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Sample records for aflp transcriptional profiling

  1. Differential transcript profiling through cDNA-AFLP showed complexity of rutin biosynthesis and accumulation in seeds of a nutraceutical food crop (Fagopyrum spp.)

    OpenAIRE

    Gupta Nidhi; Naik Pradeep; Chauhan Rajinder

    2012-01-01

    Abstract Background Buckwheat, consisting of two cultivated species Fagopyrum tataricum and F. esculentum, is the richest source of flavonoid rutin. Vegetative tissues of both the Fagopyrum species contain almost similar amount of rutin; however, rutin content in seed of F. tataricum are ~50 folds of that in seed of F. esculentum. In order to understand the molecular basis of high rutin content in F. tataricum, differential transcript profiling through cDNA-AFLP has been utilized to decipher ...

  2. Differential transcript profiling through cDNA-AFLP showed complexity of rutin biosynthesis and accumulation in seeds of a nutraceutical food crop (Fagopyrum spp.

    Directory of Open Access Journals (Sweden)

    Gupta Nidhi

    2012-06-01

    Full Text Available Abstract Background Buckwheat, consisting of two cultivated species Fagopyrum tataricum and F. esculentum, is the richest source of flavonoid rutin. Vegetative tissues of both the Fagopyrum species contain almost similar amount of rutin; however, rutin content in seed of F. tataricum are ~50 folds of that in seed of F. esculentum. In order to understand the molecular basis of high rutin content in F. tataricum, differential transcript profiling through cDNA-AFLP has been utilized to decipher what genetic factors in addition to flavonoid structural genes contribute to high rutin content of F. tataricum compared to F. esculentum. Results Differential transcript profiling through cDNA-AFLP in seed maturing stages (inflorescence to seed maturation with 32 primer combinations generated total of 509 transcript fragments (TDFs. 167 TDFs were then eluted, cloned and sequenced from F. tataricum and F. esculentum. Categorization of TDFs on the basis of their presence/absence (qualitative variation or differences in the amount of expression (quantitative variation between both the Fagopyrum species showed that majority of variants are quantitative (64%. The TDFs represented genes controlling different biological processes such as basic and secondary metabolism (33%, regulation (18%, signal transduction (14%, transportation (13%, cellular organization (10%, and photosynthesis & energy (4%. Most of the TDFs except belonging to cellular metabolism showed relatively higher transcript abundance in F. tataricum over F. esculentum. Quantitative RT-PCR analysis of nine TDFs representing genes involved in regulation, metabolism, signaling and transport of secondary metabolites showed that all the tested nine TDFs (Ubiquitin protein ligase, ABC transporter, sugar transporter except MYB 118 showed significantly higher expression in early seed formation stage (S7 of F. tataricum compared to F. esculentum. qRT-PCR results were found to be consistent with the cDNA-AFLP

  3. Comparative transcriptional profiling under drought stress between upland and lowland rice (Oryza sativa L.) using cDNA-AFLP

    Institute of Scientific and Technical Information of China (English)

    GAO FengHua; ZHANG HongLiang; WANG HaiGuang; GAO Hong; LI ZiChao

    2009-01-01

    The continuous growth of lowland rice (LR) in paddy fields supplied with enough water over the years, and of upland rice (UR) in naturally rain-fed soils, has resulted in greater resistance to drought stress in UR compared to LR. To elucidate their differential regulation mechanisms of drought-resistance, genome-wide transcript regulation under drought stress in UR and LR was investigated using cDNA-AFLP. The results indicated that over 90% of gene expression was not affected by drought stress in the two rice genotypes, more than 8% was regulated by drought stress in both, and less than 1% was specifically expressed in UR or LR. Fifty-seven genes were specifically expressed in UR and thirty-eight specifically in LR. Genes specifically expressed in UR included cell rescue and defence genes functioning in drought-resistance, signal transduction molecules, nucleotides and amino acid biosynthesis genes required for plant growth, and the regulatory genes for growth and development. In LR, genes specifically expressed were related to protein and nucleotide degradation. Some genes were upregulated earlier in UR, and downregulated genes were inclined to be downregulated earlier in UR compared to LR, implying that more rapid regulation mechanisms caused earlier responses of UR to drought stress. Expression levels of upregulated genes in UR were higher than those in LR. The differences in gene expression between UR and LR could account for stronger regulation ability, more drought-resistance and superior growth of UR under drought stress compared to LR.

  4. Real-imaging cDNA-AFLP transcript profiling of pancreatic cancer patients: Egr-1 as a potential key regulator of muscle cachexia

    International Nuclear Information System (INIS)

    Cancer cachexia is a progressive wasting syndrome and the most prevalent characteristic of cancer in patients with advanced pancreatic adenocarcinoma. We hypothesize that genes expressed in wasted skeletal muscle of pancreatic cancer patients may determine the initiation and severity of cachexia syndrome. We studied gene expression in skeletal muscle biopsies from pancreatic cancer patients with and without cachexia utilizing Real-Imaging cDNA-AFLP-based transcript profiling for genome-wide expression analysis. Our approach yielded 183 cachexia-associated genes. Ontology analysis revealed characteristic changes for a number of genes involved in muscle contraction, actin cytoskeleton rearrangement, protein degradation, tissue hypoxia, immediate early response and acute-phase response. We demonstrate that Real-Imaging cDNA-AFLP analysis is a robust method for high-throughput gene expression studies of cancer cachexia syndrome in patients with pancreatic cancer. According to quantitative RT-PCR validation, the expression levels of genes encoding the acute-phase proteins α-antitrypsin and fibrinogen α and the immediate early response genes Egr-1 and IER-5 were significantly elevated in the skeletal muscle of wasted patients. By immunohistochemical and Western immunoblotting analysis it was shown, that Egr-1 expression is significantly increased in patients with cachexia and cancer. This provides new evidence that chronic activation of systemic inflammatory response might be a common and unifying factor of muscle cachexia

  5. A format for databasing and comparison of AFLP fingerprint profiles

    Directory of Open Access Journals (Sweden)

    Chuah Aaron

    2003-02-01

    Full Text Available Abstract Background Amplified fragment length polymorphism (AFLP is a PCR-based technique that involves restriction of genomic DNA followed by ligation of adaptors to the fragments generated and selective PCR amplification of a subset of these fragments. The amplified fragments are separated on a sequencing gel and visualized by autoradiography or fluorescent sequencing equipment. AFLP allows high-resolution genotyping but the lack of a format for databasing and comparison of AFLP fingerprint profiles limits its wider applications in profiling large numbers of biological samples. Results A scheme is described to represent a DNA fingerprint profile with a nucleotide sequence-like format in which the information line contains the minimal necessary details to interpret an AFLP DNA fingerprint profile. They include technique used, information on restriction enzymes, primer combination, biological source for DNA materials, fragment sizing and annotation. The bodylines contain information on size and relative intensity of DNA fragments by a string of defined alphabets or symbols. Algorithms for normalizing raw data, binning of fragments and comparing AFLP DNA fingerprint profiles are described. Firstly, the peak heights are normalized against their average and then represented by five symbols according to their relative intensities. Secondly, a binning algorithm based loosely on common springs and rubber bands is applied, which positions sequence fragments into their best possible integer approximations. A BLAST-like reward-penalty concept is used to compare AFLP fingerprint profiles by matching peaks using two metrics: score and percentage of similarity. A software package was developed based on our scheme and proposed algorithms. Example of use this software is given in evaluating novelty of a new tropical orchid cultivar by comparing its AFLP fingerprint profile against those of related commercial cultivars in a database. Conclusions AFLP DNA

  6. A format for databasing and comparison of AFLP fingerprint profiles

    OpenAIRE

    Chuah Aaron; Hong Yan

    2003-01-01

    Abstract Background Amplified fragment length polymorphism (AFLP) is a PCR-based technique that involves restriction of genomic DNA followed by ligation of adaptors to the fragments generated and selective PCR amplification of a subset of these fragments. The amplified fragments are separated on a sequencing gel and visualized by autoradiography or fluorescent sequencing equipment. AFLP allows high-resolution genotyping but the lack of a format for databasing and comparison of AFLP fingerprin...

  7. Distribution of Penicillium commune isolates in cheese dairies mapped using secondary metabolite profiles, morphotypes, RAPD and AFLP fingerprinting

    DEFF Research Database (Denmark)

    Lund, Flemming; Nielsen, A.B.; Skouboe, P.

    2003-01-01

    using morphotypes (colony morphology and colours) and secondary metabolite profiles. Based on production of secondary metabolites the P. commune isolates were classified into 6 groups. The genetic diversity of the P. commune isolates was assessed using randomly amplified polymorphic DNA (RAPD......) and amplified fragment length polymorphism, (AFLP). For a sub-set of 272 P. commune isolates RAPD analysis generated 33 RAPD groups whereas AFLP profiling revealed 55 AFLP groups. This study conclusively showed that the discriminatory power of AFLP was high compared to RAPD and that AFLP fingerprinting matched......In an 8-year study of the diversity and distribution of Penicillium commune contaminants in two different cheese dairies, swab and air samples were taken from the production plants, the processing environment and contaminated cheeses. A total of 321 Penicillium commune isolates were characterized...

  8. Long-Term Boron-Excess-Induced Alterations of Gene Profiles in Roots of Two Citrus Species Differing in Boron-Tolerance Revealed by cDNA-AFLP

    Science.gov (United States)

    Guo, Peng; Qi, Yi-Ping; Yang, Lin-Tong; Ye, Xin; Huang, Jing-Hao; Chen, Li-Song

    2016-01-01

    Boron (B) toxicity is observed in some citrus orchards in China. However, limited data are available on the molecular mechanisms of citrus B-toxicity and B-tolerance. Using cDNA-AFLP, we identified 20 up- and 52 down-regulated genes, and 44 up- and 66 down-regulated genes from excess B-treated Citrus sinensis and Citrus grandis roots, respectively, thereby demonstrating that gene expression profiles were more affected in the latter. In addition, phosphorus and total soluble protein concentrations were lowered only in excess B-treated C. grandis roots. Apparently, C. sinensis had higher B-tolerance than C. grandis. Our results suggested that the following several aspects were responsible for the difference in the B-tolerance between the two citrus species including: (a) B-excess induced Root Hair Defective 3 expression in C. sinensis roots, and repressed villin4 expression in C. grandis roots; accordingly, root growth was less inhibited by B-excess in the former; (b) antioxidant systems were impaired in excess B-treated C. grandis roots, hence accelerating root senescence; (c) genes related to Ca2+ signals were inhibited (induced) by B-excess in C. grandis (C. sinensis) roots. B-excess-responsive genes related to energy (i.e., alternative oxidase and cytochrome P450), lipid (i.e., Glycerol-3-phosphate acyltransferase 9 and citrus dioxygenase), and nucleic acid (i.e., HDA19, histone 4, and ribonucleotide reductase RNR1 like protein) metabolisms also possibly accounted for the difference in the B-tolerance between the two citrus species. These data increased our understanding of the mechanisms on citrus B-toxicity and B-tolerance at transcriptional level. PMID:27446128

  9. Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing

    Directory of Open Access Journals (Sweden)

    Leterrier Christine

    2010-07-01

    Full Text Available Abstract Background SNP (Single Nucleotide Polymorphism discovery is now routinely performed using high-throughput sequencing of reduced representation libraries. Our objective was to adapt 454 GS FLX based sequencing methodologies in order to obtain the largest possible dataset from two reduced representations libraries, produced by AFLP (Amplified Fragment Length Polymorphism for genomic DNA, and EST (Expressed Sequence Tag for the transcribed fraction of the genome. Findings The expressed fraction was obtained by preparing cDNA libraries without PCR amplification from quail embryo and brain. To optimize the information content for SNP analyses, libraries were prepared from individuals selected in three quail lines and each individual in the AFLP library was tagged. Sequencing runs produced 399,189 sequence reads from cDNA and 373,484 from genomic fragments, covering close to 250 Mb of sequence in total. Conclusions Both methods used to obtain reduced representations for high-throughput sequencing were successful after several improvements. The protocols may be used for several sequencing applications, such as de novo sequencing, tagged PCR fragments or long fragment sequencing of cDNA.

  10. Toxicogenomics: transcription profiling for toxicology assessment.

    Science.gov (United States)

    Zhou, Tong; Chou, Jeff; Watkins, Paul B; Kaufmann, William K

    2009-01-01

    Toxicogenomics, the application of transcription profiling to toxicology, has been widely used for elucidating the molecular and cellular actions of chemicals and other environmental stressors on biological systems, predicting toxicity before any functional damages, and classification of known or new toxicants based on signatures of gene expression. The success of a toxicogenomics study depends upon close collaboration among experts in different fields, including a toxicologist or biologist, a bioinformatician, statistician, physician and, sometimes, mathematician. This review is focused on toxicogenomics studies, including transcription profiling technology, experimental design, significant gene extraction, toxicological results interpretation, potential pathway identification, database input and the applications of toxicogenomics in various fields of toxicological study. PMID:19157067

  11. Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology

    Directory of Open Access Journals (Sweden)

    Ramina Angelo

    2008-07-01

    Full Text Available Abstract Background After 10-year-use of AFLP (Amplified Fragment Length Polymorphism technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping, as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants. This may be achieved by means of the Gene Ontology (GO, consisting in three structured vocabularies (i.e. ontologies describing genes, transcripts and proteins of any organism in terms of their associated cellular component, biological process and molecular function in a species-independent manner. In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology. Results Descriptive statistics on the type, size and nature of gene sequences obtained by means of AFLP technology were calculated. The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies. A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice, respectively. On the whole, the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results. Such an exhaustive annotation may offer a suitable platform for functional genomics, particularly useful in non-model species. Conclusion Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization

  12. Using of AFLP to evaluate gamma-irradiated amaranth mutants

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    Labajová Mária

    2013-01-01

    Full Text Available To determine which of several gamma-irradiated mutants of amaranth Ficha cultivar and K-433 hybrid are most genetically similar to their non-irradiated control genotypes, we performed amplified fragment length polymorphism (AFLP based analysis. A total of 40 selective primer combinations were used in reported analyses. First analyses of gamma-irradiated amaranth mutant lines were done used the AFLP. In the study, primers with the differentiation ability for all analysed mutant lines are reported. The very specific changes in the mutant lines´ non-coding regions based on AFLP length polymorphism were analysed. Mutant lines of the Ficha cultivar (C15, C26, C27, C82, C236 shared a genetic dissimilarity of 0,11 and their ISSR profiles are more similar to the Ficha than those of K-433 hybrid mutant lines. The K-433 mutant lines (D54, D279, D282 shared genetic dissimilarity of 0,534 but are more distinct to their control plant as a whole, as those of the Ficha mutant lines. Different AFLP fingerprints patters of the mutant lines when compared to the Ficha cultivar and K-433 hybrid AFLP profiles may be a consequence of the complex response of the intergenic space of mutant lines to the gamma-radiance. Although a genetic polymorphism was detected within accessions, the AFLP markers successfully identified all the accessions. The AFLP results are discussed by a combination of biochemical characteristics of mutant lines and their control genotypes.

  13. Identification of epididymis-specific transcripts in the mouse and rat by transcriptional profiling

    Institute of Scientific and Technical Information of China (English)

    Daniel S. Johnston; Terry T. Turner; Joshua N. Finger; Tracy L. Owtscharuk; S. Kopf; Scott A. Jelinsky

    2007-01-01

    As part of our efforts to identify novel contraceptive targets in the epididymis we performed transcriptional profiling on each of the 10 and 19 segments of the mouse and rat epididymidis, respectively, using Affymetrix whole genome microarrays. A total of 17 096 and 16 360 probe sets representing transcripts were identified as being expressed in the segmented mouse and rat epididymal transcriptomes, respectively. Comparison of the expressed murine transcripts against a mouse transcriptional profiling database derived from 22 other mouse tissues identified 77transcripts that were expressed uniquely in the epididymis. The expression of these genes was further evaluated by reverse transcription polymerase chain reaction (RT-PCR) analysis of RNA from 21 mouse tissues. RT-PCR analysis confirmed epididymis-specific expression of Defensin Beta 13 and identified two additional genes with expression restricted only to the epididymis and testis. Comparison of the 16 360 expressed transcripts in the rat epididymis with data of 21 other tissues from a rat transcriptional profiling database identified 110 transcripts specific for the epididymis.Sixty-two of these transcripts were further investigated by qPCR analysis. Only Defensin 22 (E3 epididymal protein)was shown to be completely specific for the epididymis. In addition, 14 transcripts showed more than 100-fold selective expression in the epididymis. The products of these genes might play important roles in epididymal and/or sperm function and further investigation and validation as contraceptive targets are warranted. The results of the studies described in this report are available at the Mammalian Reproductive Genetics (MRG) Database (http://mrg.genetics.washington.edu/).

  14. Gene Transcription Profile of the Detached Retina (An AOS Thesis)

    Science.gov (United States)

    Zacks, David N.

    2009-01-01

    Purpose: Separation of the neurosensory retina from the retinal pigment epithelium (RPE) yields many morphologic and functional consequences, including death of the photoreceptor cells, Müller cell hypertrophy, and inner retinal rewiring. Many of these changes are due to the separation-induced activation of specific genes. In this work, we define the gene transcription profile within the retina as a function of time after detachment. We also define the early activation of kinases that might be responsible for the detachment-induced changes in gene transcription. Methods: Separation of the retina from the RPE was induced in Brown-Norway rats by the injection of 1% hyaluronic acid into the subretinal space. Retinas were harvested at 1, 7, and 28 days after separation. Gene transcription profiles for each time point were determined using the Affymetrix Rat 230A gene microarray chip. Transcription levels in detached retinas were compared to those of nondetached retinas with the BRB-ArrayTools Version 3.6.0 using a random variance analysis of variance (ANOVA) model. Confirmation of the significant transcriptional changes for a subset of the genes was performed using microfluidic quantitative real-time polymerase chain reaction (qRT-PCR) assays. Kinase activation was explored using Western blot analysis to look for early phosphorylation of any of the 3 main families of mitogen-activated protein kinases (MAPK): the p38 family, the Janus kinase family, and the p42/p44 family. Results: Retinas separated from the RPE showed extensive alterations in their gene transcription profile. Many of these changes were initiated as early as 1 day after separation, with significant increases by 7 days. ANOVA analysis defined 144 genes that had significantly altered transcription levels as a function of time after separation when setting a false discovery rate at ≤0.1. Confirmatory RT-PCR was performed on 51 of these 144 genes. Differential transcription detected on the microarray

  15. What can digital transcript profiling reveal about human cancers?

    Directory of Open Access Journals (Sweden)

    J.M. Cerutti

    2003-08-01

    Full Text Available Important biological and clinical features of malignancy are reflected in its transcript pattern. Recent advances in gene expression technology and informatics have provided a powerful new means to obtain and interpret these expression patterns. A comprehensive approach to expression profiling is serial analysis of gene expression (SAGE, which provides digital information on transcript levels. SAGE works by counting transcripts and storing these digital values electronically, providing absolute gene expression levels that make historical comparisons possible. SAGE produces a comprehensive profile of gene expression and can be used to search for candidate tumor markers or antigens in a limited number of samples. The Cancer Genome Anatomy Project has created a SAGE database of human gene expression levels for many different tumors and normal reference tissues and provides online tools for viewing, comparing, and downloading expression profiles. Digital expression profiling using SAGE and informatics have been useful for identifying genes that have a role in tumor invasion and other aspects of tumor progression.

  16. Genetic relatedness among Campylobacter jejuni serotyped isolates of diverse origin as determined by numerical analysis of amplified fragment length polymorphism (AFLP) profiles

    DEFF Research Database (Denmark)

    Siemer, B.L.; Harrington, C.S.; Nielsen, E.M.;

    2004-01-01

    Aims: To use amplified fragment length polymorphism (AFLP) analysis to evaluate the genetic relatedness among 254 Campylobacter jejuni reference and field strains of diverse origin representing all defined 'Penner' serotypes for this species. Methods and Results: Field strains (n = 207) from human...... health. The remaining 30 groups contained isolates from humans, chickens and associated food products, cattle, sheep, turkeys, ostriches and/or dogs. Strains assigned to serotypes 2, 6/7, 11 and 12 formed major clusters at the 77.6% S-level. Most other serotypes did not form homogeneous clusters...

  17. Transcriptional profiling of putative human epithelial stem cells

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    Koçer Salih S

    2008-07-01

    Full Text Available Abstract Background Human interfollicular epidermis is sustained by the proliferation of stem cells and their progeny, transient amplifying cells. Molecular characterization of these two cell populations is essential for better understanding of self renewal, differentiation and mechanisms of skin pathogenesis. The purpose of this study was to obtain gene expression profiles of alpha 6+/MHCI+, transient amplifying cells and alpha 6+/MHCI-, putative stem cells, and to compare them with existing data bases of gene expression profiles of hair follicle stem cells. The expression of Major Histocompatibility Complex (MHC class I, previously shown to be absent in stem cells in several tissues, and alpha 6 integrin were used to isolate MHCI positive basal cells, and MHCI low/negative basal cells. Results Transcriptional profiles of the two cell populations were determined and comparisons made with published data for hair follicle stem cell gene expression profiles. We demonstrate that presumptive interfollicular stem cells, alpha 6+/MHCI- cells, are enriched in messenger RNAs encoding surface receptors, cell adhesion molecules, extracellular matrix proteins, transcripts encoding members of IFN-alpha family proteins and components of IFN signaling, but contain lower levels of transcripts encoding proteins which take part in energy metabolism, cell cycle, ribosome biosynthesis, splicing, protein translation, degradation, DNA replication, repair, and chromosome remodeling. Furthermore, our data indicate that the cell signaling pathways Notch1 and NF-κB are downregulated/inhibited in MHC negative basal cells. Conclusion This study demonstrates that alpha 6+/MHCI- cells have additional characteristics attributed to stem cells. Moreover, the transcription profile of alpha 6+/MHCI- cells shows similarities to transcription profiles of mouse hair follicle bulge cells known to be enriched for stem cells. Collectively, our data suggests that alpha 6+/MHCI- cells

  18. cDNA-AFLP Analysis on Transcripts Associated Gene with Broodiness in Muscovy Duck%番鸭就巢性状相关基因表达的cDNA-AFLP分析

    Institute of Scientific and Technical Information of China (English)

    吴旭; 严美姣; 刘丽平; 傅星源; 连森阳; 李昂

    2012-01-01

    [目的]寻找与番鸭就巢性状相关的表达基因,了解其就巢调控的分子机理.[方法]采用cDNA-AFLP(cDNA-amplified fragment length polymorphism)技术分析遗传背景相近的RF系白羽番鸭就巢个体和非就巢个体脑垂体基因表达差异.[结果]筛选到与就巢行为相关差异表达片段82条,选取其中15条进行测序.将测序结果在GenBank数据库进行BLAST比较和分析,发现8个片段(53.3%)与已知基因具有较高同源性,涉及与繁殖性能紧密相关的下丘脑-垂体-性腺轴(hypothalamic-pituitary-gonadal,HPG)上的功能基因,如GnRH基因、FSH基因,同时也分离到位于GH/IGF轴上的功能基因,即GH基因;以及在功能上属于信号传导、转录调控、代谢的调节基因,如超氧化物歧化酶基因、角蛋白关联蛋白基因、硫氰酸酶释放硫基转移酶基因等.2个片段与未知功能的基因有同源性,5个与数据库中现有的基因没有明显的相似性.随机选择3个片段进行RT-PCR验证,检测片段的表达模式与cDNA-AFLP结果一致.[结论]揭示番鸭不同就巢性状基因表达调控模式,进一步阐明番鸭就巢的分子机理.%[Objective] The objective of this experiment is to identify differentially expressed genes of Muscovy Duck broodiness. [ Method ] cDNA-AFLP approach was employed to analyze genes differentially expressed in broodiness and non-broodiness Muscovy Duck individuals derived from a single RF white feathers line. [Result] There were 82 differentially expressed bands associated with broodiness behaviors, 15 bands of them were subject to sequence analysis. Database searches indicate that 8 cDNA fragments show high homology to known genes, which include some function genes in hypothalamic-pituitary-gonadal axis regulating reproduction, such as GnRH gene and FSH gene. Meanwhile genes were also found in GH-IGF axis, such as GH gene. Other genes participated in signal transduction, transcription, metabolism biological

  19. RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease.

    Science.gov (United States)

    Schaker, Patricia D C; Palhares, Alessandra C; Taniguti, Lucas M; Peters, Leila P; Creste, Silvana; Aitken, Karen S; Van Sluys, Marie-Anne; Kitajima, João P; Vieira, Maria L C; Monteiro-Vitorello, Claudia B

    2016-01-01

    Sugarcane smut disease is caused by the biotrophic fungus Sporisorium scitamineum. The disease is characterized by the development of a whip-like structure from the primary meristems, where billions of teliospores are produced. Sugarcane smut also causes tillering and low sucrose and high fiber contents, reducing cane productivity. We investigated the biological events contributing to disease symptoms in a smut intermediate-resistant sugarcane genotype by examining the transcriptional profiles (RNAseq) shortly after inoculating the plants and immediately after whip emission. The overall picture of disease progression suggests that premature transcriptional reprogramming of the shoot meristem functions continues until the emergence of the whip. The guidance of this altered pattern is potentially primarily related to auxin mobilization in addition to the involvement of other hormonal imbalances. The consequences associated with whip emission are the modulation of typical meristematic functions toward reproductive organ differentiation, requiring strong changes in carbon partitioning and energy production. These changes include the overexpression of genes coding for invertases and trehalose-6P synthase, as well as other enzymes from key metabolic pathways, such as from lignin biosynthesis. This is the first report describing changes in the transcriptional profiles following whip development, providing a hypothetical model and candidate genes to further study sugarcane smut disease progression. PMID:27583836

  20. Transcriptional profile of a myotube starvation model of atrophy

    Science.gov (United States)

    Stevenson, Eric J.; Koncarevic, Alan; Giresi, Paul G.; Jackman, Robert W.; Kandarian, Susan C.

    2005-01-01

    Skeletal muscle wasting is a pervasive phenomenon that can result from a wide range of pathological conditions as well as from habitual muscular inactivity. The present work describes a cell-culture condition that induces significant atrophy in skeletal muscle C2C12 myotubes. The failure to replenish differentiation media in mature myotubes leads to rapid atrophy (53% in diameter), which is referred to here as starvation. Affymetrix microarrays were used to develop a transcriptional profile of control (fed) vs. atrophied (nonfed) myotubes. Myotube starvation was characterized by an upregulation of genes involved in translational inhibition, amino acid biosynthesis and transport, and cell cycle arrest/apoptosis, among others. Downregulated genes included several structural and regulatory elements of the extracellular matrix as well as several elements of Wnt/frizzled and TGF-beta signaling pathways. Interestingly, the characteristic transcriptional upregulation of the ubiquitin-proteasome system, calpains, and cathepsins known to occur in multiple in vivo models of atrophy were not seen during myotube starvation. With the exception of the downregulation of extracellular matrix genes, serine protease inhibitor genes, and the upregulation of the translation initiation factor PHAS-I, this model of atrophy in cell culture has a transcriptional profile quite distinct from any study published to date with atrophy in whole muscle. These data show that, although the gross morphology of atrophied muscle fibers may be similar in whole muscle vs. myotube culture, the processes by which this phenotype is achieved differ markedly.

  1. Global transcriptional profiles of Trichophyton rubrum in response to Flucytosine

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Trichophyton rubrum (T.rubrum) is one of the most common human fungal pathogens that cause chronic infections of the skin and nails. To identify antifungal responsive genes, cDNA microarray analysis was performed for T. rubrum to reveal global transcriptional profiles of drug-specific responses to 5-Flucytosine (5-FC). cDNA microarray was constructed from the T. rubrum expressed sequence tag (ESTs) database, the minimum inhibitory concentration (MIC) of 5-FC was determined, and microarray hybridization and data analysis were applied. The expression pattern of 7 genes observed by microarray was confirmed by the quantitative real-time reverser transcription polymerase chain reaction (RT-PCR). Data analysis indicated that a total of 474 genes were found differentially expressed, 196 showed an increase in expression and 278 showed a decrease in expression. Marked down-regulation of genes involved in nucleotide metabolism (such as CDC21), transcription (such as E2F1), and RNA processing (such as SGN1, RIM4 and NOP1) was observed. Other genes involved in signal transduction, chaperones, inorganic ion transport, secondary metabolite biosynthesis, amino acid transport, lipid transport and potential drug resistance mechanism were also affected by 5-FC. Quantitative real-time RT-PCR of the selected genes confirmed the reliability of the microarray results. This is the first analysis of transcriptional profiles in response to 5-FC for T. rubrum. The findings may be valuable for the identification of genes involved in mechanisms of action and mechanisms of antifungal drug resistance of 5-FC.

  2. Transcriptional Profiling of Egg Allergy and Relationship to Disease Phenotype

    Science.gov (United States)

    Kosoy, Roman; Agashe, Charuta; Grishin, Alexander; Leung, Donald Y.; Wood, Robert A.; Sicherer, Scott H.; Jones, Stacie M.; Burks, A. Wesley; Davidson, Wendy F.; Lindblad, Robert W.; Dawson, Peter; Merad, Miriam; Kidd, Brian A.; Dudley, Joel T.; Sampson, Hugh A.

    2016-01-01

    Background Egg allergy is one of the most common food allergies of childhood. There is a lack of information on the immunologic basis of egg allergy beyond the role of IgE. Objective To use transcriptional profiling as a novel approach to uncover immunologic processes associated with different phenotypes of egg allergy. Methods Peripheral blood mononuclear cells (PBMCs) were obtained from egg-allergic children who were defined as reactive (BER) or tolerant (BET) to baked egg, and from food allergic controls (AC) who were egg non-allergic. PBMCs were stimulated with egg white protein. Gene transcription was measured by microarray after 24 h, and cytokine secretion by multiplex assay after 5 days. Results The transcriptional response of PBMCs to egg protein differed between BER and BET versus AC subjects. Compared to the AC group, the BER group displayed increased expression of genes associated with allergic inflammation as well as corresponding increased secretion of IL-5, IL-9 and TNF-α. A similar pattern was observed for the BET group. Further similarities in gene expression patterns between BER and BET groups, as well as some important differences, were revealed using a novel Immune Annotation resource developed for this project. This approach identified several novel processes not previously associated with egg allergy, including positive associations with TLR4-stimulated myeloid cells and activated NK cells, and negative associations with an induced Treg signature. Further pathway analysis of differentially expressed genes comparing BER to BET subjects showed significant enrichment of IFN-α and IFN-γ response genes, as well as genes associated with virally-infected DCs. Conclusions Transcriptional profiling identified several novel pathways and processes that differed when comparing the response to egg allergen in BET, BER, and AC groups. We conclude that this approach is a useful hypothesis-generating mechanism to identify novel immune processes associated

  3. Novel transcriptional profile in wrist muscles from cerebral palsy patients

    Directory of Open Access Journals (Sweden)

    Subramaniam Shankar

    2009-07-01

    Full Text Available Abstract Background Cerebral palsy (CP is an upper motor neuron disease that results in a progressive movement disorder. Secondary to the neurological insult, muscles from CP patients often become spastic. Spastic muscle is characterized by an increased resistance to stretch, but often develops the further complication of contracture which represents a prominent disability in children with CP. This study's purpose is to characterize alterations of spastic muscle on the transcriptional level. Increased knowledge of spastic muscle may lead to novel therapies to improve the quality of life for children with CP. Method The transcriptional profile of spastic muscles were defined in children with cerebral palsy and compared to control patients using Affymetrix U133A chips. Expression data were verified using quantitative-PCR (QPCR and validated with SDS-PAGE for select genes. Significant genes were determined using a 2 × 2 ANOVA and results required congruence between 3 preprocessing algorithms. Results CP patients clustered independently and 205 genes were significantly altered, covering a range of cellular processes. Placing gene expression in the context of physiological pathways, the results demonstrated that spastic muscle in CP adapts transcriptionally by altering extracellular matrix, fiber type, and myogenic potential. Extracellular matrix adaptations occur primarily in the basal lamina although there is increase in fibrillar collagen components. Fiber type is predominately fast compared to normal muscle as evidenced by contractile gene isoforms and decrease in oxidative metabolic gene transcription, despite a paradoxical increased transcription of slow fiber pathway genes. We also found competing pathways of fiber hypertrophy with an increase in the anabolic IGF1 gene in parallel with a paradoxical increase in myostatin, a gene responsible for stopping muscle growth. We found evidence that excitation-contraction coupling genes are altered in

  4. A transcriptional profile of aging in the human kidney.

    Science.gov (United States)

    Rodwell, Graham E J; Sonu, Rebecca; Zahn, Jacob M; Lund, James; Wilhelmy, Julie; Wang, Lingli; Xiao, Wenzhong; Mindrinos, Michael; Crane, Emily; Segal, Eran; Myers, Bryan D; Brooks, James D; Davis, Ronald W; Higgins, John; Owen, Art B; Kim, Stuart K

    2004-12-01

    In this study, we found 985 genes that change expression in the cortex and the medulla of the kidney with age. Some of the genes whose transcripts increase in abundance with age are known to be specifically expressed in immune cells, suggesting that immune surveillance or inflammation increases with age. The age-regulated genes show a similar aging profile in the cortex and the medulla, suggesting a common underlying mechanism for aging. Expression profiles of these age-regulated genes mark not only age, but also the relative health and physiology of the kidney in older individuals. Finally, the set of aging-regulated kidney genes suggests specific mechanisms and pathways that may play a role in kidney degeneration with age.

