Application of restriction display PCR technique in the preparation of cDNA microarray probes

AIM: To develop a simplified and efficient method for the preparation of hepatitis C virus (HCV) cDNA microarray probes.METHODS: With the technique of restriction display PCR (RD-PCR), restriction enzyme Sau3A I was chosen to digest the full-length HCV cDNAs. The products were classified and re-amplified by RD-PCR. We separated the differential genes by polyacrylamide gel electrophoresis and silver staining. Single bands cut out from the polyacrylamide gel were isolated. The third-round PCR was performed using the single bands as PCR template.The RD-PCR fragments were purified and cloned into the pMD18-T vector. The recombinant plasmids were extracted from positive clones, and the target gene fragments were sequenced. The cDNA microarray was prepared by spotting RD-PCR products to the surface of amino-modified glass slides using a robot. We validated the detection of microarray by hybridization and sequence analysis.RESULTS: A total of 24 different cDNA fragments ranging from 200 to 800 bp were isolated and sequenced,which were the specific gene fragments of HCV. These fragments could be further used as probes in microarray preparation. The diagnostic capability of the microarray was evaluated after the washing and scanning steps. The results of hybridization and sequence analysis showed that the specificity, sensitivity, accuracy, reproducibility,and linearity in detecting HCV RNA were satisfactory.CONCLUSION: The RD-PCR technique is of great value in obtaining a large number of size-comparable gene probes, which provides a speedy protocol in generating probes for the preparation of microarrays. Microarray prepared as such could be further optimized and applied in the clinical diagnosis of HCV.

A Strategy to Optimize the Oligo-Probes for Microarray-based Detection of Viruses

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.

Progress in Mechanical Modeling of Implantable Flexible Neural Probes

Implanted neural probes can detect weak discharges of neurons in the brain by piercing soft brain tissue,thus as important tools for brain science research,as well as diagnosis and treatment of brain diseases.However,the rigid neural probes,such as Utah arrays,Michigan probes,and metal microfilament electrodes,are mechanically unmatched with brain tissue and are prone to rejection and glial scarring after implantation,which leads to a significant degradation in the signal quality with the implantation time.In recent years,flexible neural electrodes are rapidly developed with less damage to biological tissues,excellent biocompatibility,and mechanical compliance to alleviate scarring.Among them,the mechanical modeling is important for the optimization of the structure and the implantation process.In this review,the theoretical calculation of the flexible neural probes is firstly summarized with the processes of buckling,insertion,and relative interaction with soft brain tissue for flexible probes from outside to inside.Then,the corresponding mechanical simulation methods are organized considering multiple impact factors to realize minimally invasive implantation.Finally,the technical difficulties and future trends of mechanical modeling are discussed for the next-generation flexible neural probes,which is critical to realize low-invasiveness and long-term coexistence in vivo.

Lift-Off Effect of Koch and Circular Differential Pickup Eddy Current Probes

A flexible or planar eddy current probe with a differential structure can suppress the lift-off noise during the inspection of defects.However,the extent of the lift-off effect on differential probes,including different coil structures,varies.In this study,two planar eddy current probes with differential pickup structures and the same size,Koch and circular probes,were used to compare lift-off effects.The eddy current distributions of the probes perturbed by 0°and 90°cracks were obtained by finite element analysis.The analysis results show that the 90°crack can impede the eddy current induced by the Koch probe even further at relatively low lift-off distance.The peak-to-peak values of the signal output from the two probes were compared at different lift-off distances using finite element analysis and experimental methods.In addition,the effects of different frequencies on the lift-off were studied experimentally.The results show that the signal peak-to-peak value of the Koch probe for the inspection of cracks in 90°orientation is larger than that of the circular probe when the lift-off distance is smaller than 1.2 mm.In addition,the influence of the lift-off distance on the peak-to-peak signal value of the two probes was studied via normalization.This indicates that the influence becomes more evident with an increase in excitation frequency.This research discloses the lift-off effect of differential planar eddy current probes with different coil shapes and proves the detection merit of the Koch probe for 90°cracks at low lift-off distances.

