AIM： To determine DNA aneuploidy in mucosal biopsies of achalasia patients for subsequent rapid diagnosis. METHODS： Biopsies from the middle third of the esophagus were obtained in 15 patients with achalasia. Immuno...AIM： To determine DNA aneuploidy in mucosal biopsies of achalasia patients for subsequent rapid diagnosis. METHODS： Biopsies from the middle third of the esophagus were obtained in 15 patients with achalasia. Immunohistochemical staining was carried out with monoclonal antibodies MIB-1 for Ki67 and PAb 1801 for p53, in addition to the conventional histologic examination for dysplasia. Nuclei of fresh biopsy material were enzymatically and mechanically isolated, and the DNA content was determined with image cytometry after Feulgen staining. DNA grading of malignancy was assessed according to Boecking to determine the variability of DNA values noted around the normal diploid peak. Further indices measured included the aneuploid rate, and the 5c-, 7c- and 9c-exceeding rate. RESULTS： The histological examination did not demonstrate dysplasia; while MIB-1 （basal） showed a positive reaction in 8/15 achalasia specimens, p53 was negative in all specimens. Image cytometric DNA analysis detected aneuploidy in 4/15 （26.7%） specimens. Samples from 15 patients with squamous cell carcinoma as well as specimens obtained exclusively 2 cm proximal to the tumor served as reference tests. All carcinomas （15/15） as well as 9 of the peritumoral samples （9/15） were aneuploid. The comparison of biopsies from achalasia patients with peritumoral and carcinoma specimens revealed statistically significant differences regarding the aneuploid rate （diploid： P 〈 0.0001; tetraploid： P = 0.001）, grading of malignancy according to Boecking （P 〈 0.0001） and the 5c- （P 〈 0.0001）, 7c-（P 〈 0.0001）, and 9c- （P = 0.0001） exceeding rate with progredient DNA alterations in the respective order. CONCLUSION： The finding that DNA aneuploidy was identified by image cytometry in esophageal specimens of patients with achalasia, which may be due to specific chromosomal alterations presenting as precancerous lesions in 27% of patients, leads us to conclude that image cytometry represents a valuable screening tool.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
Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between
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
Seoul virus(SEOV), which is predominantly carried by Rattus norvegicus, is one of the major causes of hemorrhagic fever with renal syndrome(HFRS) in China. Hubei province, located in the central south of China, has ex...Seoul virus(SEOV), which is predominantly carried by Rattus norvegicus, is one of the major causes of hemorrhagic fever with renal syndrome(HFRS) in China. Hubei province, located in the central south of China, has experienced some of the most severe epidemics of HFRS. To investigate the mitochondrial DNA(mt DNA)-based phylogenetics of wild rats in Hubei, and the relationship with SEOV infection, 664 wild rats were captured from five trapping sites in Hubei from2000–2009 and 2014–2015. Using reverse-transcription(RT)-PCR, 41(6.17%) rats were found to be positive for SEOV infection. The SEOV-positive percentage in Yichang was significantly lower than that in other areas. The mt DNA D-loop and cytochrome b(cyt-b) genes of 103 rats were sequenced.Among these animals, 37 were SEOV-positive. The reconstruction of the phylogenetic relationship(based on the complete D-loop and cyt-b sequences) allowed the rats to be categorized into two lineages, R. norvegicus and Rattus nitidus, with the former including the majority of the rats. For both the D-loop and cyt-b genes, 18 haplotypes were identified. The geographic distributions of the different haplotypes were significantly different. There were no significant differences in the SEOVpositive percentages between different haplotypes. There were three sub-lineages for the D-loop,and two for cyt-b. The SEOV-positive percentages for each of the sub-lineages did not significantly differ. This indicates that the SEOV-positive percentage is not related to the mt DNA D-loop or cyt-b haplotype or the sub-lineage of rats from Hubei.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
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
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
Total or severe teratospermia affects the prognosis of fertility and causes serious problems for patients undergoing assisted reproduction[1].The pathophysiological mechanism of teratospermia is unclear.It has been sh...Total or severe teratospermia affects the prognosis of fertility and causes serious problems for patients undergoing assisted reproduction[1].The pathophysiological mechanism of teratospermia is unclear.It has been shown that patients with sperm parameters abnormalities and abnormal morphology have a high rate of fragmentation and sperm DNA decondensation[2,3],and that sperm DNA fragmentation analysis could be used as a predictor factor of fertility potential[4].展开更多
