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Gene expression profiles of the swimming crab Portunus trituberculatus exposed to salinity stress

MARINE BIOLOGY 2011年第10期158卷 2161-2172页

作者： Xu, Qianghua Liu, Yang Shanghai Ocean Univ Coll Marine Sci Minist Educ Key Lab Sustainable Exploitat Ocean Fisheries Res Shanghai 201306 Peoples R China Shanghai Ocean Univ Key Lab Shanghai Educ Commiss Ocean Fisheries Res Shanghai 201306 Peoples R China

The swimming crab, Portunus trituberculatus, is an important marine fishery and aquaculture species. Although P. trituberculatus is a euryhaline species, water salinity condition influenced its distribution, migration route, and artificial propagations. To investigate gene expression in the P. trituberculatus exposed to different salinity stresses, 2426 expressed sequence tags (ESTs) from gill cDNA library were selected to spot on a cDNA microarray chip. In total, 417 differentially expressed genes were identified and grouped into eight clusters by hierarchical clustering analysis. Approximately 71.5% of grouped genes belonged to three independent expression patterns, indicating that these three expression patterns may represent three important stress tolerance pathways or networks in P. trituberculatus. Moreover, our cDNA microarray data suggested that there were differences in gene expression patterns of P. trituberculatus for low salinity and high salinity acclimation, suggesting that two salinity challenges resulted in a wide variation of gene expression in P. trituberculatus. In addition, a series of genes such as CCAAT/enhancer-binding protein, Na/K ATPase beta-subunit, and heat shock proteins (HSPs) genes were suggested to be key elements during salinity acclimation process. Overall, this work represented an important step toward understanding the molecular processes and mechanisms involved in salinity acclimation of the swimming crab.

关键词： GENE expression SWIMMING crabs SALINITY -- Environmental aspects EFFECT of environment on animals ANIMAL migration microarray technology

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MicroRNA-126 Regulates DNA Methylation in CD4+T Cells and Contributes to Systemic Lupus Erythematosus by Targeting DNA Methyltransferase 1

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ARTHRITIS AND RHEUMATISM 2011年第5期63卷 1376-1386页

作者： Zhao, Sha Wang, Yu Liang, Yunsheng Zhao, Ming Long, Hai Ding, Shu Yin, Heng Lu, Qianjin Cent S Univ Xiangya Hosp 2 Dept Dermatol Hunan Key Lab Med Epigenom Changsha 410011 Hunan Peoples R China

Objective. To identify microRNA genes with abnormal expression in the CD4+ T cells of patients with systemic lupus erythematosus (SLE) and to determine the role of microRNA-126 (miR-126) in the etiology of SLE. Methods. MicroRNA expression patterns in CD4+ T cells from patients with SLE and healthy control subjects were analyzed by microRNA microarray and stem loop quantitative polymerase chain reaction (qPCR). Luciferase reporter gene assays were performed to identify miR-126 targets. Dnmt1, CD11a, and CD70 messenger RNA and protein levels were determined by real-time qPCR, Western blotting, and flow cytometry. CD11a, CD70, and EGFL7 promoter methylation levels were detected by bisulfite sequencing. IgG levels in T cell-B cell cocultures were determined by enzyme-linked immunosorbent assay. Results. The expression of 11 microRNA was significantly increased or decreased in CD4+ T cells from patients with SLE relative to that in CD4+ T cells from control subjects. Among these, miR-126 was up-regulated, and its degree of overexpression was inversely correlated with Dnmt1 protein levels. We demonstrated that miR-126 directly inhibits Dnmt1 translation via interaction with its 3'-untranslated region, and that overexpression of miR-126 in CD4+ T cells can significantly reduce Dnmt1 protein levels. The overexpression of miR-126 in CD4+ T cells from healthy donors caused the demethylation and up-regulation of genes encoding CD11a and CD70, thereby causing T cell and B cell hyperactivity. The inhibition of miR-126 in CD4+ T cells from patients with SLE had the opposite effects. Expression of the miR-126 host gene EGFL7 was also up-regulated in CD4+ T cells from patients with SLE, possibly in a hypomethylation-dependent manner. Conclusion. Our data suggest that miR-126 regulates DNA methylation in CD4+ T cells and contributes to T cell autoreactivity in SLE by directly targeting Dnmt1.

