DNA methylation has been extensively investigated in recent years,not least because of its known relationship with various diseases.Progress in analytical methods can greatly increase the relevance of DNA methylation ...DNA methylation has been extensively investigated in recent years,not least because of its known relationship with various diseases.Progress in analytical methods can greatly increase the relevance of DNA methylation studies to both clinical medicine and scientific research.Microflu-idic chips are excellent carriers for molecular analysis,and their use can provide improvements from multiple aspects.On-chip molecular analysis has received extensive attention owing to its advantages of portability,high throughput,low cost,and high efficiency.In recent years,the use of novel microfluidic chips for DNA methylation analysis has been widely reported and has shown obvious superiority to conventional methods.In this review,wefirst focus on DNA methylation and its applications.Then,we discuss advanced microfluidic-based methods for DNA methylation analysis and describe the great progress that has been made in recent years.Finally,we summarize the advantages that microfluidic technology brings to DNA methylation analysis and describe several challenges and perspectives for on-chip DNA methylation analysis.This review should help researchers improve their understanding and make progress in developing microfluidic-based methods for DNA methylation analysis.展开更多
[Objective] The sequences of mitochondrial DNA D-loop region of Xinjiang Goose with three different colors of plumage were analyzed in order to study the genetic diversity of Xinjiang Goose, as well as the phylogeny a...[Objective] The sequences of mitochondrial DNA D-loop region of Xinjiang Goose with three different colors of plumage were analyzed in order to study the genetic diversity of Xinjiang Goose, as well as the phylogeny and evolution. [Method] Ten geese were selected randomly from the core populations of grey-, mosaic- and white-plumaged Xinjiang Goose respectively with a total number of thirty as experi- mental materials, of which the blood samples were collected from the largest vein under the wing （brachial vein） for DNA extraction. Sequences of mitochondrial DNA D-loop regions were determined using DNA sequencing technology to analyze the polymorphism. In addition, the genetic distances among different populations were estimated through the comparison with the reference sequences. [Resull] The con- tents of A, G, C and T nucleotides in the D-loop region of Xinjiang Goose were 28.85%, 17.05%, 25.38% and 28.72%, respectively. The average haplotype diversity and nucleotide diversity of Xinjiang Goose were 0.583 and 0.056. Xinjiang Goose and Greylag Goose were clustered into the same group. [Conclusion] The results showed that Xinjiang Geese with three different colors of plumage all descend from Greylag Goose （Anser anser）.展开更多
DNA methylation,especially methylation of cytosine in eukaryotic organisms,has been implicated in gene regulation,genomic imprinting,the timing of DNA replication,and determination of chromatin structure.It was report...DNA methylation,especially methylation of cytosine in eukaryotic organisms,has been implicated in gene regulation,genomic imprinting,the timing of DNA replication,and determination of chromatin structure.It was reported that 6.5% of the whole cytosine residues in the nuclear DNA in展开更多
Our previously described environmental DNA extraction method has been widely used in environmental microbial community analysis. However, residual humic substances may remain with obtained environmental DNA, which int...Our previously described environmental DNA extraction method has been widely used in environmental microbial community analysis. However, residual humic substances may remain with obtained environmental DNA, which interferes downstream molecular analyses. To remedy this situation, two DNA extraction buffers （PIPES and Tris-HCl） and four purification strategies including our new modified low melting point gel purification method and three commercial kits from QIAEX, Omega and Promega were evaluated with diverse soil samples. The PIPES buffer （pH 6.5） is found to be more effective for removing the humic substances, but it leads to lower DNA yield and causes more severe DNA shearing than using the Tris-HC1 buffer （pH 8.0）. Gel purification and the Promega purification kit achieve much higher DNA recoveries than QIAEX or Omega kit, and higher purity of DNA is obtained by gel purification than by the Promega kit with both DNA extraction buffers mentioned above. Considering all results together, two alternative methods for DNA extraction and purification are proposed： one uses Tris-HCl buffer extraction and gel purification as the primary approach when the amount of soil or biomass is not a major concern, and the other uses PIPES buffer extraction and the Promega kit purification when severe DNA shearing and/or limited biomass occurs. Purified DNA samples by both methods are amenable for use as templates for whole community genome amplifications and PCR amplifications of bacterial 16S rRNA genes. It is demonstrated that these two alternative methods could be applied to a wide variety of environmental samples.展开更多
