BACKGROUND Genetic tests are increasingly performed for the management of unresectable pancreatic cancer.For genotyping aimed samples current guidelines recommend using core specimens,although based on moderate qualit...BACKGROUND Genetic tests are increasingly performed for the management of unresectable pancreatic cancer.For genotyping aimed samples current guidelines recommend using core specimens,although based on moderate quality evidence.However,in clinical practice among the endoscopic ultrasound(EUS) guided tissue acquisition methods,fine needle aspiration(FNA) is the most widely performed.AIM To assess the adequacy for next generation sequencing(NGS) of the DNA yielded from EUS-FNA pancreatic adenocarcinoma(PDAC) samples.METHODS Between November 2018 and December 2021,105 patients with PDAC confirmed by EUS-FNA were included in the study at our tertiary gastroenterology center.Either 22 gauge(G) or 19G FNA needles were used.One pass was dedicated to DNA extraction.DNA concentration and purity(A260/280,A260/230) were assessed by spectrophotometry.We assessed the differences in DNA parameters according to needle size and tumor characteristics(size,location) and the adequacy of the extracted DNA for NGS(defined as A260/280 ≥ 1.7,and DNA yield:≥ 10 ng for amplicon based NGS,≥ 50 ng for whole exome sequencing [WES],≥ 100 ng for whole genome sequencing [WGS]) by analysis of variance and ttest respectively.Moreover,we compared DNA purity parameters across the different DNA yield categories.RESULTS Our cohort included 49% male patients,aged 67.02 ± 8.38 years.The 22G needle was used in 71%of the cases.The DNA parameters across our samples varied as follows:DNA yield:1289 ng(inter quartile range:534.75-3101),A260/280 = 1.85(1.79-1.86),A260/230 = 2.2(1.72-2.36).DNA yield was > 10 ng in all samples and > 100 ng in 93% of them(one sample < 50 ng).There were no significant differences in the concentration and A260/280 between samples by needle size.Needle size was the only independent predictor of A260/230 which was higher in the 22G samples(P =0.038).NGS adequacy rate was 90% for 19G samples regardless of NGS type,and for 22G samples it reached 89% for WGS adequacy and 91% for WES and amplicon based NGS.Samples with DNA yield > 100 ng had significantly higher A260/280(1.89 ± 0.32 vs 1.34 ± 0.42,P = 0.013).Tumor characteristics were not corelated with the DNA parameters.CONCLUSION EUS-FNA PDAC samples yield DNA adequate for subsequent NGS.DNA amount was similar between 22G and 19G FNA needles.DNA purity parameters may vary indirectly with needle size.展开更多
Silicon phthalocyanine derivatives 1a and 1b were synthesized and characterized by UV, <sup>1</sup>H-NMR and MS. The photophysical properties of the compounds in DMSO were investigated. The maximum absorpt...Silicon phthalocyanine derivatives 1a and 1b were synthesized and characterized by UV, <sup>1</sup>H-NMR and MS. The photophysical properties of the compounds in DMSO were investigated. The maximum absorption peaks of compounds 1a and 1b at the Q-band are 681 nm. With ZnPc (Φ<sub>F</sub> = 0.20, Φ<sub>Δ</sub> = 0.67) as a reference, the fluorescence quantum yield (Φ<sub>F</sub>) of 1a and 1b are 0.20 and 0.31 respectively, and the singlet oxygen quantum yield (Φ<sub>Δ</sub>) are 0.66 and 0.59 respectively. The DNA-photocleavage activities of compounds 1a and 1b were studied by gel electrophoresis. Compounds 1a and 1b possess good photocleavage activity to pBR322 DNA. The results demonstrate that compounds 1a and 1b are potential photosensitizers for tumor therapy.展开更多
【目的】通过荧光定量PCR技术对土壤微生物目标基因进行绝对定量,其定量结果的准确性容易受到DNA提取得率以及腐殖酸抑制性的影响。【方法】采用内参基因加标法,利用构建的突变质粒DNA,对供试水稻土壤样品中的微生物16S r RNA目标基因...【目的】通过荧光定量PCR技术对土壤微生物目标基因进行绝对定量,其定量结果的准确性容易受到DNA提取得率以及腐殖酸抑制性的影响。【方法】采用内参基因加标法,利用构建的突变质粒DNA,对供试水稻土壤样品中的微生物16S r RNA目标基因的绝对拷贝数进行荧光定量PCR检测,用来表征该样品中细菌群落总体丰度。在定量前通过双向引物扩增方法验证突变质粒中的内参基因对供试土壤的特异性。【结果】不同水稻土壤样品的DNA提取量在样品间差异较大。通过内参基因加标法对DNA提取量进行校正,显著提高了16S r RNA基因绝对定量的精确度。不同水稻土壤样品间的变异系数为17.8,与未加标处理相比降低了66.7%。在此基础上,进一步通过内参基因加标法对土壤有机质和含水率均呈现典型空间特征差异的6处亚热带湿地土壤样品中的16S r RNA基因进行绝对定量。16S r RNA基因绝对拷贝数与土壤微生物生物量碳具有显著的线性相关性(R2=0.694,P<0.001),表明内参校正后的16S r RNA基因绝对拷贝数可以准确反映单位质量土壤中微生物的丰度。【结论】内参基因加标法可以对DNA提取得率以及腐殖酸对PCR扩增的抑制性进行校正,从而提高绝对定量的准确性。基于内参基因加标法的目标基因绝对定量PCR检测,可作为土壤微生物生物量测量,以及微生物功能基因绝对丰度定量的一种核酸检测方法。展开更多