Due to frequent soil Cd contamination and wide use of butachlor in China,there is a need to assess their combined toxicity to soil microorganisms.The combined effects of cadmium(Cd,10 mg kg-1 soil) and herbicide butac...Due to frequent soil Cd contamination and wide use of butachlor in China,there is a need to assess their combined toxicity to soil microorganisms.The combined effects of cadmium(Cd,10 mg kg-1 soil) and herbicide butachlor(10,50,and 100 mg kg-1 soil) on enzyme activities and microbial community structure in a paddy soil were assessed using the traditional enzyme assays and random amplified polymorphic DNA(RAPD) analysis.The results showed that urease and phosphatase activities were significantly reduced by high butachlor concentration(100 mg kg-1 soil).When the concentrations of Cd and butachlor added were at a ratio of 1:10,urease and phosphatase activities were significantly decreased whereas enzyme activities were greatly improved at the ratio of 1:5,which indicated that the combined effects of Cd and butachlor on soil urease and phosphatase activities depended largely on their addition concentration ratios.Random amplified polymorphic DNA(RAPD) analysis showed loss of original bands and appearance of new bands when compared with the control soil.Random amplified polymorphic DNA fingerprints suggested substantial differences between the control and treated soil samples,with apparent changes in the number and size of amplified DNA fragments.The addition of high concentration butachlor and the combined impacts of Cd and butachlor significantly affected the diversity of the microbial community.RAPD analysis in conjunction with other biomarkers such as soil enzyme parameters would prove a powerful ecotoxicological tool.Further investigations should be carried out to understand the clear link between RAPD patterns and enzyme activity.展开更多
AIM:To compare the differences between dideoxy sequencing/KRAS StripAssay/pyrosequencing for detection of KRAS mutation in Chinese colorectal cancer (CRC) patients.METHODS:Formalin-f ixed, paraff in-embedded (FFPE) sa...AIM:To compare the differences between dideoxy sequencing/KRAS StripAssay/pyrosequencing for detection of KRAS mutation in Chinese colorectal cancer (CRC) patients.METHODS:Formalin-f ixed, paraff in-embedded (FFPE) samples with tumor cells ≥ 50% were collected from 100 Chinese CRC patients at Beijing Cancer Hospital. After the extraction of genome DNA from FFPE samples, fragments contained codons 12 and 13 of KRAS exon 2 were amplified by polymerase chain reaction and analyzed by dideoxy sequencing, the KRAS Strip Assay and pyrosequencing. In addition, the sensitivities of the 3 methods were compared on serial dilutions (contents of mutant DNA: 100%,50%,20%, 5%,10%, 5%,1%,0%) of A549 cell line DNA (carrying the codon 12 Gly>Ser mutation) into wild-type DNA (human normal intestinal mucosa). The results of dideoxy sequencing,the KRAS StripAssay and pyrosequencing were analyzed by Chromas Software, Collector forKRAS Strip Assay and the pyrosequencing PyroMarkTM Q24 system, respectively.RESULTS: Among 100 patients, KRAS mutations were identif ied in 34%, 37% and 37% of patients by dideoxy sequencing, the KRAS StripAssay and pyrosequencing, respectively. The sensitivity was highest with the KRAS Strip Assay (1%), followed by pyrosequencing (5%), and dideoxy sequencing was lowest (15%). Six different mutation types were found in this study with 3 main mutations Gly12 Asp (GGT>GAT), Gly12 Val (GGT>GTT) and Gly13 Asp (GGC>GAC). Thirty-three patients were identifi ed to have KRAS mutations by the 3 methods, and a total of 8 patients had conflicting results between 3 methods: 4 mutations not detected by dideoxy sequencing and the KRAS StripAssay were identified by pyrosequencing; 3 mutations not detected by dideoxy sequencing and pyrosequencing were identif ied by the KRAS StripAssay; and 1 mutation not detected by pyrosequencing was conf irmed by dideoxy sequencing and the KRAS StripAssay. Among these discordant results, the results identif ied by dideoxy sequencing were consistent either with the KRAS StripAssay or with pyrosequencing, which indicated that the accuracy of dideoxy sequencing was high. CONCLUSION: Taking a worldwide view of reports and our results,dideoxy sequencing remains the most popular method because of its low cost and high accuracy.展开更多