DNA is a biological macromolecule that carries genetic information in organisms.It provides a series of predominant bio-logical advantages,such as sequence programmability,high biocompatibility,and low biotoxicity.As ...DNA is a biological macromolecule that carries genetic information in organisms.It provides a series of predominant bio-logical advantages,such as sequence programmability,high biocompatibility,and low biotoxicity.As such,it is a unique polymer material that shows great potential for application in biological and medical fields.DNA aptamers are short DNA sequences with a specific ability of molecular recognition.With its discovery,the application prospect of DNA materials has broadened,especially for the separation and analysis of biological particles.In this review,the functions and characteristics of DNA aptamers are introduced,and the applications of DNA materials in cell/exosome separation and cancer detection are summarized.The application prospect and possible challenges of DNA materials are predicted.展开更多
Plasmid DNA was irradiated or implanted by mixed particle field(CR) or lithium-ion-beam to detect strand breaks.The primary results showed that mixed particle field could induce single and double strand breaks with po...Plasmid DNA was irradiated or implanted by mixed particle field(CR) or lithium-ion-beam to detect strand breaks.The primary results showed that mixed particle field could induce single and double strand breaks with positive linear-dose-effects;most of sequence changes induced by CR were point mutant.Lithium-ion-beam could induce strand breaks also,but it was only at dose of 20Gy.展开更多
The DNA content of tumor all was analyzed by flow cytometry on parafflnembedded specimens in 73 patients with epithelial ovarian tumor, and its clinical significance was evaluated. One of the 5 benign (20%), 2 of the ...The DNA content of tumor all was analyzed by flow cytometry on parafflnembedded specimens in 73 patients with epithelial ovarian tumor, and its clinical significance was evaluated. One of the 5 benign (20%), 2 of the 11 borderline (18.18%), and 30 of the 57 malignant (52. 63%) tumors were aneuplold. The occurrence rate of aneuploidy In malignant tumors was higher than In benign and borderline tumors ( P < 0. 05 ). Furthermore, aneuploidy was more frequently In the advanced stages (Ⅲ -Ⅳ ) (77. 7%) than in the early stages (Ⅰ - Ⅱ ) (9. 5%) (P<0. 005). The occurrence rate of DNA aneuploidy was higher in patients associated with ascites and the residual tumor≥.2 cm. Patients with aneuploid tumors had more of ten ascites (P<0. 005) and residual tumor size≥2cm (P< 0.005). There was no apparent correlation between the DNA ptoidy and the histologic grade, histologic type of the tumors. G0/G1 cell proportion of DNA diplold tumors in advanced carcinoma (64. 6%) was less than those of early stage carcinoma (75. 9% ) (P<0. 05). The survival rate of diplold tumor patients was higher than that of aneuploid tumor patients in the different time after operation, and the median survival time was 30. 2 months and 10. 3 months, respectively. Multivariate analysis revealed that cellular DNA ploidy was the most Important predictive factor (P = 0. 007) of prognosis, followed by residual tumor size (P= 0. 05). Different tumor specimen of the same patient can exhibit variation sometime (38. 9%).The results revealed that the DNA ploidy may reflect tumor biological characteristics, I. e. , Its proliferative ability. Analysis of cellular DNA content of epithelial ovarian tumors would help us to predict the prognosis of the patients better.展开更多
Studies were performed to determine the extent of nuclear DNA degradation induced by iron, iron-ascorbate, or iron-bleomycin under aerobic conditions in a model system using isolated rat liver nuclei. The effects of f...Studies were performed to determine the extent of nuclear DNA degradation induced by iron, iron-ascorbate, or iron-bleomycin under aerobic conditions in a model system using isolated rat liver nuclei. The effects of five antioxidants (catalase, superoxide dismutase, dimethyl sulfoxide, glutathione and diallyl sulfide) on this oxidative nuclear damage were also investigated. At the 0.05 level for statistical significance, iron induced concentration-dependent DNA degradation, and this effect was enhanced by ascorbate and bleomycin. The antioxidants catalase, dimethyl sulfoxide, and diallyl sulfide significantly reduced the iron-ascorbate-induced DNA damage, whereas superoxide dismutase and dimethyl sulfoxide significantly reduced iron-bleomycin-induced damage. Glutathione significantly increased the iron-bleomycin-induced DNA damage. These results suggest that the reactive oxygen species generated by iron, iron-ascorbate, and iron-bleomycin are responsible for the DNA strand breaks in isolated rat liver nuclei.展开更多