It is important to obtain a considerable quantity of DNA from oligotrophic environments such as a drinking water distribution system(DWDS)to study microbial communities by molecular biotechnology,and DNA yield is alwa...It is important to obtain a considerable quantity of DNA from oligotrophic environments such as a drinking water distribution system(DWDS)to study microbial communities by molecular biotechnology,and DNA yield is always one of the biggest problems when performing metagenomic sequencing on drinking water samples.To obtain as many microbes as possible,ultrasound has been widely used in cell detachment,but studies on the optimal ultrasonic parameters for biofilm in DWDS have rarely been seen.The effects of three ultrasonic parameters,including power,duration,and the number of ultrasound treatments(USTs)on the selected monoculture bacteria(Pelomonas sp.)biofilm were studied first.Then the optimal values of each ultrasonic parameter were initially determined.Based on these values,three levels of each ultrasonic parameter were selected,and then an orthogonal experiment was conducted to further study drinking water biofilm,and finally the optimal ultrasonic parameters for the effective separation of biofilm cells in DWDS were determined.The results showed that the optimal ultrasonic power,duration,and the number of USTs are 13 W,1 min,and 15,respectively.A 20-min interval is needed between two USTs.The present optimal UST,which does not lose DNA quality,can increase the amount of extractable DNA by at least 4.78 times compared to samples without UST.This study provides a pretreatment methodology for extracting more and reliable DNA from biofilm in DWDS,and can better solve the problem of DNA collection in oligotrophic environments.展开更多
基金The Executive Agency for Higher Education,Research,Development and Innovation Funding-research,No.PN-Ⅲ-P1-1.2-PCCDI-2017-0797 (PANCNGS)
文摘BACKGROUND Genetic tests are increasingly performed for the management of unresectable pancreatic cancer.For genotyping aimed samples current guidelines recommend using core specimens,although based on moderate quality evidence.However,in clinical practice among the endoscopic ultrasound(EUS) guided tissue acquisition methods,fine needle aspiration(FNA) is the most widely performed.AIM To assess the adequacy for next generation sequencing(NGS) of the DNA yielded from EUS-FNA pancreatic adenocarcinoma(PDAC) samples.METHODS Between November 2018 and December 2021,105 patients with PDAC confirmed by EUS-FNA were included in the study at our tertiary gastroenterology center.Either 22 gauge(G) or 19G FNA needles were used.One pass was dedicated to DNA extraction.DNA concentration and purity(A260/280,A260/230) were assessed by spectrophotometry.We assessed the differences in DNA parameters according to needle size and tumor characteristics(size,location) and the adequacy of the extracted DNA for NGS(defined as A260/280 ≥ 1.7,and DNA yield:≥ 10 ng for amplicon based NGS,≥ 50 ng for whole exome sequencing [WES],≥ 100 ng for whole genome sequencing [WGS]) by analysis of variance and ttest respectively.Moreover,we compared DNA purity parameters across the different DNA yield categories.RESULTS Our cohort included 49% male patients,aged 67.02 ± 8.38 years.The 22G needle was used in 71%of the cases.The DNA parameters across our samples varied as follows:DNA yield:1289 ng(inter quartile range:534.75-3101),A260/280 = 1.85(1.79-1.86),A260/230 = 2.2(1.72-2.36).DNA yield was > 10 ng in all samples and > 100 ng in 93% of them(one sample < 50 ng).There were no significant differences in the concentration and A260/280 between samples by needle size.Needle size was the only independent predictor of A260/230 which was higher in the 22G samples(P =0.038).NGS adequacy rate was 90% for 19G samples regardless of NGS type,and for 22G samples it reached 89% for WGS adequacy and 91% for WES and amplicon based NGS.Samples with DNA yield > 100 ng had significantly higher A260/280(1.89 ± 0.32 vs 1.34 ± 0.42,P = 0.013).Tumor characteristics were not corelated with the DNA parameters.CONCLUSION EUS-FNA PDAC samples yield DNA adequate for subsequent NGS.DNA amount was similar between 22G and 19G FNA needles.DNA purity parameters may vary indirectly with needle size.
