Bioinformatics analyses of differentially expressed genes associated with spinal cord injury:a microarray-based analysis in a mouse model

Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new opportunity for investigating diagnosis,treatment,and prognosis of spinal cord injury.However,differentially expressed genes are not consistent among studies,and many key genes and signaling pathways have not yet been accurately studied.GSE5296 was retrieved from the Gene Expression Omnibus DataSet.Differentially expressed genes were obtained using R/Bioconductor software(expression changed at least two-fold;P < 0.05).Database for Annotation,Visualization and Integrated Discovery was used for functional annotation of differentially expressed genes and Animal Transcription Factor Database for predicting potential transcription factors.The resulting transcription regulatory protein interaction network was mapped to screen representative genes and investigate their diagnostic and therapeutic value for disease.In total,this study identified 109 genes that were upregulated and 30 that were downregulated at 0.5,4,and 24 hours,and 3,7,and 28 days after spinal cord injury.The number of downregulated genes was smaller than the number of upregulated genes at each time point.Database for Annotation,Visualization and Integrated Discovery analysis found that many inflammation-related pathways were upregulated in injured spinal cord.Additionally,expression levels of these inflammation-related genes were maintained for at least 28 days.Moreover,399 regulation modes and 77 nodes were shown in the protein-protein interaction network of upregulated differentially expressed genes.Among the 10 upregulated differentially expressed genes with the highest degrees of distribution,six genes were transcription factors.Among these transcription factors,ATF3 showed the greatest change.ATF3 was upregulated within 30 minutes,and its expression levels remained high at28 days after spinal cord injury.These key genes screened by bioinformatics tools can be used as biological markers to diagnose diseases and provide a reference for identifying therapeutic targets.

Protein microarray analysis of cytokine expression changes in distal stumps after sciatic nerve transection

A large number of chemokines,cytokines,other trophic factors and the extracellular matrix molecules form a favorable microenvironment for peripheral nerve regeneration.This microenvironment is one of the major factors for regenerative success.Therefore,it is important to investigate the key molecules and regulators affecting nerve regeneration after peripheral nerve injury.However,the identities of specific cytokines at various time points after sciatic nerve injury have not been determined.The study was performed by transecting the sciatic nerve to establish a model of peripheral nerve injury and to analyze,by protein microarray,the expression of different cytokines in the distal nerve after injury.Results showed a large number of cytokines were up-regulated at different time points post injury and several cytokines,e.g.,ciliary neurotrophic factor,were downregulated.The construction of a protein-protein interaction network was used to screen how the proteins interacted with differentially expressed cytokines.Kyoto Encyclopedia of Genes and Genomes pathway and Gene ontology analyses indicated that the differentially expressed cytokines were significantly associated with chemokine signaling pathways,Janus kinase/signal transducers and activators of transcription,phosphoinositide 3-kinase/protein kinase B,and notch signaling pathway.The cytokines involved in inflammation,immune response and cell chemotaxis were up-regulated initially and the cytokines involved in neuronal apoptotic processes,cell-cell adhesion,and cell proliferation were up-regulated at 28 days after injury.Western blot analysis showed that the expression and changes of hepatocyte growth factor,glial cell line-derived neurotrophic factor and ciliary neurotrophic factor were consistent with the results of protein microarray analysis.The results provide a comprehensive understanding of changes in cytokine expression and changes in these cytokines and classical signaling pathways and biological functions during Wallerian degeneration,as well as a basis for potential treatments of peripheral nerve injury.The study was approved by the Institutional Animal Care and Use Committee of the Chinese PLA General Hospital,China(approval number:2016-x9-07)in September 2016.