Summary： To determining the postmortem interval （PMI） through quantitative analysis of the DNA degradation of cell nucleus in human brain and spleen by using image analysis technique （IAT）. The brain and spleen t...Summary： To determining the postmortem interval （PMI） through quantitative analysis of the DNA degradation of cell nucleus in human brain and spleen by using image analysis technique （IAT）. The brain and spleen tissues from 32 cadavers with known PMI were collected, subjected to cell smear every 1 h within the first 5-36 h after death, stained by Feulgen-Van＇s staining, Three indices reflecting DNA in brain cells （astrocytes） and splenic lymphocytes, including integral optical density （IOD）, average optical density （AOD）, average gray （AG） were measured by employing the mage analysis instrument. The results showed that IOD and AOD declined and AG increased with the prolongation of dead time within 5 36 h. A correlation between the PMI and gray parameters （IOD,AOD and AG） was identified and the corresponding regression equation was obtained. The parameters （IOD, AOD and AG） were proved to be effective quantitative indicators for accurate estimation of PMI within 5-36 h after death.展开更多
MtDNA was successfully extracted from ten individual bones (femurs) in the tombs of ancient Jushi in Turfan basin, dated back to the year about 3 000-2 500 years ago. By means of four overlapping primers, we got nucl...MtDNA was successfully extracted from ten individual bones (femurs) in the tombs of ancient Jushi in Turfan basin, dated back to the year about 3 000-2 500 years ago. By means of four overlapping primers, we got nucleotide sequence of the 218bp length. Ancient mtDNA was analyzed by the sequencing of hypervariable region Ⅰ of the mtDNA control region. The result shows that 9 haplotypes with 24 polymorphic sites were obtained. The phylogenetic analysis indicated that Mongolians and Altai are the population genetically closest to the Jushi groups and Jushi mtDNA pool being an admixture of eastern Asian and European lineages. So our preliminary data imply that an ancient mingling of Euro-Asian population had existed in Turfan basin prior to the early Iron Age.展开更多
The changes of retinal nuclear DNA content in rats after death was detected and the relationship between degradation of retinal nuclear DNA and postmortem interval （PMI） was analyzed. Ninety healthy adult SD rats, f...The changes of retinal nuclear DNA content in rats after death was detected and the relationship between degradation of retinal nuclear DNA and postmortem interval （PMI） was analyzed. Ninety healthy adult SD rats, female, weighing 250±10 g, were randomly divided into 15 groups. At 20 ℃, the retinal cells were withdrawn every 2 h within 0 to 28 h after death and stained with Feulgen-Vans. Index of density （ID）, integral absorbance （IA） and average absorbance （AA） in retinal nucleus were analyzed by image analysis system. And the obtained data were subjected to linear regression analysis by using SPSS12.0 software. The results showed that in retinal nucleus, AA and IA were gradually declined with the prolongation of PMI, while ID had an increased tendency. Within 28 h after PMI, the regression equations were as follows： YAA=-0.009XAA＋0.590 （R^2=0.949）, YIA=0.097XIA＋18.903 （R^2=0.968）, YID=0.122XID＋2.246 （R^2=0.951）. It was concluded that retinal nuclear DNA after death in rats was degraded gradually and had a good correlation with PMI.展开更多
Shrimps of genus Artemia are the inhabitants of continental and marine waters with salinity of 70 to 350 g/l and above.Artemia is able to survive in the conditions in which other animals cannot exist.This is due to ad...Shrimps of genus Artemia are the inhabitants of continental and marine waters with salinity of 70 to 350 g/l and above.Artemia is able to survive in the conditions in which other animals cannot exist.This is due to adaptations:effective osmoregulation system,the ability to synthesize of respiratory pigment(hemoglobin)and diapauses cysts(Litvinenko at.al.,2009).Cysts of this展开更多
Normal mode analysis in dihedral angle space was carried out on two X ray crystal structures and one model structure responded to the same sequence of duplex DNA: d(CGCGAATTCGCG). Comparing these results indicates th...Normal mode analysis in dihedral angle space was carried out on two X ray crystal structures and one model structure responded to the same sequence of duplex DNA: d(CGCGAATTCGCG). Comparing these results indicates that it is reliable and meaningful to carry out normal mode analysis on model structures. The reliability is greater except for the ends of helix.展开更多
基金support from the National Key R&D Program of China(Grant No.2018YFE0118700)the National Natural Science Foundation of China(NSFC Grant No.62174119)+1 种基金the 111 Project(Grant No.B07014)the Foundation for Talent Scientists of Nanchang Institute for Microtechnology of Tianjin University.