文摘Silicon phthalocyanine derivatives 1a and 1b were synthesized and characterized by UV, <sup>1</sup>H-NMR and MS. The photophysical properties of the compounds in DMSO were investigated. The maximum absorption peaks of compounds 1a and 1b at the Q-band are 681 nm. With ZnPc (Φ<sub>F</sub> = 0.20, Φ<sub>Δ</sub> = 0.67) as a reference, the fluorescence quantum yield (Φ<sub>F</sub>) of 1a and 1b are 0.20 and 0.31 respectively, and the singlet oxygen quantum yield (Φ<sub>Δ</sub>) are 0.66 and 0.59 respectively. The DNA-photocleavage activities of compounds 1a and 1b were studied by gel electrophoresis. Compounds 1a and 1b possess good photocleavage activity to pBR322 DNA. The results demonstrate that compounds 1a and 1b are potential photosensitizers for tumor therapy.
文摘【目的】通过荧光定量PCR技术对土壤微生物目标基因进行绝对定量,其定量结果的准确性容易受到DNA提取得率以及腐殖酸抑制性的影响。【方法】采用内参基因加标法,利用构建的突变质粒DNA,对供试水稻土壤样品中的微生物16S r RNA目标基因的绝对拷贝数进行荧光定量PCR检测,用来表征该样品中细菌群落总体丰度。在定量前通过双向引物扩增方法验证突变质粒中的内参基因对供试土壤的特异性。【结果】不同水稻土壤样品的DNA提取量在样品间差异较大。通过内参基因加标法对DNA提取量进行校正,显著提高了16S r RNA基因绝对定量的精确度。不同水稻土壤样品间的变异系数为17.8,与未加标处理相比降低了66.7%。在此基础上,进一步通过内参基因加标法对土壤有机质和含水率均呈现典型空间特征差异的6处亚热带湿地土壤样品中的16S r RNA基因进行绝对定量。16S r RNA基因绝对拷贝数与土壤微生物生物量碳具有显著的线性相关性(R2=0.694,P<0.001),表明内参校正后的16S r RNA基因绝对拷贝数可以准确反映单位质量土壤中微生物的丰度。【结论】内参基因加标法可以对DNA提取得率以及腐殖酸对PCR扩增的抑制性进行校正,从而提高绝对定量的准确性。基于内参基因加标法的目标基因绝对定量PCR检测,可作为土壤微生物生物量测量,以及微生物功能基因绝对丰度定量的一种核酸检测方法。
基金Project supported by the Major Science and Technology Program for Water Pollution Control and Treatment(No.2017ZX07201004)the National Natural Science Foundation of China(No.51678520)。
文摘It is important to obtain a considerable quantity of DNA from oligotrophic environments such as a drinking water distribution system(DWDS)to study microbial communities by molecular biotechnology,and DNA yield is always one of the biggest problems when performing metagenomic sequencing on drinking water samples.To obtain as many microbes as possible,ultrasound has been widely used in cell detachment,but studies on the optimal ultrasonic parameters for biofilm in DWDS have rarely been seen.The effects of three ultrasonic parameters,including power,duration,and the number of ultrasound treatments(USTs)on the selected monoculture bacteria(Pelomonas sp.)biofilm were studied first.Then the optimal values of each ultrasonic parameter were initially determined.Based on these values,three levels of each ultrasonic parameter were selected,and then an orthogonal experiment was conducted to further study drinking water biofilm,and finally the optimal ultrasonic parameters for the effective separation of biofilm cells in DWDS were determined.The results showed that the optimal ultrasonic power,duration,and the number of USTs are 13 W,1 min,and 15,respectively.A 20-min interval is needed between two USTs.The present optimal UST,which does not lose DNA quality,can increase the amount of extractable DNA by at least 4.78 times compared to samples without UST.This study provides a pretreatment methodology for extracting more and reliable DNA from biofilm in DWDS,and can better solve the problem of DNA collection in oligotrophic environments.