IM To determine the incidence of hepatitis B virus (HBV) intrauterine infection and to explore the relationship between HBV viremia level of pregnant women and HBV intrauterine infection.METHODS Sixtynine pregnant w...IM To determine the incidence of hepatitis B virus (HBV) intrauterine infection and to explore the relationship between HBV viremia level of pregnant women and HBV intrauterine infection.METHODS Sixtynine pregnant women were divided into three groups. Group A, 41 HBsAg positive patients, 14 of them were HBeAg positive (group A1), and 27 HBeAg negative (group A2); Group B, 12 HBsAg negative patients, but positive for antiHBs and/or antiHBe and/or antiHBc; and Group C, 16 patients negative for all HBV markers. Blood samples of mothers were taken at delivery, samples of their infants were collected within 24 hours after birth (before injection of HBIG and HBV vaccine). All the serum samples were stored at -20℃. HBV serum markers were tested by radioimmunoassay and HBV NDA were detected by nested polymerase chain reaction.RESULTS In group C, all of 16 newborns were negative for HBsAg and HBV DNA. In group A, 7 infants were HBsAg positive (171%), and 17 (415%) were HBV DNA positive (P<005). The incidence of intrauterine HBV infection was much higher in group A1 than that in group A2 (HBsAg 429% vs 37%, HBV DNA 929% vs 148%, P<005). The incidence of HBV intrauterine infection was significantly different between high and low HBV viremia of mothers (933% vs 429%, P<005).CONCLUSION The incidence of HBV intrauterine infection is high when HBV DNA in newborns detected with nested PCR is used as a marker of HBV infection. It is related to HBV viremia level of mothers.展开更多
Random Amplified Polymorphic DNA (RAPD) analysis is a new technology of molecular marking which has proved very powerful in detecting genetic diversity at the level of population. The genomic DNAs used in our experime...Random Amplified Polymorphic DNA (RAPD) analysis is a new technology of molecular marking which has proved very powerful in detecting genetic diversity at the level of population. The genomic DNAs used in our experiment were extracted from fresh leaves taken from 59 individuals sampled from three natural populations in Yan An, Shanxi Province. Through more than 2,000 PCRs, deep-going RAPD analysis was carried out on DNA samples from 49 inviduals. The percentage of polymorphic RAPD loci found in these three populations were respectively 27.2 %, 18.6 % and 5.4 %; the average genetic distances within population, 0.055, 0.036 and 0.008; the average genetic distances between populations (Ⅰ-Ⅱ), (Ⅰ-Ⅲ) and (Ⅱ-Ⅲ), 0.105, 0.096 and 0.060. The genetic diversity of A. brachypus within and between populations was found, for the first time, to be rather poor,thus revealing innate factors as the cause contributing to its endangered status. In addition, our work also provides basic materials for elucidating the underlying cause of its endangerment and for its protection biology.展开更多
Objective To determine the DNA damaging potential and the genotoxicity of individual compounds in pesticide contaminated soil. Methods In the present study, DNA damaging potential of pesticide-contaminated soil and th...Objective To determine the DNA damaging potential and the genotoxicity of individual compounds in pesticide contaminated soil. Methods In the present study, DNA damaging potential of pesticide-contaminated soil and the genotoxicity of individual compounds present in the soil were assessed using fluofimetdc analysis of DNA unwinding assay. Results The contaminated soil sample showed 79% （P〈0.001） of DNA strand break, whereas technical grade of major catbaryl and α-naphthol constituents of the contaminated soil showed 64% （P〈0.01） and 60% （P〈0.02） damage respectively. Conclusion Our results indicate that the toxicity caused by contaminated soil is mainly due to carbatyl and α -napthol, which are the major constituents of the soil sample analyzed by CrC-MS.展开更多
Analysis of patient＇s materials like cells or nucleic acids obtained in a minimally invasive or noninvasive manner through the sampling of blood or other body fluids serves as liquid biopsies, which has huge potentia...Analysis of patient＇s materials like cells or nucleic acids obtained in a minimally invasive or noninvasive manner through the sampling of blood or other body fluids serves as liquid biopsies, which has huge potential for numerous diagnostic applications. Circulating cell-free DNA（cfDNA） is explored as a prognostic or predictive marker of liquid biopsies with the improvements in genomic and molecular methods. DNA methylation is an important epigenetic marker known to affect gene expression. cfDNA methylation detection is a very promising approach as abnormal distribution of DNA methylation is one of the hallmarks of many cancers and methylation changes occur early during carcinogenesis. This re？view summarizes the various investigational applications of cfDNA methylation and its oxidized de？rivatives as biomarkers for cancer diagnosis, prenatal diagnosis and organ transplantation monitoring.The review also provides a brief overview of the technologies for cfDNA methylation analysis based on next generation sequencing.展开更多