文摘DNA methylation has been extensively investigated in recent years,not least because of its known relationship with various diseases.Progress in analytical methods can greatly increase the relevance of DNA methylation studies to both clinical medicine and scientific research.Microflu-idic chips are excellent carriers for molecular analysis,and their use can provide improvements from multiple aspects.On-chip molecular analysis has received extensive attention owing to its advantages of portability,high throughput,low cost,and high efficiency.In recent years,the use of novel microfluidic chips for DNA methylation analysis has been widely reported and has shown obvious superiority to conventional methods.In this review,wefirst focus on DNA methylation and its applications.Then,we discuss advanced microfluidic-based methods for DNA methylation analysis and describe the great progress that has been made in recent years.Finally,we summarize the advantages that microfluidic technology brings to DNA methylation analysis and describe several challenges and perspectives for on-chip DNA methylation analysis.This review should help researchers improve their understanding and make progress in developing microfluidic-based methods for DNA methylation analysis.
基金Supported by the Fond for Open Projects of Xinjiang Key Laboratory of Herbivore Nutrition for Meat&Milk Production~~
文摘[Objective] The sequences of mitochondrial DNA D-loop region of Xinjiang Goose with three different colors of plumage were analyzed in order to study the genetic diversity of Xinjiang Goose, as well as the phylogeny and evolution. [Method] Ten geese were selected randomly from the core populations of grey-, mosaic- and white-plumaged Xinjiang Goose respectively with a total number of thirty as experi- mental materials, of which the blood samples were collected from the largest vein under the wing （brachial vein） for DNA extraction. Sequences of mitochondrial DNA D-loop regions were determined using DNA sequencing technology to analyze the polymorphism. In addition, the genetic distances among different populations were estimated through the comparison with the reference sequences. [Resull] The con- tents of A, G, C and T nucleotides in the D-loop region of Xinjiang Goose were 28.85%, 17.05%, 25.38% and 28.72%, respectively. The average haplotype diversity and nucleotide diversity of Xinjiang Goose were 0.583 and 0.056. Xinjiang Goose and Greylag Goose were clustered into the same group. [Conclusion] The results showed that Xinjiang Geese with three different colors of plumage all descend from Greylag Goose （Anser anser）.