关键词： SYSTEMIC lupus erythematosus COMPUTER software ENZYME-linked immunosorbent assay FLOW cytometry POLYMERASE chain reaction STATISTICS T-test (Statistics) WESTERN immunoblotting DATA analysis EQUIPMENT & supplies REVERSE transcriptase polymerase chain reaction microarray technology GENETIC aspects

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Rgtsp: a generalized top scoring pairs package for class prediction

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BIOINFORMATICS 2011年第12期27卷 1729-1730页

作者： Popovici, Vlad Budinska, Eva Delorenzi, Mauro Swiss Inst Bioinformat Bioinformat Core Facil CH-1015 Lausanne Switzerland Ecole Polytech Fed Lausanne Sch Life Sci Swiss Natl Ctr Competence Res Mol Oncol CH-1015 Lausanne Switzerland Masaryk Univ Inst Biostat & Anal Brno Czech Republic

A top scoring pair (TSP) classifier consists of a pair of variables whose relative ordering can be used for accurately predicting the class label of a sample. This classification rule has the advantage of being easily interpretable and more robust against technical variations in data, as those due to different microarray platforms. Here we describe a parallel implementation of this classifier which significantly reduces the training time, and a number of extensions, including a multi-class approach, which has the potential of improving the classification performance.

关键词： microarray technology C++ (Computer program language) SOURCE code (Computer science) COMPUTER software BIOINFORMATICS COMPUTERS in biology

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Temperature Affects Sole Carbon Utilization Patterns of Campylobacter coli 49941

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CURRENT MICROBIOLOGY 2011年第3期62卷 821-825页

作者： Line, John Hiett, Kelli Guard, Jean Seal, Bruce ARS USDA PMSRU Athens GA USA ARS USDA ESQRU Athens GA USA

Campylobacter spp. are small, asaccharolytic bacteria exhibiting unique nutritional and environmental requirements. Campylobacter spp. exist as commensal organisms in some animal species, yet are estimated to be the most common causative agents of foodborne illness in humans. C. jejuni is most often associated with poultry, while C. coli are more frequently associated with swine. Temperature has been suggested to trigger potential colonization or virulence factors in C. jejuni, and recent studies have demonstrated temperature-dependent genes are important to colonization. It is possible that temperature-dependent colonization factors are in part responsible for the species-specific colonization characteristics of C. coli also. We determined utilization of 190 different sole carbon substrates by C. coli ATCC 49941 at 37 and 42A degrees C using phenotype microarray (PM) technology. Temperature did affect amino acid utilization. l-asparagine and l-serine allowed significantly (P = 0.004) more respiration by C. coli ATCC 49941 at the lower temperature of 37A degrees C as compared to 42A degrees C. Conversely, l-glutamine was utilized to a significantly greater extent (P = 0.015) at the higher temperature of 42A degrees C. Other organic substrates exhibited temperature-dependent utilization including succinate, d,l-malate, and propionate which all supported active respiration by C. coli to a significantly greater extent at 42A degrees C. Further investigation is needed to determine the basis for the temperature-dependent utilization of substrates by Campylobacter spp. and their possible role in species-specific colonization.

关键词： CAMPYLOBACTER jejuni ANIMALS -- Classification VIRULENCE (Microbiology) ESCHERICHIA coli microarray technology

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Successful application of microarray technology to microdissected formalin-fixed, paraffin-embedded tissue

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JOURNAL OF MOLECULAR DIAGNOSTICS 2007年第1期9卷 70-79页

作者： Coudry, Renata A. Meireles, Sibele I. Stoyanova, Radka Cooper, Harry S. Carpino, Alan Wang, Xianqun Engstrom, Paul F. Clapper, Margie L. Fox Chase Canc Ctr Div Populat Sci Philadelphia PA 19111 USA Fox Chase Canc Ctr Div Med Sci Philadelphia PA 19111 USA Arcturus Biosci Sunnyvale CA USA

The establishment of a reliable method for using RNA from formalin-fixed, paraffin-embedded (FFPE) tissue would provide an opportunity to obtain novel gene expression data from the vast amounts of archived tissue. A custom-designed 22,000 oligonucleotide array was used in the present study to compare the gene expression profile of colonic epithelial cells isolated by laser capture microdissection from FFPE-archived samples with that of the same cell population from matched frozen samples, the preferred source of RNA. Total RNA was extracted from FFPE tissues, amplified, and labeled using the Paradise Reagent System. The quality of the input RNA was assessed by the Bioanalyzer profile, reverse transcriptase-polymerase chain reaction, and agarose gel electrophoresis. The results demonstrate that it is possible to obtain reliable microarray data from FFPE samples using RNA acquired by laser capture microdissection. The concordance between matched FFPE and frozen samples was evaluated and expressed as a Pearson's correlation coefficient, with values ranging from 0.80 to 0.97. The presence of ribosomal RNA peaks in FFPE-derived RNA was reflected by a high correlation with paired frozen samples. A set of practical recommendations for evaluating the RNA integrity and quality in FFPE samples is reported.

