Prospects of DNA microarray application in management of chronic obstructive pulmonary disease:A systematic review

Chronic obstructive pulmonary disease(COPD)is incurable chronic disease which kills 3.3 million each year worldwide.Number of global cases of COPD is steadily rising alongside with life expectancy,disproportionally hitting middle-income countries like Russia and China,in such conditions,new approaches to the COPD management are desperately needed.DNA microarray technology is a powerful genomic tool that has the potential to uncover underlying COPD biological alteration and brings up revolutionized treatment option to clinicians.We executed systematic review studies of studies published in last 10 years regarding DNA microarray application in COPD management,with complacence to PRISMA criteria and using PubMed and Medline data bases as data source.Out of 920 identified papers,39 were included in the final analysis.We concluded that Genome-wide expression profiling using DNA microarray technology has great potential in enhancing COPD management.Current studied proofed this method is reliable and possesses many potential applications such as individual at risk of COPD development recognition,early diagnosis of disease,COPD phenotype identification,exacerbation prediction,personalized treatment optioning and prospect of oncogenesis evaluation in patients with COPD.Despite all the proofed benefits of this technology,researchers are still in the early stage of exploring it’s potential.Therefore,large clinical trials are still needed to set up standard for DNA microarray techniques usage implementation in COPD management guidelines,subsequently giving opportunity to clinicians for controlling or even eliminating COPD entirely.

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.

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.

Polyurethane Molecular Stamps for the in situ Synthesis of DNA Microarray

Fabrication of polyurethane molecular stamps (PU stamps) based on polypropylene glycol (PPG) and toluene diisocyanate (TDI), using 3, 3-dichloro-4, 4-methylenedianiline (MOCA) as the crosslinker, is reported. It was shown from the contact angle measurement that PU stamps surface has good affinity with acetonitrile, guaranteeing the well distribution of DNA monomers on patterned stamps. Laser confocal fluorescence microscopy images of oligonucleotide arrays after hybridization confirmed polyurethane is an excellent material for molecular stamps when transferring polar chemicals and conducting reactions on interfaces by stamping.

Characterization of the genes involved in nitrogen cycling in wastewater treatment plants using DNA microarray and most probable number-PCR

To improve nitrogen removal performance of wastewater treatment plants （WWTPs）, it is essential to understand the behavior of nitrogen cycling communities, which comprise various microorganisms. This study characterized the quantity and diversity of nitrogen cycling genes in various processes of municipal WWTPs by employing two molecular-based methods：most probable number-polymerase chain reaction （MPN-PCR） and DNA microarray. MPN-PCR analysis revealed that gene quantities were not statistically different among processes, suggesting that conventional actwated sludge processes （CAS） are similar to nitrogen removal processes in their ability to retain an adequate population of nitrogen cycling microorganisms. Furthermore, most processes in the WWTPs that were researched shared a pattern：the nitS and the bacterial amoA genes were more abundant than the nirK and archaeal amoA genes, respectivelv. DNA microarray analysis revealed that several kinds of nitrification and denitrification genes were detected in both CAS and anaerobic-oxic processes （AO）, whereas limited genes were detected in nitrogen removal processes. Results of this study suggest that CAS maintains a diverse community of nitrogen cycling microorganisms; moreover, the microbial communities in nitrogen removal processes may be specific.

DNA microarray technology and its application in fish biology and aquaculture

Fishery is an important industry in China as well as in the rest of the world,and it provides a human food resource containing high-quality protein.Best practice in aquaculture requires a full understanding of the genomic controls and transcriptional profiles of cultured fish species.Improvements in aquaculture can be made by regulation of the expression of functional genes.Microarray technology is a powerful tool for rapid screening of genes or transcriptional profiles in a particular fish or for a particular economic character;for example,genes that are related to growth and disease control in the fish.This review provides a brief introduction to microarray technology and its methods and applications,together with a discussion of the achievements in fish biology that have resulted from this technology.