Comparative study of microarray and experimental data on Schwann cells in peripheral nerve degeneration and regeneration: big data analysis

A Schwann cell has regenerative capabilities and is an important cell in the peripheral nervous system.This microarray study is part of a bioinformatics study that focuses mainly on Schwann cells. Microarray data provide information on differences between microarray-based and experiment-based gene expression analyses. According to microarray data, several genes exhibit increased expression(fold change) but they are weakly expressed in experimental studies(based on morphology, protein and mRNA levels). In contrast, some genes are weakly expressed in microarray data and highly expressed in experimental studies;such genes may represent future target genes in Schwann cell studies. These studies allow us to learn about additional genes that could be used to achieve targeted results from experimental studies. In the current big data study by retrieving more than 5000 scientific articles from PubMed or NCBI, Google Scholar, and Google, 1016(up-and downregulated) genes were determined to be related to Schwann cells. However,no experiment was performed in the laboratory; rather, the present study is part of a big data analysis. Our study will contribute to our understanding of Schwann cell biology by aiding in the identification of genes.Based on a comparative analysis of all microarray data, we conclude that the microarray could be a good tool for predicting the expression and intensity of different genes of interest in actual experiments.

HER2 in gastric cancer: Comparative analysis of three different antibodies using whole-tissue sections and tissue microarrays

AIM:To compare the performance of three commercially available anti-human epidermalgrowth factor receptor 2(HER2)antibodies in whole-tissue sections and tissue microarrays(TMAs)of a series of gastric tumors.METHODS:We present a comparative analysis of three anti-HER2 antibodies(HercepTest,4B5 and SP3)using TMA and whole-tissue sections prepared from the same paraffin blocks of 199 gastric adenocarcinomas operated upon between January 2004 and December2008 at a Brazilian cancer hospital.The data on the patients’age,sex,the anatomical location of the tumor and the Lauren’s histological classification were collected from clinical and pathological records.The immunohistochemical(IHC)results were examined by two pathologists and the cases were classified as positive(3+),equivocal(2+)and negative(0 or 1+),according to the criteria of the IHC scoring system of gastric cancer.TMAs and whole-tissue sections were evaluated separately and independently.All cases yielding discordant IHC results and/or scored as 2+were subjected to dual-color in situ hybridization in order to determine the final HER2 status.Besides determining the sensitivity and predictive value for HER2-positive status,we measured the accuracy of each antibody by calculating the area under the receiver operating characteristic(ROC)curve.The agreement between the results obtained using the TMAs and those obtained using the whole-tissue sections was assessed by means of Kappa coefficient.RESULTS:Intratumoral heterogeneity of HER2 expression was observed with all antibodies.HER2-positive expression(3+)in the whole-tissue sections was observed in 23 cases(11.6%)using the 4B5 antibody,in 18 cases(9.1%)using the SP3 antibody and in 10 cases(5.1%)using the HercepTest antibody.In the TMAs,11 positive cases(5.6%)were identified using SP3 antibody,9(4.6%)using the 4B5 antibody and 6(3%)using the HercepTest antibody.The sensitivity using whole-tissue sections and TMA,respectively,was 95.2%and 42.9%with 4B5,90.5%and 66.7%with SP3 and 47.6%and42.9%with HercepTest.The accuracy,calculated from the area under the ROC curve,using whole-tissue sections and TMA,respectively,was 0.91 and 0.79 by 4B5,0.86 and 0.80 by SP3 and 0.73 and 0.71 by HercepTest.The concordance of the results obtained using wholetissue sections and TMA was 97.4%(Kappa 0.75)using HercepTest,85.6%(Kappa 0.56)using SP3 and 84.1%(Kappa 0.38)using 4B5.CONCLUSION:The use of the 4B5 antibody on wholetissue sections was the most accurate IHC method for evaluating HER2 expression in gastric adenocarcinoma.