关键词： RNA Tissues microarray technology microdissection success

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Aberrant Signaling Pathways in Squamous Cell Lung Carcinoma

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CANCER INFORMATICS 2011年第10期10卷 273-285页

作者： Shi, Ivy Sadraei, Nooshin Hashemi Duan, Zhong-Hui Shi, Ting Cleveland Clin Fdn Lerner Res Inst Dept Canc Biol Cleveland OH 44195 USA Hudson High Sch Hudson OH 44236 USA Cleveland Clin Fdn Taussig Canc Inst Dept Solid Tumor Oncol Cleveland OH 44195 USA Univ Akron Dept Comp Sci Akron OH 44236 USA Univ Akron Program Integrated Biosci Akron OH 44236 USA

Lung cancer is the second most commonly occurring non-cutaneous cancer in the United States with the highest mortality rate among both men and women. In this study, we utilized three lung cancer microarray datasets generated by previous researchers to identify differentially expressed genes, altered signaling pathways, and assess the involvement of Hedgehog (Hh) pathway. The three datasets contain the expression levels of tens of thousands genes in normal lung tissues and squamous cell lung carcinoma. The datasets were combined and analyzed. The dysregulated genes and altered signaling pathways were identified using statistical methods. We then performed Fisher's exact test on the significance of the association of Hh pathway downstream genes and squamous cell lung carcinoma. 395 genes were found commonly differentially expressed in squamous cell lung carcinoma. The genes encoding fibrous structural-protein keratins and cell cycle dependent genes encoding cyclin-dependent kinases were significantly up-regulated while the ones encoding LIM domains were down. Over 100 signaling pathways were implicated in squamous cell lung carcinoma, including cell cycle regulation pathway, p53 tumor-suppressor pathway, IL-8 signaling, Wnt-beta-catenin pathway, mTOR signaling and EGF signaling. In addition, 37 out of 223 downstream molecules of Hh pathway were altered. The P-value from the Fisher's exact test indicates that Hh signaling is implicated in squamous cell lung carcinoma. Numerous genes were altered and multiple pathways were dysfunctional in squamous cell lung carcinoma. Many of the altered genes have been implicated in different types of carcinoma while some are organ-specific. Hh signaling is implicated in squamous cell lung cancer, opening the door for exploring new cancer therapeutic treatment using GLI antagonist GANT 61.

关键词： biomarkers drug targets signaling pathways microarray technology non-small cell lung cancer cancer treatment

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A New Generationmicroarray for the Simultaneous Detection and Identification of Yersinia pestis and Bacillus anthracis in Food

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JOURNAL OF PATHOGENS 2012年第unknown期2012卷 627036-627036页

作者： Goji, Noriko MacMillan, Trevor Amoako, Kingsley Kwaku Canadian Food Inspect Agcy Natl Ctr Anim Dis Lethbridge Lab POB 640 Lethbridge AB T1J 3Z4 Canada Univ Lethbridge Dept Biol Sci Lethbridge AB T1K 3M4 Canada

The use of microarrays as a multiple analytic system has generated increased interest and provided a powerful analytical tool for the simultaneous detection of pathogens in a single experiment. A wide array of applications for this technology has been reported. A low density oligonucleotide microarray was generated from the genetic sequences of Y. pestis and B. anthracis and used to fabricate a microarray chip. The new generation chip, consisting of 2,240 spots in 4 quadrants with the capability of stripping/rehybridization, was designated as "Y-PESTIS/B-ANTHRACIS 4x2K Array." The chip was tested for specificity using DNA from a panel of bacteria that may be potentially present in food. In all, 37 unique Y. pestis-specific and 83 B. anthracis-specific probes were identified. The microarray assay distinguished Y. pestis and B. anthracis from the other bacterial species tested and correctly identified the Y. pestis-specific oligonucleotide probes using DNA extracted from experimentally inoculated milk samples. Using a whole genome amplification method, the assay was able to detect as low as 1 ng genomic DNA as the start sample. The results suggest that oligonucleotide microarray can specifically detect and identify Y. pestis and B. anthracis and may be a potentially useful diagnostic tool for detecting and confirming the organisms in food during a bioterrorism event.

关键词： BACILLUS anthracis YERSINIA pestis DETECTION of pathogenic microorganisms microarray technology OLIGONUCLEOTIDE arrays FOOD pathogens

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Structural and functional networks in complex systems with delay

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Physical Review E 2011年第5期83卷 056113-056113页

作者： Víctor M. Eguíluz Toni Pérez Javier Borge-Holthoefer Alex Arenas Instituto de Física Interdisciplinar y Sistemas Complejos IFISC (CSIC-UIB) E-07122 Palma de Mallorca Spain Physics Department Lehigh University Bethlehem Pennsylvania 18015 USA Departament d’Enginyeria Informàtica i Matemàtiques Universitat Rovira i Virgili E-43007 Tarragona Spain

Functional networks of complex systems are obtained from the analysis of the temporal activity of their components, and are often used to infer their unknown underlying connectivity. We obtain the equations relating topology and function in a system of diffusively delay-coupled elements in complex networks. We solve exactly the resulting equations in motifs (directed structures of three nodes) and in directed networks. The mean-field solution for directed uncorrelated networks shows that the clusterization of the activity is dominated by the in-degree of the nodes, and that the locking frequency decreases with increasing average degree. We find that the exponent of a power law degree distribution of the structural topology γ is related to the exponent of the associated functional network as α=(2−γ)−1 for γ<2.

