目的设计用于人巨细胞病毒(HCM V)诊断的60-m er长链寡核苷酸探针及微阵列。方法利用生物学软件A rray D es igner2.0,针对HCM V特异且保守的序列设计60-m er探针,利用BLA ST功能将设计探针在G enB ank数据库进行序列比对分析,筛选得到H...目的设计用于人巨细胞病毒(HCM V)诊断的60-m er长链寡核苷酸探针及微阵列。方法利用生物学软件A rray D es igner2.0,针对HCM V特异且保守的序列设计60-m er探针,利用BLA ST功能将设计探针在G enB ank数据库进行序列比对分析,筛选得到HCM V特异性O ligo探针,根据各探针的属性特点设计芯片阵列。结果设计得到24条解链温度(Tm值)相近、长度均一的60-m er O ligo探针及其芯片阵列,拟打印成DNA芯片用于HCM V检测。结论利用病原体的生物信息学资料及A rray D es igner2.0生物软件,能有效的进行病毒检测芯片的设计。展开更多
In this study, blood culture and PCR-microarray analysis were used to examine 172 cases of suspected septicemia. Primers and oligonucleotide probes, based on the sequences of bacterial 16 SrRNA gene, were arrayed by i...In this study, blood culture and PCR-microarray analysis were used to examine 172 cases of suspected septicemia. Primers and oligonucleotide probes, based on the sequences of bacterial 16 SrRNA gene, were arrayed by imprinting on microar ray slides. Blood specimens collected from 172 cases of suspected septicemia wer e cultured and then tested separately by PCR for the bacterial 16S rRNA. Of the 172 clinical cases, 17 cases tested positive by PCR. The number of positives ide ntified by PCR (9.88%) was significantly higher than the number of positives id entified by the blood culture (4.65%). When blood culture was used as control, the sensitivity of PCR was 100%, the specificity was 97.85%, and the index of accurate diagnosis was 0.979. When the 17 PCR positive specimens were further an alyzed by hybridization against the microarrays, five were found to be probe pos itive for E. coli, four were positive for S. epidermidis, four were positive for CoNS, and two were positive for Bacillus and Propionibacterium, respectively. I n the eight specimens showing positive results by both PCR and blood culture, th e species determined by microarray analysis corresponded with the result obtaine d from blood culture. Detection of the bacterial 16S rRNA genes in clinical spec imens by PCR and microarray analysis can be used to accurately diagnose neonatal sepsis. This method has a higher sensitivity and specificity than blood culture and can provide a rapid way for the etiological diagnosis of neonatal septicemi a.展开更多
DNA microarrays have been acknowledged to represent a promising approach for the detection of viral pathogens. However, the probes designed for current arrays could cover only part of the given viral variants, that co...DNA microarrays have been acknowledged to represent a promising approach for the detection of viral pathogens. However, the probes designed for current arrays could cover only part of the given viral variants, that could result in false-negative or ambiguous data. If all the variants are to be covered, the requirement for more probes would render much higher spot density and thus higher cost of the arrays. Here we have developed a new strategy for oligonucleotide probe design. Using type I human immunodeficiency virus (HIV-1) tat gene as an example, we designed the array probes and validated the optimized parameters in silico. Results show that the oligo number is significantly reduced comparing with the existing methods, while specificity and hybridization efficiency remain intact. The adoption of this method in reducing the oligo numbers could increase the detection capacity for DNA microarrays, and would significantly lower the manufacturing cost for making array chips.展开更多
文摘目的设计用于人巨细胞病毒(HCM V)诊断的60-m er长链寡核苷酸探针及微阵列。方法利用生物学软件A rray D es igner2.0,针对HCM V特异且保守的序列设计60-m er探针,利用BLA ST功能将设计探针在G enB ank数据库进行序列比对分析,筛选得到HCM V特异性O ligo探针,根据各探针的属性特点设计芯片阵列。结果设计得到24条解链温度(Tm值)相近、长度均一的60-m er O ligo探针及其芯片阵列,拟打印成DNA芯片用于HCM V检测。结论利用病原体的生物信息学资料及A rray D es igner2.0生物软件,能有效的进行病毒检测芯片的设计。
文摘In this study, blood culture and PCR-microarray analysis were used to examine 172 cases of suspected septicemia. Primers and oligonucleotide probes, based on the sequences of bacterial 16 SrRNA gene, were arrayed by imprinting on microar ray slides. Blood specimens collected from 172 cases of suspected septicemia wer e cultured and then tested separately by PCR for the bacterial 16S rRNA. Of the 172 clinical cases, 17 cases tested positive by PCR. The number of positives ide ntified by PCR (9.88%) was significantly higher than the number of positives id entified by the blood culture (4.65%). When blood culture was used as control, the sensitivity of PCR was 100%, the specificity was 97.85%, and the index of accurate diagnosis was 0.979. When the 17 PCR positive specimens were further an alyzed by hybridization against the microarrays, five were found to be probe pos itive for E. coli, four were positive for S. epidermidis, four were positive for CoNS, and two were positive for Bacillus and Propionibacterium, respectively. I n the eight specimens showing positive results by both PCR and blood culture, th e species determined by microarray analysis corresponded with the result obtaine d from blood culture. Detection of the bacterial 16S rRNA genes in clinical spec imens by PCR and microarray analysis can be used to accurately diagnose neonatal sepsis. This method has a higher sensitivity and specificity than blood culture and can provide a rapid way for the etiological diagnosis of neonatal septicemi a.
基金Research funding for undergraduate students of Nankai UniversityNSFC grant (30270308)+1 种基金NSFC grant (30370053)Tianjin grant (05YFJZJC01301).
文摘DNA microarrays have been acknowledged to represent a promising approach for the detection of viral pathogens. However, the probes designed for current arrays could cover only part of the given viral variants, that could result in false-negative or ambiguous data. If all the variants are to be covered, the requirement for more probes would render much higher spot density and thus higher cost of the arrays. Here we have developed a new strategy for oligonucleotide probe design. Using type I human immunodeficiency virus (HIV-1) tat gene as an example, we designed the array probes and validated the optimized parameters in silico. Results show that the oligo number is significantly reduced comparing with the existing methods, while specificity and hybridization efficiency remain intact. The adoption of this method in reducing the oligo numbers could increase the detection capacity for DNA microarrays, and would significantly lower the manufacturing cost for making array chips.