  5. A transcriptional profile of aging in the human kidney.

    Directory of Open Access Journals (Sweden)

    Graham E J Rodwell

    2004-12-01

    Full Text Available In this study, we found 985 genes that change expression in the cortex and the medulla of the kidney with age. Some of the genes whose transcripts increase in abundance with age are known to be specifically expressed in immune cells, suggesting that immune surveillance or inflammation increases with age. The age-regulated genes show a similar aging profile in the cortex and the medulla, suggesting a common underlying mechanism for aging. Expression profiles of these age-regulated genes mark not only age, but also the relative health and physiology of the kidney in older individuals. Finally, the set of aging-regulated kidney genes suggests specific mechanisms and pathways that may play a role in kidney degeneration with age.

  6. Statistical modelling of transcript profiles of differentially regulated genes

    Directory of Open Access Journals (Sweden)

    Sergeant Martin J

    2008-07-01

    Full Text Available Abstract Background The vast quantities of gene expression profiling data produced in microarray studies, and the more precise quantitative PCR, are often not statistically analysed to their full potential. Previous studies have summarised gene expression profiles using simple descriptive statistics, basic analysis of variance (ANOVA and the clustering of genes based on simple models fitted to their expression profiles over time. We report the novel application of statistical non-linear regression modelling techniques to describe the shapes of expression profiles for the fungus Agaricus bisporus, quantified by PCR, and for E. coli and Rattus norvegicus, using microarray technology. The use of parametric non-linear regression models provides a more precise description of expression profiles, reducing the "noise" of the raw data to produce a clear "signal" given by the fitted curve, and describing each profile with a small number of biologically interpretable parameters. This approach then allows the direct comparison and clustering of the shapes of response patterns between genes and potentially enables a greater exploration and interpretation of the biological processes driving gene expression. Results Quantitative reverse transcriptase PCR-derived time-course data of genes were modelled. "Split-line" or "broken-stick" regression identified the initial time of gene up-regulation, enabling the classification of genes into those with primary and secondary responses. Five-day profiles were modelled using the biologically-oriented, critical exponential curve, y(t = A + (B + CtRt + ε. This non-linear regression approach allowed the expression patterns for different genes to be compared in terms of curve shape, time of maximal transcript level and the decline and asymptotic response levels. Three distinct regulatory patterns were identified for the five genes studied. Applying the regression modelling approach to microarray-derived time course data

  7. Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency

    NARCIS (Netherlands)

    Stölting, K.N.; Gort, G.; Wüst, C.; Wilson, A.B.

    2009-01-01

    Background - Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP) is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. In spite of the frequent application of this method, studies on th

  8. Transcriptional profiling of nitrogen fixation in Azotobacter vinelandii.

    Science.gov (United States)

    Hamilton, Trinity L; Ludwig, Marcus; Dixon, Ray; Boyd, Eric S; Dos Santos, Patricia C; Setubal, João C; Bryant, Donald A; Dean, Dennis R; Peters, John W

    2011-09-01

    Most biological nitrogen (N(2)) fixation results from the activity of a molybdenum-dependent nitrogenase, a complex iron-sulfur enzyme found associated with a diversity of bacteria and some methanogenic archaea. Azotobacter vinelandii, an obligate aerobe, fixes nitrogen via the oxygen-sensitive Mo nitrogenase but is also able to fix nitrogen through the activities of genetically distinct alternative forms of nitrogenase designated the Vnf and Anf systems when Mo is limiting. The Vnf system appears to replace Mo with V, and the Anf system is thought to contain Fe as the only transition metal within the respective active site metallocofactors. Prior genetic analyses suggest that a number of nif-encoded components are involved in the Vnf and Anf systems. Genome-wide transcription profiling of A. vinelandii cultured under nitrogen-fixing conditions under various metal amendments (e.g., Mo or V) revealed the discrete complement of genes associated with each nitrogenase system and the extent of cross talk between the systems. In addition, changes in transcript levels of genes not directly involved in N(2) fixation provided insight into the integration of central metabolic processes and the oxygen-sensitive process of N(2) fixation in this obligate aerobe. The results underscored significant differences between Mo-dependent and Mo-independent diazotrophic growth that highlight the significant advantages of diazotrophic growth in the presence of Mo. PMID:21724999

  9. AFLP fingerprinting of elite varieties (clones) from the genus Populus

    Institute of Scientific and Technical Information of China (English)

    GAO Jianming; ZHANG Shougong; QI Liwang; ZHANG Yong; WANG Chunguo; CHEN Ruiyang; SONG Wenqin

    2007-01-01

    Accurate identification of varieties (clones) and knowledge of their genetic relationships are essential for poplar breeding and variety management.In this study,21 elite poplar varieties of Tacamahaca and Aigeiros in China were fingerprinted using amplified fragment length polymorphism (AFLP) markers.Four AFLP primer pairs developed generated totally 181 AFLP polymorphic fragments,and in particular,each primer pair generated fingerprint profiles specific to each of the tested varieties.The genetic relationships among the varieties were evaluated by dendrograms and multidimensional scaling (MDS).The results showed that the tested poplar can be classified into five groups,and indicated the clear separation of varieties of different sections of poplar and the primary distinction between native and exotic poplar varieties.This study indicated that tested poplar varieties could be identified by their fingerprint profiles and that genetic relationships deduced from the study were consistent with their genealogy.In addition,our results demonstrated that AFLP could be used to construct DNA fingerprints of poplar clones at a large-scale level and to determine genetic relationships of poplar varieties.

  10. Spatiotemporal profiles of arginine vasopressin transcription in cultured suprachiasmatic nucleus.

    Science.gov (United States)

    Yoshikawa, Tomoko; Nakajima, Yoshihiro; Yamada, Yoshiko; Enoki, Ryosuke; Watanabe, Kazuto; Yamazaki, Maya; Sakimura, Kenji; Honma, Sato; Honma, Ken-ichi

    2015-11-01

    Arginine vasopressin (AVP), a major neuropeptide in the suprachiasmatic nucleus (SCN), is postulated to mediate the output of the circadian oscillation. Mice carrying a reporter gene of AVP transcription (AVP(ELuc)) were produced by knocking-in a cDNA of Emerald-luciferase (ELuc) in the translational initiation site. Homozygous mice did not survive beyond postnatal day 7. Using the heterozygous (AVP(ELuc/+)) mice, a bioluminescence reporter system was developed that enabled to monitor AVP transcription through AVP-ELuc measurement in real time for more than 10 cycles in the cultured brain slice. AVP(ELuc/+) mice showed circadian behaviour rhythms and light responsiveness indistinguishable from those of the wild-type. Robust circadian rhythms in AVP-ELuc were detected in the cultured SCN slice at a single cell as well as tissue levels. The circadian rhythm of the whole SCN slice was stable, with the peak at the mid-light phase of a light-dark cycle, while that of a single cell was more variable. By comparison, rhythmicity in the paraventricular nucleus and supraoptic nucleus in the hypothalamus was unstable and damped rapidly. Spatiotemporal profiles of AVP expression at the pixel level revealed significant circadian rhythms in the entire area of AVP-positive cells in the SCN, and at least two clusters that showed different circadian oscillations. Contour analysis of bioluminescence intensity in a cell-like region demonstrated the radiation area was almost identical to the cell size. This newly developed reporter system for AVP gene expression is a useful tool for the study of circadian rhythms. PMID:26342201

  11. Transcription Profiling of the Stringent Response in Escherichia coli▿ †

    Science.gov (United States)

    Durfee, Tim; Hansen, Anne-Marie; Zhi, Huijun; Blattner, Frederick R.; Jin, Ding Jun

    2008-01-01

    The bacterial stringent response serves as a paradigm for understanding global regulatory processes. It can be triggered by nutrient downshifts or starvation and is characterized by a rapid RelA-dependent increase in the alarmone (p)ppGpp. One hallmark of the response is the switch from maximum-growth-promoting to biosynthesis-related gene expression. However, the global transcription patterns accompanying the stringent response in Escherichia coli have not been analyzed comprehensively. Here, we present a time series of gene expression profiles for two serine hydroxymate-treated cultures: (i) MG1655, a wild-type E. coli K-12 strain, and (ii) an isogenic relAΔ251 derivative defective in the stringent response. The stringent response in MG1655 develops in a hierarchical manner, ultimately involving almost 500 differentially expressed genes, while the relAΔ251 mutant response is both delayed and limited in scope. We show that in addition to the down-regulation of stable RNA-encoding genes, flagellar and chemotaxis gene expression is also under stringent control. Reduced transcription of these systems, as well as metabolic and transporter-encoding genes, constitutes much of the down-regulated expression pattern. Conversely, a significantly larger number of genes are up-regulated. Under the conditions used, induction of amino acid biosynthetic genes is limited to the leader sequences of attenuator-regulated operons. Instead, up-regulated genes with known functions, including both regulators (e.g., rpoE, rpoH, and rpoS) and effectors, are largely involved in stress responses. However, one-half of the up-regulated genes have unknown functions. How these results are correlated with the various effects of (p)ppGpp (in particular, RNA polymerase redistribution) is discussed. PMID:18039766

  12. Transcriptional profile of maize roots under acid soil growth

    Directory of Open Access Journals (Sweden)

    Mattiello Lucia

    2010-09-01

    Full Text Available Abstract Background Aluminum (Al toxicity is one of the most important yield-limiting factors of many crops worldwide. The primary symptom of Al toxicity syndrome is the inhibition of root growth leading to poor water and nutrient absorption. Al tolerance has been extensively studied using hydroponic experiments. However, unlike soil conditions, this method does not address all of the components that are necessary for proper root growth and development. In the present study, we grew two maize genotypes with contrasting tolerance to Al in soil containing toxic levels of Al and then compared their transcriptomic responses. Results When grown in acid soil containing toxic levels of Al, the Al-sensitive genotype (S1587-17 showed greater root growth inhibition, more Al accumulation and more callose deposition in root tips than did the tolerant genotype (Cat100-6. Transcriptome profiling showed a higher number of genes differentially expressed in S1587-17 grown in acid soil, probably due to secondary effects of Al toxicity. Genes involved in the biosynthesis of organic acids, which are frequently associated with an Al tolerance response, were not differentially regulated in both genotypes after acid soil exposure. However, genes related to the biosynthesis of auxin, ethylene and lignin were up-regulated in the Al-sensitive genotype, indicating that these pathways might be associated with root growth inhibition. By comparing the two maize lines, we were able to discover genes up-regulated only in the Al-tolerant line that also presented higher absolute levels than those observed in the Al-sensitive line. These genes encoded a lipase hydrolase, a retinol dehydrogenase, a glycine-rich protein, a member of the WRKY transcriptional family and two unknown proteins. Conclusions This work provides the first characterization of the physiological and transcriptional responses of maize roots when grown in acid soil containing toxic levels of Al. The

  13. Transcription Profiling Analysis of Mango–Fusarium mangiferae Interaction

    Science.gov (United States)

    Liu, Feng; Wu, Jing-bo; Zhan, Ru-lin; Ou, Xiong-chang

    2016-01-01

    Malformation caused by Fusarium mangiferae is one of the most destructive mango diseases affecting the canopy and floral development, leading to dramatic reduction in fruit yield. To further understand the mechanism of interaction between mango and F. mangiferae, we monitored the transcriptome profiles of buds from susceptible mango plants, which were challenged with F. mangiferae. More than 99 million reads were deduced by RNA-sequencing and were assembled into 121,267 unigenes. Based on the sequence similarity searches, 61,706 unigenes were identified, of which 21,273 and 50,410 were assigned to gene ontology categories and clusters of orthologous groups, respectively, and 33,243 were mapped to 119 KEGG pathways. The differentially expressed genes of mango were detected, having 15,830, 26,061, and 20,146 DEGs respectively, after infection for 45, 75, and 120 days. The analysis of the comparative transcriptome suggests that basic defense mechanisms play important roles in disease resistance. The data also show the transcriptional responses of interactions between mango and the pathogen and more drastic changes in the host transcriptome in response to the pathogen. These results could be used to develop new methods to broaden the resistance of mango to malformation, including the over-expression of key mango genes.

  14. Subgroup-specific intrinsic disorder profiles of arabidopsis NAC transcription factors

    DEFF Research Database (Denmark)

    Stender, Emil G.; O'Shea, Charlotte; Skriver, Karen

    2015-01-01

    Protein intrinsic disorder (ID), referring to the lack of a fixed tertiary structure, is significant in signaling and transcription. We recently characterized ID in 6 phylogenetically representative Arabidopsis thaliana NAC transcription factors. Their transcription regulatory domains are mostly.......g. transcriptional activation and interactions. Based on our analysis, we suggest that ID profiling of regulatory proteins in general can be used to guide identification of interaction partners of network proteins....

  15. The Human Adult Skeletal Muscle Transcriptional Profile Reconstructed by a Novel Computational Approach

    OpenAIRE

    Bortoluzzi, Stefania; d'Alessi, Fabio; Romualdi, Chiara; Danieli, Gian Antonio

    2000-01-01

    By applying a novel software tool, information on 4080 UniGene clusters was retrieved from three adult human skeletal muscle cDNA libraries, which were selected for being neither normalized nor subtracted. Reconstruction of a transcriptional profile of the corresponding tissue was attempted by a computational approach, classifying each transcript according to its level of expression. About 25% of the transcripts accounted for about 80% of the detected transcriptional activity, whereas most ge...

  16. Leveraging transcript quantification for fast computation of alternative splicing profiles.

    Science.gov (United States)

    Alamancos, Gael P; Pagès, Amadís; Trincado, Juan L; Bellora, Nicolás; Eyras, Eduardo

    2015-09-01

    Alternative splicing plays an essential role in many cellular processes and bears major relevance in the understanding of multiple diseases, including cancer. High-throughput RNA sequencing allows genome-wide analyses of splicing across multiple conditions. However, the increasing number of available data sets represents a major challenge in terms of computation time and storage requirements. We describe SUPPA, a computational tool to calculate relative inclusion values of alternative splicing events, exploiting fast transcript quantification. SUPPA accuracy is comparable and sometimes superior to standard methods using simulated as well as real RNA-sequencing data compared with experimentally validated events. We assess the variability in terms of the choice of annotation and provide evidence that using complete transcripts rather than more transcripts per gene provides better estimates. Moreover, SUPPA coupled with de novo transcript reconstruction methods does not achieve accuracies as high as using quantification of known transcripts, but remains comparable to existing methods. Finally, we show that SUPPA is more than 1000 times faster than standard methods. Coupled with fast transcript quantification, SUPPA provides inclusion values at a much higher speed than existing methods without compromising accuracy, thereby facilitating the systematic splicing analysis of large data sets with limited computational resources. The software is implemented in Python 2.7 and is available under the MIT license at https://bitbucket.org/regulatorygenomicsupf/suppa. PMID:26179515

  17. Sputum is a surrogate for bronchoalveolar lavage for monitoring Mycobacterium tuberculosis transcriptional profiles in TB patients.

    Science.gov (United States)

    Garcia, Benjamin J; Loxton, Andre G; Dolganov, Gregory M; Van, Tran T; Davis, J Lucian; de Jong, Bouke C; Voskuil, Martin I; Leach, Sonia M; Schoolnik, Gary K; Walzl, Gerhard; Strong, Michael; Walter, Nicholas D

    2016-09-01

    Pathogen-targeted transcriptional profiling in human sputum may elucidate the physiologic state of Mycobacterium tuberculosis (M. tuberculosis) during infection and treatment. However, whether M. tuberculosis transcription in sputum recapitulates transcription in the lung is uncertain. We therefore compared M. tuberculosis transcription in human sputum and bronchoalveolar lavage (BAL) samples from 11 HIV-negative South African patients with pulmonary tuberculosis. We additionally compared these clinical samples with in vitro log phase aerobic growth and hypoxic non-replicating persistence (NRP-2). Of 2179 M. tuberculosis transcripts assayed in sputum and BAL via multiplex RT-PCR, 194 (8.9%) had a p-value <0.05, but none were significant after correction for multiple testing. Categorical enrichment analysis indicated that expression of the hypoxia-responsive DosR regulon was higher in BAL than in sputum. M. tuberculosis transcription in BAL and sputum was distinct from both aerobic growth and NRP-2, with a range of 396-1020 transcripts significantly differentially expressed after multiple testing correction. Collectively, our results indicate that M. tuberculosis transcription in sputum approximates M. tuberculosis transcription in the lung. Minor differences between M. tuberculosis transcription in BAL and sputum suggested lower oxygen concentrations or higher nitric oxide concentrations in BAL. M. tuberculosis-targeted transcriptional profiling of sputa may be a powerful tool for understanding M. tuberculosis pathogenesis and monitoring treatment responses in vivo.

  18. Influence of mRNA decay rates on the computational prediction of transcription rate profiles from gene expression profiles

    Indian Academy of Sciences (India)

    Chi-Fang Chin; Arthur Chun-Chieh Shih; Kuo-Chin Fan

    2007-12-01

    The abundance of an mRNA species depends not only on the transcription rate at which it is produced, but also on its decay rate, which determines how quickly it is degraded. Both transcription rate and decay rate are important factors in regulating gene expression. With the advance of the age of genomics, there are a considerable number of gene expression datasets, in which the expression profiles of tens of thousands of genes are often non-uniformly sampled. Recently, numerous studies have proposed to infer the regulatory networks from expression profiles. Nevertheless, how mRNA decay rates affect the computational prediction of transcription rate profiles from expression profiles has not been well studied. To understand the influences, we present a systematic method based on a gene dynamic regulation model by taking mRNA decay rates, expression profiles and transcription profiles into account. Generally speaking, an expression profile can be regarded as a representation of a biological condition. The rationale behind the concept is that the biological condition is reflected in the changing of gene expression profile. Basically, the biological condition is either associated to the cell cycle or associated to the environmental stresses. The expression profiles of genes that belong to the former, so-called cell cycle data, are characterized by periodicity, whereas the expression profiles of genes that belong to the latter, so-called condition-specific data, are characterized by a steep change after a specific time without periodicity. In this paper, we examine the systematic method on the simulated expression data as well as the real expression data including yeast cell cycle data and condition-specific data (glucose-limitation data). The results indicate that mRNA decay rates do not significantly influence the computational prediction of transcription-rate profiles for cell cycle data. On the contrary, the magnitudes and shapes of transcription-rate profiles for

  19. Genotyping and genetic diversity of Arcobacter butzleri by amplified fragment length polymorphism (AFLP) analysis

    DEFF Research Database (Denmark)

    On, Stephen L.W.; Atabay, H.I.; Amisu, K.O.;

    2004-01-01

    strains homogeneous with respect to their respective source of isolation. However, contemporaneous strains from the same source could also be distinguished. Conclusions: AFLP profiling is an effective method for typing the genetically diverse organism A. butzleri. Significance and Impact of the Study......: The study represents a comprehensive analysis of the genetic diversity of A. butzleri by use of isolates from six countries spanning three continents and also shows that several distinct A. butzleri genotypes may be found in a given environment. AFLP profiling appears to have considerable potential......Aims: To investigate the potential of amplified fragment length polymorphism (AFLP) profiling for genotyping Arcobacter butzleri and to obtain further data on the genetic diversity of this organism. Methods and Results: Seventy-three isolates of Danish, British, Turkish, Swedish, Nigerian and North...

  20. Intracellular biology and virulence determinants of Francisella tularensis revealed by transcriptional profiling inside macrophages

    OpenAIRE

    Wehrly, Tara D.; Chong, Audrey; Virtaneva, Kimmo; Sturdevant, Dan E.; Child, Robert; Edwards, Jessica A.; Brouwer, Dedeke; Nair, Vinod; Fischer, Elizabeth R.; Wicke, Luke; Curda, Alissa J.; Kupko, John J.; Martens, Craig; Crane, Deborah D.; Bosio, Catharine M.

    2009-01-01

    The highly infectious bacterium Francisella tularensis is a facultative intracellular pathogen, whose virulence requires proliferation inside host cells, including macrophages. Here we have performed a global transcriptional profiling of the highly virulent F. tularensis subsp. tularensis Schu S4 strain during its intracellular cycle within primary murine macrophages, to characterize its intracellular biology and identify pathogenic determinants based on their intracellular expression profile...

  1. Transcriptional Profile of Haemophilus influenzae: Effects of Iron and Heme

    OpenAIRE

    Whitby, Paul W.; VanWagoner, Timothy M.; Seale, Thomas W.; Morton, Daniel J; Stull, Terrence L.

    2006-01-01

    Haemophilus influenzae requires either heme or a porphyrin and iron source for growth. Microarray studies of H. influenzae strain Rd KW20 identified 162 iron/heme-regulated genes, representing ∼10% of the genome, with ≥1.5-fold changes in transcription in response to iron/heme availability in vitro. Eighty genes were preferentially expressed under iron/heme restriction; 82 genes were preferentially expressed under iron/heme-replete conditions.

  2. Transcriptional Profiling of Caudal Fin Regeneration in Zebrafish

    Directory of Open Access Journals (Sweden)

    Michael Schebesta

    2006-01-01

    Full Text Available Regeneration of severed limbs in adult animals is restricted to urodele amphibians. Mammals, including humans, have very limited regenerative capabilities and even with proper treatment, only the tips of our digits can grow back. Teleost fish can regenerate amputated fins, the evolutionary ancestors of limbs. To elucidate the principles of limb-fin regeneration, we performed an Affymetrix microarray screen on regenerating caudal fins 12, 24, 48, and 72 h post amputation. Approximately 15,000 zebrafish transcripts were analyzed, identifying 829 transcripts as differentially expressed during regeneration. Of those, 563 were up-regulated and 266 were down-regulated. We constructed a comprehensive database containing expression data, functional assignment, and background information from the literature for each differentially expressed transcript. In order to validate our findings, we employed three approaches: (1 microarray expression analysis of genes previously implicated in fin regeneration, (2 RT-PCR analysis of genes newly identified as differentially expressed during regeneration, and (3 in situ hybridization of the up-regulated genes bambi, dlx5A, and her6. Moreover, we show that Smad 1/5/8 proteins, effector molecules of Bmp signaling, are phosphorylated during fin regeneration. Taken together, we provide a comprehensive database of fin regeneration that will serve as an important tool for understanding the molecular mechanisms of regeneration.

  3. Identification of a novel reference gene for apple transcriptional profiling under postharvest conditions.

    Science.gov (United States)

    Storch, Tatiane Timm; Pegoraro, Camila; Finatto, Taciane; Quecini, Vera; Rombaldi, Cesar Valmor; Girardi, César Luis

    2015-01-01

    Reverse Transcription quantitative PCR (RT-qPCR) is one of the most important techniques for gene expression profiling due to its high sensibility and reproducibility. However, the reliability of the results is highly dependent on data normalization, performed by comparisons between the expression profiles of the genes of interest against those of constitutively expressed, reference genes. Although the technique is widely used in fruit postharvest experiments, the transcription stability of reference genes has not been thoroughly investigated under these experimental conditions. Thus, we have determined the transcriptional profile, under these conditions, of three genes commonly used as reference--ACTIN (MdACT), PROTEIN DISULPHIDE ISOMERASE (MdPDI) and UBIQUITIN-CONJUGATING ENZYME E2 (MdUBC)--along with two novel candidates--HISTONE 1 (MdH1) and NUCLEOSSOME ASSEMBLY 1 PROTEIN (MdNAP1). The expression profile of the genes was investigated throughout five experiments, with three of them encompassing the postharvest period and the other two, consisting of developmental and spatial phases. The transcriptional stability was comparatively investigated using four distinct software packages: BestKeeper, NormFinder, geNorm and DataAssist. Gene ranking results for transcriptional stability were similar for the investigated software packages, with the exception of BestKeeper. The classic reference gene MdUBC ranked among the most stably transcribed in all investigated experimental conditions. Transcript accumulation profiles for the novel reference candidate gene MdH1 were stable throughout the tested conditions, especially in experiments encompassing the postharvest period. Thus, our results present a novel reference gene for postharvest experiments in apple and reinforce the importance of checking the transcription profile of reference genes under the experimental conditions of interest.

  4. Identification of a novel reference gene for apple transcriptional profiling under postharvest conditions.

    Directory of Open Access Journals (Sweden)

    Tatiane Timm Storch

    Full Text Available Reverse Transcription quantitative PCR (RT-qPCR is one of the most important techniques for gene expression profiling due to its high sensibility and reproducibility. However, the reliability of the results is highly dependent on data normalization, performed by comparisons between the expression profiles of the genes of interest against those of constitutively expressed, reference genes. Although the technique is widely used in fruit postharvest experiments, the transcription stability of reference genes has not been thoroughly investigated under these experimental conditions. Thus, we have determined the transcriptional profile, under these conditions, of three genes commonly used as reference--ACTIN (MdACT, PROTEIN DISULPHIDE ISOMERASE (MdPDI and UBIQUITIN-CONJUGATING ENZYME E2 (MdUBC--along with two novel candidates--HISTONE 1 (MdH1 and NUCLEOSSOME ASSEMBLY 1 PROTEIN (MdNAP1. The expression profile of the genes was investigated throughout five experiments, with three of them encompassing the postharvest period and the other two, consisting of developmental and spatial phases. The transcriptional stability was comparatively investigated using four distinct software packages: BestKeeper, NormFinder, geNorm and DataAssist. Gene ranking results for transcriptional stability were similar for the investigated software packages, with the exception of BestKeeper. The classic reference gene MdUBC ranked among the most stably transcribed in all investigated experimental conditions. Transcript accumulation profiles for the novel reference candidate gene MdH1 were stable throughout the tested conditions, especially in experiments encompassing the postharvest period. Thus, our results present a novel reference gene for postharvest experiments in apple and reinforce the importance of checking the transcription profile of reference genes under the experimental conditions of interest.

  5. Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays

    Directory of Open Access Journals (Sweden)

    Müller Marlen

    2012-06-01

    Full Text Available Abstract Microarrays are routine tools for transcript profiling, and genomic tiling arrays such as the Arabidopsis AGRONOMICS1 arrays have been found to be highly suitable for such experiments because changes in genome annotation can be easily integrated at the data analysis level. In a transcript profiling experiment, RNA labeling is a critical step, most often initiated by oligo-dT-primed reverse transcription. Although this has been found to be a robust and reliable method, very long transcripts or non-polyadenylated transcripts might be labeled inefficiently. In this study, we first provide data handling methods to analyze AGRONOMICS1 tiling microarrays based on the TAIR10 genome annotation. Second, we describe methods to easily quantify antisense transcripts on such tiling arrays. Third, we test a random-primed RNA labeling method, and find that on AGRONOMICS1 arrays this method has similar general performance as the conventional oligo-dT-primed method. In contrast to the latter, however, the former works considerably better for long transcripts and for non-polyadenylated transcripts such as found in mitochondria and plastids. We propose that researchers interested in organelle function use the random-primed method to unleash the full potential of genomic tiling arrays.

  6. Transcriptional responses in Honey Bee larvae infected with chalkbrood fungus

    Directory of Open Access Journals (Sweden)

    Murray Keith D

    2010-06-01

    Full Text Available Abstract Background Diseases and other stress factors working synergistically weaken honey bee health and may play a major role in the losses of bee populations in recent years. Among a large number of bee diseases, chalkbrood has been on the rise. We present here the experimental identification of honey bee genes that are differentially expressed in response to infection of honey bee larvae with the chalkbrood fungus, Ascosphaera apis. Results We used cDNA-AFLP ®Technology to profile transcripts in infected and uninfected bee larvae. From 64 primer combinations, over 7,400 transcriptionally-derived fragments were obtained A total of 98 reproducible polymorphic cDNA-AFLP fragments were excised and sequenced, followed by quantitative real-time RT-PCR (qRT-PCR analysis of these and additional samples. We have identified a number of differentially-regulated transcripts that are implicated in general mechanisms of stress adaptation, including energy metabolism and protein transport. One of the most interesting differentially-regulated transcripts is for a chitinase-like enzyme that may be linked to anti-fungal activities in the honey bee larvae, similarly to gut and fat-body specific chitinases found in mosquitoes and the red flour beetle. Surprisingly, we did not find many components of the well-characterized NF-κB intracellular signaling pathways to be differentially-regulated using the cDNA-AFLP approach. Therefore, utilizing qRT-PCR, we probed some of the immune related genes to determine whether the lack of up-regulation of their transcripts in our analysis can be attributed to lack of immune activation or to limitations of the cDNA-AFLP approach. Conclusions Using a combination of cDNA-AFLP and qRT-PCR analyses, we were able to determine several key transcriptional events that constitute the overall effort in the honey bee larvae to fight natural fungal infection. Honey bee transcripts identified in this study are involved in critical

  7. Olive phenolic compounds: metabolic and transcriptional profiling during fruit development

    OpenAIRE

    Alagna Fiammetta; Mariotti Roberto; Panara Francesco; Caporali Silvia; Urbani Stefania; Veneziani Gianluca; Esposto Sonia; Taticchi Agnese; Rosati Adolfo; Rao Rosa; Perrotta Gaetano; Servili Maurizio; Baldoni Luciana

    2012-01-01

    Abstract Background Olive (Olea europaea L.) fruits contain numerous secondary metabolites, primarily phenolics, terpenes and sterols, some of which are particularly interesting for their nutraceutical properties. This study will attempt to provide further insight into the profile of olive phenolic compounds during fruit development and to identify the major genetic determinants of phenolic metabolism. Results The concentration of the major phenolic compounds, such as oleuropein, demethyloleu...

  8. Transcriptional profiling of apoptosis-deficient Drosophila mutants

    Directory of Open Access Journals (Sweden)

    Fumiaki Obata

    2014-12-01

    Full Text Available Apoptosis is a fundamental way to remove damaged or unwanted cells during both developmental and post-developmental stages. Apoptosis deficiency leads to various diseases including cancer. To know the physiological changes in apoptosis-deficient mutants, we conducted non-biased transcriptomic analysis of Drosophila darkcd4 mutants. As recently reported, combined with metabolome and genetic analysis, we identified systemic immune response, energy wasting, as well as alteration in S-adenosyl-methionine metabolism in response to necrotic cells [1]. Here, we describe in detail how we obtained validated microarray dataset deposited in Gene Expression Omnibus (GSE47853. Our data provide a resource for searching transcriptional alterations in Drosophila apoptosis-deficient mutants.

  9. Isolation, classification and transcription profiles of the AP2/ERF transcription factor superfamily in citrus.

    Science.gov (United States)

    Xie, Xiu-lan; Shen, Shu-ling; Yin, Xue-ren; Xu, Qian; Sun, Chong-de; Grierson, Donald; Ferguson, Ian; Chen, Kun-song

    2014-07-01

    The AP2/ERF gene family encodes plant-specific transcription factors. In model plants, AP2/ERF genes have been shown to be expressed in response to developmental and environmental stimuli, and many function downstream of the ethylene, biotic, and abiotic stress signaling pathways. In citrus, ethylene is effective in regulation citrus fruit quality, such as degreening and aroma. However, information about the citrus AP2/ERF family is limited, and would enhance our understanding of fruit responses to environmental stress, fruit development and quality. CitAP2/ERF genes were isolated using the citrus genome database, and their expression patterns analyzed by real-time PCR using various orange organs and samples from a fruit developmental series. 126 sequences with homologies to AP2/ERF proteins were identified from the citrus genome, and, on the basis of their structure and sequence, assigned to the ERF family (102), AP2 family (18), RAV family (4) and Soloist (2). MEME motif analysis predicted the defining AP2/ERF domain and EAR repressor domains. Analysis of transcript accumulation in Citrus sinensis cv. 'Newhall' indicated that CitAP2/ERF genes show organ-specific and temporal expression, and provided a framework for understanding the transcriptional regulatory roles of AP2/ERF gene family members in citrus. Hierarchical cluster analysis and t tests identified regulators that potentially function during orange fruit growth and development. PMID:24566692

  10. Isolation, classification and transcription profiles of the AP2/ERF transcription factor superfamily in citrus.

    Science.gov (United States)

    Xie, Xiu-lan; Shen, Shu-ling; Yin, Xue-ren; Xu, Qian; Sun, Chong-de; Grierson, Donald; Ferguson, Ian; Chen, Kun-song

    2014-07-01

    The AP2/ERF gene family encodes plant-specific transcription factors. In model plants, AP2/ERF genes have been shown to be expressed in response to developmental and environmental stimuli, and many function downstream of the ethylene, biotic, and abiotic stress signaling pathways. In citrus, ethylene is effective in regulation citrus fruit quality, such as degreening and aroma. However, information about the citrus AP2/ERF family is limited, and would enhance our understanding of fruit responses to environmental stress, fruit development and quality. CitAP2/ERF genes were isolated using the citrus genome database, and their expression patterns analyzed by real-time PCR using various orange organs and samples from a fruit developmental series. 126 sequences with homologies to AP2/ERF proteins were identified from the citrus genome, and, on the basis of their structure and sequence, assigned to the ERF family (102), AP2 family (18), RAV family (4) and Soloist (2). MEME motif analysis predicted the defining AP2/ERF domain and EAR repressor domains. Analysis of transcript accumulation in Citrus sinensis cv. 'Newhall' indicated that CitAP2/ERF genes show organ-specific and temporal expression, and provided a framework for understanding the transcriptional regulatory roles of AP2/ERF gene family members in citrus. Hierarchical cluster analysis and t tests identified regulators that potentially function during orange fruit growth and development.