Expression of a novel bHLH-Zip gene in human testis

<abstract>Aim: To identify specifically expressed genes in the adult and fetal testes. Methods: A human testis cDNA microarray was established. Then the mRNA of adult and fetal testis was purified and probes were prepared by a reverse transcription reaction with the testis mRNA as template. The microarray was hybridized with probes of adult and fetal testes. The nucleic sequences of differentially expressed genes were determined and homologies were searched in the databases of the GenBank. Results: When hybridized with adult or fetal testis probes, the positive clones were 96.8 % and 95.4 %, respectively. Among these genes, one was a new testis-specific gene, which was named TSP1. TSP1 was highly expressed in human adult testis. The cDNA of TSP1 was 1,484 bp in length. The cDNA sequence of this clone was deposited in the Genbank (AF333098). TSP1 was also determined as Interim Gen Symbol (Unigene, No. Hs.98266). Protein analysis showed that TSP1 contained two functional domains: an N-terminal basic helix-loop-helix (bHLH) and a C-terminal leucine zipper (Zip). Homologous analysis showed that the 430 amino acid sequences deduced from the 1,293 bp open reading frame (ORF) had a homology with the human gene FLJ2509 (AK098575). TSP1 had also a sequence homology with Spz 1 protein of mouse. Expression profiles showed that TSP1 was specifically and strongly expressed in the testis. Conclusion: TSP1 is a gene highly expressed in adult testis. It may play an important role in spermatogenesis in the humans.

Analysis of Gene Expression Pattern of Lumbar Intervertebral Disc Degeneration in Human

ObjectiveTo investigate the gene expression changes in normal and degeneration lumbar intervertebral disc in humans, providing information for clinical. MethodsThe PCR products of 4096 human genes were spotted onto a kind of chemical-material-coated-glass slides. The total RNAs were isolated from the tissues. Both the mRNAs from the degeneration and normal lumbar intervertebral disc in humans were reversely transcribed to the cDNAs, which used as the hybridization probes with the incorporations of fluorescent dUTP. The mixed probes were then hybridized to the cDNA microarray. After high-stringent washing, the cDNA microarray was scanned for the fluorescent signals and analyzed with computer image analysis. ResultsAmong the 4096 targets, there were 706 genes whose expression levels differed between the degeneration and normal lumbar intervertebral disc in all cases, comprising 298 up-regulated and 358 down-regulated ones. ConclusionDNA microarray technology is an effective technique in screening for differently expressed genes between the degeneration and normal lumbar intervertebral disc. Cell apoptosis plays an important role in the process of lumbar intervertebral disc degeneration.

Chronic hepatitis B liver disease in patients living in the Amazon region: S gene mutations and genotypes characterization

The Amazon region is considered to be a high endemic area for Hepatitis B Virus (HBV) infections, Rond&ocirc;nia state having the highest prevalence. The aim of this study was to identify molecular genotypes and mutations in the S gene region of HBV viral genomes from 20 patients using a DNA microarray. Results: Serological tests showed that 88% of patients were HBeAg negative, 82% had anti-HBe antibodies and 33% were co-infected with Hepatitis Delta Virus. Sixteen percent of the patients were considered cirrhotic, and 11% have been transfused. The microarray technique identified the genotypes A (4 patients), D (7 patients) and F (7 patients) in 18 samples. Mutations were detected in all 3 genotypes and, overall, A159G, which has been associated with a reduced antigenicity of the virus, was detected most frequently. In genotype A, G119E was the most frequently detected mutation followed by mutations A159G, F134Y, W172C, Y161F and T143S. A159G was detected in all genotype D and F samples followed by mutations T143S, Y161F, N131T, T114S and G119E in genotype D and mutations T143S, Y161F, N131T, T114S and G119E in genotype F. Conclusion: The analysis of mutations repartition among genotypes suggests that some of them are preferentially or exclusively associated with genotype A, D or F. This type of tool is adapted for clinical and therapy monitoring of patient as well as for molecular epidemiology research on HBV.

Retinoic acid induction of genes associated with neural tube developmental defects

To date, little information has been available regarding genes involved in the regulation of embryonic cell development, which participate in retinoic acid-induced neural tube defects in mice. Previous studies have revealed seven differentially expressed genes involved in neural tube developmental defects. However, gene expression and regulation is a complex process. Therefore, gene expression differences between normal and defective neural tubes at 9.5 and 10.5 days were compared. A total of eight differentially expressed genes exhibited coincident alterations at embryonic 9.5 and 10.5 days. In mice with retinoic acid-induced neural tube defects, NeK7, IGFBP5 ZW10, Csf3r, PSMC6, Cdk5, and Rbl expressions were downregulated, but Apoa-4 expression was upregulated. These results were confirmed by Northern blot hybridization. Results suggested that NeK7, IGFBP5, ZW10, Csf3r, PSMC6, Cdk5, Rb1, and Apoa-4 are important regulatory factors involved in neural tube defects.