Microarray Analysis of Transcriptomic Response of <i>Escherichia coli</i>to Nonthermal Plasma-Treated PBS Solution

We developed a technique of generating nonthermal atmospheric plasma-activated solution that had broad-spectrum antibacterial properties. Plasma-activated phosphate-buffered saline (PBS) causes rapid inactivation of bacteria following generation of oxidative stress. However, dose optimization requires understanding of cellular mechanisms. The objective of this study was to explore genome-wise response to develop gene expression profile of Escherichia coli using DNA microarray following exposure to plasma-activated PBS solution. Upon exposure to plasma-treated PBS solution, E. coli cells had differentially expressed genes involved in oxidative stress, and cell envelope and membrane associated porin and transporters. The genes involved in house-keeping and metabolism, energy generation, motility and virulence were conversely downregulated. This is the first report which demonstrates a severe oxidative stress induced in E. coli cells in response to an exposure to nonequilibrium nonthermal dielectric-barrier discharge plasma-activated PBS solution, and the genes that are responsive to reactive oxygen species appeared to play a role in cellular stress. Such studies are important to identify targets of inactivation, and to understand plasma-treated solution and bacterial cell interactions.

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。

CGH-based microarray detection of cryptic and novel copy number alterations and balanced translocations in cytogenetically abnormal cases of b-cell all

Acute lymphoblastic leukemia (ALL) is the most common malignancy in children, with the majority of cases being of precursor B-cell phenoltype. Conventional cytogenetic analysis plays an important role in the diagnosis of B-cell ALL, identifying characteristic chromosomal abnormalities associated with a given prognosis therein facilitating optimized treatment. The more recent introduction of microarray technology to the analysis of B-cell ALL has afforded both higher resolution for the detection of known abnormalities and an ability to identify novel copy number abnormalities (CNAs) with potential clinical relevance. In the current study, microarray analysis was performed on 20 cytogenetically abnormal B-cell ALL cases (10 pediatric and 10 adult), while a novel microarray-based balanced-translocation detection methodology (translocation CGH or tCGH) was applied to that subset of cases with a known or suspected recurrent balanced translocation. Standard microarray analysis identified that CNAs was not detected by previous conventional cytogenetics in 75% (15/20) cases. tCGH identified 9/9 (100%) balanced translocations defining BCR/ABL1 (x4), ETV6/RUNX1 (x3), and MLL/AFF1 (x2) breakpoints with high resolution. The results illustrate the improved molecular detail afforded by these technologies and a comparison of translocation breakpoints, CNAs and patient age offers new insights into tumor biology with potential prognostic significance.

Expression profile of microRNAs in gastrointestinal stromal tumors revealed by high throughput quantitative RT-PCR microarray

AIM: To investigate the microRNA(miRNA) expression profile in gastrointestinal stromal tumor(GIST) tissues that could serve as a novel diagnostic biomarker for GIST detection.METHODS: We performed a quantitative real-time quantitative reverse transcriptase polymerase chain reaction assay to analyze the expression of 1888 miRNAs in a sample set that included 54 GIST tissue samples.RESULTS: We found that dysregulation of several miRNAs may be related to the malignant potential of GISTs. Six of these miRNAs, hsa-let-7c, miR-218,miR-488#, miR-4683, miR-34c-5p and miR-4773, were selected as the final list of biomarkers to separate the malignant GISTs(M group) from the benign GISTs(B group). In addition, MiR-29b-2#, hsa-let-7c, miR-891 b, miR-218, miR-204, miR-204-3p, miR-628-5p,miR-744, miR-29c#, miR-625 and miR-196 a were used to distinguish between the borderline(BO group) and M groups. There were 11 common miRNAs selected to separate the benign and borderline(BB) group from the M group, including hsa-let-7c, miR-218, miR-628-5p,miR-204-3p, miR-204, miR-891 b, miR-488#, miR-145,miR-891 a, miR-34c-5p and miR-196 a.CONCLUSION: The identified miRNAs appear tobe novel biomarkers to distinguish malignant from benign GISTs, which may be helpful to understand the mechanisms of GIST oncogenesis and progression,and to further elucidate the characteristics of GIST subtypes.