The aim of this study was to evaluate the effect of naringin on experimentally induced inflammatory bowel dis- ease in rats. Naringin （20, 40 and 80 mg/kg） was given orally for 7 days to Wistar rats before induction...The aim of this study was to evaluate the effect of naringin on experimentally induced inflammatory bowel dis- ease in rats. Naringin （20, 40 and 80 mg/kg） was given orally for 7 days to Wistar rats before induction of colitis by intrarectal instillation of 2 mL of 4% （v/v） acetic acid solution. The degree of colonic mucosal damage was analyzed by examining mucosal damage, ulcer area, ulcer index and stool consistency. Intrarectal administration of 4% acetic acid resulted in significant modulation of serum alkaline phosphatase, lactate dehydrogenase, superoxide dismutase （SOD）, glutathione （GSH）, malondialdehyde （MDA） and myeloperoxidase （MPO） content along with colonic nitric oxide （NO）, xanthine oxidase （XO） level and protein carbonyl content in the colonic tissue as well as in blood. Naringin （40 and 80 mg/kg） exerted a dose dependent （P 〈 0.05） ameliorative effect, as it significantly increased hematological parameter as well as colonic SOD and GSH. There was a significant （P 〈 0.05） and dose dependant inhibition of macroscopical score, ulcer area along with colonic MDA, MPO activity by the 7 days of pretreatment of naringin （40 and 80 mg/kg）. Biochemical studies revealed a significant （P 〈 0.05） dose dependant inhibition in serum alkaline phosphatase （ALP） and lactate dehydrogenase （LDH） levels by pretreatment of naringin. Increased levels of colonic NO, XO, protein carbonyl content and DNA damage were also sig- nificantly decreased by naringin pretreatment. The findings of the present investigation propose that naringin has an anti-inflammatory, anti-oxidant and anti-apoptotic potential effect at colorectal sites as it modulates the production and expression of oxidative mediators such as MDA, MPO, NO and XO, thus reducing DNA damage.展开更多
AIM: To develop and optimize cDNA representational difference analysis (cDNA RDA) method and to identify and clone garlic up-regulated genes in human gastric cancer (HGC) cells. METHODS: We performed cDNA RDA method b...AIM: To develop and optimize cDNA representational difference analysis (cDNA RDA) method and to identify and clone garlic up-regulated genes in human gastric cancer (HGC) cells. METHODS: We performed cDNA RDA method by using abundant double-stranded cDNA messages provided by two self-constructed cDNA libraries (Allitridi-treated and paternal HGC cell line BGC823 cells cDNA libraries respectively). Bam H I and Xho I restriction sites harbored in the library vector were used to select representations. Northern and Slot blots analyses were employed to identify the obtained difference products. RESULTS: Fragments released from the cDNA library vector after restriction endonuclease digestion acted as good marker indicating the appropriate digestion degree for library DNA. Two novel expressed sequence tags (ESTs) and a recombinant gene were obtained. Slot blots result showed a 8-fold increase of glia-derived nexin/protease nexin 1 (GDN/PN1) gene expression level and 4-fold increase of hepatitis B virus x-interacting protein (XIP) mRNA level in BGC823 cells after Allitridi treatment for 72h. CONCLUSION: Elevated levels of GDN/PN1 and XIP mRNAs induced by Allitridi provide valuable molecular evidence for elucidating the garlic's efficacies against neurodegenerative and inflammatory diseases. Isolation of a recombinant gene and two novel ESTs further show cDNA RDA based on cDNA libraries to be a powerful method with high specificity and reproducibility in cloning differentially expressed genes.展开更多