文摘DNA methylation,especially methylation of cytosine in eukaryotic organisms,has been implicated in gene regulation,genomic imprinting,the timing of DNA replication,and determination of chromatin structure.It was reported that 6.5% of the whole cytosine residues in the nuclear DNA in
基金Project(51104189)supported by the National Natural Science Foundation of ChinaProject(2010CB630901)supported by the National Basic Research Program of China+1 种基金Project(1343-77341)supported by the Graduate Education Innovative Program of Central South University,ChinaProject(DOE-ER64125)supported by Department of Energy,Office of Science under the Environmental Remediation Science Program of the United States
文摘Our previously described environmental DNA extraction method has been widely used in environmental microbial community analysis. However, residual humic substances may remain with obtained environmental DNA, which interferes downstream molecular analyses. To remedy this situation, two DNA extraction buffers （PIPES and Tris-HCl） and four purification strategies including our new modified low melting point gel purification method and three commercial kits from QIAEX, Omega and Promega were evaluated with diverse soil samples. The PIPES buffer （pH 6.5） is found to be more effective for removing the humic substances, but it leads to lower DNA yield and causes more severe DNA shearing than using the Tris-HC1 buffer （pH 8.0）. Gel purification and the Promega purification kit achieve much higher DNA recoveries than QIAEX or Omega kit, and higher purity of DNA is obtained by gel purification than by the Promega kit with both DNA extraction buffers mentioned above. Considering all results together, two alternative methods for DNA extraction and purification are proposed： one uses Tris-HCl buffer extraction and gel purification as the primary approach when the amount of soil or biomass is not a major concern, and the other uses PIPES buffer extraction and the Promega kit purification when severe DNA shearing and/or limited biomass occurs. Purified DNA samples by both methods are amenable for use as templates for whole community genome amplifications and PCR amplifications of bacterial 16S rRNA genes. It is demonstrated that these two alternative methods could be applied to a wide variety of environmental samples.
文摘DNA is a biological macromolecule that carries genetic information in organisms.It provides a series of predominant bio-logical advantages,such as sequence programmability,high biocompatibility,and low biotoxicity.As such,it is a unique polymer material that shows great potential for application in biological and medical fields.DNA aptamers are short DNA sequences with a specific ability of molecular recognition.With its discovery,the application prospect of DNA materials has broadened,especially for the separation and analysis of biological particles.In this review,the functions and characteristics of DNA aptamers are introduced,and the applications of DNA materials in cell/exosome separation and cancer detection are summarized.The application prospect and possible challenges of DNA materials are predicted.
文摘Plasmid DNA was irradiated or implanted by mixed particle field(CR) or lithium-ion-beam to detect strand breaks.The primary results showed that mixed particle field could induce single and double strand breaks with positive linear-dose-effects;most of sequence changes induced by CR were point mutant.Lithium-ion-beam could induce strand breaks also,but it was only at dose of 20Gy.
文摘The DNA content of tumor all was analyzed by flow cytometry on parafflnembedded specimens in 73 patients with epithelial ovarian tumor, and its clinical significance was evaluated. One of the 5 benign (20%), 2 of the 11 borderline (18.18%), and 30 of the 57 malignant (52. 63%) tumors were aneuplold. The occurrence rate of aneuploidy In malignant tumors was higher than In benign and borderline tumors ( P < 0. 05 ). Furthermore, aneuploidy was more frequently In the advanced stages (Ⅲ -Ⅳ ) (77. 7%) than in the early stages (Ⅰ - Ⅱ ) (9. 5%) (P<0. 005). The occurrence rate of DNA aneuploidy was higher in patients associated with ascites and the residual tumor≥.2 cm. Patients with aneuploid tumors had more of ten ascites (P<0. 005) and residual tumor size≥2cm (P< 0.005). There was no apparent correlation between the DNA ptoidy and the histologic grade, histologic type of the tumors. G0/G1 cell proportion of DNA diplold tumors in advanced carcinoma (64. 6%) was less than those of early stage carcinoma (75. 9% ) (P<0. 05). The survival rate of diplold tumor patients was higher than that of aneuploid tumor patients in the different time after operation, and the median survival time was 30. 2 months and 10. 3 months, respectively. Multivariate analysis revealed that cellular DNA ploidy was the most Important predictive factor (P = 0. 007) of prognosis, followed by residual tumor size (P= 0. 05). Different tumor specimen of the same patient can exhibit variation sometime (38. 9%).The results revealed that the DNA ploidy may reflect tumor biological characteristics, I. e. , Its proliferative ability. Analysis of cellular DNA content of epithelial ovarian tumors would help us to predict the prognosis of the patients better.