  11. ProbeSelect: selecting differentially expressed probes in transcriptional profile data

    OpenAIRE

    Hosur, Raghavendra; Szak, Suzanne; Thai, Alice; Allaire, Norm; Bienkowska, Jadwiga

    2013-01-01

    Summary: Transcriptional profiling still remains one of the most popular techniques for identifying relevant biomarkers in patient samples. However, heterogeneity in the population leads to poor statistical evidence for selection of most relevant biomarkers to pursue. In particular, human transcriptional differences can be subtle, making it difficult to tease out real differentially expressed biomarkers from the variability inherent in the population. To address this issue, we propose a simpl...

  12. Hippocampal CA1 transcriptional profile of sleep deprivation: relation to aging and stress.

    Directory of Open Access Journals (Sweden)

    Nada M Porter

    Full Text Available BACKGROUND: Many aging changes seem similar to those elicited by sleep-deprivation and psychosocial stress. Further, sleep architecture changes with age suggest an age-related loss of sleep. Here, we hypothesized that sleep deprivation in young subjects would elicit both stress and aging-like transcriptional responses. METHODOLOGY/PRINCIPAL FINDINGS: F344 rats were divided into control and sleep deprivation groups. Body weight, adrenal weight, corticosterone level and hippocampal CA1 transcriptional profiles were measured. A second group of animals was exposed to novel environment stress (NES, and their hippocampal transcriptional profiles measured. A third cohort exposed to control or SD was used to validate transcriptional results with Western blots. Microarray results were statistically contrasted with prior transcriptional studies. Microarray results pointed to sleep pressure signaling and macromolecular synthesis disruptions in the hippocampal CA1 region. Animals exposed to NES recapitulated nearly one third of the SD transcriptional profile. However, the SD-aging relationship was more complex. Compared to aging, SD profiles influenced a significant subset of genes. mRNA associated with neurogenesis and energy pathways showed agreement between aging and SD, while immune, glial, and macromolecular synthesis pathways showed SD profiles that opposed those seen in aging. CONCLUSIONS/SIGNIFICANCE: We conclude that although NES and SD exert similar transcriptional changes, selective presynaptic release machinery and Homer1 expression changes are seen in SD. Among other changes, the marked decrease in Homer1 expression with age may represent an important divergence between young and aged brain response to SD. Based on this, it seems reasonable to conclude that therapeutic strategies designed to promote sleep in young subjects may have off-target effects in the aged. Finally, this work identifies presynaptic vesicular release and intercellular

  13. The Human Adult Skeletal Muscle Transcriptional Profile Reconstructed by a Novel Computational Approach

    Science.gov (United States)

    Bortoluzzi, Stefania; d'Alessi, Fabio; Romualdi, Chiara; Danieli, Gian Antonio

    2000-01-01

    By applying a novel software tool, information on 4080 UniGene clusters was retrieved from three adult human skeletal muscle cDNA libraries, which were selected for being neither normalized nor subtracted. Reconstruction of a transcriptional profile of the corresponding tissue was attempted by a computational approach, classifying each transcript according to its level of expression. About 25% of the transcripts accounted for about 80% of the detected transcriptional activity, whereas most genes showed a low level of expression. This in silico transcriptional profile was then compared with data obtained by a SAGE study. A fairly good agreement between the two methods was observed. About 400 genes, highly expressed in skeletal muscle or putatively skeletal muscle-specific, may represent the minimal set of genes needed to determine the tissue specificity. These genes could be used as a convenient reference to monitor major changes in the transcriptional profile of adult human skeletal muscle in response to different physiological or pathological conditions, thus providing a framework for designing DNA microarrays and initiating biological studies. PMID:10720575

  14. Sputum is a surrogate for bronchoalveolar lavage for monitoring Mycobacterium tuberculosis transcriptional profiles in TB patients.

    Science.gov (United States)

    Garcia, Benjamin J; Loxton, Andre G; Dolganov, Gregory M; Van, Tran T; Davis, J Lucian; de Jong, Bouke C; Voskuil, Martin I; Leach, Sonia M; Schoolnik, Gary K; Walzl, Gerhard; Strong, Michael; Walter, Nicholas D

    2016-09-01

    Pathogen-targeted transcriptional profiling in human sputum may elucidate the physiologic state of Mycobacterium tuberculosis (M. tuberculosis) during infection and treatment. However, whether M. tuberculosis transcription in sputum recapitulates transcription in the lung is uncertain. We therefore compared M. tuberculosis transcription in human sputum and bronchoalveolar lavage (BAL) samples from 11 HIV-negative South African patients with pulmonary tuberculosis. We additionally compared these clinical samples with in vitro log phase aerobic growth and hypoxic non-replicating persistence (NRP-2). Of 2179 M. tuberculosis transcripts assayed in sputum and BAL via multiplex RT-PCR, 194 (8.9%) had a p-value pathogenesis and monitoring treatment responses in vivo. PMID:27553415

  15. What we have learned from transcript profile analyses of male and female gametes in flowering plants

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Double fertilization is one of the predominant features of sexual reproduction in flowering plants but, because of the physical inaccessibility of gametes, the essential molecular mechanisms in these processes are largely unknown. Based on the techniques for isolating highly purified gametes from several species and well-developed methods for manipulating RNA from limited quantities of gametes, genome-wide investigations of gamete transcription profiles were recently conducted in flowering plants. In this review, we survey the accumulated knowledge on gamete collection and purification, cDNA library construction, and transcript profile analysis to assess our understanding of the molecular mechanisms of gamete specialization and fertilization.

  16. Transcription Profile of Aging and Cognition-Related Genes in the Medial Prefrontal Cortex

    Science.gov (United States)

    Ianov, Lara; Rani, Asha; Beas, Blanca S.; Kumar, Ashok; Foster, Thomas C.

    2016-01-01

    Cognitive function depends on transcription; however, there is little information linking altered gene expression to impaired prefrontal cortex function during aging. Young and aged F344 rats were characterized on attentional set shift and spatial memory tasks. Transcriptional differences associated with age and cognition were examined using RNA sequencing to construct transcriptomic profiles for the medial prefrontal cortex (mPFC), white matter, and region CA1 of the hippocampus. The results indicate regional differences in vulnerability to aging. Age-related gene expression in the mPFC was similar to, though less robust than, changes in the dorsolateral PFC of aging humans suggesting that aging processes may be similar. Importantly, the pattern of transcription associated with aging did not predict cognitive decline. Rather, increased mPFC expression of genes involved in regulation of transcription, including transcription factors that regulate the strength of excitatory and inhibitory inputs, and neural activity-related immediate-early genes was observed in aged animals that exhibit delayed set shift behavior. The specificity of impairment on a mPFC-dependent task, associated with a particular mPFC transcriptional profile indicates that impaired executive function involves altered transcriptional regulation and neural activity/plasticity processes that are distinct from that described for impaired hippocampal function. PMID:27242522

  17. Transcriptional profiling of foam cells in response to hypercholesterolemia.

    Science.gov (United States)

    Goo, Young-Hwa; Yechoor, Vijay K; Paul, Antoni

    2016-09-01

    Hypercholesterolemia is a main risk factor for atherosclerosis development. Arterial macrophages, or foam cells, take-up and process lipoprotein particles deposited in arteries, and store much of the cholesterol carried by these particles in their cytoplasm. However, the effects of exposure to different cholesterol levels on foam cells remain poorly understood. Given the remarkable plasticity of macrophages in response to environmental variables, studies on macrophage biology should ideally be performed in the environment where they exert their physiological functions, namely atherosclerotic lesions in the case of foam cells. We used a mouse model of atherosclerosis, the apolipoprotein E-deficient mouse, to study in vivo the transcriptional response of foam cells to short- and long-term elevations in plasma cholesterol, induced by feeding mice a western type diet. The microarray data sets from this study have been deposited in NCBI's Gene Expression Omnibus under the accession number GSE70619. Here we provide detailed information on the experimental set-up, on the isolation of RNA by laser capture microdissection, and on the methodology used for RNA amplification and analysis by microarray and quantitative real-time PCR. PMID:27408807

  18. Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

    OpenAIRE

    Chiu, Isaac M; Barrett, Lee B.; Williams, Erika K.; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D.; Lou, Shan; Bryman, Gregory S; Roberson, David P.; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos del Moral, Enrique Jos??; Cheryl L. Stucky

    2014-01-01

    The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1)...

  19. Global transcriptional profiling reveals Streptococcus agalactiae genes controlled by the MtaR transcription factor

    Directory of Open Access Journals (Sweden)

    Cvek Urska

    2008-12-01

    Full Text Available Abstract Background Streptococcus agalactiae (group B Streptococcus; GBS is a significant bacterial pathogen of neonates and an emerging pathogen of adults. Though transcriptional regulators are abundantly encoded on the GBS genome, their role in GBS pathogenesis is poorly understood. The mtaR gene encodes a putative LysR-type transcriptional regulator that is critical for the full virulence of GBS. Previous studies have shown that an mtaR- mutant transports methionine at reduced rates and grows poorly in normal human plasma not supplemented with methionine. The decreased virulence of the mtaR mutant was correlated with a methionine transport defect; however, no MtaR-regulated genes were identified. Results Microarray analysis of wild-type GBS and an mtaR mutant revealed differential expression of 12 genes, including 1 upregulated and 11 downregulated genes in the mtaR mutant. Among the downregulated genes, we identified a cluster of cotranscribed genes encoding a putative methionine transporter (metQ1NP and peptidase (pdsM. The expression of four genes potentially involved in arginine transport (artPQ and arginine biosynthesis (argGH was downregulated and these genes localized to two transcriptional units. The virulence factor cspA, which encodes an extracellular protease, was downregulated. Additionally, the SAN_1255 locus, which putatively encodes a protein displaying similarity to plasminogen activators, was downregulated. Conclusion To our knowledge, this is the first study to describe the global influence of MtaR on GBS gene expression. This study implicates the metQ1NP genes as encoding the MtaR-regulated methionine transporter, which may provide a mechanistic explanation for the methionine-dependent growth defect of the mtaR mutant. In addition to modulating the expression of genes involved in metabolism and amino acid transport, inactivation of mtaR affected the expression of other GBS genes implicated in pathogenesis. These findings

  20. Collision probabilities for AFLP bands, with an application to simple measures of genetic similarity

    NARCIS (Netherlands)

    Gort, G.; Koopman, W.J.M.; Stein, A.; Eeuwijk, van F.A.

    2008-01-01

    AFLP is a frequently used DNA fingerprinting technique that is popular in the plant sciences. A problem encountered in the interpretation and comparison of individual plant profiles, consisting of band presence-absence patterns, is that multiple DNA fragments of the same length can be generated that

  1. On some surprising statistical properties of a DNA fingerprinting technique called AFLP

    NARCIS (Netherlands)

    Gort, G.

    2010-01-01

    AFLP is a widely used DNA fingerprinting technique, resulting in band absence - presence profiles, like a bar code. Bands represent DNA fragments, sampled from the genome of an individual plant or other organism. The DNA fragments travel through a lane of an electrophoretic gel or microcapillary sys

  2. Comparative transcriptional profiling and preliminary study on heterosis mechanism of super-hybrid rice

    NARCIS (Netherlands)

    Song, G.S.; Zhai, H.L.; Peng, Y.G.; Zhang, L.; Wei, G.; Chen, X.Y.; Xiao, Y.G.; Wang, L.; Chen, Y.J.; Wu, B.; Chen, B.; Zhang, Y.; Chen, H.; Feng, X.J.; Gong, W.K.; Liu, Y.; Yin, Z.J.; Wang, F.; Liu, G.Z.; Xu, H.L.; Wei, X.L.; Zhao, X.L.; Ouwerkerk, P.B.F.; Hankemeier, T.; Reijmers, T.; Heijden, R. van der; Lu, C.M.; Wang, M.; Greef, J. van der; Zhu, Z.

    2010-01-01

    Heterosis is a biological phenomenon whereby the offspring from two parents show improved and superior performance than either inbred parental lines. Hybrid rice is one of the most successful apotheoses in crops utilizing heterosis. Transcriptional profiling of F1 super-hybrid rice Liangyou-2186 and

  3. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

    DEFF Research Database (Denmark)

    Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T;

    2009-01-01

    JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database...

  4. Transcriptional profiling identifies physicochemical properties of nanomaterials that are determinants of the in vivo pulmonary response

    DEFF Research Database (Denmark)

    Halappanavar, Sabina; Saber, Anne Thoustrup; Decan, Nathalie;

    2015-01-01

    We applied transcriptional profiling to elucidate the mechanisms associated with pulmonary responses to titanium dioxide (TiO2) nanoparticles (NPs) of different sizes and surface coatings, and to determine if these responses are modified by NP size, surface area, surface modification, and embedding...

  5. Transcription profiles of non-immortalized breast cancer cell lines

    International Nuclear Information System (INIS)

    Searches for differentially expressed genes in tumours have made extensive use of array technology. Most samples have been obtained from tumour biopsies or from established tumour-derived cell lines. Here we compare cultures of non-immortalized breast cancer cells, normal non-immortalized breast cells and immortalized normal and breast cancer cells to identify which elements of a defined set of well-known cancer-related genes are differentially expressed. Cultures of cells from pleural effusions or ascitic fluids from breast cancer patients (MSSMs) were used in addition to commercially-available normal breast epithelial cells (HMECs), established breast cancer cell lines (T-est) and established normal breast cells (N-est). The Atlas Human Cancer 1.2 cDNA expression array was employed. The data obtained were analysed using widely-available statistical and clustering software and further validated through real-time PCR. According to Significance Analysis of Microarray (SAM) and AtlasImage software, 48 genes differed at least 2-fold in adjusted intensities between HMECs and MSSMs (p < 0.01). Some of these genes have already been directly linked with breast cancer, metastasis and malignant progression, whilst others encode receptors linked to signal transduction pathways or are otherwise related to cell proliferation. Fifty genes showed at least a 2.5-fold difference between MSSMs and T-est cells according to AtlasImage, 2-fold according to SAM. Most of these classified as genes related to metabolism and cell communication. The expression profiles of 1176 genes were determined in finite life-span cultures of metastatic breast cancer cells and of normal breast cells. Significant differences were detected between the finite life-span breast cancer cell cultures and the established breast cancer cell lines. These data suggest caution in extrapolating information from established lines for application to clinical cancer research

  6. Inference of transcription modification in long-live yeast strains from their expression profiles

    Directory of Open Access Journals (Sweden)

    Longo Valter D

    2007-07-01

    Full Text Available Abstract Background Three kinases: Sch9, PKA and TOR, are suggested to be involved in both the replicative and chronological ageing in yeast. They function in pathways whose down-regulation leads to life span extension. Several stress response proteins, including two transcription factors Msn2 and Msn4, mediate the longevity extension phenotype associated with decreased activity of either Sch9, PKA, or TOR. However, the mechanisms of longevity, especially the underlying transcription program have not been fully understood. Results We measured the gene expression profiles in wild type yeast and three long-lived mutants: sch9Δ, ras2Δ, and tor1Δ. To elucidate the transcription program that may account for the longevity extension, we identified the transcription factors that are systematically and significantly associated with the expression differentiation in these mutants with respect to wild type by integrating microarray expression data with motif and ChIP-chip data, respectively. Our analysis suggests that three stress response transcription factors, Msn2, Msn4 and Gis1, are activated in all the three mutants. We also identify some other transcription factors such as Fhl1 and Hsf1, which may also be involved in the transcriptional modification in the long-lived mutants. Conclusion Combining microarray expression data with other data sources such as motif and ChIP-chip data provides biological insights into the transcription modification that leads to life span extension. In the chronologically long-lived mutant: sch9Δ, ras2Δ, and tor1Δ, several common stress response transcription factors are activated compared with the wild type according to our systematic transcription inference.

  7. Root-Specific Transcript Profiling of Contrasting Rice Genotypes in Response to Salinity Stress

    Institute of Scientific and Technical Information of China (English)

    Olivier Cotsaftis; Darren Plett; Alexander A.T. Johnson; Harkamal Walia; Clyde Wilson; Abdelbagi M. Ismail; Timothy J. Close; Mark Tester; Ute Baumann

    2011-01-01

    Elevated salinity imposes osmotic and ion toxicity stresses on living cells and requires a multitude of responses in order to enable plant survival. Building on earlier work profiling transcript levels in rice (Oryza sativa) shoots of FL478, a salt-tolerant indica recombinant inbred line, and IR29, a salt-sensitive cultivar, transcript levels were compared in roots of these two accessions as well as in the roots of two additional salt-tolerant indica genotypes, the landrace Pokkali and the recombinant inbred line IR63731. The aim of this study was to compare transcripts in the sensitive and the tolerant lines in order to identify genes likely to be involved in plant salinity tolerance, rather than in responses to salinity perse. Transcript profiles of several gene families with known links to salinity tolerance are described (e.g. HKTs,NHXs). The putative function of a set of genes identified through their salt responsiveness, transcript levels, and/or chro-mosomal location (i.e. Underneath QTLs for salinity tolerance) is also discussed. Finally, the parental origin of the Saltol region in FL478 is further investigated. Overall, the dataset presented appears to be robust and it seems likely that this system could provide a reliable strategy for the discovery of novel genes involved in salinity tolerance.

  8. Transcription profiles of mitochondrial genes correlate with mitochondrial DNA haplotypes in a natural population of Silene vulgaris

    Directory of Open Access Journals (Sweden)

    Olson Matthew S

    2010-01-01

    Full Text Available Abstract Background Although rapid changes in copy number and gene order are common within plant mitochondrial genomes, associated patterns of gene transcription are underinvestigated. Previous studies have shown that the gynodioecious plant species Silene vulgaris exhibits high mitochondrial diversity and occasional paternal inheritance of mitochondrial markers. Here we address whether variation in DNA molecular markers is correlated with variation in transcription of mitochondrial genes in S. vulgaris collected from natural populations. Results We analyzed RFLP variation in two mitochondrial genes, cox1 and atp1, in offspring of ten plants from a natural population of S. vulgaris in Central Europe. We also investigated transcription profiles of the atp1 and cox1 genes. Most DNA haplotypes and transcription profiles were maternally inherited; for these, transcription profiles were associated with specific mitochondrial DNA haplotypes. One individual exhibited a pattern consistent with paternal inheritance of mitochondrial DNA; this individual exhibited a transcription profile suggestive of paternal but inconsistent with maternal inheritance. We found no associations between gender and transcript profiles. Conclusions Specific transcription profiles of mitochondrial genes were associated with specific mitochondrial DNA haplotypes in a natural population of a gynodioecious species S. vulgaris. Our findings suggest the potential for a causal association between rearrangements in the plant mt genome and transcription product variation.

  9. Berry flesh and skin ripening features in Vitis vinifera as assessed by transcriptional profiling.

    Directory of Open Access Journals (Sweden)

    Diego Lijavetzky

    Full Text Available BACKGROUND: Ripening of fleshy fruit is a complex developmental process involving the differentiation of tissues with separate functions. During grapevine berry ripening important processes contributing to table and wine grape quality take place, some of them flesh- or skin-specific. In this study, transcriptional profiles throughout flesh and skin ripening were followed during two different seasons in a table grape cultivar 'Muscat Hamburg' to determine tissue-specific as well as common developmental programs. METHODOLOGY/PRINCIPAL FINDINGS: Using an updated GrapeGen Affymetrix GeneChip® annotation based on grapevine 12×v1 gene predictions, 2188 differentially accumulated transcripts between flesh and skin and 2839 transcripts differentially accumulated throughout ripening in the same manner in both tissues were identified. Transcriptional profiles were dominated by changes at the beginning of veraison which affect both pericarp tissues, although frequently delayed or with lower intensity in the skin than in the flesh. Functional enrichment analysis identified the decay on biosynthetic processes, photosynthesis and transport as a major part of the program delayed in the skin. In addition, a higher number of functional categories, including several related to macromolecule transport and phenylpropanoid and lipid biosynthesis, were over-represented in transcripts accumulated to higher levels in the skin. Functional enrichment also indicated auxin, gibberellins and bHLH transcription factors to take part in the regulation of pre-veraison processes in the pericarp, whereas WRKY and C2H2 family transcription factors seems to more specifically participate in the regulation of skin and flesh ripening, respectively. CONCLUSIONS/SIGNIFICANCE: A transcriptomic analysis indicates that a large part of the ripening program is shared by both pericarp tissues despite some components are delayed in the skin. In addition, important tissue differences are

  10. Genetic Comparison of B. Anthracis and its Close Relatives Using AFLP and PCR Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, P.J.; Hill, K.K.; Laker, M.T.; Ticknor, L.O.; Keim, P.S.

    1999-02-01

    Amplified Fragment length Polymorphism (AFLP) analysis allows a rapid, relatively simple analysis of a large portion of a microbial genome, providing information about the species and its phylogenetic relationship to other microbes (Vos, et al., 1995). The method simply surveys the genome for length and sequence polymorphisms. The pattern identified can be used for comparison to the genomes of other species. Unlike other methods, it does not rely on analysis of a single genetic locus that may bias the interpretation of results and it does not require any prior knowledge of the targeted organism. Moreover, a standard set of reagents can be applied to any species without using species-specific information or molecular probes. The authors are using AFLP's to rapidly identify different bacterial species. A comparison of AFLP profiles generated from a large battery of B. anthracis strains shows very little variability among different isolates (Keim, et al., 1997). By contrast, there is a significant difference between AFLP profiles generated for any B. anthracis strain and even the most closely related Bacillus species. Sufficient variability is apparent among all known microbial species to allow phylogenetic analysis based on large numbers of genetically unlinked loci. These striking differences among AFLP profiles allow unambiguous identification of previously identified species and phylogenetic placement of newly characterized isolates relative to known species based on a large number of independent genetic loci. Data generated thus far show that the method provides phylogenetic analyses that are consistent with other widely accepted phylogenetic methods. However, AFLP analysis provides a more detailed analysis of the targets and samples a much larger portion of the genome. Consequently, it provides an inexpensive, rapid means of characterizing microbial isolates to further differentiate among strains and closely related microbial species. Such information

  11. AFLP variation in 25 Avena species.

    Science.gov (United States)

    Fu, Yong-Bi; Williams, David J

    2008-08-01

    Current molecular characterization of ex situ plant germplasm has placed more emphasis on cultivated gene pools and less on exotic gene pools representing wild relative species. This study attempted to characterize a selected set of germplasm accessions representing various Avena species with the hope to establish a reference set of exotic oat germplasm for oat breeding and research. The amplified fragment length polymorphism (AFLP) technique was applied to screen 163 accessions of 25 Avena species with diverse geographic origins. For each accession, 413 AFLP polymorphic bands detected by five AFLP primer pairs were scored. The frequencies of polymorphic bands ranged from 0.006 to 0.994 and averaged 0.468. Analysis of molecular variance revealed 59.5% of the total AFLP variation resided among 25 oat species, 45.9% among six assessed sections of the genus, 36.1% among three existing ploidy levels, and 50.8% among eight defined genome types. All the species were clustered together according to their ploidy levels. The C genome diploids appeared to be the most distinct, followed by the Ac genome diploid A. canariensis. The Ac genome seemed to be the oldest in all the A genomes, followed by the As, Al and Ad genomes. The AC genome tetraploids were more related to the ACD genome hexaploids than the AB genome tetraploids. Analysis of AFLP similarity suggested that the AC genome tetraploid A. maroccana was likely derived from the Cp genome diploid A. eriantha and the As genome diploid A. wiestii, and might be the progenitor of the ACD genome hexaploids. These AFLP patterns are significant for our understanding of the evolutionary pathways of Avena species and genomes, for establishing reference sets of exotic oat germplasm, and for exploring new exotic sources of genes for oat improvement.

  12. Overview on the application of transcription profiling using selected nephrotoxicants for toxicology assessment.

    OpenAIRE

    Kramer, Jeffrey A; Pettit, Syril D.; Amin, Rupesh P; Bertram, Timothy A; Car, Bruce; Cunningham, Michael; Curtiss, Sandra W.; Davis, John W.; Kind, Clive; Lawton, Michael; Naciff, Jorge M; Oreffo, Victor; Roman, Richard J.; Sistare, Frank D.; Stevens, James

    2004-01-01

    Microarrays allow for the simultaneous measurement of changes in the levels of thousands of messenger RNAs within a single experiment. As such, the potential for the application of transcription profiling to preclinical safety assessment and mechanism-based risk assessment is profound. However, several practical and technical challenges remain. Among these are nomenclature issues, platform-specific data formats, and the lack of uniform analysis methods and tools. Experiments were designed to ...

  13. Transcriptional profiling uncovers a network of cholesterol-responsive atherosclerosis target genes.

    Directory of Open Access Journals (Sweden)

    Josefin Skogsberg

    2008-03-01

    Full Text Available Despite the well-documented effects of plasma lipid lowering regimes halting atherosclerosis lesion development and reducing morbidity and mortality of coronary artery disease and stroke, the transcriptional response in the atherosclerotic lesion mediating these beneficial effects has not yet been carefully investigated. We performed transcriptional profiling at 10-week intervals in atherosclerosis-prone mice with human-like hypercholesterolemia and a genetic switch to lower plasma lipoproteins (Ldlr(-/-Apo(100/100Mttp(flox/flox Mx1-Cre. Atherosclerotic lesions progressed slowly at first, then expanded rapidly, and plateaued after advanced lesions formed. Analysis of lesion expression profiles indicated that accumulation of lipid-poor macrophages reached a point that led to the rapid expansion phase with accelerated foam-cell formation and inflammation, an interpretation supported by lesion histology. Genetic lowering of plasma cholesterol (e.g., lipoproteins at this point all together prevented the formation of advanced plaques and parallel transcriptional profiling of the atherosclerotic arterial wall identified 37 cholesterol-responsive genes mediating this effect. Validation by siRNA-inhibition in macrophages incubated with acetylated-LDL revealed a network of eight cholesterol-responsive atherosclerosis genes regulating cholesterol-ester accumulation. Taken together, we have identified a network of atherosclerosis genes that in response to plasma cholesterol-lowering prevents the formation of advanced plaques. This network should be of interest for the development of novel atherosclerosis therapies.

  14. Transcriptome response of the Pacific oyster (Crassostrea gigas) to infection with Vibrio tubiashii using cDNA AFLP differential display

    Science.gov (United States)

    We used qualitative complementary DNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) differential display analysis and real-time, quantitative PCR (RT-qPCR) to identify genes in the Pacific oyster Crassostrea gigas whose transcription either changes in response to exposure to a pathogenic bacter...

  15. Resequencing of Curcuma longa L. cv. Kedaram through transcriptome profiling reveals various novel transcripts.

    Science.gov (United States)

    Sahoo, Ambika; Jena, Sudipta; Sahoo, Suprava; Nayak, Sanghamitra; Kar, Basudeba

    2016-09-01

    Curcuma longa L. (Turmeric), of the family Zingiberaceae, is one of the economically as well as medicinally important plant species. It is a sterile, polyploid and vegetatively propagated spice crop cultivated usually in Southeast Asia. In the current study, we carried out re-sequencing through transcriptome profiling of Curcuma longa cv. Kedaram (Cl_Ked_6). We acquired a total of 1 GB raw data by resequencing through paired-end sequencing using Nextseq 500 platform. The raw data obtained in this study can be accessible in NCBI database with accession number of SRR3928562 with bioproject accession number PRJNA324755. Cufflinks-2.2.1 tool was used for transcriptome assembly which resulted in 39,554 numbers of transcripts. The transcript length ranged from 76 to 15,568, having N50 value of 1221 and median transcript length of 860. We annotated the transcripts using multiple databases. This data will be beneficial for studying sequence variations particularly SNPs between cultivars of turmeric towards authentic identification and discovery of novel functional transcripts in Kedaram. PMID:27595066

  16. Transcript profiling of Elf5+/- mammary glands during pregnancy identifies novel targets of Elf5.

    Directory of Open Access Journals (Sweden)

    Renee L Rogers

    Full Text Available BACKGROUND: Elf5, an epithelial specific Ets transcription factor, plays a crucial role in the pregnancy-associated development of the mouse mammary gland. Elf5(-/- embryos do not survive, however the Elf5(+/- mammary gland displays a severe pregnancy-associated developmental defect. While it is known that Elf5 is crucial for correct mammary development and lactation, the molecular mechanisms employed by Elf5 to exert its effects on the mammary gland are largely unknown. PRINCIPAL FINDINGS: Transcript profiling was used to investigate the transcriptional changes that occur as a result of Elf5 haploinsufficiency in the Elf5(+/- mouse model. We show that the development of the mouse Elf5(+/- mammary gland is delayed at a transcriptional and morphological level, due to the delayed increase in Elf5 protein in these glands. We also identify a number of potential Elf5 target genes, including Mucin 4, whose expression, is directly regulated by the binding of Elf5 to an Ets binding site within its promoter. CONCLUSION: We identify novel transcriptional targets of Elf5 and show that Muc4 is a direct target of Elf5, further elucidating the mechanisms through which Elf5 regulates proliferation and differentiation in the mammary gland.

  17. Transcriptional Profiling of Endobronchial Ultrasound-Guided Lymph Node Samples Aids Diagnosis of Mediastinal Lymphadenopathy

    Science.gov (United States)

    Tomlinson, Gillian S.; Thomas, Niclas; Chain, Benjamin M.; Best, Katharine; Simpson, Nandi; Hardavella, Georgia; Brown, James; Bhowmik, Angshu; Navani, Neal; Janes, Samuel M.; Miller, Robert F.; Noursadeghi, Mahdad

    2016-01-01

    Background Endobronchial ultrasound (EBUS)-guided biopsy is the mainstay for investigation of mediastinal lymphadenopathy for laboratory diagnosis of malignancy, sarcoidosis, or TB. However, improved methods for discriminating between TB and sarcoidosis and excluding malignancy are still needed. We sought to evaluate the role of genomewide transcriptional profiling to aid diagnostic processes in this setting. Methods Mediastinal lymph node samples from 88 individuals were obtained by EBUS-guided aspiration for investigation of mediastinal lymphadenopathy and subjected to transcriptional profiling in addition to conventional laboratory assessments. Computational strategies were used to evaluate the potential for using the transcriptome to distinguish between diagnostic categories. Results Molecular signatures associated with granulomas or neoplastic and metastatic processes were clearly discernible in granulomatous and malignant lymph node samples, respectively. Support vector machine (SVM) learning using differentially expressed genes showed excellent sensitivity and specificity profiles in receiver operating characteristic curve analysis with area under curve values > 0.9 for discriminating between granulomatous and nongranulomatous disease, TB and sarcoidosis, and between cancer and reactive lymphadenopathy. A two-step decision tree using SVM to distinguish granulomatous and nongranulomatous disease, then between TB and sarcoidosis in granulomatous cases, and between cancer and reactive lymphadenopathy in nongranulomatous cases, achieved > 90% specificity for each diagnosis and afforded greater sensitivity than existing tests to detect TB and cancer. In some diagnostically ambiguous cases, computational classification predicted granulomatous disease or cancer before pathologic abnormalities were evident. Conclusions Machine learning analysis of transcriptional profiling in mediastinal lymphadenopathy may significantly improve the clinical utility of EBUS

  18. Breeding response of transcript profiling in developing seeds of Brassica napus

    Directory of Open Access Journals (Sweden)

    Li Xiaodan

    2009-05-01

    Full Text Available Abstract Background The upgrading of rapeseed cultivars has resulted in a substantial improvement in yield and quality in China over the past 30 years. With the selective pressure against fatty acid composition and oil content, high erucic acid- and low oil-content cultivars have been replaced by low erucic acid- and high oil-content cultivars. The high erucic acid cultivar Zhongyou 821 and its descendent, low erucic acid cultivar Zhongshuang 9, are representatives of two generations of the most outstanding Chinese rapeseed cultivars (B. napus developed the past 2 decades. This paper compares the transcriptional profiles of Zhongshuang 9 and Zhongyou 821 for 32 genes that are principally involved in lipid biosynthesis during seed development in order to elucidate how the transcriptional profiles of these genes responded to quality improvement over the past 20 years. Results Comparison of the cultivar Zhongyou 821 with its descendent, Zhongshuang 9, shows that the transcriptional levels of seven of the 32 genes were upregulated by 30% to 109%, including FAD3, ACCase, FAE1, GKTP, Caleosin, GAPDH, and PEPC. Of the 32 genes, 10 (KAS3, β-CT, BcRK6, P450, FatA, Oleosin, FAD6, FatB, α-CT and SUC1 were downregulated by at least 20% and most by 50%. The Napin gene alone accounted for over 75% of total transcription from all 32 genes assessed in both cultivars. Most of the genes showed significant correlation with fatty acid accumulation, but the correlation in ZS9 was significantly different from that in ZY821. Higher KCR2 activity is associated with higher C16:0, C18:0, and C18:2 in both cultivars, lower C22:1 and total fatty acid content in ZY821, and lower 18:1 in ZS9. Conclusion This paper illustrates the response of the transcription levels of 32 genes to breeding in developing rapeseed seeds. Both cultivars showed similar transcription profiles, with the Napin gene predominantly transcribed. Selective pressure for zero erucic acid, low

  19. AFLP fingerprinting of tartary buckwheat accessions (Fagopyrum tataricum) displaying rutin content variation.

    Science.gov (United States)

    Gupta, Nidhi; Sharma, Sunil K; Rana, Jai C; Chauhan, Rajinder S

    2012-09-01

    In light of the economic importance of buckwheat as well as existence of enormous accessions of Fagopyrum species in the Himalayan regions of India, the characterization of tartary buckwheat for rutin content variation vis-à-vis DNA fingerprinting was undertaken so as to identify fingerprint profiles unique to high rutin content accessions. Rutin content analysis in mature seeds of 195 accessions of Fagopyrum tataricum showed a wide range of variation (6 μg/mg to 30 μg/mg D.W.) with most of the accessions (81%) containing 10-16 μg/mg of rutin followed by 14% accessions with significantly higher rutin content (17 μg/mg to 30 μg/mg) and 5% accessions with low rutin content (≤10 μg/mg). AFLP fingerprinting of 18 accessions having high (≥17 μg/mg) and low rutin content (≤10 μg/mg) with 19 EcoRI/MseI primer combinations yielded 136 polymorphic fragments out of total 907. The hierarchical and model-based cluster analyses of AFLP data strongly suggested that the 18 populations of F. tataricum were clustered into two separate groups. The high and low rutin content accessions were clustered into two separate groups based on AFLP fingerprinting. The AFLP fingerprints associated with high rutin content accessions of F. tataricum are expected to be useful for evaluation, conservation and genetic improvement of buckwheat.