A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the “fine structure” of nucleotide sequences. The approach is bas...A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the “fine structure” of nucleotide sequences. The approach is based on the assumption that nucleotides have an inner abstract characteristic, the determinative degree, which reflects genetic code phenomenological prop-erties and is adjusted to nucleotides physical properties. We consider each codon position independently, which gives three separate walks characterized by different angles and lengths, and that such an object is called triander which reflects the “strength” of branch. A general method for identifying DNA sequence “by triander” which can be treated as a unique “genogram” (or “gene passport”) is proposed. The two- and three-dimensional trianders are considered. The difference of sequences fine structure in genes and the intergenic space is shown. A clear triplet signal in coding sequences was found which is absent in the intergenic space and is independent from the sequence length. This paper presents the topological classification of trianders which can allow us to provide a detailed working out signatures of functionally different genomic regions.展开更多
文摘AIM： To determine DNA aneuploidy in mucosal biopsies of achalasia patients for subsequent rapid diagnosis. METHODS： Biopsies from the middle third of the esophagus were obtained in 15 patients with achalasia. Immunohistochemical staining was carried out with monoclonal antibodies MIB-1 for Ki67 and PAb 1801 for p53, in addition to the conventional histologic examination for dysplasia. Nuclei of fresh biopsy material were enzymatically and mechanically isolated, and the DNA content was determined with image cytometry after Feulgen staining. DNA grading of malignancy was assessed according to Boecking to determine the variability of DNA values noted around the normal diploid peak. Further indices measured included the aneuploid rate, and the 5c-, 7c- and 9c-exceeding rate. RESULTS： The histological examination did not demonstrate dysplasia; while MIB-1 （basal） showed a positive reaction in 8/15 achalasia specimens, p53 was negative in all specimens. Image cytometric DNA analysis detected aneuploidy in 4/15 （26.7%） specimens. Samples from 15 patients with squamous cell carcinoma as well as specimens obtained exclusively 2 cm proximal to the tumor served as reference tests. All carcinomas （15/15） as well as 9 of the peritumoral samples （9/15） were aneuploid. The comparison of biopsies from achalasia patients with peritumoral and carcinoma specimens revealed statistically significant differences regarding the aneuploid rate （diploid： P 〈 0.0001; tetraploid： P = 0.001）, grading of malignancy according to Boecking （P 〈 0.0001） and the 5c- （P 〈 0.0001）, 7c-（P 〈 0.0001）, and 9c- （P = 0.0001） exceeding rate with progredient DNA alterations in the respective order. CONCLUSION： The finding that DNA aneuploidy was identified by image cytometry in esophageal specimens of patients with achalasia, which may be due to specific chromosomal alterations presenting as precancerous lesions in 27% of patients, leads us to conclude that image cytometry represents a valuable screening tool.
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Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between
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 grants from the National Natural Science Foundation of China(81402728,81371865)
文摘Seoul virus(SEOV), which is predominantly carried by Rattus norvegicus, is one of the major causes of hemorrhagic fever with renal syndrome(HFRS) in China. Hubei province, located in the central south of China, has experienced some of the most severe epidemics of HFRS. To investigate the mitochondrial DNA(mt DNA)-based phylogenetics of wild rats in Hubei, and the relationship with SEOV infection, 664 wild rats were captured from five trapping sites in Hubei from2000–2009 and 2014–2015. Using reverse-transcription(RT)-PCR, 41(6.17%) rats were found to be positive for SEOV infection. The SEOV-positive percentage in Yichang was significantly lower than that in other areas. The mt DNA D-loop and cytochrome b(cyt-b) genes of 103 rats were sequenced.Among these animals, 37 were SEOV-positive. The reconstruction of the phylogenetic relationship(based on the complete D-loop and cyt-b sequences) allowed the rats to be categorized into two lineages, R. norvegicus and Rattus nitidus, with the former including the majority of the rats. For both the D-loop and cyt-b genes, 18 haplotypes were identified. The geographic distributions of the different haplotypes were significantly different. There were no significant differences in the SEOVpositive percentages between different haplotypes. There were three sub-lineages for the D-loop,and two for cyt-b. The SEOV-positive percentages for each of the sub-lineages did not significantly differ. This indicates that the SEOV-positive percentage is not related to the mt DNA D-loop or cyt-b haplotype or the sub-lineage of rats from Hubei.