Activatable fluorescent probes for imaging and diagnosis of rheumatoid arthritis

Rheumatoid arthritis(RA)is a systemic autoimmune disease that is primarily manifested as synovitis and polyarticular opacity and typically leads to serious joint damage and irreversible disability,thus adversely affecting locomotion ability and life quality.Consequently,good prognosis heavily relies on the early diagnosis and effective therapeutic monitoring of RA.Activatable fluorescent probes play vital roles in the detection and imaging of biomarkers for disease diagnosis and in vivo imaging.Herein,we review the fluorescent probes developed for the detection and imaging of RA biomarkers,namely reactive oxygen/nitrogen species(hypochlorous acid,peroxynitrite,hydroxyl radical,nitroxyl),pH,and cysteine,and address the related challenges and prospects to inspire the design of novel fluorescent probes and the improvement of their performance in RA studies.

超高速细胞分选平台结合cDNA microarray技术筛查宫颈癌细胞潜在分子标志物

目的:通过超高速细胞分选平台结合cDNA microarray技术,筛查宫颈癌细胞可能潜在的分子标志物。方法:采用MoFlo XDP型超高速细胞分选平台纯化细胞膜表面表达CD38和不表达CD38的宫颈癌细胞,利用RNAlater技术得到cDNA microarray实验所需RNA,然后进行基因芯片分析。结果:利用MoFlo XDP型超高速细胞分选平台可以获得纯度为99.0%以上的CD38阳性表达宫颈癌细胞。结论:cDNA microarray分析发现了RORA、PLIN4、AUTS2、IFITM1等宫颈癌细胞潜在分子标志物,为宫颈癌研究提供了新的技术方法。

Expression and Significance of Survivin mRNA in Lung Cancer of Different Progression Stages by FISH and Tissue Microarray Technology*

Objective： To investigate the expression of Survivin mRNA in lung cancer progression tissue microarray by FISH （fluorescence in situ hybridization） method and determine its role and significance in lung cancer genesis and progress. Methods： The expression of Survivin mRNA was detected by FISH method and tissue microarray technology. 89 cases of primary lung cancer, 12 cases of lymph node metastasis of lung cancer, 12 cases of precancerous lesion and 10 cases of normal lung tissue were examined. Results： 69.7% of primary lung cancer express Survivin mRNA; the positive ratio of primary lung cancer and precancerous lesion were both significantly higher than that of normal lung tissue （P〈0.05）; the expression of Survivin mRNA was related to the differentiation degree, lymph node metastasis and clinical stages （P〈0.05）. Conclusion： FISH has good sensitivity and stability. Tissue microarray technology has many advantages, such as high efficiency, high throughput, etc; it may have good prospect in pathology. Survivin mRNA was highly expressed in lung cancer and precancerous lesion; it was related to the progress and malignant behavior; it may play a promotion role in lung cancer genesis and progress and offer basis to early diagnosis, prognosis estimate and treatment.

Expression of COX-2 in Different Subtypes of Gastric Intestinal Metaplasia and Gastric Carcinoma by Tissue Microarray

Objective: To study the expression of cyclooxygenase-2 (COX-2) protein in different subtypes of intestinal metaplasia (IM) and gastric carcinoma, evaluate the possibility of COX-2 forecasting the risk of malignant potential of IM, and the relationship between COX-2 expression and gastric carcinogenesis. Methods: Forty cases of chronic atrophic gastritis (CAG) with IM, 40 cases of gastric carcinoma and corresponding paracancerous tissues were selected to construct a tissue microarray. High iron diamine/alcian blue (HID/AB) staining and Hematoxylin and Eosin (HE) staining was used to classify IM and gastric carcinoma, and the expression of COX-2 protein detected in different subtypes of IM and gastric cancer by using immunohistochemistry. Results: The positive expression rate of COX-2 was 45.65%, 59.38% and 77.27% in IM foci in CAG, IM foci in paracancerous tissues, and intestinal-type gastric carcinoma, respectively, significantly higher than in diffuse-type gastric cancer (16.67%)(P<0.05, 0.005 and 0.005, respectively), and the expression intensity of COX-2 protein showed a increased tendency gradually in the sequence of IM foci in CAG→IM foci in paracancerous tissues→intestinal-type gastric carcinoma (P<0.005). The positive expression rate of COX-2 protein in type Ⅲ IM was significantly higher than in type Ⅰ and type Ⅱ IM (P<0.005 and 0.05, respectively), and the expression intensity also showed a increased tendency gradually from type Ⅰ to type Ⅲ IM (P<0.005). Conclusion: The expression level of COX-2 was increased gradually along with the increase of the risk of malignancy of IM, and its expression level may be a useful index to forecast the risk of malignant potential of IM. COX-2 expression was associated with intestinal-type gastric carcinoma, but it might also have some role in the carcinogenesis of diffuse-type gastric carcinoma.