  20. Comparison of susceptibility and transcription profile of the new antifungal hassallidin A with caspofungin

    International Nuclear Information System (INIS)

    This is First report on the antifungal effects of the new glycolipopeptide hassallidin A. Due to related molecular structure moieties between hassallidin A and the established antifungal drug caspofungin we assumed parallels in the effects on cell viability. Therefore we compared hassallidin A with caspofungin by antifungal susceptibility testing and by analysing the genome-wide transcriptional profile of Candida albicans. Furthermore, we examined modifications in ultracellular structure due to hassallidin A treatment by electron microscopy. Hassallidin A was found to be fungicidal against all tested Candida species and Cryptococcus neoformans isolates. MICs ranged from 4 to 8 μg/ml, independently from the species. Electron microscopy revealed noticeable ultrastructural changes in C. albicans cells exposed to hassallidin A. Comparing the transcriptional profile of C. albicans cells treated with hassallidin A to that of cells exposed to caspofungin, only 20 genes were found to be similarly up- or down-regulated in both assays, while 227 genes were up- or down-regulated induced by hassallidin A specifically. Genes up-regulated in cells exposed to hassallidin A included metabolic and mitotic genes, while genes involved in DNA repair, vesicle docking, and membrane fusion were down-regulated. In summary, our data suggest that, although hassallidin A and caspofungin have similar structures, however, the effects on susceptibility and transcriptional response to yeasts seem to be different

  1. Transcription profiling provides insights into gene pathways involved in horn and scurs development in cattle

    Directory of Open Access Journals (Sweden)

    Lehnert Sigrid A

    2010-06-01

    Full Text Available Abstract Background Two types of horns are evident in cattle - fixed horns attached to the skull and a variation called scurs, which refers to small loosely attached horns. Cattle lacking horns are referred to as polled. Although both the Poll and Scurs loci have been mapped to BTA1 and 19 respectively, the underlying genetic basis of these phenotypes is unknown, and so far, no candidate genes regulating these developmental processes have been described. This study is the first reported attempt at transcript profiling to identify genes and pathways contributing to horn and scurs development in Brahman cattle, relative to polled counterparts. Results Expression patterns in polled, horned and scurs tissues were obtained using the Agilent 44 k bovine array. The most notable feature when comparing transcriptional profiles of developing horn tissues against polled was the down regulation of genes coding for elements of the cadherin junction as well as those involved in epidermal development. We hypothesize this as a key event involved in keratinocyte migration and subsequent horn development. In the polled-scurs comparison, the most prevalent differentially expressed transcripts code for genes involved in extracellular matrix remodelling, which were up regulated in scurs tissues relative to polled. Conclusion For this first time we describe networks of genes involved in horn and scurs development. Interestingly, we did not observe differential expression in any of the genes present on the fine mapped region of BTA1 known to contain the Poll locus.

  2. Transcriptional profiling of the pea shoot apical meristem reveals processes underlying its function and maintenance

    Directory of Open Access Journals (Sweden)

    Singh Mohan B

    2008-06-01

    Full Text Available Abstract Background Despite the importance of the shoot apical meristem (SAM in plant development and organ formation, our understanding of the molecular mechanisms controlling its function is limited. Genomic tools have the potential to unravel the molecular mysteries of the SAM, and legume systems are increasingly being used in plant-development studies owing to their unique characteristics such as nitrogen fixation, secondary metabolism, and pod development. Garden pea (Pisum sativum is a well-established classic model species for genetics studies that has been used since the Mendel era. In addition, the availability of a plethora of developmental mutants makes pea an ideal crop legume for genomics studies. This study aims to utilise genomics tools in isolating genes that play potential roles in the regulation of SAM activity. Results In order to identify genes that are differentially expressed in the SAM, we generated 2735 ESTs from three cDNA libraries derived from freshly micro-dissected SAMs from 10-day-old garden peas (Pisum sativum cv Torsdag. Custom-designed oligonucleotide arrays were used to compare the transcriptional profiles of pea SAMs and non-meristematic tissues. A total of 184 and 175 transcripts were significantly up- or down-regulated in the pea SAM, respectively. As expected, close to 61% of the transcripts down-regulated in the SAM were found in the public database, whereas sequences from the same source only comprised 12% of the genes that were expressed at higher levels in the SAM. This highlights the under-representation of transcripts from the meristematic tissues in the current public pea protein database, and demonstrates the utility of our SAM EST collection as an essential genetic resource for revealing further information on the regulation of this developmental process. In addition to unknowns, many of the up-regulated transcripts are known to encode products associated with cell division and proliferation

  3. Dynamic Metabolite Profiling in an Archaeon Connects Transcriptional Regulation to Metabolic Consequences.

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    Horia Todor

    Full Text Available Previous work demonstrated that the TrmB transcription factor is responsible for regulating the expression of many enzyme-coding genes in the hypersaline-adapted archaeon Halobacterium salinarum via a direct interaction with a cis-regulatory sequence in their promoters. This interaction is abolished in the presence of glucose. Although much is known about the effects of TrmB at the transcriptional level, it remains unclear whether and to what extent changes in mRNA levels directly affect metabolite levels. In order to address this question, here we performed a high-resolution metabolite profiling time course during a change in nutrients using a combination of targeted and untargeted methods in wild-type and ΔtrmB strain backgrounds. We found that TrmB-mediated transcriptional changes resulted in widespread and significant changes to metabolite levels across the metabolic network. Additionally, the pattern of growth complementation using various purines suggests that the mis-regulation of gluconeogenesis in the ΔtrmB mutant strain in the absence of glucose results in low phosphoribosylpyrophosphate (PRPP levels. We confirmed these low PRPP levels using a quantitative mass spectrometric technique and found that they are associated with a metabolic block in de novo purine synthesis, which is partially responsible for the growth defect of the ΔtrmB mutant strain in the absence of glucose. In conclusion, we show how transcriptional regulation of metabolism affects metabolite levels and ultimately, phenotypes.

  4. Dynamic Metabolite Profiling in an Archaeon Connects Transcriptional Regulation to Metabolic Consequences.

    Science.gov (United States)

    Todor, Horia; Gooding, Jessica; Ilkayeva, Olga R; Schmid, Amy K

    2015-01-01

    Previous work demonstrated that the TrmB transcription factor is responsible for regulating the expression of many enzyme-coding genes in the hypersaline-adapted archaeon Halobacterium salinarum via a direct interaction with a cis-regulatory sequence in their promoters. This interaction is abolished in the presence of glucose. Although much is known about the effects of TrmB at the transcriptional level, it remains unclear whether and to what extent changes in mRNA levels directly affect metabolite levels. In order to address this question, here we performed a high-resolution metabolite profiling time course during a change in nutrients using a combination of targeted and untargeted methods in wild-type and ΔtrmB strain backgrounds. We found that TrmB-mediated transcriptional changes resulted in widespread and significant changes to metabolite levels across the metabolic network. Additionally, the pattern of growth complementation using various purines suggests that the mis-regulation of gluconeogenesis in the ΔtrmB mutant strain in the absence of glucose results in low phosphoribosylpyrophosphate (PRPP) levels. We confirmed these low PRPP levels using a quantitative mass spectrometric technique and found that they are associated with a metabolic block in de novo purine synthesis, which is partially responsible for the growth defect of the ΔtrmB mutant strain in the absence of glucose. In conclusion, we show how transcriptional regulation of metabolism affects metabolite levels and ultimately, phenotypes.

  5. Analysis of subtelomeric virulence gene families in Plasmodium falciparum by comparative transcriptional profiling.

    Science.gov (United States)

    Witmer, Kathrin; Schmid, Christoph D; Brancucci, Nicolas M B; Luah, Yen-Hoon; Preiser, Peter R; Bozdech, Zbynek; Voss, Till S

    2012-04-01

    The Plasmodium falciparum genome is equipped with several subtelomeric gene families that are implicated in parasite virulence and immune evasion. Members of these families are uniformly positioned within heterochromatic domains and are thus subject to variegated expression. The best-studied example is that of the var family encoding the major parasite virulence factor P. falciparum erythrocyte membrane protein 1 (PfEMP1). PfEMP1 undergoes antigenic variation through switches in mutually exclusive var gene transcription. var promoters function as crucial regulatory elements in the underlying epigenetic control strategy. Here, we analysed promoters of upsA, upsB and upsC var, rifA1-type rif, stevor, phist and pfmc-2tm genes and investigated their role in endogenous gene transcription by comparative genome-wide expression profiling of transgenic parasite lines. We find that the three major var promoter types are functionally equal and play an essential role in singular gene choice. Unlike var promoters, promoters of non-var families are not silenced by default, and transcription of non-var families is not subject to the same mode of mutually exclusive transcription as has been observed for var genes. Our findings identified a differential logic in the regulation of var and other subtelomeric virulence gene families, which will have important implications for our understanding and future analyses of phenotypic variation in malaria parasites. PMID:22435676

  6. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

    DEFF Research Database (Denmark)

    Mathelier, Anthony; Fornes, Oriol; Arenillas, David J;

    2016-01-01

    JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we...

  7. A multi-gene transcriptional profiling approach to the discovery of cell signature markers.

    Science.gov (United States)

    Wada, Youichiro; Li, Dan; Merley, Anne; Zukauskas, Andrew; Aird, William C; Dvorak, Harold F; Shih, Shou-Ching

    2011-01-01

    A profile of transcript abundances from multiple genes constitutes a molecular signature if the expression pattern is unique to one cell type. Here we measure mRNA copy numbers per cell by normalizing per million copies of 18S rRNA and identify 6 genes (TIE1, KDR, CDH5, TIE2, EFNA1 and MYO5C) out of 79 genes tested as excellent molecular signature markers for endothelial cells (ECs) in vitro. The selected genes are uniformly expressed in ECs of 4 different origins but weakly or not expressed in 4 non-EC cell lines. A multi-gene transcriptional profile of these 6 genes clearly distinguishes ECs from non-ECs in vitro. We conclude that (i) a profile of mRNA copy numbers per cell from a well-chosen multi-gene panel can act as a sensitive and accurate cell type signature marker, and (ii) the method described here can be applied to in vivo cell fingerprinting and molecular diagnosis. PMID:20972619

  8. Genome-wide transcriptional profiling of human glioblastoma cells in response to ITE treatment.

    Science.gov (United States)

    Kang, Bo; Zhou, Yanwen; Zheng, Min; Wang, Ying-Jie

    2015-09-01

    A ligand-activated transcription factor aryl hydrocarbon receptor (AhR) is recently revealed to play a key role in embryogenesis and tumorigenesis (Feng et al. [1], Safe et al. [2]) and 2-(1'H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE) (Song et al. [3]) is an endogenous AhR ligand that possesses anti-tumor activity. In order to gain insights into how ITE acts via the AhR in embryogenesis and tumorigenesis, we analyzed the genome-wide transcriptional profiles of the following three groups of cells: the human glioblastoma U87 parental cells, U87 tumor sphere cells treated with vehicle (DMSO) and U87 tumor sphere cells treated with ITE. Here, we provide the details of the sample gathering strategy and show the quality controls and the analyses associated with our gene array data deposited into the Gene Expression Omnibus (GEO) under the accession code of GSE67986.

  9. Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences

    Science.gov (United States)

    Halperin, Yonit; Linhart, Chaim; Ulitsky, Igor; Shamir, Ron

    A key goal of gene expression analysis is the characterization of transcription factors (TFs) and micro-RNAs (miRNAs) regulating specific transcriptional programs. The most common approach to address this task is a two-step methodology: In the first step, a clustering procedure is executed to partition the genes into groups that are believed to be co-regulated, based on expression profile similarity. In the second step, a motif discovery tool is applied to search for over-represented cis-regulatory motifs within each group. In an effort to obtain better results by simultaneously utilizing all available information, several studies have suggested computational schemes for a single-step combined analysis of expression and sequence data. Despite extensive research, reverse engineering complex regulatory networks from microarray measurements remains a difficult challenge with limited success, especially in metazoans.

  10. Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes

    Directory of Open Access Journals (Sweden)

    Deyholos Michael K

    2006-10-01

    Full Text Available Abstract Background Roots are an attractive system for genomic and post-genomic studies of NaCl responses, due to their primary importance to agriculture, and because of their relative structural and biochemical simplicity. Excellent genomic resources have been established for the study of Arabidopsis roots, however, a comprehensive microarray analysis of the root transcriptome following NaCl exposure is required to further understand plant responses to abiotic stress and facilitate future, systems-based analyses of the underlying regulatory networks. Results We used microarrays of 70-mer oligonucleotide probes representing 23,686 Arabidopsis genes to identify root transcripts that changed in relative abundance following 6 h, 24 h, or 48 h of hydroponic exposure to 150 mM NaCl. Enrichment analysis identified groups of structurally or functionally related genes whose members were statistically over-represented among up- or down-regulated transcripts. Our results are consistent with generally observed stress response themes, and highlight potentially important roles for underappreciated gene families, including: several groups of transporters (e.g. MATE, LeOPT1-like; signalling molecules (e.g. PERK kinases, MLO-like receptors, carbohydrate active enzymes (e.g. XTH18, transcription factors (e.g. members of ZIM, WRKY, NAC, and other proteins (e.g. 4CL-like, COMT-like, LOB-Class 1. We verified the NaCl-inducible expression of selected transcription factors and other genes by qRT-PCR. Conclusion Micorarray profiling of NaCl-treated Arabidopsis roots revealed dynamic changes in transcript abundance for at least 20% of the genome, including hundreds of transcription factors, kinases/phosphatases, hormone-related genes, and effectors of homeostasis, all of which highlight the complexity of this stress response. Our identification of these transcriptional responses, and groups of evolutionarily related genes with either similar or divergent

  11. Transcriptional profiling of subcutaneous adipose tissue in Italian Large White pigs divergent for backfat thickness.

    Science.gov (United States)

    Zambonelli, P; Gaffo, E; Zappaterra, M; Bortoluzzi, S; Davoli, R

    2016-06-01

    Fat deposition is a widely studied trait in pigs because of its implications with animal growth efficiency, technological and nutritional characteristics of meat products, but the global framework of the biological and molecular processes regulating fat deposition in pigs is still incomplete. This study describes the backfat tissue transcription profile in Italian Large White pigs and reports genes differentially expressed between fat and lean animals according to RNA-seq data. The backfat transcription profile was characterised by the expression of 23 483 genes, of which 54.1% were represented by known genes. Of 63 418 expressed transcripts, about 80% were non-previously annotated isoforms. By comparing the expression level of fat vs. lean pigs, we detected 86 robust differentially expressed transcripts, 72 more highly expressed (e.g. ACP5, BCL2A1, CCR1, CD163, CD1A, EGR2, ENPP1, GPNMB, INHBB, LYZ, MSR1, OLR1, PIK3AP1, PLIN2, SPP1, SLC11A1, STC1) and 14 lower expressed (e.g. ADSSL1, CDO1, DNAJB1, HSPA1A, HSPA1B, HSPA2, HSPB8, IGFBP5, OLFML3) in fat pigs. The main functional categories enriched in differentially expressed genes were immune system process, response to stimulus, cell activation and skeletal system development, for the overexpressed genes, and unfolded protein binding and stress response, for the underexpressed genes, which included five heat shock proteins. Adipose tissue alterations and impaired stress response are linked to inflammation and, in turn, to adipose tissue secretory activity, similar to what is observed in human obesity. Our results provide the opportunity to identify biomarkers of carcass fat traits to improve the pig production chain and to identify genetic factors that regulate the observed differential expression. PMID:26931818

  12. Comparative transcriptional profiling of human Merkel cells and Merkel cell carcinoma.

    Science.gov (United States)

    Mouchet, Nicolas; Coquart, Nolwenn; Lebonvallet, Nicolas; Le Gall-Ianotto, Christelle; Mogha, Ariane; Fautrel, Alain; Boulais, Nicholas; Dréno, Brigitte; Martin, Ludovic; Hu, Weiguo; Galibert, Marie-Dominique; Misery, Laurent

    2014-12-01

    Merkel cell carcinoma is believed to be derived from Merkel cells after infection by Merkel cell polyomavirus (MCPyV) and other poorly understood events. Transcriptional profiling using cDNA microarrays was performed on cells from MCPy-negative and MCPy-positive Merkel cell carcinomas and isolated normal Merkel cells. This microarray revealed numerous significantly upregulated genes and some downregulated genes. The extensive list of genes that were identified in these experiments provides a large body of potentially valuable information of Merkel cell carcinoma carcinogenesis and could represent a source of potential targets for cancer therapy.

  13. A multi-gene transcriptional profiling approach to the discovery of cell signature markers

    OpenAIRE

    Wada, Youichiro; Li, Dan; Merley, Anne; Zukauskas, Andrew; Aird, William C.; Dvorak, Harold F.; Shih, Shou-Ching

    2010-01-01

    A profile of transcript abundances from multiple genes constitutes a molecular signature if the expression pattern is unique to one cell type. Here we measure mRNA copy numbers per cell by normalizing per million copies of 18S rRNA and identify 6 genes (TIE1, KDR, CDH5, TIE2, EFNA1 and MYO5C) out of 79 genes tested as excellent molecular signature markers for endothelial cells (ECs) in vitro. The selected genes are uniformly expressed in ECs of 4 different origins but weakly or not expressed ...

  14. Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain.

    Science.gov (United States)

    Krienen, Fenna M; Yeo, B T Thomas; Ge, Tian; Buckner, Randy L; Sherwood, Chet C

    2016-01-26

    The human brain is patterned with disproportionately large, distributed cerebral networks that connect multiple association zones in the frontal, temporal, and parietal lobes. The expansion of the cortical surface, along with the emergence of long-range connectivity networks, may be reflected in changes to the underlying molecular architecture. Using the Allen Institute's human brain transcriptional atlas, we demonstrate that genes particularly enriched in supragranular layers of the human cerebral cortex relative to mouse distinguish major cortical classes. The topography of transcriptional expression reflects large-scale brain network organization consistent with estimates from functional connectivity MRI and anatomical tracing in nonhuman primates. Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across the cerebral cortex of postmortem human brains (n = 6). Unimodal sensory and motor zones have similar molecular profiles, despite being distributed across the cortical mantle. Sensory/motor profiles were anticorrelated with paralimbic and certain distributed association network profiles. Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii) genes cortically enriched in humans relative to nonhuman primates, (iii) genes related to connectivity in rodents, (iv) genes associated with human and mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies. Molecular innovations of upper cortical layers may be an important component in the evolution of long-range corticocortical projections.

  15. Transcriptional profiling of endocrine cerebro-osteodysplasia using microarray and next-generation sequencing.

    Directory of Open Access Journals (Sweden)

    Piya Lahiry

    Full Text Available BACKGROUND: Transcriptome profiling of patterns of RNA expression is a powerful approach to identify networks of genes that play a role in disease. To date, most mRNA profiling of tissues has been accomplished using microarrays, but next-generation sequencing can offer a richer and more comprehensive picture. METHODOLOGY/PRINCIPAL FINDINGS: ECO is a rare multi-system developmental disorder caused by a homozygous mutation in ICK encoding intestinal cell kinase. We performed gene expression profiling using both cDNA microarrays and next-generation mRNA sequencing (mRNA-seq of skin fibroblasts from ECO-affected subjects. We then validated a subset of differentially expressed transcripts identified by each method using quantitative reverse transcription-polymerase chain reaction (qRT-PCR. Finally, we used gene ontology (GO to identify critical pathways and processes that were abnormal according to each technical platform. Methodologically, mRNA-seq identifies a much larger number of differentially expressed genes with much better correlation to qRT-PCR results than the microarray (r² = 0.794 and 0.137, respectively. Biologically, cDNA microarray identified functional pathways focused on anatomical structure and development, while the mRNA-seq platform identified a higher proportion of genes involved in cell division and DNA replication pathways. CONCLUSIONS/SIGNIFICANCE: Transcriptome profiling with mRNA-seq had greater sensitivity, range and accuracy than the microarray. The two platforms generated different but complementary hypotheses for further evaluation.

  16. The application of AFLP fingerprinting in breeding of Brassica napus

    OpenAIRE

    Cuřínová, Petra

    2008-01-01

    AFLP markers are widely used in breeding in some other crops, but their utilization in breeding of Brassica crops is not so frequent. AFLP markers are used for molecular characterization of particular varieties or genotypes and for evaluation of genetic diversity. The aim of this thesis was the application of this method in breeding of rapeseed and in comparative study of genetic variability of different oil seed rape cultivars of Czech, Czechoslovak and German origin. AFLP is based on select...

  17. Age-related behaviors have distinct transcriptional profiles in Caenorhabditis elegans.

    Science.gov (United States)

    Golden, Tamara R; Hubbard, Alan; Dando, Caroline; Herren, Michael A; Melov, Simon

    2008-12-01

    There has been a great deal of interest in identifying potential biomarkers of aging. Biomarkers of aging would be useful to predict potential vulnerabilities in an individual that may arise well before they are chronologically expected, due to idiosyncratic aging rates that occur between individuals. Prior attempts to identify biomarkers of aging have often relied on the comparisons of long-lived animals to a wild-type control. However, the effect of interventions in model systems that prolong lifespan (such as single gene mutations or caloric restriction) can sometimes be difficult to interpret due to the manipulation itself having multiple unforeseen consequences on physiology, unrelated to aging itself. The search for predictive biomarkers of aging therefore is problematic, and the identification of metrics that can be used to predict either physiological or chronological age would be of great value. One methodology that has been used to identify biomarkers for numerous pathologies is gene expression profiling. Here, we report whole-genome expression profiles of individual wild-type Caenorhabditis elegans covering the entire wild-type nematode lifespan. Individual nematodes were scored for either age-related behavioral phenotypes, or survival, and then subsequently associated with their respective gene expression profiles. This facilitated the identification of transcriptional profiles that were highly associated with either physiological or chronological age. Overall, our approach serves as a paradigm for identifying potential biomarkers of aging in higher organisms that can be repeatedly sampled throughout their lifespan.

  18. Dynamic transcriptional profiling provides insights into tuberous root development in Rehmannia glutinosa

    Directory of Open Access Journals (Sweden)

    Peng eSun

    2015-06-01

    Full Text Available Rehmannia glutinosa, a herb of the Scrophulariaceae family, is widely cultivated in the Northern part of China. The tuberous root has well known medicinal properties; however, yield and quality are threatened by abiotic and biotic stresses. Understanding the molecular process of tuberous root development may help identify novel targets for its control. In the present study, we used Illumina sequencing and de novo assembly strategies to obtain a reference transcriptome that is relevant to tuberous root development. We then conducted RNA-seq quantification analysis to determine gene expression profiles of the adventitious root (AR, thickening adventitious root (TAR, and the developing tuberous root (DTR. Expression profiling identified a total of 6,974 differentially expressed unigenes during root developmental. Bioinformatics analysis and gene expression profiling revealed changes in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone biosynthesis during root development. Moreover, we identified and allocated putative functions to the genes involved in tuberous root development, including genes related to major carbohydrate metabolism, hormone metabolism, and transcription regulation. The present study provides the initial description of gene expression profiles of AR, TAR, and DTR, which facilitates identification of genes of interest. Moreover, our work provides insights into the molecular mechanisms underlying tuberous root development and may assist in the design and development of improved breeding schemes for different R. glutinosa varieties through genetic manipulation.

  19. Genome-wide transcriptional profiling linked to social class in asthma

    Science.gov (United States)

    Chen, E; Miller, G E; Walker, H A; Arevalo, J M; Sung, C Y; Cole, S W

    2009-01-01

    Objectives Low socioeconomic status (SES) is one of the most robust social factors associated with disease morbidity, including more severe asthma in childhood. However, our understanding of the biological processes that explain this link is limited. This study tested whether the social environment could get “under the skin” to alter genomic activity in children with asthma. Design and participants Two group design of children with physician diagnosed asthma who came from low or high SES families. Outcomes Genome-wide transcriptional profiles from T lymphocytes of children with asthma. Results Children with asthma from a low SES background showed overexpression of genes regulating inflammatory processes, including those involved in chemokine activity, stress responses and wound responses, compared with children with asthma from a high SES background. Bioinformatic analysis suggested that decreased activity of cyclic AMP response element binding protein and nuclear factor Y and increased nuclear factor κB transcriptional signalling mediated these effects. These pathways are known to regulate catecholamine and inflammatory signalling in immune cells. Conclusions This study provides the first evidence in a sample of paediatric patients diagnosed with asthma that the larger social environment can affect processes at the genomic level. Specifically, gene transcription control pathways that regulate inflammation and catecholamine signalling were found to vary by SES in children with asthma. Because these pathways are the primary targets of many asthma medications, these findings suggest that the larger social environment may alter molecular mechanisms that have implications for the efficacy of asthma therapeutics. PMID:19001005

  20. Transcript profiling reveals rewiring of iron assimilation gene expression in Candida albicans and C. dubliniensis.

    LENUS (Irish Health Repository)

    Moran, Gary P

    2012-12-01

    Hyphal growth is repressed in Candida albicans and Candida dubliniensis by the transcription factor Nrg1. Transcript profiling of a C. dubliniensis NRG1 mutant identified a common group of 28 NRG1-repressed genes in both species, including the hypha-specific genes HWP1, ECE1 and the regulator of cell elongation UME6. Unexpectedly, C. dubliniensis NRG1 was required for wild-type levels of expression of 10 genes required for iron uptake including seven ferric reductases, SIT1, FTR1 and RBT5. However, at alkaline pH and during filamentous growth in 10% serum, most of these genes were highly induced in C. dubliniensis. Conversely, RBT5, PGA10, FRE10 and FRP1 did not exhibit induction during hyphal growth when NRG1 is downregulated, indicating that in C. dubliniensis NRG1 is also required for optimal expression of these genes in alkaline environments. In iron-depleted medium at pH 4.5, reduced growth of the NRG1 mutant relative to wild type was observed; however, growth was restored to wild-type levels or greater at pH 6.5, indicating that alkaline induction of iron assimilation gene expression could rescue this phenotype. These data indicate that transcriptional control of iron assimilation and pseudohypha formation has been separated in C. albicans, perhaps promoting growth in a wider range of niches.

  1. Circulating Human Eosinophils Share a Similar Transcriptional Profile in Asthma and Other Hypereosinophilic Disorders.

    Directory of Open Access Journals (Sweden)

    Cindy Barnig

    Full Text Available Eosinophils are leukocytes that are released into the peripheral blood in a phenotypically mature state and are capable of being recruited into tissues in response to appropriate stimuli. Eosinophils, traditionally considered cytotoxic effector cells, are leukocytes recruited into the airways of asthma patients where they are believed to contribute to the development of many features of the disease. This perception, however, has been challenged by recent findings suggesting that eosinophils have also immunomodulatory functions and may be involved in tissue homeostasis and wound healing. Here we describe a transcriptome-based approach-in a limited number of patients and controls-to investigate the activation state of circulating human eosinophils isolated by flow cytometry. We provide an overview of the global expression pattern in eosinophils in various relevant conditions, e.g., eosinophilic asthma, hypereosinophilic dermatological diseases, parasitosis and pulmonary aspergillosis. Compared to healthy subjects, circulating eosinophils isolated from asthma patients differed in their gene expression profile which is marked by downregulation of transcripts involved in antigen presentation, pathogen recognition and mucosal innate immunity, whereas up-regulated genes were involved in response to non-specific stimulation, wounding and maintenance of homeostasis. Eosinophils from other hypereosinophilic disorders displayed a very similar transcriptional profile. Taken together, these observations seem to indicate that eosinophils exhibit non-specific immunomodulatory functions important for tissue repair and homeostasis and suggest new roles for these cells in asthma immunobiology.

  2. Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity.

    Science.gov (United States)

    Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

    2014-01-01

    The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4(+)SNS-Cre/TdTomato(+), 2) IB4(-)SNS-Cre/TdTomato(+), and 3) Parv-Cre/TdTomato(+) cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. PMID:25525749

  3. Circulating Human Eosinophils Share a Similar Transcriptional Profile in Asthma and Other Hypereosinophilic Disorders

    Science.gov (United States)

    Barnig, Cindy; Dembélé, Doulaye; Paul, Nicodème; Poirot, Anh; Uring-Lambert, Béatrice; Georgel, Philippe; de Blay, Fréderic; Bahram, Seiamak

    2015-01-01

    Eosinophils are leukocytes that are released into the peripheral blood in a phenotypically mature state and are capable of being recruited into tissues in response to appropriate stimuli. Eosinophils, traditionally considered cytotoxic effector cells, are leukocytes recruited into the airways of asthma patients where they are believed to contribute to the development of many features of the disease. This perception, however, has been challenged by recent findings suggesting that eosinophils have also immunomodulatory functions and may be involved in tissue homeostasis and wound healing. Here we describe a transcriptome-based approach–in a limited number of patients and controls—to investigate the activation state of circulating human eosinophils isolated by flow cytometry. We provide an overview of the global expression pattern in eosinophils in various relevant conditions, e.g., eosinophilic asthma, hypereosinophilic dermatological diseases, parasitosis and pulmonary aspergillosis. Compared to healthy subjects, circulating eosinophils isolated from asthma patients differed in their gene expression profile which is marked by downregulation of transcripts involved in antigen presentation, pathogen recognition and mucosal innate immunity, whereas up-regulated genes were involved in response to non-specific stimulation, wounding and maintenance of homeostasis. Eosinophils from other hypereosinophilic disorders displayed a very similar transcriptional profile. Taken together, these observations seem to indicate that eosinophils exhibit non-specific immunomodulatory functions important for tissue repair and homeostasis and suggest new roles for these cells in asthma immunobiology. PMID:26524763

  4. Transcriptional profiling of Actinobacillus pleuropneumoniae during the acute phase of a natural infection in pigs

    Directory of Open Access Journals (Sweden)

    Harel Josée

    2010-02-01

    Full Text Available Abstract Background Actinobacillus pleuropneumoniae is the etiological agent of porcine pleuropneumonia, a respiratory disease which causes great economic losses worldwide. Many virulence factors are involved in the pathogenesis, namely capsular polysaccharides, RTX toxins, LPS and many iron acquisition systems. In order to identify genes that are expressed in vivo during a natural infection, we undertook transcript profiling experiments with an A. pleuropneumoniae DNA microarray, after recovery of bacterial mRNAs from serotype 5b-infected porcine lungs. AppChip2 contains 2033 PCR amplicons based on the genomic sequence of App serotype 5b strain L20, representing more than 95% of ORFs greater than 160 bp in length. Results Transcriptional profiling of A. pleuropneumoniae recovered from the lung of a pig suffering from a natural infection or following growth of the bacterial isolate in BHI medium was performed. An RNA extraction protocol combining beadbeating and hot-acid-phenol was developed in order to maximize bacterial mRNA yields and quality following total RNA extraction from lung lesions. Nearly all A. pleuropneumoniae transcripts could be detected on our microarrays, and 150 genes were deemed differentially expressed in vivo during the acute phase of the infection. Our results indicate that, for example, gene apxIVA from an operon coding for RTX toxin ApxIV is highly up-regulated in vivo, and that two genes from the operon coding for type IV fimbriae (APL_0878 and APL_0879 were also up-regulated. These transcriptional profiling data, combined with previous comparative genomic hybridizations performed by our group, revealed that 66 out of the 72 up-regulated genes are conserved amongst all serotypes and that 3 of them code for products that are predicted outer membrane proteins (genes irp and APL_0959, predicted to code for a TonB-dependent receptor and a filamentous hemagglutinin/adhesin respectively or lipoproteins (gene APL_0920. Only 4

  5. Transcriptional profiling of trait deterioration in the insect pathogenic nematode Heterorhabditis bacteriophora

    Directory of Open Access Journals (Sweden)

    Shapiro-Ilan David I

    2009-12-01

    Full Text Available Abstract Background The success of a biological control agent depends on key traits, particularly reproductive potential, environmental tolerance, and ability to be cultured. These traits can deteriorate rapidly when the biological control agent is reared in culture. Trait deterioration under laboratory conditions has been widely documented in the entomopathogenic nematode (EPN Heterorhabditis bacteriophora (Hb but the specific mechanisms behind these genetic processes remain unclear. This research investigates the molecular mechanisms of trait deterioration of two experimental lines of Hb, an inbred line (L5M and its original parental line (OHB. We generated transcriptional profiles of two experimental lines of Hb, identified the differentially expressed genes (DEGs and validated their differential expression in the deteriorated line. Results An expression profiling study was performed between experimental lines L5M and OHB of Hb with probes for 15,220 ESTs from the Hb transcriptome. Microarray analysis showed 1,185 DEGs comprising of 469 down- and 716 up-regulated genes in trait deteriorated nematodes. Analysis of the DEGs showed that trait deterioration involves massive changes of the transcripts encoding enzymes involved in metabolism, signal transduction, virulence and longevity. We observed a pattern of reduced expression of enzymes related to primary metabolic processes and induced secondary metabolism. Expression of sixteen DEGs in trait deteriorated nematodes was validated by quantitative reverse transcription-PCR (qRT-PCR which revealed similar expression kinetics for all the genes tested as shown by microarray. Conclusion As the most closely related major entomopathogen to C. elegans, Hb provides an attractive near-term application for using a model organism to better understand interspecies interactions and to enhance our understanding of the mechanisms underlying trait deterioration in biological control agents. This information

  6. Molecular characterization of BZR transcription factor family and abiotic stress induced expression profiling in Brassica rapa.