A novel strategy for in situ maskless synthesis of biochips:Self-driving micro-fluid porous type printing (SMPTP)

A novel maskless technique, self-driving micro-fluid porous type printing （SMPTP）, was reported to in situ synthesize oligonucleotide arrays on glass slide, which has the merits of low cost, high quality and simple craft. In SMPTP for fabricating gene- chips, porous fiber tubes with a number of nanometric or micron channels functioned as ＂active letters＂ and were assembled in designed patterns, which are identical to the distribution of monomers in each layer of the array, and four patterns were needed for each layer. By means of capillarity, the synthesis solution was automatically taken into porous tubes assembled in a printing plate and reached the surface. An oligonucleotide array of 160 features with four different 15-mer probes was in situ synthesized using this technique. The four specific oligonucleotide probes, including the matched and the mismatched by the fluorescent target sequence, gave obviously different hybridization fluorescent signals.

A New Optimized Wrapper Gene Selection Method for Breast Cancer Prediction

Machine-learning algorithms have been widely used in breast cancer diagnosis to help pathologists and physicians in the decision-making process.However,the high dimensionality of genetic data makes the classification process a challenging task.In this paper,we propose a new optimized wrapper gene selection method that is based on a nature-inspired algorithm(simulated annealing(SA)),which will help select the most informative genes for breast cancer prediction.These optimal genes will then be used to train the classifier to improve its accuracy and efficiency.Three supervised machine-learning algorithms,namely,the support vector machine,the decision tree,and the random forest were used to create the classifier models that will help to predict breast cancer.Two different experiments were conducted using three datasets:Gene expression(GE),deoxyribonucleic acid(DNA)methylation,and a combination of the two.Six measures were used to evaluate the performance of the proposed algorithm,which include the following:Accuracy,precision,recall,specificity,area under the curve(AUC),and execution time.The effectiveness of the proposed classifiers was evaluated through comprehensive experiments.The results demonstrated that our approach outperformed the conventional classifiers as expected in terms of accuracy and execution time.High accuracy values of 99.77%,99.45%,and 99.45%have been achieved by SA-SVM for GE,DNA methylation,and the combined datasets,respectively.The execution time of the proposed approach was significantly reduced,in comparison to that of the traditional classifiers and the best execution time has been reached by SA-SVM,which was 0.02,0.03,and 0.02 on GE,DNA methylation,and the combined datasets respectively.In regard to precision and specificity,SA-RF obtained the best result of 100 on GE dataset.While SA-SVM attained the best recall result of 100 on GE dataset.

Expression Profile of a Novel Germ Cell-specific Gene,TSCPA,in Mice and Human

In order to identify novel genes involved in spermatogenesis, testis cDNA samples from Balb/C mice of different postnatal days were hybridized with the whole mouse genome Affymetrix chip to screen the testis-specific genes. The characteristics of the selected genes were analyzed by RT-PCR as well as other bioinformatic tools. A novel differentially expressed testis-specific gene （GenBank Accession No： NM_029042） in the developmental stages of testes was identified, and named TSCPA. Cellular mapping prediction of TSCPA indicated that its protein was probably expressed in nuclei, and one putative domain （aa 332 377） was anchoring domain of cAMP-dependent type Ⅱ PK. The result of subcellular localization of GFP-TSCPA fusion protein in Cos-7 cells showed that TSCPA protein was expressed in nuclei. RT-PCR analysis revealed that TSCPA was expressed specifically in mouse and human testis. TSCPA gene was expressed weakly in 21-day-old mouse testis and the expression was increased gradually from 38th day to 6th month of mouse testes. No expression of hTSCPA was found in cryptorchidism and Sertoli-cell-only syndrome patients. It was concluded that the expression profile of TSCPA in human and mice indicated that TSCPA might play an important role in spermatogenesis.