Identification of p63 expression in human lung cancer: analysis by complementary DNA and tissue microarray

Objective: To evaluate p63 expression at mRNA transcripts and protein levels in lung squamous cell cancer (SCC), adenocarcinoma, large cell lung cancer (LCLC) and small cell lung cancer (SCLC) and their matched metastatic tumors. The association between p63 expression and p63 locus at chromosomal 3q27 q29 was also investigated. Methods: p63 mRNA expression levels in a large series of lung cancers including SCC, adenocarcinoma, LCLC, SCLC and their matched metastatic tumors were analyzed by cDNA microarray technology. A tissue microarray from 150 primary lung cancer specimens was constructed and used for immunohistochemical detection of p63 protein expression. Chromosomal imbalances at the p63 locus in 70 primary lung cancers samples were studied by comparative genomic hybridization (CGH) technology. Results: mRNA levels were 10 fold in SCC compared to LCLC, SCLC, and adenocarcinoma. Interestingly, the mRNA expression of p63 in metastatic carcinomas was significantly higher than that in their matched primary tumors ( P <0 001). Immunohistochemistry demonstrated that p63 expression was 94.64% in SCC but only 1 79% in lung adenocarcinoma and 2 of 4 LCLC were positive staining. All the results in of SCLC were negative. There was a statistically significant difference for p63 positivity between pT1 tumors and those of higher stage ( P =0 035). The CGH results indicated that p63 locus at chromosomal 3q27 q29 was overrepresented in SCC. p63 immunopositivity correlated significantly with pronounced gains of the p63 locus at chromosomal 3q27 q29 (P=0.0001), indicating that strong expression of p63 in lung SCC correlated with increased gene amplification. Conclusion: p63 might play an important role not only in squamous differentiation of lung cancer but also in tumor development and progression.

α粒子诱发BEP2D细胞转化过程中肺癌相关基因表达的cDNA Microarray研究

目的：探讨辐射诱发人支气管上皮细胞(BEP2D)转化过程中肺癌相关基因的表达。方法：用Cartesian PixSys5500 cDNA Microarray点样仪将60个肺癌相关基因以微阵列形式点布于醛基化的玻璃片上。提取α离子辐射前BEP2D细胞（原代）和α粒子辐射后20代、35代细胞总RNA，经长片段反转录和线性扩增标记成荧光探针后与微阵列中cDNA进行杂交。结果：原代细胞中检测到40个基因表达；20代检测到47个基因表达；35代检测到20个基因表达。所检测的基因中，抑癌基因的mRNA丰度在原代和20代后细胞中急剧下降；大多数癌基因的表达丰度在20代以后细胞中仅轻微下降；生长因子类基因大都在20代细胞表达。结论：在辐射诱发的人支气管上皮转化细胞中，抑癌基因的失活可能与细胞恶化有关；癌基因及生长因子类基因可能促进了细胞的转化。

Screening of Serum Biomarkers for Distinguishing between Latent and Active Tuberculosis Using Proteome Microarray