    Science.gov (United States)

    Saha, Gopal; Park, Jong-In; Jung, Hee-Jeong; Ahmed, Nasar Uddin; Kayum, Md Abdul; Kang, Jong-Goo; Nou, Ill-Sup

    2015-07-01

    BRASSINAZOLE-RESISTANT (BZR) transcription factors (TFs) are primarily well known as positive regulators of Brassinosteroid (BR) signal transduction in different plants. BR is a plant specific steroid hormone, which has multiple stress resistance functions besides various growth regulatory roles. Being an important regulator of the BR synthesis, BZR TFs might have stress resistance related activities. However, no stress resistance related functional study of BZR TFs has been reported in any crop plants so far. Therefore, this study identified 15 BZR TFs of Brassica rapa (BrBZR) from a genome-wide survey and characterized them through sequence analysis and expression profiling against several abiotic stresses. Various systematic in silico analysis of these TFs validated the fundamental properties of BZRs, where a high degree of similarity also observed with recognized BZRs of other plant species from the comparison studies. In the organ specific expression analyses, 6 BrBZR TFs constitutively expressed in flower developmental stages indicating their flower specific functions. Subsequently, from the stress resistance related expression profiles differential transcript abundance levels were observed by 6 and 11 BrBZRs against salt and drought stresses, respectively. All BrBZRs showed several folds up-regulation against exogenous ABA treatment. All BrBZRs also showed differential expression against low temperature stress treatments and these TFs were proposed as transcriptional activators of CBF cold response pathway of B. rapa. Notably, three BrBZRs gave co-responsive expression against all the stresses tested here, suggesting their multiple stress resistance related functions. Thus, the findings would be helpful in resolving the complex regulatory mechanism of BZRs in stress resistance and further functional genomics study of these potential TFs in different Brassica crops. PMID:25931321

  7. Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection.

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    Lisa Marcinowski

    2012-09-01

    Full Text Available During viral infections cellular gene expression is subject to rapid alterations induced by both viral and antiviral mechanisms. In this study, we applied metabolic labeling of newly transcribed RNA with 4-thiouridine (4sU-tagging to dissect the real-time kinetics of cellular and viral transcriptional activity during lytic murine cytomegalovirus (MCMV infection. Microarray profiling on newly transcribed RNA obtained at different times during the first six hours of MCMV infection revealed discrete functional clusters of cellular genes regulated with distinct kinetics at surprising temporal resolution. Immediately upon virus entry, a cluster of NF-κB- and interferon-regulated genes was induced. Rapid viral counter-regulation of this coincided with a very transient DNA-damage response, followed by a delayed ER-stress response. Rapid counter-regulation of all three clusters indicated the involvement of novel viral regulators targeting these pathways. In addition, down-regulation of two clusters involved in cell-differentiation (rapid repression and cell-cycle (delayed repression was observed. Promoter analysis revealed all five clusters to be associated with distinct transcription factors, of which NF-κB and c-Myc were validated to precisely match the respective transcriptional changes observed in newly transcribed RNA. 4sU-tagging also allowed us to study the real-time kinetics of viral gene expression in the absence of any interfering virion-associated-RNA. Both qRT-PCR and next-generation sequencing demonstrated a sharp peak of viral gene expression during the first two hours of infection including transcription of immediate-early, early and even well characterized late genes. Interestingly, this was subject to rapid gene silencing by 5-6 hours post infection. Despite the rapid increase in viral DNA load during viral DNA replication, transcriptional activity of some viral genes remained remarkably constant until late-stage infection, or was

  8. Transcriptional profiling reveals regulated genes in the hippocampus during memory formation

    Science.gov (United States)

    Donahue, Christine P.; Jensen, Roderick V.; Ochiishi, Tomoyo; Eisenstein, Ingrid; Zhao, Mingrui; Shors, Tracey; Kosik, Kenneth S.

    2002-01-01

    Transcriptional profiling (TP) offers a powerful approach to identify genes activated during memory formation and, by inference, the molecular pathways involved. Trace eyeblink conditioning is well suited for the study of regional gene expression because it requires the hippocampus, whereas the highly parallel task, delay conditioning, does not. First, we determined when gene expression was most regulated during trace conditioning. Rats were exposed to 200 trials per day of paired and unpaired stimuli each day for 4 days. Changes in gene expression were most apparent 24 h after exposure to 200 trials. Therefore, we profiled gene expression in the hippocampus 24 h after 200 trials of trace eyeblink conditioning, on multiple arrays using additional animals. Of 1,186 genes on the filter array, seven genes met the statistical criteria and were also validated by real-time polymerase chain reaction. These genes were growth hormone (GH), c-kit receptor tyrosine kinase (c-kit), glutamate receptor, metabotropic 5 (mGluR5), nerve growth factor-beta (NGF-beta), Jun oncogene (c-Jun), transmembrane receptor Unc5H1 (UNC5H1), and transmembrane receptor Unc5H2 (UNC5H2). All these genes, except for GH, were downregulated in response to trace conditioning. GH was upregulated; therefore, we also validated the downregulation of the GH inhibitor, somatostatin (SST), even though it just failed to meet criteria on the arrays. By during situ hybridization, GH was expressed throughout the cell layers of the hippocampus in response to trace conditioning. None of the genes regulated in trace eyeblink conditioning were similarly affected by delay conditioning, a task that does not require the hippocampus. These findings demonstrate that transcriptional profiling can exhibit a repertoire of genes sensitive to the formation of hippocampal-dependent associative memories.

  9. Transcript profiling distinguishes complete treatment responders with locally advanced cervical cancer.

    Science.gov (United States)

    Fernandez-Retana, Jorge; Lasa-Gonsebatt, Federico; Lopez-Urrutia, Eduardo; Coronel-Martínez, Jaime; Cantu De Leon, David; Jacobo-Herrera, Nadia; Peralta-Zaragoza, Oscar; Perez-Montiel, Delia; Reynoso-Noveron, Nancy; Vazquez-Romo, Rafael; Perez-Plasencia, Carlos

    2015-04-01

    Cervical cancer (CC) mortality is a major public health concern since it is the second cause of cancer-related deaths among women. Patients diagnosed with locally advanced CC (LACC) have an important rate of recurrence and treatment failure. Conventional treatment for LACC is based on chemotherapy and radiotherapy; however, up to 40% of patients will not respond to conventional treatment; hence, we searched for a prognostic gene signature able to discriminate patients who do not respond to the conventional treatment employed to treat LACC. Tumor biopsies were profiled with genome-wide high-density expression microarrays. Class prediction was performed in tumor tissues and the resultant gene signature was validated by quantitative reverse transcription-polymerase chain reaction. A 27-predictive gene profile was identified through its association with pathologic response. The 27-gene profile was validated in an independent set of patients and was able to distinguish between patients diagnosed as no response versus complete response. Gene expression analysis revealed two distinct groups of tumors diagnosed as LACC. Our findings could provide a strategy to select patients who would benefit from neoadjuvant radiochemotherapy-based treatment. PMID:25926073

  10. Transcript profiling reveals expression differences in wild-type and glabrous soybean lines

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    Stromvik Martina

    2011-10-01

    Full Text Available Abstract Background Trichome hairs affect diverse agronomic characters such as seed weight and yield, prevent insect damage and reduce loss of water but their molecular control has not been extensively studied in soybean. Several detailed models for trichome development have been proposed for Arabidopsis thaliana, but their applicability to important crops such as cotton and soybean is not fully known. Results Two high throughput transcript sequencing methods, Digital Gene Expression (DGE Tag Profiling and RNA-Seq, were used to compare the transcriptional profiles in wild-type (cv. Clark standard, CS and a mutant (cv. Clark glabrous, i.e., trichomeless or hairless, CG soybean isoline that carries the dominant P1 allele. DGE data and RNA-Seq data were mapped to the cDNAs (Glyma models predicted from the reference soybean genome, Williams 82. Extending the model length by 250 bp at both ends resulted in significantly more matches of authentic DGE tags indicating that many of the predicted gene models are prematurely truncated at the 5' and 3' UTRs. The genome-wide comparative study of the transcript profiles of the wild-type versus mutant line revealed a number of differentially expressed genes. One highly-expressed gene, Glyma04g35130, in wild-type soybean was of interest as it has high homology to the cotton gene GhRDL1 gene that has been identified as being involved in cotton fiber initiation and is a member of the BURP protein family. Sequence comparison of Glyma04g35130 among Williams 82 with our sequences derived from CS and CG isolines revealed various SNPs and indels including addition of one nucleotide C in the CG and insertion of ~60 bp in the third exon of CS that causes a frameshift mutation and premature truncation of peptides in both lines as compared to Williams 82. Conclusion Although not a candidate for the P1 locus, a BURP family member (Glyma04g35130 from soybean has been shown to be abundantly expressed in the CS line and very

  11. Genetic analysis of maize by using the AFLP (R) method

    NARCIS (Netherlands)

    Vuylsteke, M.J.R.

    1999-01-01

    Methylation AFLP® is a novel PCR-based method to detect methylation of restriction sites randomly over the genome.In framework of the AFLP®-related technology development, a modification of the AFLP method was developed, called the methylation AFLP® method. Several features of the methylation AFLP a

  12. An AFLP-based genome-wide mapping strategy.

    NARCIS (Netherlands)

    Peters, J.L.; Cnops, G.; Neyt, P.; Zethof, J.; Cornelis, K.; Lijsebettens, M. van; Gerats, A.G.M.

    2004-01-01

    To efficiently determine the chromosomal location of phenotypic mutants, we designed a genome-wide mapping strategy that can be used in any crop for which a dense AFLP (Amplified Fragment Length Polymorphism) map is available or can be made. The AFLP technique is particularly suitable to initiate ma

  13. Age-related behaviors have distinct transcriptional profiles in C.elegans

    Science.gov (United States)

    Golden, Tamara R.; Hubbard, Alan; Dando, Caroline; Herren, Michael A.; Melov, Simon

    2008-01-01

    Summary There has been a great deal of interest in identifying potential biomarkers of aging (Butler et al. 2004). Biomarkers of aging would be useful to predict potential vulnerabilities in an individual that may arise well before they are chronologically expected, due to idiosyncratic aging rates that occur between individuals. Prior attempts to identify biomarkers of aging have often relied on the comparisons of long-lived animals to a wild-type control (Dhahbi et al. 2004). However, the effect of interventions in model systems that prolong lifespan (such as single gene mutations, or caloric restriction) can sometimes be difficult to interpret due to the manipulation itself having multiple unforeseen consequences on physiology, unrelated to aging itself (Gems et al. 2002; Partridge & Gems 2006). The search for predictive biomarkers of aging therefore is problematic, and the identification of metrics that can be used to predict either physiological or chronological age would be of great value (Butler et al. 2004). One methodology which has been used to identify biomarkers for numerous pathologies is gene expression profiling. Here, we report whole-genome expression profiles of individual wild-type Caenorhabditis elegans covering the entire wild-type nematode life span. Individual nematodes were scored for either age-related behavioral phenotypes, or survival, and then subsequently associated with their respective gene expression profiles. This facilitated the identification of transcriptional profiles that were highly associated with either physiological or chronological age. Overall, our approach serves as a paradigm for identifying potential biomarkers of aging in higher organisms that can be repeatedly sampled throughout their lifespan. PMID:18778409

  14. Human embryonic stem cells derived from embryos at different stages of development share similar transcription profiles.

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    Gnanaratnam Giritharan

    Full Text Available We have derived hESC from biopsied blastomeres of cleavage stage embryos under virtually the same conditions we used for the derivation of hESC lines from inner cell mass of blastocyst stage embryos. Blastomere-derived hESC lines exhibited all the standard characteristics of hESC including undifferentiated proliferation, genomic stability, expression of pluripotency markers and the ability to differentiate into the cells of all three germ layers both in vitro and in vivo. To examine whether hESC lines derived from two developmental stages of the embryo differ in gene expression, we have subjected three blastomere-derived hESC lines and two ICM-derived hESC lines grown under identical culture conditions to transcriptome analysis using gene expression arrays. Unlike previously reported comparisons of hESC lines which demonstrated, apart from core hESC-associated pluripotency signature, significant variations in gene expression profiles of different lines, our data show that hESC lines derived and grown under well-controlled defined culture conditions adopt nearly identical gene expression profiles. Moreover, blastomere-derived and ICM-derived hESC exhibited very similar transcriptional profiles independent of the developmental stage of the embryo from which they originated. Furthermore, this profile was evident in very early passages of the cells and did not appear to be affected by extensive passaging. These results suggest that during derivation process cells which give rise to hESC acquire virtually identical stable phenotype and are not affected by the developmental stage of the starting cell population.

  15. Nanosilver pathophysiology in earthworms: Transcriptional profiling of secretory proteins and the implication for the protein corona

    DEFF Research Database (Denmark)

    Hayashi, Yuya; Miclaus, Teodora; Engelmann, Péter;

    2016-01-01

    Previously we have identified lysenin as a key protein constituent of the secretome from Eisenia fetida coelomocytes and revealed its critical importance in priming interactions between the cells and the protein corona around nanosilver. As alterations of the protein environment can directly affect...... the corona composition, the extent to which nanoparticles influence the cells’ protein secretion profile is of remarkable interest that has rarely acquired attention. Here, we have probed transcriptional responses of E. fetida coelomocytes to the representative nanosilver NM-300K (15 nm) in a time...... suppressed over time indicating a negative feedback cycle. This may limit further enrichment of lysenin in the corona and thereby decrease the lysenin-assisted uptake of the nanoparticles. Other differentially expressed genes were those involved in metal stress (likewise in AgNO3-stressed cells) and in Toll...

  16. Study on differential transcriptional profile in human hepatocyte exposed to different doses γ ray

    International Nuclear Information System (INIS)

    The study analyzed the differential transcriptional profile of normal human hepatic cell and human hepatic cell radiated with three different doses (0.5 Gy, 2 Gy, 4 Gy γ ray) by gene chip technique. The results showed that the whole differentially expressed genes of three different doses have 284 in 14112 human genes analyzed, in which 261 genes were up-regulated and 23 genes were down-regulated. These genes are mainly associated with interferon receptor, mitochondrial regulation, homo sapiens hepatitis A virus cellular receptor, cell cycle regulation, kinase and zinc finger protein etc. RT-PCR results indicated that up-regulated expression of gene HAVcr-1, HAVcr-2, MFTC, MOAP1 and down-regulated expression of gene TRIP12, DCN are consistent with gene chip data. (authors)

  17. A strong anti-inflammatory signature revealed by liver transcription profiling of Tmprss6-/- mice.

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    Michela Riba

    Full Text Available Control of systemic iron homeostasis is interconnected with the inflammatory response through the key iron regulator, the antimicrobial peptide hepcidin. We have previously shown that mice with iron deficiency anemia (IDA-low hepcidin show a pro-inflammatory response that is blunted in iron deficient-high hepcidin Tmprss6 KO mice. The transcriptional response associated with chronic hepcidin overexpression due to genetic inactivation of Tmprss6 is unknown. By using whole genome transcription profiling of the liver and analysis of spleen immune-related genes we identified several functional pathways differentially expressed in Tmprss6 KO mice, compared to IDA animals and thus irrespective of the iron status. In the effort of defining genes potentially targets of Tmprss6 we analyzed liver gene expression changes according to the genotype and independently of treatment. Tmprss6 inactivation causes down-regulation of liver pathways connected to immune and inflammatory response as well as spleen genes related to macrophage activation and inflammatory cytokines production. The anti-inflammatory status of Tmprss6 KO animals was confirmed by the down-regulation of pathways related to immunity, stress response and intracellular signaling in both liver and spleen after LPS treatment. Opposite to Tmprss6 KO mice, Hfe(-/- mice are characterized by iron overload with inappropriately low hepcidin levels. Liver expression profiling of Hfe(-/- deficient versus iron loaded mice show the opposite expression of some of the genes modulated by the loss of Tmprss6. Altogether our results confirm the anti-inflammatory status of Tmprss6 KO mice and identify new potential target pathways/genes of Tmprss6.

  18. Discrimination of Carcinogens by Hepatic Transcript Profiling in Rats Following 28-day Administration

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    Hiroshi Matsumoto

    2009-11-01

    Full Text Available This study aimed at discriminating carcinogens on the basis of hepatic transcript profiling in the rats administrated with a variety of carcinogens and non-carcinogens. We conducted 28-day toxicity tests in male F344 rats with 47 carcinogens and 26 non- carcinogens, and then investigated periodically the hepatic gene expression profiles using custom microarrays. By hierarchical cluster analysis based on significantly altered genes, carcinogens were clustered into three major groups (Group 1 to 3. The formation of these groups was not affected by the gene sets used as well as the administration period, indicating that the grouping of carcinogens was universal independent of the conditions of both statistical analysis and toxicity testing. Seventeen carcinogens belonging to Group 1 were composed of mainly rat hepatocarcinogens, most of them being mutagenic ones. Group 2 was formed by three subgroups, which were composed of 23 carcinogens exhibiting distinct properties in terms of genotoxicity and target tissues, namely nonmutagenic hepatocarcinogens, and mutagenic and nonmutagenic carcinogens both of which are targeted to other tissues. Group 3 contained 6 carcinogens including 4 estrogenic substances, implying the group of estrogenic carcinogens. Gene network analyses revealed that the significantly altered genes in Group 1 included Bax, Tnfrsf6, Btg2, Mgmt and Abcb1b, suggesting that p53-mediated signaling pathway involved in early pathologic alterations associated with preceding mutagenic carcinogenesis. Thus, the common transcriptional signatures for each group might reflect the early molecular events of carcinogenesis and hence would enable us to identify the biomarker genes, and then to develop a new assay for carcinogenesis prediction.

  19. Transcriptional profiling of midgut immunity response and degeneration in the wandering silkworm, Bombyx mori.

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    Qiuyun Xu

    Full Text Available BACKGROUND: Lepidoptera insects have a novel development process comprising several metamorphic stages during their life cycle compared with vertebrate animals. Unlike most Lepidoptera insects that live on nectar during the adult stage, the Bombyx mori silkworm adults do not eat anything and die after egg-laying. In addition, the midguts of Lepidoptera insects produce antimicrobial proteins during the wandering stage when the larval tissues undergo numerous changes. The exact mechanisms responsible for these phenomena remain unclear. PRINCIPAL FINDINGS: We used the silkworm as a model and performed genome-wide transcriptional profiling of the midgut between the feeding stage and the wandering stage. Many genes concerned with metabolism, digestion, and ion and small molecule transportation were down-regulated during the wandering stage, indicating that the wandering stage midgut loses its normal functions. Microarray profiling, qRT-PCR and western blot proved the production of antimicrobial proteins (peptides in the midgut during the wandering stage. Different genes of the immune deficiency (Imd pathway were up-regulated during the wandering stage. However, some key genes belonging to the Toll pathway showed no change in their transcription levels. Unlike butterfly (Pachliopta aristolochiae, the midgut of silkworm moth has a layer of cells, indicating that the development of midgut since the wandering stage is not usual. Cell division in the midgut was observed only for a short time during the wandering stage. However, there was extensive cell apoptosis before pupation. The imbalance of cell division and apoptosis probably drives the continuous degeneration of the midgut in the silkworm since the wandering stage. CONCLUSIONS: This study provided an insight into the mechanism of the degeneration of the silkworm midgut and the production of innate immunity-related proteins during the wandering stage. The imbalance of cell division and apoptosis

  20. Transcriptional profiling of Petunia seedlings reveals candidate regulators of the cold stress response

    Directory of Open Access Journals (Sweden)

    Bei eLi

    2015-03-01

    Full Text Available Petunias are important ornamentals with the capacity for cold acclimation. So far, there is limited information concerning gene regulation and signaling pathways related to the cold stress response in petunias. A custom-designed petunia microarray representing 24816 genes was used to perform transcriptome profiling in petunia seedlings subjected to cold at 2°C for 0.5 h, 2 h, 24 h and 5 d. A total of 2071 transcripts displayed differential expression patterns under cold stress, of which 1149 were up-regulated and 922 were down-regulated. Gene ontology enrichment analysis demarcated related biological processes, suggesting a possible link between flavonoid metabolism and plant adaptation to low temperatures. Many novel stress-responsive regulators were revealed, suggesting that diverse regulatory pathways may exist in petunias in addition to the well-characterized CBF pathway. The expression changes of selected genes under cold and other abiotic stress conditions were confirmed by real-time RT-PCR. Furthermore, weighted gene co-expression network analysis divided the petunia genes on the array into 65 modules that showed high co-expression and identified stress-specific hub genes with high connectivity. Our identification of these transcriptional responses and groups of differentially expressed regulators will facilitate the functional dissection of the molecular mechanism in petunias responding to environment stresses and extend our ability to improve cold tolerance in plants.

  1. Comparative Transcriptional Profiling of Primed and Non-primed Rice Seedlings under Submergence Stress

    Science.gov (United States)

    Hussain, Saddam; Yin, Hanqi; Peng, Shaobing; Khan, Faheem A.; Khan, Fahad; Sameeullah, Muhammad; Hussain, Hafiz A.; Huang, Jianliang; Cui, Kehui; Nie, Lixiao

    2016-01-01

    Submergence stress is a limiting factor for direct-seeded rice systems in rainfed lowlands and flood-prone areas of South and Southeast Asia. The present study demonstrated that submergence stress severely hampered the germination and seedling growth of rice, however, seed priming alleviated the detrimental effects of submergence stress. To elucidate the molecular basis of seed priming-induced submergence tolerance, transcriptome analyses were performed using 4-day-old primed (selenium-Se and salicylic acid-SA priming) and non-primed rice seedlings under submergence stress. Genomewide transcriptomic profiling identified 2371 and 2405 transcripts with Se- and SA-priming, respectively, that were differentially expressed in rice compared with non-priming treatment under submergence. Pathway and gene ontology term enrichment analyses revealed that genes involved in regulation of secondary metabolism, development, cell, transport, protein, and metal handling were over-represented after Se- or SA-priming. These coordinated factors might have enhanced the submergence tolerance and maintained the better germination and vigorous seedling growth of primed rice seedlings. It was also found that many genes involved in cellular and metabolic processes such as carbohydrate metabolism, cellular, and metabolic biosynthesis, nitrogen compound metabolic process, transcription, and response to oxidative stress were induced and overlapped in seed priming treatments, a finding which reveals the common mechanism of seed priming-induced submergence tolerance. Taken together, these results may provide new avenues for understanding and advancing priming-induced responses to submergence tolerance in crop plants.

  2. Comparative Transcriptional Profiling of Primed and Non-primed Rice Seedlings under Submergence Stress

    Science.gov (United States)

    Hussain, Saddam; Yin, Hanqi; Peng, Shaobing; Khan, Faheem A.; Khan, Fahad; Sameeullah, Muhammad; Hussain, Hafiz A.; Huang, Jianliang; Cui, Kehui; Nie, Lixiao

    2016-01-01

    Submergence stress is a limiting factor for direct-seeded rice systems in rainfed lowlands and flood-prone areas of South and Southeast Asia. The present study demonstrated that submergence stress severely hampered the germination and seedling growth of rice, however, seed priming alleviated the detrimental effects of submergence stress. To elucidate the molecular basis of seed priming-induced submergence tolerance, transcriptome analyses were performed using 4-day-old primed (selenium-Se and salicylic acid-SA priming) and non-primed rice seedlings under submergence stress. Genomewide transcriptomic profiling identified 2371 and 2405 transcripts with Se- and SA-priming, respectively, that were differentially expressed in rice compared with non-priming treatment under submergence. Pathway and gene ontology term enrichment analyses revealed that genes involved in regulation of secondary metabolism, development, cell, transport, protein, and metal handling were over-represented after Se- or SA-priming. These coordinated factors might have enhanced the submergence tolerance and maintained the better germination and vigorous seedling growth of primed rice seedlings. It was also found that many genes involved in cellular and metabolic processes such as carbohydrate metabolism, cellular, and metabolic biosynthesis, nitrogen compound metabolic process, transcription, and response to oxidative stress were induced and overlapped in seed priming treatments, a finding which reveals the common mechanism of seed priming-induced submergence tolerance. Taken together, these results may provide new avenues for understanding and advancing priming-induced responses to submergence tolerance in crop plants. PMID:27516766

  3. AFLP analysis of Xanthomonas axonopodis and X. arboricola strains used in xanthan production studies reveal high levels of polymorphism

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    Laurí Mayer

    2010-10-01

    Full Text Available Amplified fragment length polymorphism (AFLP was used to analyze the genetic diversity of 14 strains of Xanthomonas arboricola pv. pruni and seven strains of X. axonopodis pv. phaseoli, which are used in xanthan production studies. Relationships identified by the AFLP profiles were assessed for xanthan production capacity, geographical location and host plant. Strains were isolated from 10 different geographic regions in South and Southeast States in Brazil. Data were analyzed for genetic similarity using the Dice coefficient and subjected to UPGMA cluster analysis. A total of 128 AFLP fragments were generated from four primer combinations: EcoRI+C/MseI+0, EcoRI+A/MseI+0, EcoRI+G/MseI+T and EcoRI+G/MseI+A. Of these, 96.1% were polymorphic. X. axonopodis pv. phaseoli (S D = 0.27 was shown to be more polymorphic than X. arboricola pv. pruni (S D = 0.58. All 14 pathovar pruni strains were included in a single main group (S D = 0.58, while the pathovar phaseoli strains were divided into three separate groups, with one group containing five strains (S D = 0.38 and two isolated groups (S D = 0.31 and 0.27 composed of only one strain each. Species were distinguished by three and eight specific AFLP markers present in the pathovar phaseoli and the pathovar pruni, respectively. For the unique strain without xanthan production capacity (X. axonopodis pv. phaseoli str. 48, nine specific AFLP bands were found. There was no evidence that geographic area or host plant influenced genetic heterogeneity. Correlations between AFLP patterns and xanthan production capacity were found in some strains, but were not consistent enough to establish a relationship.

  4. Quantitative profiling of housekeeping and Epstein-Barr virus gene transcription in Burkitt lymphoma cell lines using an oligonucleotide microarray

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    Niggli Felix K

    2006-06-01

    Full Text Available Abstract Background The Epstein-Barr virus (EBV is associated with lymphoid malignancies, including Burkitt's lymphoma (BL, and can transform human B cells in vitro. EBV-harboring cell lines are widely used to investigate lymphocyte transformation and oncogenesis. Qualitative EBV gene expression has been extensively described, but knowledge of quantitative transcription is lacking. We hypothesized that transcription levels of EBNA1, the gene essential for EBV persistence within an infected cell, are similar in BL cell lines. Results To compare quantitative gene transcription in the BL cell lines Namalwa, Raji, Akata, Jijoye, and P3HR1, we developed an oligonucleotide microarray chip, including 17 housekeeping genes, six latent EBV genes (EBNA1, EBNA2, EBNA3A, EBNA3C, LMP1, LMP2, and four lytic EBV genes (BZLF1, BXLF2, BKRF2, BZLF2, and used the cell line B95.8 as a reference for EBV gene transcription. Quantitative polymerase chain reaction assays were used to validate microarray results. We found that transcription levels of housekeeping genes differed considerably among BL cell lines. Using a selection of housekeeping genes with similar quantitative transcription in the tested cell lines to normalize EBV gene transcription data, we showed that transcription levels of EBNA1 were quite similar in very different BL cell lines, in contrast to transcription levels of other EBV genes. As demonstrated with Akata cells, the chip allowed us to accurately measure EBV gene transcription changes triggered by treatment interventions. Conclusion Our results suggest uniform EBNA1 transcription levels in BL and that microarray profiling can reveal novel insights on quantitative EBV gene transcription and its impact on lymphocyte biology.

  5. Transcriptional profile of Taxus chinensis cells in response to methyl jasmonate

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    Li Shu-tao

    2012-07-01

    Full Text Available Abstract Background Methyl jasmonate (MeJA has been successfully used as an effective elicitor to enhance production of taxol and other taxanes in cultured Taxus cells. However the mechanism of MeJA-mediated taxane biosynthesis remains unclear. Genomic information for species in the genus Taxus is currently unavailable. Therefore, information about the transcriptome of Taxus cells and specifically, description of changes in gene expression in response to MeJA, is needed for the better exploration of the biological mechanisms of MeJA-mediated taxane biosynthesis. Results In this research, the transcriptome profiles of T. chinensis cells at 16 hours (T16 after MeJA treatment and of mock-treated cells (T0 were analyzed by “RNA-seq” to investigate the transcriptional alterations of Taxus cell in response to MeJA elicitation. More than 58 million reads (200 bp in length of cDNA from both samples were generated, and 46,581 unigenes were found. There were 13,469 genes found to be expressed differentially between the two timepoints, including all of the known jasmonate (JA biosynthesis/JA signaling pathway genes and taxol-related genes. The qRT-PCR results showed that the expression profiles of 12 randomly selected DEGs and 10 taxol biosynthesis genes were found to be consistent with the RNA-Seq data. MeJA appeared to stimulate a large number of genes involved in several relevant functional categories, such as plant hormone biosynthesis and phenylpropanoid biosynthesis. Additionally, many genes encoding transcription factors were shown to respond to MeJA elicitation. Conclusions The results of a transcriptome analysis suggest that exogenous application of MeJA could induce JA biosynthesis/JA signaling pathway/defence responses, activate a series of transcription factors, as well as increase expression of genes in the terpenoid biosynthesis pathway responsible for taxol synthesis. This comprehensive description of gene expression information could

  6. Translation by polysome: theory of ribosome profile on a single mRNA transcript

    CERN Document Server

    Sharma, Ajeet K

    2011-01-01

    The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called {\\it translation}. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the track. Often several ribosomes may translate the same (mRNA) simultaneously. The ribosomes bound simultaneously to a single mRNA transcript are the members of a polyribosome (or, simply, {\\it polysome}). Experimentally measured {\\it polysome profile} gives the distribution of polysome {\\it sizes}. Recently a breakthrough in determining the instantaneous {\\it positions} of the ribosomes on a given mRNA track has been achieved and the technique is called {\\it ribosome profiling} \\cite{ingolia10,guo10}. Motivated by the success of these techniques, we have studied the spatio-temporal organization of ribosomes by extending a theoretical model that we have reported elsewhere \\cite{sharma11}. This extended version of our model incorporates not only (i) mechano-chemical cycle of indivi...

  7. Non-additive transcriptional profiles underlie dikaryotic superiority in Pleurotus ostreatus laccase activity.

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    Raúl Castanera

    Full Text Available BACKGROUND: The basidiomycete Pleurotus ostreatus is an efficient producer of laccases, a group of enzymes appreciated for their use in multiple industrial processes. The aim of this study was to reveal the molecular basis of the superiority of laccase production by dikaryotic strains compared to their parental monokaryons. METHODOLOGY/PRINCIPAL FINDINGS: We bred and studied a set of dikaryotic strains starting from a meiotic population of monokaryons. We then completely characterised the laccase allelic composition, the laccase gene expression and activity profiles in the dikaryotic strain N001, in two of its meiotic full-sib monokaryons and in the dikaryon formed from their mating. CONCLUSIONS/SIGNIFICANCE: Our results suggested that the dikaryotic superiority observed in laccase activity was due to non-additive transcriptional increases in lacc6 and lacc10 genes. Furthermore, the expression of these genes was divergent in glucose- vs. lignocellulose-supplemented media and was highly correlated to the detected extracellular laccase activity. Moreover, the expression profile of lacc2 in the dikaryotic strains was affected by its allelic composition, indicating a putative single locus heterozygous advantage.

  8. Transcriptional profile in response to ionizing radiation at low dose in Deinococcus radiodurans

    Institute of Scientific and Technical Information of China (English)

    Chen Huan; Xu Zhenjian; Tian Bing; Chen Weiwei; Hu Songnian; Hua Yuejin

    2007-01-01

    The genome-wide transcription profile of Deinococcus radiodurans cells was investigated after treatment with low dose irradiation (2 kGy). From the expression profile, we found that the process of DNA repair was induced in order, i.e. genes involved in base excision repair, nucleotide excision repair and single-strand annealing were induced immediately after ionizing radiation, and genes for recombination repair, including recA, recD and recQ were then activated. Especially, recD and recQ were specifically induced at low dose irradiation, and this phenomenon informed us that these two genes would play a certain role in anti-oxidation. Some genes such as ddrA and ssb were activated during the whole repair phase. Furthermore, the response of oxidative stress-related genes under low dose irradiation showed a different pattern from that of the acute high-level irradiation, many anti-oxidative genes were induced to scavenge reactive oxygen species directly, other associated systems also changed their expression patterns during the recovery time, such as iron metabolism systems, intracellular mutagenic precursors sanitize systems. These characteristics indicate that there is a powerful and orderly recovery process in Deinococcus radiodurans.