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
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Total or severe teratospermia affects the prognosis of fertility and causes serious problems for patients undergoing assisted reproduction[1].The pathophysiological mechanism of teratospermia is unclear.It has been shown that patients with sperm parameters abnormalities and abnormal morphology have a high rate of fragmentation and sperm DNA decondensation[2,3],and that sperm DNA fragmentation analysis could be used as a predictor factor of fertility potential[4].
基金supported by the National Key Basic Research Program of China (No.2004CB418503)the National Natural Science Foundation of China (No.40801203)
文摘Due to frequent soil Cd contamination and wide use of butachlor in China,there is a need to assess their combined toxicity to soil microorganisms.The combined effects of cadmium(Cd,10 mg kg-1 soil) and herbicide butachlor(10,50,and 100 mg kg-1 soil) on enzyme activities and microbial community structure in a paddy soil were assessed using the traditional enzyme assays and random amplified polymorphic DNA(RAPD) analysis.The results showed that urease and phosphatase activities were significantly reduced by high butachlor concentration(100 mg kg-1 soil).When the concentrations of Cd and butachlor added were at a ratio of 1:10,urease and phosphatase activities were significantly decreased whereas enzyme activities were greatly improved at the ratio of 1:5,which indicated that the combined effects of Cd and butachlor on soil urease and phosphatase activities depended largely on their addition concentration ratios.Random amplified polymorphic DNA(RAPD) analysis showed loss of original bands and appearance of new bands when compared with the control soil.Random amplified polymorphic DNA fingerprints suggested substantial differences between the control and treated soil samples,with apparent changes in the number and size of amplified DNA fragments.The addition of high concentration butachlor and the combined impacts of Cd and butachlor significantly affected the diversity of the microbial community.RAPD analysis in conjunction with other biomarkers such as soil enzyme parameters would prove a powerful ecotoxicological tool.Further investigations should be carried out to understand the clear link between RAPD patterns and enzyme activity.
文摘AIM:To compare the differences between dideoxy sequencing/KRAS StripAssay/pyrosequencing for detection of KRAS mutation in Chinese colorectal cancer (CRC) patients.METHODS:Formalin-f ixed, paraff in-embedded (FFPE) samples with tumor cells ≥ 50% were collected from 100 Chinese CRC patients at Beijing Cancer Hospital. After the extraction of genome DNA from FFPE samples, fragments contained codons 12 and 13 of KRAS exon 2 were amplified by polymerase chain reaction and analyzed by dideoxy sequencing, the KRAS Strip Assay and pyrosequencing. In addition, the sensitivities of the 3 methods were compared on serial dilutions (contents of mutant DNA: 100%,50%,20%, 5%,10%, 5%,1%,0%) of A549 cell line DNA (carrying the codon 12 Gly>Ser mutation) into wild-type DNA (human normal intestinal mucosa). The results of dideoxy sequencing,the KRAS StripAssay and pyrosequencing were analyzed by Chromas Software, Collector forKRAS Strip Assay and the pyrosequencing PyroMarkTM Q24 system, respectively.RESULTS: Among 100 patients, KRAS mutations were identif ied in 34%, 37% and 37% of patients by dideoxy sequencing, the KRAS StripAssay and pyrosequencing, respectively. The sensitivity was highest with the KRAS Strip Assay (1%), followed by pyrosequencing (5%), and dideoxy sequencing was lowest (15%). Six different mutation types were found in this study with 3 main mutations Gly12 Asp (GGT>GAT), Gly12 Val (GGT>GTT) and Gly13 Asp (GGC>GAC). Thirty-three patients were identifi ed to have KRAS mutations by the 3 methods, and a total of 8 patients had conflicting results between 3 methods: 4 mutations not detected by dideoxy sequencing and the KRAS StripAssay were identified by pyrosequencing; 3 mutations not detected by dideoxy sequencing and pyrosequencing were identif ied by the KRAS StripAssay; and 1 mutation not detected by pyrosequencing was conf irmed by dideoxy sequencing and the KRAS StripAssay. Among these discordant results, the results identif ied by dideoxy sequencing were consistent either with the KRAS StripAssay or with pyrosequencing, which indicated that the accuracy of dideoxy sequencing was high. CONCLUSION: Taking a worldwide view of reports and our results,dideoxy sequencing remains the most popular method because of its low cost and high accuracy.