Computational Analysis Reveals MicroRNA-mRNA Regulatory Network in Esophageal Squamous Cell Carcinoma

Micro RNAs（mi RNAs） are known to regulate post-transcriptional gene expression.They are involved in carcinogenesis and tumor progression.The aim of this study was to explore the micro RNA-m RNA regulatory network in esophageal squamous cell carcinoma（ESCC） using comprehensive computational approaches.In this study we have selected a total of 11 mi RNAs from one previously reported study in ESCC.The m RNA targets of these mi RNAs were predicted using various algorithms.The expression profiles of these m RNA targets were identified on DNA microarray experiment dataset across ESCC tissue samples.Based on the mi RNA-m RNA regulatory relationships,the network was inferred.A total of 23 mi RNA-m RNA regulatory interactions,with 11 mi RNAs and 13 m RNA targets,were inferred in ESCC.The mi RNA-m RNA regulatory network with increased confidence provides insights into the progression of ESCC and may serve as a biomarker for prognosis or the aggressiveness of ESCC.However,the results should be examined with further experimental validation.

Gene expression profiles in the peri-infarct brain cortex in a rat model of stroke-prone renovascular hypertension

BACKGROUND： Previous studies have focused on gene expression acutely following stroke onset. However, there have been a few reports of gene expression during later stages of cerebral infarction. OBJECTIVE： To determine gene expression profiling in the peri-infarct brain cortex 7 days after ischemia in a rat model of cerebral infarction in renovascular hypertensive rats. DESIGN, TIME AND SETTING： An in vivo, molecular experiment was performed at the Experimental Animal Center of Sun Yat-sen University and CapitalBio, Beijing, China between February 2004 and August 2005. MATERIALS： A 70-mer oligo chip containing 5 705 rat genes was supplied by CapitalBio, Beijing, China; and the Oligo rat gene bank was provided by Qiagen, the Netherlands. METHODS： Six Sprague Dawiey rats were utilized to establish a stroke-prone renovascular hypertensive model using the two-kidney and two-clip method. The rats were subsequently randomly assigned to two groups： middle cerebral artery occlusion and sham-operation, with three rats in each group. The middle cerebral artery occlusion model was induced by intraluminal suture method. Incisions were sutured following isolation of carotid arteries in the sham-operation group. MAIN OUTCOME MEASURES： Total RNA was extracted from the peri-infarct cerebral cortex 7 days after surgery. Following fluorescent labeling, RNA was hybridized to an Oligo chip containing 5 705 genes and was then scanned. Images were collected and the differentially expressed genes （number and category） were selected by data analysis. RESULTS： A total of 174 genes were upregulated, and 23 were downregulated, in the peri-infarct cerebral cortex 7 days after ischemia. The upregulated genes were distributed among 12 functional categories, and the downregulated genes belonged to categories of transport, transcription regulators, signals, response to stress, metabolism, and cell adhesion. The expression of some cytoskeletal genes was upregulated, including VIM, A2M, B2M, ACTR3, and ARPClB. Expression of a few cell adhesion-related genes （such as NLGN1, LGALS1, LGALS3, COLIA1, COL2A1, and SPP1） and other inflammation-related genes （such as CIQB, ClS, C4, C5R1, CFH, CD14, CD164, CD47, CD48, CD53, CD8B, IFNGR, and TFITM2） were upregulated. The glutamate-receptor gene GRIK5 was downregulated, which is related to the excitatory neurotransmitter glutamate. However, expression of the inhibitory neurotransmitter GABA-related genes was bidirectional - namely, GABRA5 downregulation and GABARAP upregulation. CONCLUSION： Upregulation of many cell adhesion and inflammation related genes and downregulation of excitatory glutamate-related receptor genes revealed active gene expression during later stages of cerebral infarction, which suggested molecular mechanisms of injury or repair.

Characteristics of mRNA dynamic expression related to spinal cord ischemia/reperfusion injury:a transcriptomics study