  9. Comprehensive analysis and expression profile of the homeodomain leucine zipper IV transcription factor family in tomato.

    Science.gov (United States)

    Gao, Yanna; Gao, Shenghua; Xiong, Cheng; Yu, Gang; Chang, Jiang; Ye, Zhibiao; Yang, Changxian

    2015-11-01

    Homeodomain leucine zipper IV (HD-ZIP IV) proteins are plant-specific transcription factors that play important roles in development of epidermal cell layers and cuticle formation. The functions of two HD-ZIP IV family genes, CD2 and Wo, have been well characterized in tomato (Solanum lycopersicum). CD2 and Wo are involved in cuticle biosynthesis and trichome formation, respectively. In this study, we identified 13 novel tomato HD-ZIP IV (SlHDZIV) genes. We analyzed the structures, chromosome locations, phylogeny, protein motifs, and expression profiles of these SlHDZIV genes. Gene structure analysis revealed that a module of 11 exons and 10 introns existed in the SlHDZIV genes. These genes were asymmetrically distributed on chromosomes, except on chromosome 4 and 5. Segmental duplication possibly contributed to the expansion of tomato HD-ZIP IV genes. The expression profiles of these genes revealed their broad expression pattern and high expression in young leaves and flowers. Each gene responded to more than one of different phytohormones [abscisic acid, ethephon, 4-(indolyl)-butyric acid, jasmonic acid, salicylic acid, gibberellic acid, and 6-benzylaminopurine] and four abiotic stress treatments (cold, heat, salt, and drought). This study provided significant insights into the diverse roles of SlHDZIV genes in tomato growth and development.

  10. Gene Transcriptional and Metabolic Profile Changes in Mimetic Aging Mice Induced by D-Galactose.

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    Yue-Yue Zhou

    Full Text Available D-galactose injection has been shown to induce many changes in mice that represent accelerated aging. This mouse model has been widely used for pharmacological studies of anti-aging agents. The underlying mechanism of D-galactose induced aging remains unclear, however, it appears to relate to glucose and 1ipid metabolic disorders. Currently, there has yet to be a study that focuses on investigating gene expression changes in D-galactose aging mice. In this study, integrated analysis of gas chromatography/mass spectrometry-based metabonomics and gene expression profiles was used to investigate the changes in transcriptional and metabolic profiles in mimetic aging mice injected with D-galactose. Our findings demonstrated that 48 mRNAs were differentially expressed between control and D-galactose mice, and 51 potential biomarkers were identified at the metabolic level. The effects of D-galactose on aging could be attributed to glucose and 1ipid metabolic disorders, oxidative damage, accumulation of advanced glycation end products (AGEs, reduction in abnormal substance elimination, cell apoptosis, and insulin resistance.

  11. Transcriptional profiling of the murine cutaneous response during initial and subsequent infestations with Ixodes scapularis nymphs

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    Heinze Dar M

    2012-02-01

    Full Text Available Abstract Background Ixodes scapularis ticks are hematophagous arthropods capable of transmitting many infectious agents to humans. The process of blood feeding is an extended and continuous interplay between tick and host responses. While this process has been studied extensively in vitro, no global understanding of the host response to ticks has emerged. Methods To address this issue, we used PCR-arrays to measure skin-specific expression of 233 discrete genes at 8 time points during primary and secondary infestations of mice with pathogen-free I. scapularis nymphs. Selected results were then validated at the mRNA and protein levels by additional real-time PCR and bioplex assay. Results Primary infestation was characterized by the late induction of an innate immune response. Lectin pattern recognition receptors, cytokines, and chemokines were upregulated consistent with increased neutrophil and macrophage migration. Gene ontology and pathway analyses of downregulated genes suggested inhibition of gene transcription and Th17 immunity. During the secondary infestation, additional genes were modulated suggesting a broader involvement of immune cells including CD8 and CD4 positive T lymphocytes. The cytokine response showed a mixed Th1/Th2 profile with a potential for T regulatory cell activity. Key gene ontology clusters observed during the secondary infestation were cell migration and activation. Matrix metalloproteinases were upregulated, apoptosis-related genes were differentially modulated, and immunoreceptor signaling molecules were upregulated. In contrast, transcripts related to mitogenic, WNT, Hedgehog, and stress pathways were downregulated. Conclusions Our results support a model of tick feeding where lectin pattern recognition receptors orchestrate an innate inflammatory response during primary infestation that primes a mixed Th1/Th2 response upon secondary exposure. Tick feeding inhibits gene transcription and Th17 immunity. Salivary

  12. Global transcript profiling of transgenic plants constitutively overexpressing the RNA-binding protein AtGRP7

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    Hennig Lars

    2010-10-01

    Full Text Available Abstract Background The clock-controlled RNA-binding protein AtGRP7 influences circadian oscillations of its own transcript at the post-transcriptional level. To identify additional targets that are regulated by AtGRP7, transcript profiles of transgenic plants constitutively overexpressing AtGRP7 (AtGRP7-ox and wild type plants were compared. Results Approximately 1.4% of the transcripts represented on the Affymetrix ATH1 microarray showed changes in steady-state abundance upon AtGRP7 overexpression. One third of the differentially expressed genes are controlled by the circadian clock, and they show a distinct bias of their phase: The up-regulated genes preferentially peak around dawn, roughly opposite to the AtGRP7 peak abundance whereas the down-regulated genes preferentially peak at the end of the day. Further, transcripts responsive to abiotic and biotic stimuli were enriched among AtGRP7 targets. Transcripts encoding the pathogenesis-related PR1 and PR2 proteins were elevated in AtGRP7-ox plants but not in plants overexpressing AtGRP7 with a point mutation in the RNA-binding domain, indicating that the regulation involves RNA binding activity of AtGRP7. Gene set enrichment analysis uncovered components involved in ribosome function and RNA metabolism among groups of genes upregulated in AtGRP7-ox plants, consistent with its role in post-transcriptional regulation. Conclusion Apart from regulating a suite of circadian transcripts in a time-of-day dependent manner AtGRP7, both directly and indirectly, affects other transcripts including transcripts responsive to abiotic and biotic stimuli. This suggests a regulatory role of AtGRP7 in the output of the endogenous clock and a complex network of transcripts responsive to external stimuli downstream of the AtGRP7 autoregulatory circuit.

  13. Molecular Characterization and Expression Profiling of NAC Transcription Factors in Brachypodium distachyon L.

    Science.gov (United States)

    Zhu, Gengrui; Chen, Guanxing; Zhu, Jiantang; Zhu, Yan; Lu, Xiaobing; Li, Xiaohui; Hu, Yingkao; Yan, Yueming

    2015-01-01

    NAC (NAM, ATAF1/2, CUC2) transcription factors are involved in regulating plant developmental processes and response to environmental stresses. Brachypodium distachyon is an emerging model system for cereals, temperate grasses and biofuel crops. In this study, a comprehensive investigation of the molecular characterizations, phylogenetics and expression profiles under various abiotic stresses of the NAC gene family in Brachypodium distachyon was performed. In total, 118 BNAC genes in B. distachyon were identified, of which 22 (18.64%) were tandemly duplicated and segmentally duplicated, respectively. The Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC) algorithms showed that they were divided into two clades and fourteen subfamilies, supported by similar motif compositions within one subfamily. Some critical amino acids detected using DIVERGE v3.0 might contribute to functional divergence among subfamilies. The different exon-intron organizations among subfamilies revealed structural differentiation. Promoter sequence predictions showed that the BNAC genes were involved in various developmental processes and diverse stress responses. Three NAC domain-encoding genes (BNAC012, BNAC078 and BNAC108), orthologous of NAC1, were targeted by five miRNA164 (Bdi-miR164a-c, e, f), suggesting that they might function in lateral organ enlargement, floral development and the responses to abiotic stress. Eleven (~9.32%) BNAC proteins containing α-helical transmembrane motifs were identified. 23 representative BNAC genes were analyzed by quantitative real-time PCR, showing different expression patterns under various abiotic stresses, of which 18, 17 and 11 genes were up-regulated significantly under drought, H2O2 and salt stresses, respectively. Only four and two genes were up-regulated under cold and cadmium stresses, respectively. Dynamic transcriptional expression analysis revealed that six genes showed constitutive expression and period

  14. Molecular Characterization and Expression Profiling of NAC Transcription Factors in Brachypodium distachyon L.

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    Gengrui Zhu

    Full Text Available NAC (NAM, ATAF1/2, CUC2 transcription factors are involved in regulating plant developmental processes and response to environmental stresses. Brachypodium distachyon is an emerging model system for cereals, temperate grasses and biofuel crops. In this study, a comprehensive investigation of the molecular characterizations, phylogenetics and expression profiles under various abiotic stresses of the NAC gene family in Brachypodium distachyon was performed. In total, 118 BNAC genes in B. distachyon were identified, of which 22 (18.64% were tandemly duplicated and segmentally duplicated, respectively. The Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC algorithms showed that they were divided into two clades and fourteen subfamilies, supported by similar motif compositions within one subfamily. Some critical amino acids detected using DIVERGE v3.0 might contribute to functional divergence among subfamilies. The different exon-intron organizations among subfamilies revealed structural differentiation. Promoter sequence predictions showed that the BNAC genes were involved in various developmental processes and diverse stress responses. Three NAC domain-encoding genes (BNAC012, BNAC078 and BNAC108, orthologous of NAC1, were targeted by five miRNA164 (Bdi-miR164a-c, e, f, suggesting that they might function in lateral organ enlargement, floral development and the responses to abiotic stress. Eleven (~9.32% BNAC proteins containing α-helical transmembrane motifs were identified. 23 representative BNAC genes were analyzed by quantitative real-time PCR, showing different expression patterns under various abiotic stresses, of which 18, 17 and 11 genes were up-regulated significantly under drought, H2O2 and salt stresses, respectively. Only four and two genes were up-regulated under cold and cadmium stresses, respectively. Dynamic transcriptional expression analysis revealed that six genes showed constitutive expression and period

  15. Global Transcriptional Profile of Tranosema rostrale lchnovirus Genes in Infected Lepidopteran Hosts and Wasp Ovaries

    Institute of Scientific and Technical Information of China (English)

    Asieh Rasoolizadeh; Frédéric Dallaire; Don Stewart; Catherine Béliveau; Renée Lapointe; Michel Cusson

    2009-01-01

    The ichnovirus TrIV, transmitted by the endoparasitic wasp Tranosema rostrale to its lepidopteran host during oviposition, replicates asymptomatically in wasp ovaries and causes physiological dysfunctions in parasitized caterpillars. The need to identify ichnoviral genes responsible for disturbances induced in lepidopteran hosts has provided the impetus for the sequencing and annotation of ichnovirus genomes, including that of TrIV. In the latter, 86 putative genes were identified, including 35 that could be assigned to recognized ichnoviral gene families. With the aim of assessing the relative importance of each TrIV gene, as inferred from its level of expression, and evaluating the accuracy of the gene predictions made during genome annotation, the present study builds on an earlier qPCR quantification of transcript abundance of TrIV rep ORFs, in both lepidopteran and wasp hosts, extending it to other gene families as well as to a sample of unassigned ORFs. We show that the majority (91%) of putative ORFs assigned to known gene families are expressed in infected larvae, while this proportion is lower (67%) for a sample taken among the remaining ORFs. Selected members of the TrV and rep gene families are shown to be transcribed in infected larvae at much higher levels than genes from any other TrIV gene family, pointing to their likely involvement in host subjugation. In wasp ovaries, the transcriptional profile is dominated by a rep gene and a member of a newly described gene family encoding secreted proteins displaying a novel cysteine motif, which we identified among previously unassigned ORFs.

  16. Transcriptional Profiling of Hilar Nodes from Pigs after Experimental Infection with Actinobacillus Pleuropneumoniae

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    Shumin Yu

    2013-11-01

    Full Text Available The gram-negative bacterium Actinobacillus pleuropneumoniae (APP is an inhabitant of the porcine upper respiratory tract and the causative agent of porcine pleuropneumonia (PP. In recent years, knowledge about the proinflammatory cytokine and chemokine gene expression that occurs in lung and lymph node of the APP-infected swine has been advanced. However, systematic gene expression profiles on hilar nodes from pigs after infection with Actinobacillus pleuropneumoniae have not yet been reported. The transcriptional responses were studied in hilar nodes (HN from swine experimentally infected with APP and the control groupusing Agilent Porcine Genechip, including 43,603 probe sets. 9,517 transcripts were identified as differentially expressed (DE at the p ≤ 0.01 level by comparing the log2 (normalized signal of the two groups named treatment group (TG and controls (CG. Eight hundred and fifteen of these DE transcripts were annotated as pig genes in the GenBank database (DB. Two hundred and seventy-two biological process categories (BP, 75 cellular components and 171 molecular functions were substantially altered in the TG compared to CG. Many BP were involved in host immune responses (i.e., signaling, signal transmission, signal transduction, response to stimulus, oxidation reduction, response to stress, immune system process, signaling pathway, immune response, cell surface receptor linked signaling pathway. Seven DE gene pathways (VEGF signaling pathway, Long-term potentiation, Ribosome, Asthma, Allograft rejection, Type I diabetes mellitus and Cardiac muscle contraction and statistically significant associations with host responses were affected. Many cytokines (including NRAS, PI3K, MAPK14, CaM, HSP27, protein phosphatase 3, catalytic subunit and alpha isoform, mediating the proliferation and migration of endothelial cells and promoting survival and vascular permeability, were activated in TG, whilst many immunomodulatory cytokines were

  17. Identification of key transcription factors in caerulein-induced pancreatitis through expression profiling data.

    Science.gov (United States)

    Qi, Dachuan; Wu, Bo; Tong, Danian; Pan, Ye; Chen, Wei

    2015-08-01

    The current study aimed to isolate key transcription factors (TFs) in caerulein-induced pancreatitis, and to identify the difference between wild type and Mist1 knockout (KO) mice, in order to elucidate the contribution of Mist1 to pancreatitis. The gene profile of GSE3644 was downloaded from the Gene Expression Omnibus database then analyzed using the t-test. The isolated differentially expressed genes (DEGs) were mapped into a transcriptional regulatory network derived from the Integrated Transcription Factor Platform database and in the network, the interaction pairs involving at least one DEG were screened. Fisher's exact test was used to analyze the functional enrichment of the target genes. A total of 1,555 and 3,057 DEGs were identified in the wild type and Mist1KO mice treated with caerulein, respectively. DEGs screened in Mist1KO mice were predominantly enriched in apoptosis, mitogen-activated protein kinase signaling and other cancer-associated pathways. A total of 188 and 51 TFs associated with pathopoiesis were isolated in Mist1KO and wild type mice, respectively. Out of the top 10 TFs (ranked by P-value), 7 TFs, including S-phase kinase-associated protein 2 (Skp2); minichromosome maintenance complex component 3 (Mcm3); cell division cycle 6 (Cdc6); cyclin B1 (Ccnb1); mutS homolog 6 (Msh6); cyclin A2 (Ccna2); and cyclin B2 (Ccnb2), were expressed in the two types of mouse. These TFs were predominantly involved in phosphorylation, DNA replication, cell division and DNA mismatch repair. In addition, specific TFs, including minichromosome maintenance complex component 7 (Mcm7); lymphoid-specific helicase (Hells); and minichromosome maintenance complex component 6 (Mcm6), that function in the unwinding of DNA were identified to participate in Mist1KO pancreatitis. The DEGs, including Cdc6, Mcm6, Msh6 and Wdr1 are closely associated with the regulation of caerulein-induced pancreatitis. Furthermore, other identified TFs were also involved in this type of

  18. AFLP and MS-AFLP analysis of the variation within saffron crocus (Crocus sativus L. germplasm.

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    Matteo Busconi

    Full Text Available The presence and extent of genetic variation in saffron crocus are still debated, as testified by several contradictory articles providing contrasting results about the monomorphism or less of the species. Remarkably, phenotypic variations have been frequently observed in the field, such variations are usually unstable and can change from one growing season to another. Considering that gene expression can be influenced both by genetic and epigenetic changes, epigenetics could be a plausible cause of the alternative phenotypes. In order to obtain new insights into this issue, we carried out a molecular marker analysis of 112 accessions from the World Saffron and Crocus Collection. The accessions were grown for at least three years in the same open field conditions. The same samples were analysed using Amplified Fragment Length Polymorphism (AFLP and Methyl Sensitive AFLP in order to search for variation at the genetic (DNA sequence and epigenetic (cytosine methylation level. While the genetic variability was low (4.23% polymorphic peaks and twelve (12 effective different genotypes, the methyl sensitive analysis showed the presence of high epigenetic variability (33.57% polymorphic peaks and twenty eight (28 different effective epigenotypes. The pattern obtained by Factorial Correspondence Analysis of AFLP and, in particular, of MS-AFLP data was consistent with the geographical provenance of the accessions. Very interestingly, by focusing on Spanish accessions, it was observed that the distribution of the accessions in the Factorial Correspondence Analysis is not random but tends to reflect the geographical origin. Two clearly defined clusters grouping accessions from the West (Toledo and Ciudad Real and accessions from the East (Cuenca and Teruel were clearly recognised.

  19. AFLP and MS-AFLP analysis of the variation within saffron crocus (Crocus sativus L.) germplasm.

    Science.gov (United States)

    Busconi, Matteo; Colli, Licia; Sánchez, Rosa Ana; Santaella, Marcela; De-Los-Mozos Pascual, Marcelino; Santana, Omar; Roldán, Marta; Fernández, José-Antonio

    2015-01-01

    The presence and extent of genetic variation in saffron crocus are still debated, as testified by several contradictory articles providing contrasting results about the monomorphism or less of the species. Remarkably, phenotypic variations have been frequently observed in the field, such variations are usually unstable and can change from one growing season to another. Considering that gene expression can be influenced both by genetic and epigenetic changes, epigenetics could be a plausible cause of the alternative phenotypes. In order to obtain new insights into this issue, we carried out a molecular marker analysis of 112 accessions from the World Saffron and Crocus Collection. The accessions were grown for at least three years in the same open field conditions. The same samples were analysed using Amplified Fragment Length Polymorphism (AFLP) and Methyl Sensitive AFLP in order to search for variation at the genetic (DNA sequence) and epigenetic (cytosine methylation) level. While the genetic variability was low (4.23% polymorphic peaks and twelve (12) effective different genotypes), the methyl sensitive analysis showed the presence of high epigenetic variability (33.57% polymorphic peaks and twenty eight (28) different effective epigenotypes). The pattern obtained by Factorial Correspondence Analysis of AFLP and, in particular, of MS-AFLP data was consistent with the geographical provenance of the accessions. Very interestingly, by focusing on Spanish accessions, it was observed that the distribution of the accessions in the Factorial Correspondence Analysis is not random but tends to reflect the geographical origin. Two clearly defined clusters grouping accessions from the West (Toledo and Ciudad Real) and accessions from the East (Cuenca and Teruel) were clearly recognised.

  20. Transcriptional profiling of Medicago truncatula under salt stress identified a novel CBF transcription factor MtCBF4 that plays an important role in abiotic stress responses

    Directory of Open Access Journals (Sweden)

    Su Zhen

    2011-07-01

    Full Text Available Abstract Background Salt stress hinders the growth of plants and reduces crop production worldwide. However, different plant species might possess different adaptive mechanisms to mitigate salt stress. We conducted a detailed pathway analysis of transcriptional dynamics in the roots of Medicago truncatula seedlings under salt stress and selected a transcription factor gene, MtCBF4, for experimental validation. Results A microarray experiment was conducted using root samples collected 6, 24, and 48 h after application of 180 mM NaCl. Analysis of 11 statistically significant expression profiles revealed different behaviors between primary and secondary metabolism pathways in response to external stress. Secondary metabolism that helps to maintain osmotic balance was induced. One of the highly induced transcription factor genes was successfully cloned, and was named MtCBF4. Phylogenetic analysis revealed that MtCBF4, which belongs to the AP2-EREBP transcription factor family, is a novel member of the CBF transcription factor in M. truncatula. MtCBF4 is shown to be a nuclear-localized protein. Expression of MtCBF4 in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Transgenic Arabidopsis over-expressing MtCBF4 enhanced tolerance to drought and salt stress, and activated expression of downstream genes that contain DRE elements. Over-expression of MtCBF4 in M. truncatula also enhanced salt tolerance and induced expression level of corresponding downstream genes. Conclusion Comprehensive transcriptomic analysis revealed complex mechanisms exist in plants in response to salt stress. The novel transcription factor gene MtCBF4 identified here played an important role in response to abiotic stresses, indicating that it might be a good candidate gene for genetic improvement to produce stress-tolerant plants.

  1. Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling

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    Rumballe Bree A

    2011-09-01

    Full Text Available Abstract Background The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models. Results To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs. Conclusion The resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events.

  2. Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis

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    Chavez Adela

    2008-07-01

    Full Text Available Abstract Background Anaplasma phagocytophilum (Ap is an obligate intracellular bacterium and the agent of human granulocytic anaplasmosis, an emerging tick-borne disease. Ap alternately infects ticks and mammals and a variety of cell types within each. Understanding the biology behind such versatile cellular parasitism may be derived through the use of tiling microarrays to establish high resolution, genome-wide transcription profiles of the organism as it infects cell lines representative of its life cycle (tick; ISE6 and pathogenesis (human; HL-60 and HMEC-1. Results Detailed, host cell specific transcriptional behavior was revealed. There was extensive differential Ap gene transcription between the tick (ISE6 and the human (HL-60 and HMEC-1 cell lines, with far fewer differentially transcribed genes between the human cell lines, and all disproportionately represented by membrane or surface proteins. There were Ap genes exclusively transcribed in each cell line, apparent human- and tick-specific operons and paralogs, and anti-sense transcripts that suggest novel expression regulation processes. Seven virB2 paralogs (of the bacterial type IV secretion system showed human or tick cell dependent transcription. Previously unrecognized genes and coding sequences were identified, as were the expressed p44/msp2 (major surface proteins paralogs (of 114 total, through elevated signal produced to the unique hypervariable region of each – 2/114 in HL-60, 3/114 in HMEC-1, and none in ISE6. Conclusion Using these methods, whole genome transcription profiles can likely be generated for Ap, as well as other obligate intracellular organisms, in any host cells and for all stages of the cell infection process. Visual representation of comprehensive transcription data alongside an annotated map of the genome renders complex transcription into discernable patterns.

  3. Discovery of diversity in xylan biosynthetic genes by transcriptional profiling of a heteroxylan containing mucilaginous tissue

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    Jacob Kruger Jensen

    2013-06-01

    Full Text Available The exact biochemical steps of xylan backbone synthesis remain elusive. In Arabidopsis, three non-redundant genes from two glycosyltransferase (GT families, IRX9 and IRX14 from GT43 and IRX10 from GT47, are candidates for forming the xylan backbone. In other plants, evidence exists that different tissues express these three genes at widely different levels, which suggests that diversity in the makeup of the xylan synthase complex exists. Recently we have profiled the transcripts present in the developing mucilaginous tissue of psyllium (Plantago ovata Forsk. This tissue was found to have high expression levels of an IRX10 homolog, but very low levels of the two GT43 family members. This contrasts with recent wheat endosperm tissue profiling that found a relatively high abundance of the GT43 family members. We have performed an in-depth analysis of all GTs genes expressed in four developmental stages of the psyllium mucilagenous layer and in a single stage of the psyllium stem using RNA-Seq. This analysis revealed several IRX10 homologs, an expansion in GT61 (homologs of At3g18170/At3g18180, and several GTs from other GT families that are highly abundant and specifically expressed in the mucilaginous tissue. Our current hypothesis is that the four IRX10 genes present in the mucilagenous tissues have evolved to function without the GT43 genes. These four genes represent some of the most divergent IRX10 genes identified to date. Conversely, those present in the psyllium stem are very similar to those in other eudicots. This suggests these genes are under selective pressure, likely due to the synthesis of the various xylan structures present in mucilage that has a different biochemical role than that present in secondary walls. The numerous GT61 family members also show a wide sequence diversity and may be responsible for the larger number of side chain structures present in the psyllium mucilage.

  4. Gene transcript profiles in the desert plant Nitraria tangutorum during fruit development and ripening.

    Science.gov (United States)

    Wang, Jia; Dang, Zhenhua; Zhang, Huirong; Zheng, Linlin; Borjigin, Tebuqin; Wang, Yingchun

    2016-02-01

    Nitraria tangutorum Bobr., a valuable wild shrub distributed in Northwest China, produces edible and medicinal berries. However, little is known about the molecular mechanisms of its fruit development and ripening. We performed de novo transcriptome sequencing of N. tangutorum fruit using the Illumina HiSeq™ 2000 sequencing platform. More than 62.94 million reads were obtained and assembled into 69,306 unigenes (average length, 587 bp). These unigenes were annotated by querying against five databases (Nr, Swiss-Prot, GO, COG, and KEGG); 42,929 and 26,809 unigenes were found in the Nr and Swiss-Prot databases, respectively. In ortholog analyses, 33,363 unigenes were assigned with one or more GO terms, 15,537 hits were aligned to 25 COG classes, and 24,592 unigenes were classified into 128 KEGG pathways. Digital gene expression analyses were conducted on N. tangutorum fruit at the green (S1), yellow (S2), and red (S3) developmental stages. In total, 8240, 5985, and 4994 differentially expressed genes (DEGs) were detected for S1 vs. S2, S1 vs. S3, and S2 vs. S3, respectively. Cluster analyses showed that a large proportion of DEGs related to plant hormones and transcription factors (TFs) showed high expression in S1, down-regulated expression in S2, and up-regulated expression in S3. We analyzed the expression patterns of 23 genes encoding 12 putative enzymes involved in flavonoid biosynthesis. The expression profiles of 10 DEGs involved in flavonoid biosynthesis were validated by Q-PCR analysis. The assembled and annotated transcriptome sequences and gene expression profile analyses provide valuable genetic resources for research on N. tangutorum.

  5. Benzo (a) pyrene induced tumorigenesity of human immortalized oral epithelial cells: transcription profiling

    Institute of Scientific and Technical Information of China (English)

    LI Jin-zhong; PAN Hong-ya; ZHENG Jia-wei; ZHOU Xiao-jian; ZHANG Ping; CHEN Wan-tao; ZHANG Zhi-yuan

    2008-01-01

    Background The present study was designed to examine and analyze the global gene expression changes during the tumorigenesis of a human immortalized oral epithelial cell line, and search for the possible genes that may play a role in the carcinogenesis of oral cancer associated with benzo (a) pyrene.Methods The human immortalized oral epithelial cells, which have been established through transfection of E6/E7 genasof human papillomavirus type 16 and proved to be non-tumorigenic in nude mice, were treated with benzo (a) pyrene.Tumorigenesity of the treated cells were examined through nude mice subcutaneous injection. The global gene expression profiles of immortalized cells and the tumorigenic cells were acquired through hybridization of a microarray of Affymetrix U133 plus 2.0. The data were analyzed using Spring 7.0 software and treated statistically using one-way analysis of variance (ANOVA). The differentially expressed genes were classified using a Venn diagram and annotated with gene ontology. Several highlighted genes were validated in cells using a real-time polymerase chain reaction.Results There were 883 differentially expressed genes during the tumorigenesis and most of them changed expression in the early stage of tumorigenesis. These genes mainly involved in macromolecule metabolism and signal transduction,possessed the molecular function of transition metal ion binding, nucleotide binding and kinase activity; their protein products were mainly integral to membranes or localized in the nucleus and cytoskeleton. The expression patterns of IGFBP3, S100A8, MAP2K, KRT6B, GDF15, MET were validated in cells using a real-time polymerase chain reaction; the expression of IGFBP3 was further validated in clinical oral cancer specimens.Concluslona This study provides the global transcription profiling associated with the tumorigenesis of oral epithelial cells exposed to benzo (a) pyrene; IGFBP3 may play a potential role in the initiation of oral cancer related to

  6. Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites

    KAUST Repository

    Wong, Ka-Chun

    2015-04-20

    With the prevalence of chromatin immunoprecipitation (ChIP) with sequencing (ChIP-Seq) technology, massive ChIP-Seq data has been accumulated. The ChIP-Seq technology measures the genome-wide occupancy of DNA-binding proteins in vivo. It is well-known that different DNA-binding protein occupancies may result in a gene being regulated in different conditions (e.g. different cell types). To fully understand a gene\\'s function, it is essential to develop probabilistic models on multiple ChIP-Seq profiles for deciphering the gene transcription causalities. In this work, we propose and describe two probabilistic models. Assuming the conditional independence of different DNA-binding proteins\\' occupancies, the first method (SignalRanker) is developed as an intuitive method for ChIP-Seq genome-wide signal profile inference. Unfortunately, such an assumption may not always hold in some gene regulation cases. Thus, we propose and describe another method (FullSignalRanker) which does not make the conditional independence assumption. The proposed methods are compared with other existing methods on ENCODE ChIP-Seq datasets, demonstrating its regression and classification ability. The results suggest that FullSignalRanker is the best-performing method for recovering the signal ranks on the promoter and enhancer regions. In addition, FullSignalRanker is also the best-performing method for peak sequence classification. We envision that SignalRanker and FullSignalRanker will become important in the era of next generation sequencing. FullSignalRanker program is available on the following website: http://www.cs.toronto.edu/∼wkc/FullSignalRanker/ © 2015 IEEE.

  7. Transcriptional Profiling of Th2 Cells Identifies Pathogenic Features Associated with Asthma.

    Science.gov (United States)

    Seumois, Grégory; Zapardiel-Gonzalo, Jose; White, Brandie; Singh, Divya; Schulten, Veronique; Dillon, Myles; Hinz, Denize; Broide, David H; Sette, Alessandro; Peters, Bjoern; Vijayanand, Pandurangan

    2016-07-15

    Allergic asthma and rhinitis are two common chronic allergic diseases that affect the lungs and nose, respectively. Both diseases share clinical and pathological features characteristic of excessive allergen-induced type 2 inflammation, orchestrated by memory CD4(+) T cells that produce type 2 cytokines (Th2 cells). However, a large majority of subjects with allergic rhinitis do not develop asthma, suggesting divergence in disease mechanisms. Because Th2 cells play a pathogenic role in both these diseases and are also present in healthy nonallergic subjects, we performed global transcriptional profiling to determine whether there are qualitative differences in Th2 cells from subjects with allergic asthma, rhinitis, and healthy controls. Th2 cells from asthmatic subjects expressed higher levels of several genes that promote their survival as well as alter their metabolic pathways to favor persistence at sites of allergic inflammation. In addition, genes that enhanced Th2 polarization and Th2 cytokine production were also upregulated in asthma. Several genes that oppose T cell activation were downregulated in asthma, suggesting enhanced activation potential of Th2 cells from asthmatic subjects. Many novel genes with poorly defined functions were also differentially expressed in asthma. Thus, our transcriptomic analysis of circulating Th2 cells has identified several molecules that are likely to confer pathogenic features to Th2 cells that are either unique or common to both asthma and rhinitis. PMID:27271570

  8. Derivation and transcriptional profiling analysis of pluripotent stem cell lines from rat blastocysts

    Institute of Scientific and Technical Information of China (English)

    Chunliang Li; Ying Yang; Junjie Gu; Yu Ma; Ying Jin

    2009-01-01

    Embryonic stem (ES) cells are derived from blastocyst-stage embryos. Their unique properties of self-renewal and pluripotency make them an attractive tool for basic research and a potential cell resource for therapy. ES cells of mouse and human have been successfully generated and applied in a wide range of research. However, no genuine ES cell lines have been obtained from rat to date. In this study, we identified pluripotent cells in early rat embryos using specific antibodies against markers of pluripotent stem cells. Subsequently, by modifying the culture medium for rat blastocysts, we derived pluripotent rat ES-llke cell lines, which expressed pluripotency markers and formed embryoid bodies (EBs) in vitro. Importantly, these rat ES-like cells were able to produce teratomas. Both EBs and teratomas contained tissues from all three embryonic germ layers, in addition, from the rat ES-like cells, we derived a rat primitive endoderm (PrE) cell line. Furthermore, we conducted transcriptional profiling of the rat ES-like cells and identified the unique molecular signature of the rat pluripotent stem cells. Our analysis demonstrates that multiple signaling pathways, including the BMP, Activin and roTOR pathways, may be involved in keeping the rat ES-like cells in an undifferentiated state. The cell lines and information obtained in this study will accelerate our understanding of the molecular regulation underlying pluripotency and guide us in the appropriate manipulation of ES cells from a particular species.