Multiplex planar microarrays for disease prognosis, diagnosis and theranosis

Advanced diagnostic methods and algorithms for immune disorders provide qualitative and quantitative multiplex measurement for pre-clinical prognostic and clinical diagnostic biomarkers specific for diseases.Choice of therapy is confirmed by modulating diagnostic efficacy of companion, theranotic drug concentrations.Assay methods identify, monitor and manage autoimmune diseases, or risk thereof, in subjects who have,or who are related to individuals with autoimmune disease. These same diagnostic protocols also integratequalitative and quantitative assay test protocol designs for responder patient assessment, risk analysis and management of disease when integrating multiplex planar microarray diagnostic tests, patient theranostic companion diagnostic methods and test panels for simultaneous assessment and management of dysimmune and inflammatory disorders, autoimmunity, allergy and cancer. Proprietary assay methods are provided to identify, monitor and manage dysimmune conditions, or risk thereof, in subjects with pathological alterations in the immune system, or who are related to individuals with these conditions. The protocols can be used for confirmatory testing of subjects who exhibit symptoms of dysimmunity, as well as subjects who are apparently healthy and do not exhibit symptoms of altered immune function. The protocols also provide for methods of determining whether a subject has, is at risk for, or is a candidate for disease therapy, guided by companion diagnosis and immunosuppressive therapy, as well as therapeutic drug monitoring and theranostic testing of disease biomarkers in response to immunoabsorption therapy. The multiplex test panels provide the components that are integral for performing the methods to recognized clinical standards.

The Role of Combined OSR and SDF Method for Pre-Processing of Microarray Data that Accounts for Effective Denoising and Quantification

Microarray data is inherently noisy due to the noise contaminated from various sources during the preparation of microarray slide and thus it greatly affects the accuracy of the gene expression. How to eliminate the effect of the noise constitutes a challenging problem in microarray analysis. Efficient denoising is often a necessary and the first step to be taken before the image data is analyzed to compensate for data corruption and for effective utilization for these data. Hence preprocessing of microarray image is an essential to eliminate the background noise in order to enhance the image quality and effective quantification. Existing denoising techniques based on transformed domain have been utilized for microarray noise reduction with their own limitations. The objective of this paper is to introduce novel preprocessing techniques such as optimized spatial resolution (OSR) and spatial domain filtering (SDF) for reduction of noise from microarray data and reduction of error during quantification process for estimating the microarray spots accurately to determine expression level of genes. Besides combined optimized spatial resolution and spatial filtering is proposed and found improved denoising of microarray data with effective quantification of spots. The proposed method has been validated in microarray images of gene expression profiles of Myeloid Leukemia using Stanford Microarray Database with various quality measures such as signal to noise ratio, peak signal to noise ratio, image fidelity, structural content, absolute average difference and correlation quality. It was observed by quantitative analysis that the proposed technique is more efficient for denoising the microarray image which enables to make it suitable for effective quantification.

Identification of Annexin A1 protein expression in human gastric adenocarcinoma using proteomics and tissue microarray

AIM:To study the differential expression of Annexin A1(ANXA1)protein in human gastric adenocarcinoma.This study was also designed to analyze the relationship between ANXA1 expression and the clinicopathological parameters of gastric carcinoma.METHODS:Purified gastric adenocarcinoma cells(GAC)and normal gastric epithelial cells(NGEC)were obtained from 15 patients with gastric cancer by laser capture microdissection.All of the peptide specimens were labeled as18O/16O after trypsin digestion.Differential protein expressions were quantitatively identified between GAC and NGEC by nanoliter-reverse-phase liquid chromatography-mass/mass spectrometry(nanoRPLC-MS/MS).The expressions of ANXA1 in GAC and NGEC were verified by western blot analysis.The tissue microarray containing the expressed ANXA1 in 75 pairs of gastric carcinoma and paracarcinoma specimens was detected by immunohistochemistry(IHC).The relationship between ANXA1 expression and clinicopathological parametes of gastric carcinoma was analyzed.RESULTS:A total of 78 differential proteins were identified.Western blotting revealed that ANXA1 expression was significantly upregulated in GAC(2.17/1,P<0.01).IHC results showed the correlations between ANXA1protein expression and the clinicopathological parameters,including invasive depth(T stage),lymph node metastasis(N stage),distant metastasis(M stage)and tumour-lymph node metastasis stage(P<0.01).However,the correlations between ANXA1 protein expression and the remaining clinicopathological parameters,including sex,age,histological differentiation and the size of tumour were not found(P>0.05).CONCLUSION:The upregulated ANXA1 expression may be associated with carcinogenesis,progression,invasion and metastasis of GAC.This protein could be considered as a biomarker of clinical prognostic prediction and targeted therapy of GAC.