文摘Studies were performed to determine the extent of nuclear DNA degradation induced by iron, iron-ascorbate, or iron-bleomycin under aerobic conditions in a model system using isolated rat liver nuclei. The effects of five antioxidants (catalase, superoxide dismutase, dimethyl sulfoxide, glutathione and diallyl sulfide) on this oxidative nuclear damage were also investigated. At the 0.05 level for statistical significance, iron induced concentration-dependent DNA degradation, and this effect was enhanced by ascorbate and bleomycin. The antioxidants catalase, dimethyl sulfoxide, and diallyl sulfide significantly reduced the iron-ascorbate-induced DNA damage, whereas superoxide dismutase and dimethyl sulfoxide significantly reduced iron-bleomycin-induced damage. Glutathione significantly increased the iron-bleomycin-induced DNA damage. These results suggest that the reactive oxygen species generated by iron, iron-ascorbate, and iron-bleomycin are responsible for the DNA strand breaks in isolated rat liver nuclei.
文摘Summary： To determining the postmortem interval （PMI） through quantitative analysis of the DNA degradation of cell nucleus in human brain and spleen by using image analysis technique （IAT）. The brain and spleen tissues from 32 cadavers with known PMI were collected, subjected to cell smear every 1 h within the first 5-36 h after death, stained by Feulgen-Van＇s staining, Three indices reflecting DNA in brain cells （astrocytes） and splenic lymphocytes, including integral optical density （IOD）, average optical density （AOD）, average gray （AG） were measured by employing the mage analysis instrument. The results showed that IOD and AOD declined and AG increased with the prolongation of dead time within 5 36 h. A correlation between the PMI and gray parameters （IOD,AOD and AG） was identified and the corresponding regression equation was obtained. The parameters （IOD, AOD and AG） were proved to be effective quantitative indicators for accurate estimation of PMI within 5-36 h after death.
基金Supported by Fund for the Important Project of the Science and Technology DepartmentMinistry of Education
文摘MtDNA was successfully extracted from ten individual bones (femurs) in the tombs of ancient Jushi in Turfan basin, dated back to the year about 3 000-2 500 years ago. By means of four overlapping primers, we got nucleotide sequence of the 218bp length. Ancient mtDNA was analyzed by the sequencing of hypervariable region Ⅰ of the mtDNA control region. The result shows that 9 haplotypes with 24 polymorphic sites were obtained. The phylogenetic analysis indicated that Mongolians and Altai are the population genetically closest to the Jushi groups and Jushi mtDNA pool being an admixture of eastern Asian and European lineages. So our preliminary data imply that an ancient mingling of Euro-Asian population had existed in Turfan basin prior to the early Iron Age.
基金This project was supported by a grant from Hubei Provincial Natural Sciences Foundation of China (No. 2004 ABA200).
文摘The changes of retinal nuclear DNA content in rats after death was detected and the relationship between degradation of retinal nuclear DNA and postmortem interval （PMI） was analyzed. Ninety healthy adult SD rats, female, weighing 250±10 g, were randomly divided into 15 groups. At 20 ℃, the retinal cells were withdrawn every 2 h within 0 to 28 h after death and stained with Feulgen-Vans. Index of density （ID）, integral absorbance （IA） and average absorbance （AA） in retinal nucleus were analyzed by image analysis system. And the obtained data were subjected to linear regression analysis by using SPSS12.0 software. The results showed that in retinal nucleus, AA and IA were gradually declined with the prolongation of PMI, while ID had an increased tendency. Within 28 h after PMI, the regression equations were as follows： YAA=-0.009XAA＋0.590 （R^2=0.949）, YIA=0.097XIA＋18.903 （R^2=0.968）, YID=0.122XID＋2.246 （R^2=0.951）. It was concluded that retinal nuclear DNA after death in rats was degraded gradually and had a good correlation with PMI.
文摘Shrimps of genus Artemia are the inhabitants of continental and marine waters with salinity of 70 to 350 g/l and above.Artemia is able to survive in the conditions in which other animals cannot exist.This is due to adaptations:effective osmoregulation system,the ability to synthesize of respiratory pigment(hemoglobin)and diapauses cysts(Litvinenko at.al.,2009).Cysts of this
文摘Normal mode analysis in dihedral angle space was carried out on two X ray crystal structures and one model structure responded to the same sequence of duplex DNA: d(CGCGAATTCGCG). Comparing these results indicates that it is reliable and meaningful to carry out normal mode analysis on model structures. The reliability is greater except for the ends of helix.