Objective To identify potential serum biomarkers for distinguishing between latent tuberculosis infection（LTBI） and active tuberculosis（TB）. Methods A proteome microarray containing 4,262 antigens was used for screening serum biomarkers of 40 serum samples from patients with LTBI and active TB at the systems level. The interaction network and functional classification of differentially expressed antigens were analyzed using STRING 10.0 and the TB database, respectively. Enzyme-linked immunosorbent assays（ELISA） were used to validate candidate antigens further using 279 samples. The diagnostic performances of candidate antigens were evaluated by receiver operating characteristic curve（ROC） analysis. Both antigen combination and logistic regression analysis were used to improve diagnostic ability. Results Microarray results showed that levels of 152 Mycobacterium tuberculosis（Mtb）-antigenspecific IgG were significantly higher in active TB patients than in LTBI patients（P 〈 0.05）, and these differentially expressed antigens showed stronger associations with each other and were involved in various biological processes. Eleven candidate antigens were further validated using ELISA and showed consistent results in microarray analysis. ROC analysis showed that antigens Rv2031 c, Rv1408, and Rv2421 c had higher areas under the curve（AUCs） of 0.8520, 0.8152, and 0.7970, respectively. In addition, both antigen combination and logistic regression analysis improved the diagnostic ability. Conclusion Several antigens have the potential to serve as serum biomarkers for discrimination between LTBI and active TB.

Tissue microarrays in pathological examination of apoptotic acinar cells induced by dexamethasone in the pancreas of rats with severe acute pancreatitis

BACKGROUND: The good therapeutic effects of large dose of dexamethasone on severe acute pancreatitis (SAP) patients have been proved. This study was designed to investigate the influence of dexamethasone on apoptosis of acinar cells in the pancreas of rats with SAP and the protein expression of the apoptosis-regulating genes Bax and Bcl-2. METHODS: Ninety Sprague-Dawley rats with SAP were randomly divided into a model group and a dexamethasone treated group (45 rats in each group), and another 45 rats formed the sham operation group. Survival rates were calculated and gross pathological changes in the pancreas of each group were observed under a light microscope 3, 6 and 12 hours after operation. Tissue microarray technology was applied to prepare pancreatic tissue sections. The changes in Bax and Bcl-2 protein expression levels of pancreatic tissues from each group were assessed by immunohistochemical staining, and TUNEL staining was used to evaluate changes in apoptosis index. RESULTS: The model and treated groups did not differ in mortality at each time point. The pathological score for the pancreas in the treated group was significantly lower than that in the model group at 3 and 6 hours. The positive rates of Bax protein expression in the head and tail of the pancreas in the treated group at all time points were all markedly higher than those of the model group. The positive rate of Bcl-2 protein expression in the head of the pancreas in the treated group was significantly higher than that of the model group at 3 hours. TUNEL staining showed that the pancreas head and tail apoptosis indices of the treated group were markedly higher than those of the model group after 6 hours. CONCLUSIONS: Apoptosis may be a protective response. to pancreatic cell injury. The mechanism of action of dexamethasone in treating SAP may be related to the apoptosis of acinar cells in the pancreas induced by apoptosis-regulating genes such as Bax and Bcl-2. The advantages of tissue microarrays in pathological examination of the pancreas include saving of time and energy, efficiency and highly representative.

Expression of p53, p16 and COX-2 in pancreatic cancer with tissue microarray

BACKGROUND: Pancreatic cancer development and progression is driven by the accumulation of genetic changes. In this study we constructed tissue microarray containing specimens from pancreatic cancer, adjacent non-cancer tissue and normal tissue to survey the expression of p53, p16 and cyclooxyganase-2 (COX-2). METHODS: Tissue microarray containing 337 specimens from different stages of pancreatic cancer, adjacent noncancer tissue and normal tissues was constructed, and the expression of p53, p16 and COX-2 was assayed by immunohistochemistry to consecutive formalin-fixed tissue microarray sections. RESULTS: The expression of p53, p16 and COX-2 was significantly higher in tumorous tissues than in non-tumorons ones. A significant relationship was observed between p53 and COX-2, or p16 and COX-2. But no obvious correlation was seen between p53 and p16 expressions. Logistic regression analysis showed p53 and COX-2 as dependent predictors in pancreatic carcinogenesis, and a reciprocal relationship to neoplastic progression between p53 and COX-2. CONCLUSION: Combination analysis of p53 and COX-2 may be useful in predicting pancreatic carcinogenesis.