文摘IM To determine the incidence of hepatitis B virus (HBV) intrauterine infection and to explore the relationship between HBV viremia level of pregnant women and HBV intrauterine infection.METHODS Sixtynine pregnant women were divided into three groups. Group A, 41 HBsAg positive patients, 14 of them were HBeAg positive (group A1), and 27 HBeAg negative (group A2); Group B, 12 HBsAg negative patients, but positive for antiHBs and/or antiHBe and/or antiHBc; and Group C, 16 patients negative for all HBV markers. Blood samples of mothers were taken at delivery, samples of their infants were collected within 24 hours after birth (before injection of HBIG and HBV vaccine). All the serum samples were stored at -20℃. HBV serum markers were tested by radioimmunoassay and HBV NDA were detected by nested polymerase chain reaction.RESULTS In group C, all of 16 newborns were negative for HBsAg and HBV DNA. In group A, 7 infants were HBsAg positive (171%), and 17 (415%) were HBV DNA positive (P<005). The incidence of intrauterine HBV infection was much higher in group A1 than that in group A2 (HBsAg 429% vs 37%, HBV DNA 929% vs 148%, P<005). The incidence of HBV intrauterine infection was significantly different between high and low HBV viremia of mothers (933% vs 429%, P<005).CONCLUSION The incidence of HBV intrauterine infection is high when HBV DNA in newborns detected with nested PCR is used as a marker of HBV infection. It is related to HBV viremia level of mothers.
文摘Random Amplified Polymorphic DNA (RAPD) analysis is a new technology of molecular marking which has proved very powerful in detecting genetic diversity at the level of population. The genomic DNAs used in our experiment were extracted from fresh leaves taken from 59 individuals sampled from three natural populations in Yan An, Shanxi Province. Through more than 2,000 PCRs, deep-going RAPD analysis was carried out on DNA samples from 49 inviduals. The percentage of polymorphic RAPD loci found in these three populations were respectively 27.2 %, 18.6 % and 5.4 %; the average genetic distances within population, 0.055, 0.036 and 0.008; the average genetic distances between populations (Ⅰ-Ⅱ), (Ⅰ-Ⅲ) and (Ⅱ-Ⅲ), 0.105, 0.096 and 0.060. The genetic diversity of A. brachypus within and between populations was found, for the first time, to be rather poor,thus revealing innate factors as the cause contributing to its endangered status. In addition, our work also provides basic materials for elucidating the underlying cause of its endangerment and for its protection biology.
文摘Objective To determine the DNA damaging potential and the genotoxicity of individual compounds in pesticide contaminated soil. Methods In the present study, DNA damaging potential of pesticide-contaminated soil and the genotoxicity of individual compounds present in the soil were assessed using fluofimetdc analysis of DNA unwinding assay. Results The contaminated soil sample showed 79% （P〈0.001） of DNA strand break, whereas technical grade of major catbaryl and α-naphthol constituents of the contaminated soil showed 64% （P〈0.01） and 60% （P〈0.02） damage respectively. Conclusion Our results indicate that the toxicity caused by contaminated soil is mainly due to carbatyl and α -napthol, which are the major constituents of the soil sample analyzed by CrC-MS.
基金supported by grants from the National Basic Research Program of China(MOST2016YFC0900301 and 2014CB964900)the National Natural Science Foundation of China(No. 91519325)the Beijing Natural Science Foundation (No. 5162012)
文摘Analysis of patient＇s materials like cells or nucleic acids obtained in a minimally invasive or noninvasive manner through the sampling of blood or other body fluids serves as liquid biopsies, which has huge potential for numerous diagnostic applications. Circulating cell-free DNA（cfDNA） is explored as a prognostic or predictive marker of liquid biopsies with the improvements in genomic and molecular methods. DNA methylation is an important epigenetic marker known to affect gene expression. cfDNA methylation detection is a very promising approach as abnormal distribution of DNA methylation is one of the hallmarks of many cancers and methylation changes occur early during carcinogenesis. This re？view summarizes the various investigational applications of cfDNA methylation and its oxidized de？rivatives as biomarkers for cancer diagnosis, prenatal diagnosis and organ transplantation monitoring.The review also provides a brief overview of the technologies for cfDNA methylation analysis based on next generation sequencing.