Following spinal cord ischemia/reperfusion injury,an endogenous damage system is immediately activated and participates in a cascade reaction.It is difficult to interpret dynamic changes in these pathways,but the examination of the transcriptome may provide some information.The transcriptome reflects highly dynamic genomic and genetic information and can be seen as a precursor for the proteome.We used DNA microarrays to measure the expression levels of dynamic evolution-related m RNA after spinal cord ischemia/reperfusion injury in rats.The abdominal aorta was blocked with a vascular clamp for 90 minutes and underwent reperfusion for 24 and 48 hours.The simple ischemia group and sham group served as controls.After rats had regained consciousness,hindlimbs showed varying degrees of functional impairment,and gradually improved with prolonged reperfusion in spinal cord ischemia/reperfusion injury groups.Hematoxylin-eosin staining demonstrated that neuronal injury and tissue edema were most severe in the 24-hour reperfusion group,and mitigated in the 48-hour reperfusion group.There were 8,242 differentially expressed m RNAs obtained by Multi-Class Dif in the simple ischemia group,24-hour and 48-hour reperfusion groups.Sixteen m RNA dynamic expression patterns were obtained by Serial Test Cluster.Of them,five patterns were significant.In the No.28 pattern,all differential genes were detected in the 24-hour reperfusion group,and their expressions showed a trend in up-regulation.No.11 pattern showed a decreasing trend in m RNA whereas No.40 pattern showed an increasing trend in m RNA from ischemia to 48 hours of reperfusion,and peaked at 48 hours.In the No.25 and No.27 patterns,differential expression appeared only in the 24-hour and 48-hour reperfusion groups.Among the five m RNA dynamic expression patterns,No.11 and No.40 patterns could distinguish normal spinal cord from pathological tissue.No.25 and No.27 patterns could distinguish simple ischemia from ischemia/reperfusion.No.28 pattern could analyze the need for inducing reperfusion injury.The study of specific pathways and functions for different dynamic patterns can provide a theoretical basis for clinical differential diagnosis and treatment of spinal cord ischemia/reperfusion injury.

Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes

With defined culture protocol, human embryonic stem cells （hESCs） are able to generate cardiomyocytes in vitro, therefore providing a great model for human heart development, and holding great potential for car- diac disease therapies. In this study, we successfully generated a highly pure population of human cardio- myocytes （hCMs） （〉95% cTnT＋） from hESC line, which enabled us to identify and characterize an hCM-specific signature, at both the gene expression and DNA meth- ylation levels. Gene functional association network and gene-disease network analyses of these hCM-enriched genes provide new insights into the mechanisms of hCM transcriptional regulation, and stand as an informative and rich resource for investigating cardiac gene func- tions and disease mechanisms. Moreover, we show that cardiac-structural genes and cardiac-transcription fac- tors have distinct epigenetic mechanisms to regulate their gene expression, providing a better understandingof how the epigenetic machinery coordinates to regulate gene expression in different cell types.

水稻白叶枯病菌在寄主体内外不同生长条件下致病基因差异表达的分析

To demonstrate the expression profiling of Xanthomonas oryzae pv.oryzae(Xoo) in vitro and in planta,DNA microarrays of 371 genes potentially associated with pathogenicity and virulence were used to compare the transcriptional level alteration of the wild-type strain PXO99A and gene deletion mutants ΔgacAxoo and ΔfleQxoo of Xoo grown in the rich medium NBY vs.hrp-inducing minimal medium XOM2 or leaf tissues of rice.Results indicated that 17 and 38 genes of PXO99A were differentially expressed in XOM2 and the leaf tissues of rice relative to NBY,respectively.Twenty-eight genes of ΔgacAxoo grown in XOM2 and 12 genes of ΔfleQxoo in NBY were differentially expressed relative to PXO99A.The identification of differentially-expressed genes,GacAxoo-and FleQxoo-regulons and novel candidate genes of Xoo strains would provide us the target genes for further functional analysis in pathogenesis of Xoo.

Gene Expression Profiling of Human Epidermal Keratinocytes in Simulated Microgravity and Recovery Cultures

Simulated microgravity （SMG） bioreactors and DNA microarray technology are powerful tools to identify ＂space genes＂ that play key roles in cellular response to microgravity. We applied these biotechnology tools to investigate SMG and post-SMG recovery effects on human epidermal keratinocytes by exposing cells to SMG for 3, 4, 9, and 10 d using the high aspect ratio vessel bioreactor followed by recovery culturing for 15, 50, and 60 d in normal gravity. As a result, we identified 162 differentially expressed genes, 32 of which were ＂center genes＂ that were most consistently affected in the time course experiments. Eleven of the center genes were from the integrated stress response pathways and were coordinately downregulated. Another seven of the center genes, which are all metallothionein MT-Ⅰ and MT-Ⅱ isoforms, were coordinately up-regulated. In addition, HLA-G, a key gene in cellular immune response suppression, was found to be significantly upregulated during the recovery phase. Overall, more than 80% of the differentially expressed genes from the shorter exposures （≤4 d） recovered in 15 d; for longer （≥9 d） exposures, more than 50 d were needed to recover to the impact level of shorter exposures. The data indicated that shorter SMG exposure duration would lead to quicker and more complete recovery from the microgravity effect.