Analysis of gene expression profiles in pancreatic carcinoma by using cDNA microarray

OBJECTIVES: To survey the gene expression profiles in pancreatic carcinoma by using cDNA microarray and detect target genes for further study. METHODS: Three mixed samples from 2 cases of normal pancreatic tissue and 4 cases of moderate-differentiated pancreatic carcinoma were studied by means of cDNA microarray consisting of 18 000 genes. RESULTS: 1484 and 1353 different expressed genes were observed in two cancer samples respectively. We identified 455 genes altered with the same tendency in both samples, including 102 up-regulated and 353 down-regulated genes. There were 274 known genes and 181 unknown genes; 27.8% and 52.0% genes respectively had an expression level in cancer that was 2-fold higher or lower than that in normal samples. Tumor suppressor genes, growth factors and receptor genes, signal conduction genes, transcription factor genes were identified. CONCLUSIONS: cDNA microarray is an efficient and high-throughout method to investigate gene expression profiles in pancreatic carcinoma. MBD1, EDG1 and gene hypermethylation mechanism would play an important role in the pathogenesis of pancreatic carcinoma.

Detection of Genetically Modified Crops by Combination of Multiplex PCR and Low-density DNA Microarray

Objective To develop a technique for simultaneous detection of various target genes in Roundup Ready soybean by combining multiplex PCR and low-density DNA microarray. Methods Two sets of the multiplex PCR system were used to amplify the target genes in genetically modified （GM） soybean. Seventeen capture probes （PCR products） and 17 pairs of corresponding primers were designed according to the genetic characteristics of Rroundup Ready soybean （GTS40-3-2）, maize （MonS10, Nk603, GA21）, canola （T45, MS1/RF1）, and rice （SCK） in many identified GM crops. All of the probes were categorized and identified as species-specific probes. One negative probe and one positive control probe were used to assess the efficiency of all reactions, and therefore eliminate any false positive and negative results. After multiplex PCR reaction, amplicons were adulterated with Cy5-dUTP and hybridized with DNA microarray. The array was then scanned to display the specific hybridization signals of target genes. The assay was applied to the analysis of sample of certified transgenic soybean （Roundup Ready GTS40-3-2） and canola （MS1/RF1）. Results A combination technique of multiplex PCR and DNA microarray was successfully developed to identify multi-target genes in Roundup Ready soybean and MS 1/RF1 canola with a great specificity and reliability. Reliable identification of genetic characteristics of Roundup Ready of GM soybean from genetically modified crops was achieved at 0.5% transgenic events, indicating a high sensitivity. Conclusion A combination technique of multiplex PCR and low-density DNA microarray can reliably detect and identify the genetically modified crops.

Rapid Detection of rpoB Gene Mutations in Rif-resistant M.tuberculosis Isolates by Oligonucleotide Microarray

Objective To detect the specific mutations in rpoB gene of Mycobacterium tuberculosis by oligonucleotide microarray. Methods Four wild-type and 8 mutant probes were used to detect rifampin resistant strains. Target DNA of M. tuberculosis was amplified by PCR, hybridized and scanned. Direct sequencing was performed to verify the results of oligonucleotide microarray Results Of the 102 rifampin-resistant strains 98 （96.1%） had mutations in the rpoB genes. Conclusion Oligonucleotide microarray with mutation-specific probes is a reliable and useful tool for the rapid and accurate diagnosis of rifampin resistance in M. tuberculosis isolates.

抑制性消减杂交技术结合cDNA MICROARRAY技术在中国明对虾WSSV感染后差异表达基因研究上的应用

以中国明对虾WSSV感染6h的头胸部组织为实验材料,提取总RNA分别进行正反向抑制性PCRcDNA消减杂交,消减杂交后的PCR产物经纯化并克隆到T载体,进而转化成正反向消减文库。消减文库库容分别为:正向库,3.7×104;反向库,1.2×104。利用消减文库的克隆构建了cDNA表达谱芯片,共有1536个靶点,其中正、反向文库各768个。使用该cDNA芯片对WSSV感染后6h的对虾组织进行了表达谱分析,对其中80个出现明显表达调控变化的阳性克隆进行了测序。结果显示,在WSSV感染后6h,病毒基因开始大量表达,而宿主糖酵解,嘌呤、嘧啶代谢以及精氨酸代谢等代谢途径的关键基因出现明显下调。这表明病毒已在宿主体内大批量复制并开始抑制宿主代谢。病毒上调表达的WSV482可能与病毒毒力的增强有关,而宿主蛋白的管家基因如Actin,EFα的下调表达提示:在利用基因表达技术研究WSSV病毒的实验中,管家基因的选择要十分慎重。此外,根据作者已有的研究结果,TPI基因是比较好的候选管家基因。而WSV414、WSV215和WSV482是对WSSV进行RNA干涉实验较好的候选靶标基因。