  9. Gene transcriptional profiles in human lymphoblastoid cells with low and high doses of irradiation

    International Nuclear Information System (INIS)

    Objective: To compare the gene expression difference between 0.1 and 5 Gy X-ray irradiated cells,and to explore its possible mechanism. Methods: A cDNA microarray corresponding to 45033 human genes was used to analyze the transcriptional profiles of normal human lymphoblastoid AHH-1 cells at 4 h after 0.1 or 5 Gy irradiation. The genes with a fold change ≥ 2.0 were identified as the differentially expressed genes. real-lime PCR and Western blot were used to confirm the expression of PERP. Results: The microarray assay showed that there were 760 up-regulated genes and 1222 down-regulated genes in the cells at 0.1 Gy, while there were 744 genes down-regulated and 457 genes up-regulated in the cells at 5 Gy. In addition, 55 genes were commonly up-regulated and 339 genes commonly down-regulated at 0.1 and 5 Gy. The predominant biological processes of the differential genes responding to low-dose radiation include cell-cell signaling transduction and DNA damage response, and the altered genes after 5 Gy irradiation were related to cell proliferation, differentiation, and apoptosis. Moreover, the expression of PERP gene was down regulated, which was consistent with the data of microarray assay. Conclusions: The quantitative and qualitative differences in the gene expressions may contribute to the diverse biological effects induced by low or high doses of ionizing radiation. (authors)

  10. Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato

    OpenAIRE

    Gong, Pengjuan; Zhang, Junhong; Li, Hanxia; Yang, Changxian; Zhang, Chanjuan; Zhang, Xiaohui; Khurram, Ziaf; Zhang, Yuyang; Wang, Taotao; Fei, Zhangjun; Ye, Zhibiao

    2010-01-01

    To unravel the molecular mechanisms of drought responses in tomato, gene expression profiles of two drought-tolerant lines identified from a population of Solanum pennellii introgression lines, and the recurrent parent S. lycopersicum cv. M82, a drought-sensitive cultivar, were investigated under drought stress using tomato microarrays. Around 400 genes identified were responsive to drought stress only in the drought-tolerant lines. These changes in genes expression are most likely caused by ...

  11. Dormancy in potato tuber meristems: chemically induced cessation in dormancy matches the natural process based on transcript profiles.

    Science.gov (United States)

    Campbell, Michael; Segear, Erika; Beers, Lee; Knauber, Donna; Suttle, Jeffrey

    2008-11-01

    Meristem dormancy in perennial plants is a developmental process that results in repression of metabolism and growth. The cessation of dormancy results in rapid growth and should be associated with the production of nascent transcripts that encode for gene products controlling for cell division and growth. Dormancy cessation was allowed to progress normally or was chemically induced using bromoethane (BE), and microarray analysis was used to demonstrate changes in specific transcripts in response to dormancy cessation before a significant increase in cell division. Comparison of normal dormancy cessation to BE-induced dormancy cessation revealed a commonality in both up and downregulated transcripts. Many transcripts that decrease as dormancy terminates are inducible by abscisic acid particularly in the conserved BURP domain proteins, which include the RD22 class of proteins and in the storage protein patatin. Transcripts that are associated with an increase in expression encoded for proteins in the oxoglutarate-dependent oxygenase family. We conclude that BE-induced cessation of dormancy initiates transcript profiles similar to the natural processes that control dormancy. PMID:18317824

  12. Transcription profiles of endothelial cells in the rat ductus arteriosus during a perinatal period.

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    Norika Mengchia Liu

    Full Text Available Endothelial cells (ECs lining the blood vessels serve a variety of functions and play a central role in the homeostasis of the circulatory system. Since the ductus arteriosus (DA has different arterial characteristics from its connecting vessels, we hypothesized that ECs of the DA exhibited a unique gene profile involved in the regulation of DA-specific morphology and function. Using a fluorescence-activated cell sorter, we isolated ECs from pooled tissues from the DA or the descending aorta of Wistar rat fetuses at full-term of gestation (F group or neonates 30 minutes after birth (N group. Using anti-CD31 and anti-CD45 antibodies as cell surface markers for ECs and hematopoietic derived cells, respectively, cDNAs from the CD31-positive and CD45-negative cells were hybridized to the Affymetrix GeneChip® Rat Gene 1.0 ST Array. Among 26,469 gene-level probe sets, 82 genes in the F group and 81 genes in the N group were expressed at higher levels in DA ECs than in aortic ECs (p2.0. In addition to well-known endothelium-enriched genes such as Tgfb2 and Vegfa, novel DA endothelium-dominant genes including Slc38a1, Capn6, and Lrat were discovered. Enrichment analysis using GeneGo MetaCore software showed that DA endothelium-related biological processes were involved in morphogenesis and development. We identified many overlapping genes in each process including neural crest-related genes (Hoxa1, Hoxa4, and Hand2, etc and the second heart field-related genes (Tbx1, Isl1, and Fgf10, etc. Moreover, we found that regulation of epithelial-to-mesenchymal transition, cell adhesion, and retinol metabolism are the active pathways involved in the network via potential interactions with many of the identified genes to form DA-specific endothelia. In conclusion, the present study uncovered several significant differences of the transcriptional profile between the DA and aortic ECs. Newly identified DA endothelium-dominant genes may play an important role in DA

  13. Gene Transcript Profiling in Sea Otters Post-Exxon Valdez Oil Spill: A Tool for Marine Ecosystem Health Assessment

    Directory of Open Access Journals (Sweden)

    Lizabeth Bowen

    2016-06-01

    Full Text Available Using a panel of genes stimulated by oil exposure in a laboratory study, we evaluated gene transcription in blood leukocytes sampled from sea otters captured from 2006–2012 in western Prince William Sound (WPWS, Alaska, 17–23 years after the 1989 Exxon Valdez oil spill (EVOS. We compared WPWS sea otters to reference populations (not affected by the EVOS from the Alaska Peninsula (2009, Katmai National Park and Preserve (2009, Clam Lagoon at Adak Island (2012, Kodiak Island (2005 and captive sea otters in aquaria. Statistically, sea otter gene transcript profiles separated into three distinct clusters: Cluster 1, Kodiak and WPWS 2006–2008 (higher relative transcription; Cluster 2, Clam Lagoon and WPWS 2010–2012 (lower relative transcription; and Cluster 3, Alaska Peninsula, Katmai and captive sea otters (intermediate relative transcription. The lower transcription of the aryl hydrocarbon receptor (AHR, an established biomarker for hydrocarbon exposure, in WPWS 2010–2012 compared to earlier samples from WPWS is consistent with declining hydrocarbon exposure, but the pattern of overall low levels of transcription seen in WPWS 2010–2012 could be related to other factors, such as food limitation, pathogens or injury, and may indicate an inability to mount effective responses to stressors. Decreased transcriptional response across the entire gene panel precludes the evaluation of whether or not individual sea otters show signs of exposure to lingering oil. However, related studies on sea otter demographics indicate that by 2012, the sea otter population in WPWS had recovered, which indicates diminishing oil exposure.

  14. Gene transcript profiling in sea otters post-Exxon Valdez oil spill: A tool for marine ecosystem health assessment

    Science.gov (United States)

    Bowen, Lizabeth; Miles, A. Keith; Ballachey, Brenda E.; Waters, Shannon C.; Bodkin, James L.

    2016-01-01

    Using a panel of genes stimulated by oil exposure in a laboratory study, we evaluated gene transcription in blood leukocytes sampled from sea otters captured from 2006–2012 in western Prince William Sound (WPWS), Alaska, 17–23 years after the 1989 Exxon Valdez oil spill (EVOS). We compared WPWS sea otters to reference populations (not affected by the EVOS) from the Alaska Peninsula (2009), Katmai National Park and Preserve (2009), Clam Lagoon at Adak Island (2012), Kodiak Island (2005) and captive sea otters in aquaria. Statistically, sea otter gene transcript profiles separated into three distinct clusters: Cluster 1, Kodiak and WPWS 2006–2008 (higher relative transcription); Cluster 2, Clam Lagoon and WPWS 2010–2012 (lower relative transcription); and Cluster 3, Alaska Peninsula, Katmai and captive sea otters (intermediate relative transcription). The lower transcription of the aryl hydrocarbon receptor (AHR), an established biomarker for hydrocarbon exposure, in WPWS 2010–2012 compared to earlier samples from WPWS is consistent with declining hydrocarbon exposure, but the pattern of overall low levels of transcription seen in WPWS 2010–2012 could be related to other factors, such as food limitation, pathogens or injury, and may indicate an inability to mount effective responses to stressors. Decreased transcriptional response across the entire gene panel precludes the evaluation of whether or not individual sea otters show signs of exposure to lingering oil. However, related studies on sea otter demographics indicate that by 2012, the sea otter population in WPWS had recovered, which indicates diminishing oil exposure.

  15. Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids.

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    Pooi Yin Chung

    Full Text Available Staphylococcus aureus is an important human pathogen in both hospital and the community that has demonstrated resistance to all currently available antibiotics over the last two decades. Multidrug-resistant isolates of methicillin-resistant S. aureus (MRSA exhibiting decreased susceptibilities to glycopeptides has also emerged, representing a crucial challenge for antimicrobial therapy and infection control. The availability of complete whole-genome nucleotide sequence data of various strains of S. aureus presents an opportunity to explore novel compounds and their targets to address the challenges presented by antimicrobial drug resistance in this organism. Study compounds α-amyrin [3β-hydroxy-urs-12-en-3-ol (AM], betulinic acid [3β-hydroxy-20(29-lupaene-28-oic acid (BA] and betulinaldehyde [3β-hydroxy-20(29-lupen-28-al (BE] belong to pentacyclic triterpenoids and were reported to exhibit antimicrobial activities against bacteria and fungi, including S. aureus. The MIC values of these compounds against a reference strain of methicillin-resistant S. aureus (MRSA (ATCC 43300 ranged from 64 µg/ml to 512 µg/ml. However, the response mechanisms of S. aureus to these compounds are still poorly understood. The transcription profile of reference strain of MRSA treated with sub-inhibitory concentrations of the three compounds was determined using Affymetrix GeneChips. The findings showed that these compounds regulate multiple desirable targets in cell division, two-component system, ABC transporters, fatty acid biosynthesis, peptidoglycan biosynthesis, aminoacyl-tRNA synthetase, ribosome and β-lactam resistance pathways which could be further explored in the development of therapeutic agents for the treatment of S. aureus infections.

  16. Dynamic, large-scale profiling of transcription factor activity from live cells in 3D culture.

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    Michael S Weiss

    Full Text Available BACKGROUND: Extracellular activation of signal transduction pathways and their downstream target transcription factors (TFs are critical regulators of cellular processes and tissue development. The intracellular signaling network is complex, and techniques that quantify the activities of numerous pathways and connect their activities to the resulting phenotype would identify the signals and mechanisms regulating tissue development. The ability to investigate tissue development should capture the dynamic pathway activity and requires an environment that supports cellular organization into structures that mimic in vivo phenotypes. Taken together, our objective was to develop cellular arrays for dynamic, large-scale quantification of TF activity as cells organized into spherical structures within 3D culture. METHODOLOGY/PRINCIPAL FINDINGS: TF-specific and normalization reporter constructs were delivered in parallel to a cellular array containing a well-established breast cancer cell line cultured in Matrigel. Bioluminescence imaging provided a rapid, non-invasive, and sensitive method to quantify luciferase levels, and was applied repeatedly on each sample to monitor dynamic activity. Arrays measuring 28 TFs identified up to 19 active, with 13 factors changing significantly over time. Stimulation of cells with β-estradiol or activin A resulted in differential TF activity profiles evolving from initial stimulation of the ligand. Many TFs changed as expected based on previous reports, yet arrays were able to replicate these results in a single experiment. Additionally, arrays identified TFs that had not previously been linked with activin A. CONCLUSIONS/SIGNIFICANCE: This system provides a method for large-scale, non-invasive, and dynamic quantification of signaling pathway activity as cells organize into structures. The arrays may find utility for investigating mechanisms regulating normal and abnormal tissue growth, biomaterial design, or as a

  17. Transcriptional gene expression profiles of HGF/SF-met signaling pathway in colorectal carcinoma

    Institute of Scientific and Technical Information of China (English)

    Xue-Nong Li; Yan-Qing Ding; Guo-Bing Liu

    2003-01-01

    AIM: To explore the transcriptional gene expression profiles of HGF/SF-met signaling pathway in colorectal carcinoma to understand mechanisms of the signaling pathway at so gene level.METHODS: Total RNA was isolated from human colorectal carcinoma cell line LoVo treated with HGF/SF (80 ng/L)for 48 h. Fluorescent probes were prepared from RNA labeled with cy3-dUTP for the control groups and with cy5-dUTP for the HGF/SF-treated groups through reversetranscription. The probes were mixed and hybridized on the microarray at 60 ℃ for 15-20 h, then the microarray was scanned by laser scanner (GenePix 4000B). The intensity of each spot and ratios of Cy5/Cy3 were analyzed and finally the differentially expressed genes were selected by GenePix Pro 3.0 software. 6 differential expression genes (3 up-regulated genes and 3 down-regulated genes) were selected randomly and analyzed by β-actin semiquantitative RT-PCR.RESULTS: The fluorescent intensities of built-in negative control spots were less than 200, and the fluorescent intensities of positive control spots were more than 5000.Of the 4004 human genes analyzed by microarray, 129 genes (holding 3.22 % of the investigated genes) revealed differential expression in HGF/SF-treated groups compared with the control groups, of which 61 genes were up-regulated (holding 1.52 % of the investigated genes) and 68 genes were down-regulated (holding 1.70 % of the investigated genes), which supplied abundant information about target genes of HGF/SF-met signaling.CONCLUSION: HGF/SF-met signaling may up-regulate oncogenes, signal transduction genes, apoptosis-related genes, metastasis related genes, and down-regulate a number of genes. The complexity of HGF/SF-met signaling to control the gene expression is revealed as a whole by the gene chip technology.

  18. Transcriptional profiling of the bladder in urogenital schistosomiasis reveals pathways of inflammatory fibrosis and urothelial compromise.

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    Debalina Ray

    Full Text Available Urogenital schistosomiasis, chronic infection by Schistosoma haematobium, affects 112 million people worldwide. S. haematobium worm oviposition in the bladder wall leads to granulomatous inflammation, fibrosis, and egg expulsion into the urine. Despite the global impact of urogenital schistosomiasis, basic understanding of the associated pathologic mechanisms has been incomplete due to the lack of suitable animal models. We leveraged our recently developed mouse model of urogenital schistosomiasis to perform the first-ever profiling of the early molecular events that occur in the bladder in response to the introduction of S. haematobium eggs. Microarray analysis of bladders revealed rapid, differential transcription of large numbers of genes, peaking three weeks post-egg administration. Many differentially transcribed genes were related to the canonical Type 2 anti-schistosomal immune response, as reflected by the development of egg-based bladder granulomata. Numerous collagen and metalloproteinase genes were differentially transcribed over time, revealing complex remodeling and fibrosis of the bladder that was confirmed by Masson's Trichrome staining. Multiple genes implicated in carcinogenesis pathways, including vascular endothelial growth factor-, oncogene-, and mammary tumor-related genes, were differentially transcribed in egg-injected bladders. Surprisingly, junctional adhesion molecule, claudin and uroplakin genes, key components for maintaining the urothelial barrier, were globally suppressed after bladder exposure to eggs. This occurred in the setting of urothelial hyperplasia and egg shedding in urine. Thus, S. haematobium egg expulsion is associated with intricate modulation of the urothelial barrier on the cellular and molecular level. Taken together, our findings have important implications for understanding host-parasite interactions and carcinogenesis in urogenital schistosomiasis, and may provide clues for novel therapeutic

  19. Effects of Argentilactone on the Transcriptional Profile, Cell Wall and Oxidative Stress of Paracoccidioides spp.

    Science.gov (United States)

    Araújo, Felipe Souto; Coelho, Luciene Melo; Silva, Lívia do Carmo; da Silva Neto, Benedito Rodrigues; Parente-Rocha, Juliana Alves; Bailão, Alexandre Melo; de Oliveira, Cecília Maria Alves; Fernandes, Gabriel da Rocha; Hernández, Orville; Ochoa, Juan Guillermo McEwen; Soares, Célia Maria de Almeida; Pereira, Maristela

    2016-01-01

    Paracoccidioides spp., a dimorphic pathogenic fungus, is the etiologic agent of paracoccidioidomycosis (PCM). PCM is an endemic disease that affects at least 10 million people in Latin America, causing severe public health problems. The drugs used against pathogenic fungi have various side effects and limited efficacy; therefore, there is an inevitable and urgent medical need for the development of new antifungal drugs. In the present study, we evaluated the transcriptional profile of Paracoccidioides lutzii exposed to argentilactone, a constituent of the essential oil of Hyptis ovalifolia. A total of 1,058 genes were identified, of which 208 were up-regulated and 850 were down-regulated. Cell rescue, defense and virulence, with a total of 26 genes, was a functional category with a large number of genes induced, including heat shock protein 90 (hsp90), cytochrome c peroxidase (ccp), the hemoglobin ligand RBT5 (rbt5) and superoxide dismutase (sod). Quantitative real-time PCR revealed an increase in the expression level of all of those genes. An enzymatic assay showed a significant increase in SOD activity. The reduced growth of Pbhsp90-aRNA, Pbccp-aRNA, Pbsod-aRNA and Pbrbt5-aRNA isolates in the presence of argentilactone indicates the importance of these genes in the response of Paracoccidioides spp. to argentilactone. The response of the P. lutzii cell wall to argentilactone treatment was also evaluated. The results showed that argentilactone caused a decrease in the levels of polymers in the cell wall. These results suggest that argentilactone is a potential candidate for antifungal therapy. PMID:26734764

  20. Comparative Analysis of the Brassica napus Root and Leaf Transcript Profiling in Response to Drought Stress

    Directory of Open Access Journals (Sweden)

    Chunqing Liu

    2015-08-01

    Full Text Available Drought stress is one of the major abiotic factors affecting Brassica napus (B. napus productivity. In order to identify genes of potential importance to drought stress and obtain a deeper understanding of the molecular mechanisms regarding the responses of B. napus to dehydration stress, we performed large-scale transcriptome sequencing of B. napus plants under dehydration stress using the Illumina sequencing technology. In this work, a relatively drought tolerant B. napus line, Q2, identified in our previous study, was used. Four cDNA libraries constructed from mRNAs of control and dehydration-treated root and leaf were sequenced by Illumina technology. A total of 6018 and 5377 differentially expressed genes (DEGs were identified in root and leaf. In addition, 1745 genes exhibited a coordinated expression profile between the two tissues under drought stress, 1289 (approximately 74% of which showed an inverse relationship, demonstrating different regulation patterns between the root and leaf. The gene ontology (GO enrichment test indicated that up-regulated genes in root were mostly involved in “stimulus” “stress” biological process, and activated genes in leaf mainly functioned in “cell” “cell part” components. Furthermore, a comparative network related to plant hormone signal transduction and AREB/ABF, AP2/EREBP, NAC, WRKY and MYC/MYB transcription factors (TFs provided a view of different stress tolerance mechanisms between root and leaf. Some of the DEGs identified may be candidates for future research aimed at detecting drought-responsive genes and will be useful for understanding the molecular mechanisms of drought tolerance in root and leaf of B. napus.

  1. Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Bagger, Frederik Otzen; Jendholm, Johan;

    2014-01-01

    Gene expression profiling has been used extensively to characterize cancer, identify novel subtypes, and improve patient stratification. However, it has largely failed to identify transcriptional programs that differ between cancer and corresponding normal cells and has not been efficient in...... hematopoietic hierarchy, using expression profiles from normal stem/progenitor cells, and next mapped the AML patient samples to this landscape. This allowed us to identify the closest normal counterpart of individual AML samples and determine gene expression changes between cancer and normal. We find the...... cancer vs normal method (CvN method) to be superior to conventional methods in stratifying AML patients with aberrant karyotype and in identifying common aberrant transcriptional programs with potential importance for AML etiology. Moreover, the CvN method uncovered a novel poor-outcome subtype of normal...

  2. Transcriptional Profiles of Drought-Related Genes in Modulating Metabolic Processes and Antioxidant Defenses in Lolium multiflorum

    OpenAIRE

    Pan, Ling; Zhang, Xinquan; Wang, Jianping; Ma, Xiao; Zhou, Meiliang; Huang, Linkai; Nie, Gang; Wang, Pengxi; Yang, Zhongfu; Li, Ji

    2016-01-01

    Drought is a major environmental stress that limits growth and development of cool-season annual grasses. Drought transcriptional profiles of resistant and susceptible lines were studied to understand the molecular mechanisms of drought tolerance in annual ryegrass (Lolium multiflorum L.). A total of 4718 genes exhibited significantly differential expression in two L. multiflorum lines. Additionally, up-regulated genes associated with drought response in the resistant lines were compared with...

  3. Multi-transcript profiling in archival diagnostic prostate cancer needle biopsies to evaluate biomarkers in non-surgically treated men

    OpenAIRE

    Kachroo, Naveen; Warren, Anne Y; Gnanapragasam, Vincent J.

    2014-01-01

    Background Most biomarkers in prostate cancer have only been evaluated in surgical cohorts. The value of these biomarkers in a different therapy context remains unclear. Our objective was to test a panel of surgical biomarkers for prognostic value in men treated by external beam radiotherapy (EBRT) and primary androgen deprivation therapy (PADT). Methods The Fluidigm® PCR array was used for multi-transcript profiling of laser microdissected tumours from archival formalin-fixed diagnostic biop...

  4. Transcription Profiling of Malaria-Naïve and Semi-immune Colombian Volunteers in a Plasmodium vivax Sporozoite Challenge

    OpenAIRE

    Rojas-Peña, Monica L.; Vallejo, Andres; Herrera, Sócrates; Gibson, Greg; Arévalo-Herrera, Myriam

    2015-01-01

    Background Continued exposure to malaria-causing parasites in endemic regions of malaria induces significant levels of acquired immunity in adult individuals. A better understanding of the transcriptional basis for this acquired immunological response may provide insight into how the immune system can be boosted during vaccination, and into why infected individuals differ in symptomology. Methodology/Principal Findings Peripheral blood gene expression profiles of 9 semi-immune volunteers from...

  5. Gene transcription profiles associated with inter-modular hubs and connection distance in human functional magnetic resonance imaging networks.

    Science.gov (United States)

    Vértes, Petra E; Rittman, Timothy; Whitaker, Kirstie J; Romero-Garcia, Rafael; Váša, František; Kitzbichler, Manfred G; Wagstyl, Konrad; Fonagy, Peter; Dolan, Raymond J; Jones, Peter B; Goodyer, Ian M; Bullmore, Edward T

    2016-10-01

    Human functional magnetic resonance imaging (fMRI) brain networks have a complex topology comprising integrative components, e.g. long-distance inter-modular edges, that are theoretically associated with higher biological cost. Here, we estimated intra-modular degree, inter-modular degree and connection distance for each of 285 cortical nodes in multi-echo fMRI data from 38 healthy adults. We used the multivariate technique of partial least squares (PLS) to reduce the dimensionality of the relationships between these three nodal network parameters and prior microarray data on regional expression of 20 737 genes. The first PLS component defined a transcriptional profile associated with high intra-modular degree and short connection distance, whereas the second PLS component was associated with high inter-modular degree and long connection distance. Nodes in superior and lateral cortex with high inter-modular degree and long connection distance had local transcriptional profiles enriched for oxidative metabolism and mitochondria, and for genes specific to supragranular layers of human cortex. In contrast, primary and secondary sensory cortical nodes in posterior cortex with high intra-modular degree and short connection distance had transcriptional profiles enriched for RNA translation and nuclear components. We conclude that, as predicted, topologically integrative hubs, mediating long-distance connections between modules, are more costly in terms of mitochondrial glucose metabolism.This article is part of the themed issue 'Interpreting BOLD: a dialogue between cognitive and cellular neuroscience'. PMID:27574314

  6. Gene transcription profiles associated with inter-modular hubs and connection distance in human functional magnetic resonance imaging networks

    Science.gov (United States)

    Vértes, Petra E.; Rittman, Timothy; Whitaker, Kirstie J.; Romero-Garcia, Rafael; Váša, František; Wagstyl, Konrad; Fonagy, Peter; Dolan, Raymond J.; Jones, Peter B.; Goodyer, Ian M.

    2016-01-01

    Human functional magnetic resonance imaging (fMRI) brain networks have a complex topology comprising integrative components, e.g. long-distance inter-modular edges, that are theoretically associated with higher biological cost. Here, we estimated intra-modular degree, inter-modular degree and connection distance for each of 285 cortical nodes in multi-echo fMRI data from 38 healthy adults. We used the multivariate technique of partial least squares (PLS) to reduce the dimensionality of the relationships between these three nodal network parameters and prior microarray data on regional expression of 20 737 genes. The first PLS component defined a transcriptional profile associated with high intra-modular degree and short connection distance, whereas the second PLS component was associated with high inter-modular degree and long connection distance. Nodes in superior and lateral cortex with high inter-modular degree and long connection distance had local transcriptional profiles enriched for oxidative metabolism and mitochondria, and for genes specific to supragranular layers of human cortex. In contrast, primary and secondary sensory cortical nodes in posterior cortex with high intra-modular degree and short connection distance had transcriptional profiles enriched for RNA translation and nuclear components. We conclude that, as predicted, topologically integrative hubs, mediating long-distance connections between modules, are more costly in terms of mitochondrial glucose metabolism. This article is part of the themed issue ‘Interpreting BOLD: a dialogue between cognitive and cellular neuroscience’. PMID:27574314

  7. CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes

    Directory of Open Access Journals (Sweden)

    Moreau Yves

    2007-10-01

    Full Text Available Abstract Background The Complete Arabidopsis Transcript MicroArray (CATMA initiative combines the efforts of laboratories in eight European countries 1 to deliver gene-specific sequence tags (GSTs for the Arabidopsis research community. The CATMA initiative offers the power and flexibility to regularly update the GST collection according to evolving knowledge about the gene repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference. Results GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002 were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGène, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS. A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and Eu

  8. Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome

    Directory of Open Access Journals (Sweden)

    Ferrari Francesco

    2009-06-01

    Full Text Available Abstract Background Water stress during grain filling has a marked effect on grain yield, leading to a reduced endosperm cell number and thus sink capacity to accumulate dry matter. The bread wheat cultivar Chinese Spring (CS, a Chinese Spring terminal deletion line (CS_5AL-10 and the durum wheat cultivar Creso were subjected to transcriptional profiling after exposure to mild and severe drought stress at the grain filling stage to find evidences of differential stress responses associated to different wheat genome regions. Results The transcriptome analysis of Creso, CS and its deletion line revealed 8,552 non redundant probe sets with different expression levels, mainly due to the comparisons between the two species. The drought treatments modified the expression of 3,056 probe sets. Besides a set of genes showing a similar drought response in Creso and CS, cluster analysis revealed several drought response features that can be associated to the different genomic structure of Creso, CS and CS_5AL-10. Some drought-related genes were expressed at lower level (or not expressed in Creso (which lacks the D genome or in the CS_5AL-10 deletion line compared to CS. The chromosome location of a set of these genes was confirmed by PCR-based mapping on the D genome (or the 5AL-10 region. Many clusters were characterized by different level of expression in Creso, CS and CS_AL-10, suggesting that the different genome organization of the three genotypes may affect plant adaptation to stress. Clusters with similar expression trend were grouped and functional classified to mine the biological mean of their activation or repression. Genes involved in ABA, proline, glycine-betaine and sorbitol pathways were found up-regulated by drought stress. Furthermore, the enhanced expression of a set of transposons and retrotransposons was detected in CS_5AL-10. Conclusion Bread and durum wheat genotypes were characterized by a different physiological reaction to water

  9. Transcriptional profile of Mycobacterium tuberculosis replicating in type II alveolar epithelial cells.

    Directory of Open Access Journals (Sweden)

    Michelle B Ryndak

    Full Text Available Mycobacterium tuberculosis (M. tb infection is initiated by the few bacilli inhaled into the alveolus. Studies in lungs of aerosol-infected mice provided evidence for extensive replication of M. tb in non-migrating, non-antigen-presenting cells in the alveoli during the first 2-3 weeks post-infection. Alveoli are lined by type II and type I alveolar epithelial cells (AEC which outnumber alveolar macrophages by several hundred-fold. M. tb DNA and viable M. tb have been demonstrated in AEC and other non-macrophage cells of the kidney, liver, and spleen in autopsied tissues from latently-infected subjects from TB-endemic regions indicating systemic bacterial dissemination during primary infection. M. tb have also been demonstrated to replicate rapidly in A549 cells (type II AEC line and acquire increased invasiveness for endothelial cells. Together, these results suggest that AEC could provide an important niche for bacterial expansion and development of a phenotype that promotes dissemination during primary infection. In the current studies, we have compared the transcriptional profile of M. tb replicating intracellularly in A549 cells to that of M. tb replicating in laboratory broth, by microarray analysis. Genes significantly upregulated during intracellular residence were consistent with an active, replicative, metabolic, and aerobic state, as were genes for tryptophan synthesis and for increased virulence (ESAT-6, and ESAT-6-like genes, esxH, esxJ, esxK, esxP, and esxW. In contrast, significant downregulation of the DevR (DosR regulon and several hypoxia-induced genes was observed. Stress response genes were either not differentially expressed or were downregulated with the exception of the heat shock response and those induced by low pH. The intra-type II AEC M. tb transcriptome strongly suggests that AEC could provide a safe haven in which M. tb can expand dramatically and disseminate from the lung prior to the elicitation of adaptive immune

  10. Physiological Basis and Transcriptional Profiling of Three Salt-Tolerant Mutant Lines of Rice

    Science.gov (United States)

    Domingo, Concha; Lalanne, Eric; Catalá, María M.; Pla, Eva; Reig-Valiente, Juan L.; Talón, Manuel

    2016-01-01

    Salinity is a complex trait that affects growth and productivity in many crops, including rice. Mutation induction, a useful tool to generate salt tolerant plants, enables the analysis of plants with similar genetic background, facilitating the understanding of the salt tolerance mechanisms. In this work, we generated three salt tolerant mutant lines by irradiation of a salt-sensitive cultivar plants and screened M2 plants at seedling stage in the presence of high salinity. These three lines, SaT20, SaS62, and SaT58, showed different responses to salinity, but exhibited similar phenotype to wild type plants, except SaT20 that displayed shorter height when grown in the absence of salt. Under salt conditions, all three mutants and the parental line showed similar reduction in yield, although relevant differences in other physiological parameters, such as Na+ accumulation in healthy leaves of SaT20, were registered. Microarray analyses of gene expression profiles in roots revealed the occurrence of common and specific responses in the mutants. The three mutants showed up-regulation of responsive genes, the activation of oxido-reduction process and the inhibition of ion transport. The participation of jasmonate in the plant response to salt was evident by down-regulation of a gene coding for a jasmonate O-methyltransferase. Genes dealing with lipid transport and metabolism were, in general, up-regulated except in SaS62, that also exhibited down-regulation of genes involved in ion transport and Ca2+ signal transduction. The two most tolerant varieties, SaS62 and SaT20, displayed lower levels of transcripts involved in K+ uptake. The physiological study and the description of the expression analysis evidenced that the three lines showed different responses to salt: SaT20 showed a high Na+ content in leaves, SaS62 presented an inhibition of lipid metabolism and ion transport and SaT58 differs in both features in the response to salinity. The analysis of these salt

  11. Circuit-wide Transcriptional Profiling Reveals Brain Region-Specific Gene Networks Regulating Depression Susceptibility.

    Science.gov (United States)

    Bagot, Rosemary C; Cates, Hannah M; Purushothaman, Immanuel; Lorsch, Zachary S; Walker, Deena M; Wang, Junshi; Huang, Xiaojie; Schlüter, Oliver M; Maze, Ian; Peña, Catherine J; Heller, Elizabeth A; Issler, Orna; Wang, Minghui; Song, Won-Min; Stein, Jason L; Liu, Xiaochuan; Doyle, Marie A; Scobie, Kimberly N; Sun, Hao Sheng; Neve, Rachael L; Geschwind, Daniel; Dong, Yan; Shen, Li; Zhang, Bin; Nestler, Eric J

    2016-06-01

    Depression is a complex, heterogeneous disorder and a leading contributor to the global burden of disease. Most previous research has focused on individual brain regions and genes contributing to depression. However, emerging evidence in humans and animal models suggests that dysregulated circuit function and gene expression across multiple brain regions drive depressive phenotypes. Here, we performed RNA sequencing on four brain regions from control animals and those susceptible or resilient to chronic social defeat stress at multiple time points. We employed an integrative network biology approach to identify transcriptional networks and key driver genes that regulate susceptibility to depressive-like symptoms. Further, we validated in vivo several key drivers and their associated transcriptional networks that regulate depression susceptibility and confirmed their functional significance at the levels of gene transcription, synaptic regulation, and behavior. Our study reveals novel transcriptional networks that control stress susceptibility and offers fundamentally new leads for antidepressant drug discovery. PMID:27181059

  12. Transcriptional profiling of mouse uterus at pre-implantation stage under VEGF repression.

    Directory of Open Access Journals (Sweden)

    Yan Ji

    Full Text Available Uterus development during pre-implantation stage affects implantation process and embryo growth. Aberrant uterus development is associated with many human reproductive diseases. Among the factors regulating uterus development, vascular remodeling promoters are critical for uterus function and fertility. Vascular endothelial growth factor (VEGF, as one of the major members, has been found to be important in endothelial cell growth and blood vessel development, as well as in non-endothelial cells. VEGF mediation in reproduction has been broadly studied, but VEGF-induced transcriptional machinery during implantation window has not been systematically studied. In this study, a genetically repressed VEGF mouse model was used to analyze uterus transcriptome at gestation 2.5 (G2.5 by Solexa/Illumina's digital gene expression (DGE system. A number of 831 uterus-specific and 2398 VEGF-regulated genes were identified. Gene ontology (GO analysis indicated that genes actively involved in uterus development were members of collagen biosynthesis, cell proliferation and cell apoptosis. Uterus-specific genes were enriched in activities of phosphatidyl inositol phosphate kinase, histone H3-K36 demethylation and protein acetylation. Among VEGF-regulated genes, up-regulated were associated with RNA polymerase III activity while down-regulated were strongly related with muscle development. Comparable numbers of antisense transcripts were identified. Expression levels of the antisense transcripts were found tightly correlated with their sense expression levels, an indication of possibly non-specific transcripts generated around the active promoters and enhancers. The antisense transcripts with exceptionally high or low expression levels and the antisense transcripts under VEGF regulation were also identified. These transcripts may be important candidates in regulation of uterus development. This study provides a global survey on genes and antisense transcripts

  13. Characterization of CD8+ T cell differentiation following SIVΔnef vaccination by transcription factor expression profiling.