关键词： microarray technology TOPOLOGY EIGENVECTORS PROBABILITY theory NEURAL networks (Computer science)

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A Single Dose of Enterolactone Activates Estrogen Signaling and Regulates Expression of Circadian Clock Genes in Mice

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JOURNAL OF NUTRITION 2011年第9期141卷 1583-1589页

作者： Damdimopoulou, Pauliina Nurmi, Tarja Salminen, Anu Damdimopoulos, Anastasios E. Kotka, Maria van der Saag, Paul Strauss, Leena Poutanen, Matti Pongratz, Ingemar Makela, Sari Univ Turku Dept Cell Biol & Anat Inst Biomed Turku Finland Univ Turku Dept Physiol Inst Biomed Turku Finland Univ Turku Turku Ctr Dis Modeling Turku Finland Karolinska Inst Dept Biosci & Nutr Huddinge Sweden Univ Eastern Finland Dept Publ Hlth Inst Publ Hlth Clin Nutr Kuopio Finland Netherlands Acad Arts & Sci Hubrecht Inst Utrecht Netherlands

Enterolactone (EL) is an enterolignan produced by gut microbiota from dietary plant lignans. Epidemiological and experimental studies suggest that EL and plant lignans may reduce the risk of breast and prostate cancer as well as cardiovascular disease. These effects are thought to at least in part involve modulation of estrogen receptor activity. Surprisingly little is known about the in vivo estrogenicity of EL. In the present study, we investigated the target tissues of EL, the genes affected by EL treatment, and the response kinetics. Following a single dose of EL, luciferase was significantly induced in reproductive and nonreproductive tissues of male and female 3xERE-luciferase mice, indicating estrogen-like activity. microarray analysis revealed that EL regulated the expression of only 1% of 17 beta-estradiol target genes in the uterus. The majority of these genes were traditional estrogen target genes, but also members of the circadian signaling pathway were affected. Kinetic analyses showed that EL undergoes rapid phase II metabolism and is efficiently excreted. In vivo imaging demonstrated that the estrogen response followed similar, fast kinetics. We conclude that EL activates estrogen signaling in both male and female mice and that the transient responses may be due to the fast metabolism of the compound. Lastly, EL may represent a link among diet, gut microbiota, and circadian signaling. J. Nutr. 141: 1583-1589,2011.

关键词： ESTROGEN CIRCADIAN rhythms LUCIFERASES MOLECULAR clock microarray technology SEX hormones OXIDOREDUCTASES

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Complex Diel Cycles of Gene Expression in Coral-Algal Symbiosis

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SCIENCE 2011年第6014期331卷 175-175页

作者： Levy, O. Kaniewska, P. Alon, S. Eisenberg, E. Karako-Lampert, S. Bay, L. K. Reef, R. Rodriguez-Lanetty, M. Miller, D. J. Hoegh-Guldberg, O. James Cook Univ Australian Res Council Ctr Excellence Coral Reef Townsville Qld 4811 Australia Bar Ilan Univ Mina & Everard Goodman Fac Life Sci IL-52900 Ramat Gan Israel Univ Queensland Global Change Inst St Lucia Qld 4072 Australia Tel Aviv Univ Fac Life Sci Dept Neurobiol IL-69978 Tel Aviv Israel Tel Aviv Univ Raymond & Beverly Sackler Sch Phys & Astron IL-69978 Tel Aviv Israel Univ Queensland Sch Biol Sci St Lucia Qld 4072 Australia Univ Louisiana Lafayette Dept Biol Lafayette LA 70504 USA

Circadian regulation of plant-animal endosymbioses is complicated by a diversity of internal and external cues. Here, we show that stress-related genes in corals are coupled to the circadian clock, anticipating major changes in the intracellular milieu. In this regard, numerous chaperones are “hard-wired” to the clock, effectively preparing the coral for the consequences of oxidative protein damage imposed by symbiont photosynthesis (when O₂ > 250% saturation), including synexpression of antioxidant genes being light-gated. Conversely, central metabolism appears to be regulated by the hypoxia-inducible factor system in coral. These results reveal the complexity of endosymbiosis as well as the plasticity regulation downstream of the circadian clock.

关键词： CORALS CIRCADIAN rhythms RESEARCH microarray technology SYMBIOSIS ACROPORA

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