文摘The aim of this study was to evaluate the effect of naringin on experimentally induced inflammatory bowel dis- ease in rats. Naringin （20, 40 and 80 mg/kg） was given orally for 7 days to Wistar rats before induction of colitis by intrarectal instillation of 2 mL of 4% （v/v） acetic acid solution. The degree of colonic mucosal damage was analyzed by examining mucosal damage, ulcer area, ulcer index and stool consistency. Intrarectal administration of 4% acetic acid resulted in significant modulation of serum alkaline phosphatase, lactate dehydrogenase, superoxide dismutase （SOD）, glutathione （GSH）, malondialdehyde （MDA） and myeloperoxidase （MPO） content along with colonic nitric oxide （NO）, xanthine oxidase （XO） level and protein carbonyl content in the colonic tissue as well as in blood. Naringin （40 and 80 mg/kg） exerted a dose dependent （P 〈 0.05） ameliorative effect, as it significantly increased hematological parameter as well as colonic SOD and GSH. There was a significant （P 〈 0.05） and dose dependant inhibition of macroscopical score, ulcer area along with colonic MDA, MPO activity by the 7 days of pretreatment of naringin （40 and 80 mg/kg）. Biochemical studies revealed a significant （P 〈 0.05） dose dependant inhibition in serum alkaline phosphatase （ALP） and lactate dehydrogenase （LDH） levels by pretreatment of naringin. Increased levels of colonic NO, XO, protein carbonyl content and DNA damage were also sig- nificantly decreased by naringin pretreatment. The findings of the present investigation propose that naringin has an anti-inflammatory, anti-oxidant and anti-apoptotic potential effect at colorectal sites as it modulates the production and expression of oxidative mediators such as MDA, MPO, NO and XO, thus reducing DNA damage.
基金the Natural Scientific Foundation of China (NSFC3962526)National High-Technology Project-863 (102-10-01-04)
文摘AIM: To develop and optimize cDNA representational difference analysis (cDNA RDA) method and to identify and clone garlic up-regulated genes in human gastric cancer (HGC) cells. METHODS: We performed cDNA RDA method by using abundant double-stranded cDNA messages provided by two self-constructed cDNA libraries (Allitridi-treated and paternal HGC cell line BGC823 cells cDNA libraries respectively). Bam H I and Xho I restriction sites harbored in the library vector were used to select representations. Northern and Slot blots analyses were employed to identify the obtained difference products. RESULTS: Fragments released from the cDNA library vector after restriction endonuclease digestion acted as good marker indicating the appropriate digestion degree for library DNA. Two novel expressed sequence tags (ESTs) and a recombinant gene were obtained. Slot blots result showed a 8-fold increase of glia-derived nexin/protease nexin 1 (GDN/PN1) gene expression level and 4-fold increase of hepatitis B virus x-interacting protein (XIP) mRNA level in BGC823 cells after Allitridi treatment for 72h. CONCLUSION: Elevated levels of GDN/PN1 and XIP mRNAs induced by Allitridi provide valuable molecular evidence for elucidating the garlic's efficacies against neurodegenerative and inflammatory diseases. Isolation of a recombinant gene and two novel ESTs further show cDNA RDA based on cDNA libraries to be a powerful method with high specificity and reproducibility in cloning differentially expressed genes.
文摘A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the “fine structure” of nucleotide sequences. The approach is based on the assumption that nucleotides have an inner abstract characteristic, the determinative degree, which reflects genetic code phenomenological prop-erties and is adjusted to nucleotides physical properties. We consider each codon position independently, which gives three separate walks characterized by different angles and lengths, and that such an object is called triander which reflects the “strength” of branch. A general method for identifying DNA sequence “by triander” which can be treated as a unique “genogram” (or “gene passport”) is proposed. The two- and three-dimensional trianders are considered. The difference of sequences fine structure in genes and the intergenic space is shown. A clear triplet signal in coding sequences was found which is absent in the intergenic space and is independent from the sequence length. This paper presents the topological classification of trianders which can allow us to provide a detailed working out signatures of functionally different genomic regions.