MICROARRAYS AND THEIR POTENTIAL IN MEDICINE

Advancement in microarray technology can revolutionize many aspects of medicine. Microarrays have applications in gene expression profiling, genotyping, mutation analysis, gene identification, and pharmacology. This paper provides a brief review on the use of microarrays in studies of cancer, infectious diseases, chromosome disorders, neurological/mental disorders, and drugs, along with a prospect on its great potential in diagnosis, prognosis and the treatment of human diseases.

用DNA microarray快速检测淋球菌耐喹诺酮类药物基因突变

目的 研究 DNA m icroarray的制备及其检测淋球菌耐喹诺酮类药物基因突变的准确性。方法 根据淋球菌药敏及测序结果分别对淋球菌 gyr A和 par C基因的序列设计特异引物和探针并制作 DNA m icroarray。对淋球菌临床拭子进行 PCR扩增并荧光标记包含 gyr A和 par C基因的目的 DNA片段 ,与芯片杂交 ,同时以测序法进行双盲淋球菌耐喹诺酮类药物基因突变的检测。结果 87份泌尿生殖道试子全部可用 DNA m icroarray检测出来 ,芯片检测结果与药敏结果符合率为 10 0 % ,与测序结果符合率为 97.7%。结论 用 DNA microarray来检测淋球菌 gyr A和 par C基因突变快速、特异性高和灵敏度高 。

Use of blood-based biomarkers for early diagnosis and surveillance of colorectal cancer

Early screening for colorectal cancer(CRC) holds the key to combat and control the increasing global burden of CRC morbidity and mortality. However, the current available screening modalities are severely inadequate because of their high cost and cumbersome preparatory procedures that ultimately lead to a low participation rate. People simply do not like to have colonoscopies. It would be ideal, therefore, to develop an alternative modality based on blood biomarkers as the first line screening test. This will allow for the differentiation of the general population from high risk individuals. Colonoscopy would then become the secondary test, to further screen the high risk segment of the population. This will encourage participation and therefore help to reach the goal of early detection and thereby reduce the anticipated increasing global CRC incidence rate. A blood-based screening test is anappealing alternative as it is non-invasive and poses minimal risk to patients. It is easy to perform, can be repeated at shorter intervals, and therefore would likely lead to a much higher participation rate. This review surveys various blood-based test strategies currently under investigation, discusses the potency of what is available, and assesses how new technology may contribute to future test design.

Serum protein profile of yang-deficiency constitution in traditional Chinese medicine revealed by protein microarray analyses

Background:Based on the theory of traditional Chinese medicine (TCM) and preepidemiological investigation,Professor Qi Wang classified the entire human population into nine constitutions and put forward the theory of 'Nine-Constitution Medicine.' Among these constitutions,the main feature of the yang-deficiency constitution (YADC) is intolerance of the cold,which has been proven to reduce quality of life and confer susceptibility to specific diseases.Previous studies explored the genetic and transcriptional bases of YADC.In this experiment,we explored the potential mechanism of YADC using protein microarray,to deepen our understanding of its biological mechanism.Methods:Subjects identified with a YADC (n =12) or a balance constitution (BC;n =12) in accordance with the Classification and Determination Standards of Constitutions in Traditional Chinese Medicine were selected.Blood was collected to separate serum and protein microarray technology was used to analyze serum protein expression.Results:The clustering of subjects' constitutions based on protein expression profiling largely coincided with the TCM classification.Based on false discovery rate correction (P <.01) and fold change ≥ 5 or ≤ 0.2,a total of 85 proteins differentially expressed in YADC compared with their status in BC were selected,including 64 upregulated and 21 downregulated ones.Enrichment analysis suggested that subjects with YADC are susceptible to endocrine and energy metabolism disorders,as well as decline in immune function.Conclusion:This study revealed that YADC exhibits systematic differences in its protein expression profile.Moreover,we can potentially explain the characteristics of YADC partly via differentially expressed proteins.

