif ligand 19 gene(p-OmpK-CCL19)were successfully constructed.The results showed that two bicistronic DNA vaccines expressed Ompk protein of Vibrio anguillarum and CCL4/CCL19 proteins of fl ounder both in vitro and in vivo.After immunization,a large number of leucocytes in muscle were recruited at the injection site in treatment groups.The constructed vaccines induced signifi cant increases in CD4-1^(+) and CD4-2^(+) T lymphocytes,and sIgM^(+) B lymphocytes in peripheral blood,spleen,and head kidney.The percentage of T lymphocytes peaked on the 14^(th) post-vaccination day whereas that of B lymphocytes peaked in the 6^(th) post-vaccination week.Moreover,the expression profi les of 10 immune-related genes increased in muscles around the injection site,spleen,and head kidney.After the challenge,p-OmpK-CCL4 and p-OmpK-CCL19 conferred a relative percentage survival(RPS)of 74.1%and 63.3%,respectively,higher than p-OmpK alone(40.8%).In conclusion,both CCL4 and CCL19 can improve the protection of p-OmpK via evoking local immune response and then humoral and cellular immunity.CCL4 and CCL19 will be potential molecular adjuvants for use in DNA vaccines.
基金Supported by National Administration of Traditional Chinese Medicine,No.2019XZZX-EK002.
文摘BACKGROUND Xia–Gibbs syndrome(XGS,OMIM:615829),caused by mutations within the ATHook DNA-binding motif-containing protein 1(AHDC1)gene(OMIM:615790),located on the short arm of chromosome 1 within the cytogenetic band 1p36.11,contains five noncoding 5 exons,a single 4.9-kb coding exon,and a noncoding 3 exon.CASE SUMMARY In this case report,we diagnosed and treated a 6-mo-old girl with XGS.The primary clinical symptoms included global developmental delay,hypotonia,and mild dysmorphic features.Using high-throughput whole-exosome sequencing to sequence the patient and her parents,and the results showed a novel frameshift mutation of c.1155dupG(p.Arg386Alafs*3)in the AHDC1 gene.The paternal gene was wild type.CONCLUSION This report extends the mutation spectrum of the AHDC1 gene to provide the diagnostic basis for genetic counseling in families with XGS.
文摘Transcription factor SPI is a protcin present in mammalian cells that binds to GC box promoter clements of Gene and selectively activates mRNA synthesis. The gene contains functional recognition sites. It contains three continuous zinc finger motifs, which are believed being mctalloprotein structures that interact with DNA. We synthesized the second zine finger fragment of SP1 (SP1-ZF2) and its mutant (SP1-ZF2 / HT. E20→H. R23→T), we also synthesized the Cys-Cys loop (ZF6) and the His-His loop (ZF5) of SPI and linked the twoloops together using a β-turn structure to obtain a finger mimic analogue (ZF-15) by stepwise solid-phase technique. Atomic absorption studies show that SP 1-ZF2 and SP1-ZF2 / HT bind zinc cquimolarly, but ZF-15 docs not bind Zn anyway. The CD experiments demonstrate a significant change in secondary structure in the prescnce or absence of Zn to SP1-ZF2 and SP1-ZF2/ HT, but there is no change about ZF-15. Gcl-retardation clectrophoresis assays indicate that SP1-ZF2 binds to DNA sequence specifically in the presence of Zn, but SP1-ZF2 / HT docs not bind as SP 1-ZF2 did. We observed that a single zine finger like SP1-ZF2 is able to bind DNA sequence specifically.
基金financially supported by the Hundred Talents Program of the Chinese Academy of Sciences,Key Project of Chinese National Programs for Fundamental Research and Development(2009CB918502)
文摘Mammalian AlkB homologue 2(ALKBH2)is the primary housekeeping DNA demethylase,effectively repairing endogenously formed methylated lesions in double-stranded DNA.Our previous studies demonstrated that a hydrophobicβ-hairpin motif of ALKBH2 could play crucial roles in base-pair stability interrogation and damaged base flipping.Using chemical cross-linking strategy,we obtained two crystal structures of human ALKBH2 mutant bound to duplex DNA.The structural analysis suggests that theβ-hairpin motif is flexible in conformation and is likely to slide along the DNA duplex in local regions to search for damaged base.This study provides a new mechanistic insight into DNA damage detection by ALKBH2.