Subtype Identification of Avian Influenza Virus on DNA Microarray

We have developed a rapid microarray-based assay for the reliable detection of H5, H7 and H9 subtypes of avian influenza virus （AIV）. The strains used in the experiment were A/Goose/Guangdong/1/96 （H5N1）, A/African starling/983/79 （H7N1） and A/Turkey/Wiscosin/1/66 （H9N2）. The capture DNAs clones which encoding approximate 500-bp avian influenza virus gene fragments obtained by RT-PCR, were spotted on a slide-bound microarray. Cy5-labeled fluorescent cDNAs, which generated from virus RNA during reverse transcription were hybridized to these capture DNAs. These capture DNAs contained multiple fragments of the hemagglutinin and matrix protein genes of AIV respectively, for subtyping and typing AIV. The arrays were scanned to determine the probe binding sites. The hybridization pattern agreed approximately with the known grid location of each target. The results show that DNA microarray technology provides a useful diagnostic method for AIV.

Study on The Method of Quantitative Analysis of Serum Ferritin and Soluble Transferrin Receptor with Protein Microarray Technology

Objective To establish and evaluate a protein serum ferritin （SF） and soluble transferrin receptor microarray method for combined measurement of （sTfR）. Methods Microarrayer was used to print both anti-SF antibodies I and anti-sTfR antibodies I on each protein microarray. Anti-SF antibodies II and anti-sTfR antibodies II were used as detection antibodies and goat antibodies coupled to Cy3 were used as antibodies Ill. The detection conditions of the quantitative analysis method for simultaneous measurement of SF and sTfR with protein microarray were optimized and evaluated. The protein microarray was compared with commercially available traditional tests with 26 serum samples. Results By comparison experiment, mouse monoclonal antibodies were chosen as the probes and contact printing was chosen as the printing method. The concentrations of SF and sTfR probes were 0.5 mg/mL and 0.5 mg/mL respectively, while those of SF and sTfR detection antibodies were 5 μg/mL and 0.36 μg/mL respectively. Intra- and inter-assay variability was between 3.26% and 18.38% for all tests. The regression coefficients comparing protein microarray with traditional test assays were better than 0.81 for SF and sTfR. Conclusion The present study has established a protein microarray method for combined measurement of SF and sTfR.

EXPRESSION OF SURVIVIN,PTEN AND BFGF IN LUNG CANCER PROGRESSION TISSUE MICROARRAY

To investigate the expressions of survivin, PTEN and bFGF in lung cancer and precancerous lesion by tissue microarray technology. Methods: The expressions of Survivin, PTEN and bFGF were detected in 89 primary lung cancers, 12 lung cancers with lymph node metastasis, 12 precancerous lesions of lung by an immunohistochemical method, and 10 normal lung tissues were used as controls. Results: The expression of Survivin and bFGF protein were 57.3% and 66.3% in 89 primary lung cancer respectively, significantly higher than the control group (P<0.05). The positive ratio of PTEN was 42.7% in primary lung cancer, significantly lower than that of nornmal tissue (90.0%)(P<0.05). The expressions of Survivin and bFGF were significantly related to lymph node metastasis and clinical stages. The expression of PTEN was related to differentiations, lymph node metastasis and clinical stages (P<0.05). There was a negative correlation between expressions of Survivin and PTEN, a positive correlation between expressions of Survivin and bGFG (P<0.01). Conclusion: Survivin, PTEN and bFGF proteins may be related to the pathogenesis, progression and malignant behavious of lung cancer, and there are some relationships between expressions of Survivin, PTEN and bFGF. Survivin, PTEN and bFGF may play a role in prognosis assessment of lung cancer.