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.

联合应用SSH和cDNA Microarray筛选肺癌相关基因

目的 利用抑制消减杂交 (suppressionsubtractivehybridization ,SSH)和cDNAMicroarray筛选肺癌组织、肺癌旁组织和其它肿瘤组织中相互差异表达的基因。方法 将利用SSH构建的BEP2D细胞永生化阶段、恶性转化前阶段和恶性转化阶段三个cDNA文库中的克隆制作在一张芯片上 ,筛选了 15例肺癌组织、5例肺癌旁组织和其他癌组织 2 4例 (肝癌、胃癌、食管癌、乳腺癌、白血病、子宫内膜癌、脑神经胶质瘤和结肠癌各 3例 )中mRNA的表达差异。结果 获得肺癌组织高于肺癌旁组织表达的cDNA 2 6个 ,肺癌旁组织高于肺癌组织表达的 31个。二者高于其它 8种癌组织的分别为 :肺癌旁组织中 63个 ,肺癌组织中 87个。结论 联合应用SSH和cDNAMicroarray是筛选和鉴定不同样本中差异表达基因的快速和有效的方法 ;肺癌旁组织和肺癌组织中差异表达的基因 ,以及这二者与其它组织差异表达的基因 ,不仅可能是肺癌发生发展机制中的重要基因 。

Genome-wide identification of gene expression in the epididymis of infertile rat induced by alpha-chlorohydrin using oligonucleotide microarray

Objective To establish a rat model of sterility associated with epididymis and epididymal gene expression profiles relation to fertility by alpha-chlorohydrin.Methods Rats were treated with 10 mg·kg-1·d-1.alpha-chlorohydrin for 10 consecutive days.Sperm maturation and other fertility parameters were analyzed.The sperm motility and morphology were evaluated by computer-assisted sperm analysis(CASA);sperm survival rate was assessed by SYBR-14 and propidium iodide(PI)fluorescent staining;the weights of testes,epididymides,prostates and seminal vesicles were determined by electronic balance;histological examination of above tissues were evaluated by HE staining;and serumal dihydrotestosterone(DHT)and testosterone(T)of rats were detected by enzyme-labeled immunoassay.Each male rat was paired with 2 female rats in proestrus.Female rats were examined the next morning for the presence of sperm in vaginal smears and underwent a cesarean section on day 12 of gestation.Finally the reproductive indices were calculated as follows:copulation index(number of sperm positive females /number of pairings),pregnancy index(number of pregnancies /number of sperm positive females),and fertility index(number of pregnancies /number of pairings).After that we used Affymetrix Rat 230 2.0 oligo-microarray to identify epididymal special genes associated with fertility.Finally,we validated some of these genes by Real-Time quantitative polymerase chain reaction.Results The motility of spermatozoa from the cauda epididymidis of treated rats showed a significant decrease in percentage of motile,progressively motile sperm,and sperm survival rate.At the same time,the morphology of cauda epididymal spermatozoa was also adversely affected by the treatment.In addition,the serumal androgen levels of treated animals weren't changed compared with the control group.Accordingly,matings with treated males resulted in no successful pregnancy.Then,we classified general functions of the down or up regulated epididymal genes by chlorhydrin with the GeneSpring gene ontology(GO)analysis,which are involved in macromolecular metabolism and transport,primary metabolism process,cell metabolism,biological process regulation,immunology regulation,ion combination,hydratase and oxidoreductase activity.Among all the different expressed genes,we analyzed and screened the down-regulated genes associated with glucose,lipid,protein and other energy metabolism,which are considered as the major ACH action targets.Simultaneously,the up-regulated genes by chlorhydrin were detected and their characters of negative regulated sperm maturation and fertility analyzed,which are apoptosis and immune-related genes and not reported before.Conclusions We established male infertile rat model with ACH(10 mg·kg-1·d-1,po,10 days)through evaluating changes of sperm motility and morphology,mating index,fertility index and pregnancy index.Simultaneously,the ACH didn't affect the major androgen(T and DHT)metabolism and sexual ability,which is considered as the best way for male contraception.Then we determined the down-regulated epididymal genes relation to substance metabolism,which can affect the epididymal sperm maturation and presumed the major antifertility targets by ACH.Further more,we found and analyzed the epididymal up-regulated genes associated with apoptosis and immune functions,which maybe the new possible sites of action by ACH and other male antifertility agents.

Biological Significance and the Related Molecular Mechanism of Ets1 mRNA Expression in Lung Cancer by Tissue Microarray(TMA)

Objective： To investigate the expressions and proteins in the pathogenesis, progression of lung molecular mechanism of Ets-1 mRNA, and TGFβ1 and c-Met cancer by tissue microarray （TMA） method. Methods： The expressions of Ets-1 mRNA, and TGFβ1 and c-Met proteins were detected in 89 primary lung cancers, 12 lung cancer with lymph-node metastasis and 12 precancerous lesions by FISH（fluorescence in situ hybridization） and immunohistochemical method, and 10 normal lung tissues were used as controls. Results： The expressions of Ets-1 rnRNA, and TGFβ1 and c-Met proteins were significantly higher in 89 primary lung cancer than in the control group （P〈0.05）. The expressions of Ets-1 mRNA, and TGFβ1 and c-Met proteins were related to lymph node metastasis and clinical stages. There was a positive correlation between the Ets-1 mRNA expression and TGFβ1 and c-Met proteins （P〈0.05）. Conclusion： Ets-1 mRNA, TGFβ1 and c-Met proteins may be related to the pathogenesis, progression and malignant behavior of lung cancer. They may play an important role in prognosis assessment of lung cancer.

<i>Pinus taeda</i>cDNA Microarray as a Tool for Candidate Gene Identification for Local Red/Far-Red Light Adaptive Response in <i>Pinus sylvestris</i>

Light quality response is a vital environmental cue regulating plant development. Conifers, like angiosperms, respond to the changes in light quality including the level of red (R) and far-red (FR) light, which follows a latitudinal cline. R and FR wavelengths form a significant component of the entire plant life cycle, including the initial developmental stages such as seed germination, cotyledon expansion and hypocotyl elongation. With an aim to identify differentially expressed candidate genes, which would provide a clue regarding genes involved in the local adaptive response in Scots pine (Pinus sylvestris) with reference to red/far-red light;we performed a global expression analysis of Scots pine hypocotyls grown under two light treatments, continuous R (cR) and continuous FR (cFR) light;using Pinus taeda cDNA microarrays on bulked hypocotyl tissues from different individuals, which represented different genotypes. This experiment was performed with the seeds collected from northern part of Sweden (Ylinen, 68?N). Interestingly, gene expression pattern with reference to cryptochrome1, a blue light photoreceptor, was relatively high under cFR as compared to cR light treatment. Additionally, the microarray data analysis also revealed expression of 405 genes which was enhanced under cR light treatment;while the expression of 239 genes was enhanced under the cFR light treatment. Differentially expressed genes were re-annotated using Blast2GO tool. These results indicated that cR light acts as promoting factor whereas cFR antagonises the effect in most of the processes like C/N metabolism, photosynthesis and cell wall metabolism which is in accordance with former findings in Arabidopsis. We propose cryptochrome1 as a strong candidate gene to study the adaptive cline response under R and FR light in Scots pine as it shows a differential expression under the two light conditions.