    Directory of Open Access Journals (Sweden)

    James M Billingsley

    2015-03-01

    Full Text Available The onset of protective immunity against pathogenic SIV challenge in SIVΔnef-vaccinated macaques is delayed for 15-20 weeks, a process that is related to qualitative changes in CD8+ T cell responses induced by SIVΔnef. As a novel approach to characterize cell differentiation following vaccination, we used multi-target qPCR to measure transcription factor expression in naïve and memory subsets of CD8++ T cells, and in SIV-specific CD8+ T cells obtained from SIVΔnef-vaccinated or wild type SIVmac239-infected macaques. Unsupervised clustering of expression profiles organized naïve and memory CD8+ T cells into groups concordant with cell surface phenotype. Transcription factor expression patterns in SIV-specific CD8+ T cells in SIVΔnef-vaccinated animals were distinct from those observed in purified CD8+ T cell subsets obtained from naïve animals, and were intermediate to expression profiles of purified central memory and effector memory T cells. Expression of transcription factors elicited by SIVΔnef vaccination also varied over time: cells obtained at later time points, temporally associated with greater protection, appeared more central-memory like than cells obtained at earlier time points, which appeared more effector memory-like. Expression of transcription factors associated with effector differentiation, such as ID2 and RUNX3, were decreased over time, while expression of transcription factors associated with quiescence or memory differentiation, such as TCF7, BCOR and EOMES, increased. CD8+ T cells specific for a more conserved epitope expressed higher levels of TBX21 and BATF, and appeared more effector-like than cells specific for an escaped epitope, consistent with continued activation by replicating vaccine virus. These data suggest transcription factor expression profiling is a novel method that can provide additional data complementary to the analysis of memory cell differentiation based on classical phenotypic markers

  14. Transcriptional profiling of hexaploid wheat (Triticum aestivum L.) roots identifies novel, dehydration-responsive genes.

    Science.gov (United States)

    Mohammadi, Mohsen; Kav, Nat N V; Deyholos, Michael K

    2007-05-01

    We used a long-oligonucleotide microarray to identify transcripts that increased or decreased in abundance in roots of dehydration-tolerant hexaploid bread wheat, in response to withholding of water. We observed that the major classes of dehydration-responsive genes (e.g. osmoprotectants, compatible solutes, proteases, glycosyltransferases/hydrolases, signal transducers components, ion transporters) were generally similar to those observed previously in other species and osmotic stresses. More specifically, we highlighted increases in transcript expression for specific genes including those putatively related to the synthesis of asparagine, trehalose, oligopeptide transporters, metal-binding proteins, the gamma-aminobutyric acid (GABA) shunt and transcription factors. Conversely, we noted a decrease in transcript abundance for diverse classes of glutathione and sulphur-related enzymes, specific amino acids, as well as MATE-efflux carrier proteins. From these data, we identified a novel, dehydration-induced putative AP2/ERF transcription factor, which we predict to function as a transcriptional repressor. We also identified a dehydration-induced 'little protein' (LitP; predicted mass: 8 kDa) that is highly conserved across spermatophytes. Using qRT-PCR, we compared the expression patterns of selected genes between two related wheat genotypes that differed in their susceptibility to dehydration, and confirmed that these novel genes were highly inducible by water limitation in both genotypes, although the magnitude of induction differed.

  15. Transcript and protein expression profile of PF11_0394, a Plasmodium falciparum protein expressed in salivary gland sporozoites

    Directory of Open Access Journals (Sweden)

    Schlarman Maggie S

    2012-03-01

    Full Text Available Abstract Background Plasmodium falciparum malaria is a significant problem around the world today, thus there is still a need for new control methods to be developed. Because the sporozoite displays dual infectivity for both the mosquito salivary glands and vertebrate host tissue, it is a good target for vaccine development. Methods The P. falciparum gene, PF11_0394, was chosen as a candidate for study due to its potential role in the invasion of host tissues. This gene, which was selected using a data mining approach from PlasmoDB, is expressed both at the transcriptional and protein levels in sporozoites and likely encodes a putative surface protein. Using reverse transcription-polymerase chain reaction (RT-PCR and green fluorescent protein (GFP-trafficking studies, a transcript and protein expression profile of PF11_0394 was determined. Results The PF11_0394 protein has orthologs in other Plasmodium species and Apicomplexans, but none outside of the group Apicomplexa. PF11_0394 transcript was found to be present during both the sporozoite and erythrocytic stages of the parasite life cycle, but no transcript was detected during axenic exoerythrocytic stages. Despite the presence of transcript throughout several life cycle stages, the PF11_0394 protein was only detected in salivary gland sporozoites. Conclusions PF11_0394 appears to be a protein uniquely detected in salivary gland sporozoites. Even though a specific function of PF11_0394 has not been determined in P. falciparum biology, it could be another candidate for a new vaccine.

  16. Genome-wide identification and transcript profile of the whole cathepsin superfamily in the intertidal copepod Tigriopus japonicus.

    Science.gov (United States)

    Jeong, Chang-Bum; Kim, Bo-Mi; Choi, Hyeon-Jeong; Baek, Inseon; Souissi, Sami; Park, Heum Gi; Lee, Jae-Seong; Rhee, Jae-Sung

    2015-11-01

    Modulation of expression of cathepsins in innate immune response has previously been reported in mollusks and large crustaceans including crabs, lobsters, and shrimps in response to immune challenges. However, similar responses in copepods and the related cathepsin members remain under-investigated. To understand molecular and innate immune responses in the intertidal copepod Tigriopus japonicus, we identified the full spectra of cathepsin members (2 aspartyl proteases, 18 cysteine proteases, and 4 serine proteases) and also analyzed transcriptional expression of cathepsin (Tj-cathepsin) genes in developmental stages, lipopolysaccharide (LPS)- and two Vibrio species-exposed T. japonicus. The transcriptional levels of most Tj-cathepsin genes were highly increased during the molting transition from the nauplius to the copepodid stages. LPS treatment induced innate immune response via significant transcriptional increase of serine cathepsin (e.g., cathepsin As) members with induction of several cysteine cathepsin genes. However, Tj-aspartyl cathepsin E-like and a novel cysteine cathepsin were slightly reduced in response to LPS exposure. Interestingly, Vibrio species showed very low transcriptional sensitivity in the expression of entire cathepsins, while LPS induced several cathepsin gene-involved primitive immune responses in T. japonicus. In this paper, we discuss how whole cathepsin expression profiling can be linked to host defense mechanism to better understand and uncover the underlying mechanism of copepods' innate immunity. PMID:26116442

  17. Identification of genes related to Paulownia witches' broom by AFLP and MSAP.

    Science.gov (United States)

    Cao, Xibing; Fan, Guoqiang; Deng, Minjie; Zhao, Zhenli; Dong, Yanpeng

    2014-01-01

    DNA methylation is believed to play important roles in regulating gene expression in plant growth and development. Paulownia witches' broom (PaWB) infection has been reported to be related to gene expression changes in paulownia plantlets. To determine whether DNA methylation is associated with gene expression changes in response to phytoplasma, we investigated variations in genomic DNA sequence and methylation in PaWB plantlets treated with methyl methane sulfonate (MMS) using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) techniques, respectively. The results indicated that PaWB seedings recovered a normal morphology after treatment with more than 15 mg·L(-1) MMS. PaWB infection did not cause changes of the paulownia DNA sequence at the AFLP level; However, DNA methylation levels and patterns were altered. Quantitative real-time PCR (qRT-PCR) showed that three of the methylated genes were up-regulated and three were down-regulated in the MMS-treated PaWB plantlets that had regained healthy morphology. These six genes might be involved in transcriptional regulation, plant defense, signal transduction and energy. The possible roles of these genes in PaWB are discussed. The results showed that changes of DNA methylation altered gene expression levels, and that MSAP might help identify genes related to PaWB. PMID:25196603

  18. Identification of Genes Related to Paulownia Witches’ Broom by AFLP and MSAP

    Directory of Open Access Journals (Sweden)

    Xibing Cao

    2014-08-01

    Full Text Available DNA methylation is believed to play important roles in regulating gene expression in plant growth and development. Paulownia witches’ broom (PaWB infection has been reported to be related to gene expression changes in paulownia plantlets. To determine whether DNA methylation is associated with gene expression changes in response to phytoplasma, we investigated variations in genomic DNA sequence and methylation in PaWB plantlets treated with methyl methane sulfonate (MMS using amplified fragment length polymorphism (AFLP and methylation-sensitive amplification polymorphism (MSAP techniques, respectively. The results indicated that PaWB seedings recovered a normal morphology after treatment with more than 15 mg·L−1 MMS. PaWB infection did not cause changes of the paulownia DNA sequence at the AFLP level; However, DNA methylation levels and patterns were altered. Quantitative real-time PCR (qRT-PCR showed that three of the methylated genes were up-regulated and three were down-regulated in the MMS-treated PaWB plantlets that had regained healthy morphology. These six genes might be involved in transcriptional regulation, plant defense, signal transduction and energy. The possible roles of these genes in PaWB are discussed. The results showed that changes of DNA methylation altered gene expression levels, and that MSAP might help identify genes related to PaWB.

  19. Identification of Genes Related to Paulownia Witches’ Broom by AFLP and MSAP

    Science.gov (United States)

    Cao, Xibing; Fan, Guoqiang; Deng, Minjie; Zhao, Zhenli; Dong, Yanpeng

    2014-01-01

    DNA methylation is believed to play important roles in regulating gene expression in plant growth and development. Paulownia witches’ broom (PaWB) infection has been reported to be related to gene expression changes in paulownia plantlets. To determine whether DNA methylation is associated with gene expression changes in response to phytoplasma, we investigated variations in genomic DNA sequence and methylation in PaWB plantlets treated with methyl methane sulfonate (MMS) using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) techniques, respectively. The results indicated that PaWB seedings recovered a normal morphology after treatment with more than 15 mg·L−1 MMS. PaWB infection did not cause changes of the paulownia DNA sequence at the AFLP level; However, DNA methylation levels and patterns were altered. Quantitative real-time PCR (qRT-PCR) showed that three of the methylated genes were up-regulated and three were down-regulated in the MMS-treated PaWB plantlets that had regained healthy morphology. These six genes might be involved in transcriptional regulation, plant defense, signal transduction and energy. The possible roles of these genes in PaWB are discussed. The results showed that changes of DNA methylation altered gene expression levels, and that MSAP might help identify genes related to PaWB. PMID:25196603

  20. RAPD, RFLP, T-RFLP, AFLP, RISA

    International Nuclear Information System (INIS)

    focus on the conserved ribosomal regions for phylogenetic diversity studies are those that amplify up random genomic sequences. The two most common methods are random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP)

  1. Microfluidic single-cell transcriptional analysis rationally identifies novel surface marker profiles to enhance cell-based therapies.

    Science.gov (United States)

    Rennert, Robert C; Januszyk, Michael; Sorkin, Michael; Rodrigues, Melanie; Maan, Zeshaan N; Duscher, Dominik; Whittam, Alexander J; Kosaraju, Revanth; Chung, Michael T; Paik, Kevin; Li, Alexander Y; Findlay, Michael; Glotzbach, Jason P; Butte, Atul J; Gurtner, Geoffrey C

    2016-01-01

    Current progenitor cell therapies have only modest efficacy, which has limited their clinical adoption. This may be the result of a cellular heterogeneity that decreases the number of functional progenitors delivered to diseased tissue, and prevents correction of underlying pathologic cell population disruptions. Here, we develop a high-resolution method of identifying phenotypically distinct progenitor cell subpopulations via single-cell transcriptional analysis and advanced bioinformatics. When combined with high-throughput cell surface marker screening, this approach facilitates the rational selection of surface markers for prospective isolation of cell subpopulations with desired transcriptional profiles. We establish the usefulness of this platform in costly and highly morbid diabetic wounds by identifying a subpopulation of progenitor cells that is dysfunctional in the diabetic state, and normalizes diabetic wound healing rates following allogeneic application. We believe this work presents a logical framework for the development of targeted cell therapies that can be customized to any clinical application. PMID:27324848

  2. Transcriptional profiling in C. elegans suggests DNA damage dependent apoptosis as an ancient function of the p53 family

    Directory of Open Access Journals (Sweden)

    Rothblatt Jonathan

    2008-07-01

    Full Text Available Abstract Background In contrast to the three mammalian p53 family members, p53, which is generally involved in DNA damage responses, and p63 and p73 which are primarily needed for developmental regulation, cep-1 encodes for the single C. elegans p53-like gene. cep-1 acts as a transcription activator in a primordial p53 pathway that involves CEP-1 activation and the CEP-1 dependent transcriptional induction of the worm BH3 only domain encoding genes egl-1 and ced-13 to induce germ cell apoptosis. EGL-1 and CED-13 proteins inactivate Bcl-2 like CED-9 to trigger CED-4 and CED-3 caspase dependent germ cell apoptosis. To address the function of p53 in global transcriptional regulation we investigate genome-wide transcriptional responses upon DNA damage and cep-1 deficiency. Results Examining C. elegans expression profiles using whole genome Affymetrix GeneChip arrays, we found that 83 genes were induced more than two fold upon ionizing radiation (IR. None of these genes, with exception of an ATP ribosylase homolog, encode for known DNA repair genes. Using two independent cep-1 loss of function alleles we did not find genes regulated by cep-1 in the absence of IR. Among the IR-induced genes only three are dependent on cep-1, namely egl-1, ced-13 and a novel C. elegans specific gene. The majority of IR-induced genes appear to be involved in general stress responses, and qRT-PCR experiments indicate that they are mainly expressed in somatic tissues. Interestingly, we reveal an extensive overlap of gene expression changes occurring in response to DNA damage and in response to bacterial infection. Furthermore, many genes induced by IR are also transcriptionally regulated in longevity mutants suggesting that DNA damage and aging induce an overlapping stress response. Conclusion We performed genome-wide gene expression analyses which indicate that only a surprisingly small number of genes are regulated by CEP-1 and that DNA damage induced apoptosis via the

  3. Transcription Profiling of Malaria-Naive and Semi-immune Colombian Volunteers in a Plasmodium vivax Sporozoite Challenge.

    Directory of Open Access Journals (Sweden)

    Monica L Rojas-Peña

    Full Text Available Continued exposure to malaria-causing parasites in endemic regions of malaria induces significant levels of acquired immunity in adult individuals. A better understanding of the transcriptional basis for this acquired immunological response may provide insight into how the immune system can be boosted during vaccination, and into why infected individuals differ in symptomology.Peripheral blood gene expression profiles of 9 semi-immune volunteers from a Plasmodium vivax malaria prevalent region (Buenaventura, Colombia were compared to those of 7 naïve individuals from a region with no reported transmission of malaria (Cali, Colombia after a controlled infection mosquito bite challenge with P. vivax. A Fluidigm nanoscale quantitative RT-PCR array was used to survey altered expression of 96 blood informative transcripts at 7 timepoints after controlled infection, and RNASeq was used to contrast pre-infection and early parasitemia timepoints. There was no evidence for transcriptional changes prior to the appearance of blood stage parasites at day 12 or 13, at which time there was a strong interferon response and, unexpectedly, down-regulation of transcripts related to inflammation and innate immunity. This differential expression was confirmed with RNASeq, which also suggested perturbations of aspects of T cell function and erythropoiesis. Despite differences in clinical symptoms between the semi-immune and malaria naïve individuals, only subtle differences in their transcriptomes were observed, although 175 genes showed significantly greater induction or repression in the naïve volunteers from Cali.Gene expression profiling of whole blood reveals the type and duration of the immune response to P. vivax infection, and highlights a subset of genes that may mediate adaptive immunity.

  4. Global transcriptional profiling of longissimus thoracis muscle tissue in fetal and juvenile domestic goat using RNA sequencing.

    Science.gov (United States)

    Wang, Y H; Zhang, C L; Plath, M; Fang, X T; Lan, X Y; Zhou, Y; Chen, H

    2015-12-01

    Domestic goats are important meat production animals; however, data from transcriptional profiling of skeletal muscle tissue in goat have thus far been scarce. We used comparative transcriptional profiling based on RNA sequencing of longissimus thoracis muscle tissue obtained from fetal goat muscle tissue (27 512 850 clean cDNA reads) and 6-month-old goat muscle tissue (27 582 908 reads) to identify genes that are differentially expressed, novel transcript units and alternative splicing events. Gene annotation revealed that 15 960 and 14 981 genes were expressed in the fetal and juvenile libraries respectively. We detected 6432 differentially expressed genes and, when considering GO terms, found 34, 27 and 55 terms to be significantly enriched in molecular function, cellular component and biological process categories respectively. Pathway analysis revealed that larger numbers of differentially expressed genes were enriched in fetal myogenesis or cell proliferation and differentiation-related pathways (such as Wnt), genes involved in the cell cycle and the Notch signaling pathway, and most of the differentially expressed genes involved in these pathways were downregulated in the juvenile goat library. These genes may be involved in various regulation mechanisms during muscle tissue differentiation between the two development stages examined herein. The identified novel transcript units, including both non-coding and coding RNA, as well as alternative splicing events increase the level of complexity of regulation mechanisms during muscle tissue formation and differentiation. Our study provides a comparative transcriptome analysis on goat muscle tissue, which will provide a valuable genomic resource for future studies investigating the molecular basis of skeletal muscle development. PMID:26364974

  5. Transcriptional profiling of Bacillus anthracis Sterne (34F2 during iron starvation.

    Directory of Open Access Journals (Sweden)

    Paul E Carlson

    Full Text Available Lack of available iron is one of many environmental challenges that a bacterium encounters during infection and adaptation to iron starvation is important for the pathogen to efficiently replicate within the host. Here we define the transcriptional response of B. anthracis Sterne (34F(2 to iron depleted conditions. Genome-wide transcript analysis showed that B. anthracis undergoes considerable changes in gene expression during growth in iron-depleted media, including the regulation of known and candidate virulence factors. Two genes encoding putative internalin proteins were chosen for further study. Deletion of either gene (GBAA0552 or GBAA1340 resulted in attenuation in a murine model of infection. This attenuation was amplified in a double mutant strain. These data define the transcriptional changes induced during growth in low iron conditions and illustrate the potential of this dataset in the identification of putative virulence determinants for future study.

  6. Functional genomics in chickens: development of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways.

    Science.gov (United States)

    Cogburn, L A; Wang, X; Carre, W; Rejto, L; Aggrey, S E; Duclos, M J; Simon, J; Porter, T E

    2004-01-01

    The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation-fasting and re-feeding-in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken.

  7. Functional genomics in chickens: development of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways.

    Science.gov (United States)

    Cogburn, L A; Wang, X; Carre, W; Rejto, L; Aggrey, S E; Duclos, M J; Simon, J; Porter, T E

    2004-01-01

    The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation-fasting and re-feeding-in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken. PMID:18629153

  8. Transcriptional profiles of laccase genes in the brown rot fungus Postia placenta MAD-R-698.

    Science.gov (United States)

    An, Hongde; Wei, Dongsheng; Xiao, Tingting

    2015-09-01

    One of the laccase isoforms in the brown rot fungus Postia placenta is thought to contribute to the production of hydroxyl radicals, which play an important role in lignocellulose degradation. However, the presence of at least two laccase isoforms in this fungus makes it difficult to understand the details of this mechanism. In this study, we systematically investigated the transcriptional patterns of two laccase genes, Pplcc1 and Pplcc2, by quantitative PCR (qPCR) to better understand the mechanism. The qPCR results showed that neither of the two genes was expressed constitutively throughout growth in liquid culture or during the degradation of a woody substrate. Transcription of Pplcc1 was upregulated under nitrogen depletion and in response to a high concentration of copper in liquid culture, and during the initial colonization of intact aspen wafer. However, it was subject to catabolite repression by a high concentration of glucose. Transcription of Pplcc2 was upregulated by stresses caused by ferulic acid, 2, 6-dimethylbenzoic acid, and ethanol, and under osmotic stress in liquid culture. However, the transcription of Pplcc2 was downregulated upon contact with the woody substrate in solid culture. These results indicate that Pplcc1 and Pplcc2 are differentially regulated in liquid and solid cultures. Pplcc1 seems to play the major role in producing hydroxyl radicals and Pplcc2 in the stress response during the degradation of a woody substrate. PMID:26231371

  9. Quantitative transcriptional profiling of ATDC5 mouse progenitor cells during chondrogenesis

    DEFF Research Database (Denmark)

    Chen, Li; Fink, Trine; Zhang, Xiao-Yan;

    2005-01-01

    During the differentiation of a mouse chondroprogenitor cell line, ATDC5, an analysis of the transcription cartilage-related genes was carried out using real-time RT-PCR in a semiquantitative fashion. A total number of 104 genes both previously linked to chondrogenesis and hitherto not associated...

  10. Comparison Between AFLP and RFLP Markers in Detecting the Diversity of Rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    CHEN Liang; LIANG Chun-yang; SUN Chuan-qing; JIN De-min; JIANG Ting-bo; WANG Bin; WANG Xiang-kun

    2002-01-01

    AFLP and RFLP were used to study the diversity of 20 rice cultivars. 15 primer combinations were used in the AFLP analysis and 47 - 118 bands were amplified in each lane. A total of 107 polymorphic bands were detected in the RFLP analysis using 49 RFLP probes. The cluster analysis based on RFLP data showed that 20 rice cultivars could be divided into an indica group and a japonica group, as did the AFLP data; however AFLP is more suitable in detecting the difference of pedigree and ecotype among the 20 cultivars.The genetic distance based on AFLP and RFLP data showed the same tendency, but AFLP markers increased the measure of genetic distance among intra-subspecific cultivars and decreased the measure of genetic distance among inter-subspecific cultivars relative to RFLP markers. That indicated that AFLP is more suitable than RFLP in the diversity study and RFLP is more suitable to study the indica-japonica differentiation of cultivars.

  11. Transcriptional profiling of canker-resistant transgenic sweet orange (Citrus sinensis Osbeck) constitutively overexpressing a spermidine synthase gene.

    Science.gov (United States)

    Fu, Xing-Zheng; Liu, Ji-Hong

    2013-01-01

    Citrus canker disease caused by Xanthomonas citri subsp. citri (Xcc) is one of the most devastating diseases affecting the citrus industry worldwide. In our previous study, the canker-resistant transgenic sweet orange (Citrus sinensis Osbeck) plants were produced via constitutively overexpressing a spermidine synthase. To unravel the molecular mechanisms underlying Xcc resistance of the transgenic plants, in the present study global transcriptional profiling was compared between untransformed line (WT) and the transgenic line (TG9) by hybridizing with Affymetrix Citrus GeneChip. In total, 666 differentially expressed genes (DEGs) were identified, 448 upregulated, and 218 downregulated. The DEGs were classified into 33 categories after Gene ontology (GO) annotation, in which 68 genes are in response to stimulus and involved in immune system process, 12 genes are related to cell wall, and 13 genes belong to transcription factors. These genes and those related to starch and sucrose metabolism, glutathione metabolism, biosynthesis of phenylpropanoids, and plant hormones were hypothesized to play major roles in the canker resistance of TG9. Semiquantitative RT-PCR analysis showed that the transcript levels of several candidate genes in TG9 were significantly higher than in WT both before and after Xcc inoculation, indicating their potential association with canker disease.

  12. Transcriptional Profiling of Canker-Resistant Transgenic Sweet Orange (Citrus sinensis Osbeck Constitutively Overexpressing a Spermidine Synthase Gene

    Directory of Open Access Journals (Sweden)

    Xing-Zheng Fu

    2013-01-01

    Full Text Available Citrus canker disease caused by Xanthomonas citri subsp. citri (Xcc is one of the most devastating diseases affecting the citrus industry worldwide. In our previous study, the canker-resistant transgenic sweet orange (Citrus sinensis Osbeck plants were produced via constitutively overexpressing a spermidine synthase. To unravel the molecular mechanisms underlying Xcc resistance of the transgenic plants, in the present study global transcriptional profiling was compared between untransformed line (WT and the transgenic line (TG9 by hybridizing with Affymetrix Citrus GeneChip. In total, 666 differentially expressed genes (DEGs were identified, 448 upregulated, and 218 downregulated. The DEGs were classified into 33 categories after Gene ontology (GO annotation, in which 68 genes are in response to stimulus and involved in immune system process, 12 genes are related to cell wall, and 13 genes belong to transcription factors. These genes and those related to starch and sucrose metabolism, glutathione metabolism, biosynthesis of phenylpropanoids, and plant hormones were hypothesized to play major roles in the canker resistance of TG9. Semiquantitative RT-PCR analysis showed that the transcript levels of several candidate genes in TG9 were significantly higher than in WT both before and after Xcc inoculation, indicating their potential association with canker disease.

  13. A Molecular Profile of Cocaine Abuse Includes the Differential Expression of Genes that Regulate Transcription, Chromatin, and Dopamine Cell Phenotype

    Science.gov (United States)

    Bannon, Michael J; Johnson, Magen M; Michelhaugh, Sharon K; Hartley, Zachary J; Halter, Steven D; David, James A; Kapatos, Gregory; Schmidt, Carl J

    2014-01-01

    Chronic drug abuse, craving, and relapse are thought to be linked to long-lasting changes in neural gene expression arising through transcriptional and chromatin-related mechanisms. The key contributions of midbrain dopamine (DA)-synthesizing neurons throughout the addiction process provide a compelling rationale for determining the drug-induced molecular changes that occur in these cells. Yet our understanding of these processes remains rudimentary. The postmortem human brain constitutes a unique resource that can be exploited to gain insights into the pathophysiology of complex disorders such as drug addiction. In this study, we analyzed the profiles of midbrain gene expression in chronic cocaine abusers and well-matched drug-free control subjects using microarray and quantitative PCR. A small number of genes exhibited robust differential expression; many of these are involved in the regulation of transcription, chromatin, or DA cell phenotype. Transcript abundances for approximately half of these differentially expressed genes were diagnostic for assigning subjects to the cocaine-abusing vs control cohort. Identification of a molecular signature associated with pathophysiological changes occurring in cocaine abusers' midbrains should contribute to the development of biomarkers and novel therapeutic targets for drug addiction. PMID:24642598

  14. Comprehensive transcript profiling of Pto- and Prf-mediated host defense responses to infection by Pseudomonas syringae pv. tomato.

    Science.gov (United States)

    Mysore, Kirankumar S; Crasta, Oswald R; Tuori, Robert P; Folkerts, Otto; Swirsky, Peter B; Martin, Gregory B

    2002-11-01

    The disease resistance gene Pto encodes a serine/threonine protein kinase that confers resistance in tomato to Pseudomonas syringae pv. tomato strains that express the effector protein AvrPto. Pto-mediated resistance to bacterial speck disease also requires Prf, a protein with leucine-rich repeats and a putative nucleotide-binding site, although the role of Prf in the defense pathway is not known. We used GeneCalling, an open-architecture, mRNA-profiling technology, to identify genes that are either induced or suppressed in leaves 4 h after bacterial infection in the Pto- and Prf-mediated tomato-Pseudomonas(avrPto) interaction. Over 135 000 individual cDNA fragments representing an estimated 90% of the transcripts expressed in tomato leaves were examined and 432 differentially expressed genes were identified. The genes encode over 25 classes of proteins including 11 types of transcription factors and many signal transduction components. Differential expression of 91% of the genes required both Pto and Prf. Interestingly, differential expression of 32 genes did not require Pto but was dependent on Prf. Thus, our data support a role for Prf early in the Pto pathway and indicate that Prf can also function as an independent host recognition determinant of bacterial infection. Comprehensive expression profiling of the Pto-mediated defense response allows the development of many new hypotheses about the molecular basis of resistance to bacterial speck disease.

  15. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging.

    Science.gov (United States)

    Wheeler, Heather E; Metter, E Jeffrey; Tanaka, Toshiko; Absher, Devin; Higgins, John; Zahn, Jacob M; Wilhelmy, Julie; Davis, Ronald W; Singleton, Andrew; Myers, Richard M; Ferrucci, Luigi; Kim, Stuart K

    2009-10-01

    Kidneys age at different rates, such that some people show little or no effects of aging whereas others show rapid functional decline. We sequentially used transcriptional profiling and expression quantitative trait loci (eQTL) mapping to narrow down which genes to test for association with kidney aging. We first performed whole-genome transcriptional profiling to find 630 genes that change expression with age in the kidney. Using two methods to detect eQTLs, we found 101 of these age-regulated genes contain expression-associated SNPs. We tested the eQTLs for association with kidney aging, measured by glomerular filtration rate (GFR) using combined data from the Baltimore Longitudinal Study of Aging (BLSA) and the InCHIANTI study. We found a SNP association (rs1711437 in MMP20) with kidney aging (uncorrected p = 3.6 x 10(-5), empirical p = 0.01) that explains 1%-2% of the variance in GFR among individuals. The results of this sequential analysis may provide the first evidence for a gene association with kidney aging in humans.

  16. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging.

    Directory of Open Access Journals (Sweden)

    Heather E Wheeler

    2009-10-01

    Full Text Available Kidneys age at different rates, such that some people show little or no effects of aging whereas others show rapid functional decline. We sequentially used transcriptional profiling and expression quantitative trait loci (eQTL mapping to narrow down which genes to test for association with kidney aging. We first performed whole-genome transcriptional profiling to find 630 genes that change expression with age in the kidney. Using two methods to detect eQTLs, we found 101 of these age-regulated genes contain expression-associated SNPs. We tested the eQTLs for association with kidney aging, measured by glomerular filtration rate (GFR using combined data from the Baltimore Longitudinal Study of Aging (BLSA and the InCHIANTI study. We found a SNP association (rs1711437 in MMP20 with kidney aging (uncorrected p = 3.6 x 10(-5, empirical p = 0.01 that explains 1%-2% of the variance in GFR among individuals. The results of this sequential analysis may provide the first evidence for a gene association with kidney aging in humans.

  17. Transcript profiling reveals that cysteine protease inhibitors are up-regulated in tuber sprouts after extended darkness.

    Science.gov (United States)

    Grandellis, Carolina; Giammaria, Veronica; Fantino, Elisa; Cerrudo, Ignacio; Bachmann, Sandra; Santin, Franco; Ulloa, Rita M

    2016-07-01

    Potato (Solanum tuberosum L.) tubers are an excellent staple food due to its high nutritional value. When the tuber reaches physiological competence, sprouting proceeds accompanied by changes at mRNA and protein levels. Potato tubers become a source of carbon and energy until sprouts are capable of independent growth. Transcript profiling of sprouts grown under continuous light or dark conditions was performed using the TIGR 10K EST Solanaceae microarray. The profiles analyzed show a core of highly expressed transcripts that are associated to the reactivation of growth. Under light conditions, the photosynthetic machinery was fully activated; the highest up-regulation was observed for the Rubisco activase (RCA), the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and the Photosystem II 22 kDa protein (CP22) genes, among others. On the other hand, sprouts exposed to continuous darkness elongate longer, and after extended darkness, synthesis of chloroplast components was repressed, the expression of proteases was reduced while genes encoding cysteine protease inhibitors (CPIs) and metallocarboxypeptidase inhibitors (MPIs) were strongly induced. Northern blot and RT-PCR analysis confirmed that MPI levels correlated with the length of the dark period; however, CPI expression was strong only after longer periods of darkness, suggesting a feedback loop (regulation mechanism) in response to dark-induced senescence. Prevention of cysteine protease activity in etiolated sprouts exposed to extended darkness could delay senescence until they emerge to light. PMID:27075731

  18. Rice seed identification by computerized AFLP-DNA fingerprinting

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@ We developed a computerized seed identification system. Fifteen rice varieties that were widely used in China were analyzed by AFLP fingerprinting. 12 primer pairs were screened. In order to simplify the procedure and cut down the cost in seed identification, the least number of primer pairs for practical seed identification should be selected. In this study, 3 primer pairs were selected.

  19. Transcriptional profiling at different sites in lungs of pigs during acute bacterial respiratory infection

    DEFF Research Database (Denmark)

    Mortensen, Shila; Skovgaard, Kerstin; Hedegaard, Jakob;

    2011-01-01

    The local transcriptional response was studied in different locations of lungs from pigs experimentally infected with the respiratory pathogen Actinobacillus pleuropneumoniae serotype 5B, using porcine cDNA microarrays. This infection gives rise to well-demarcated infection loci in the lung......, characterized by necrotic and haemorrhagic lesions. Lung tissue was sampled from necrotic areas, from visually unaffected areas and from areas bordering on necrotic areas. Expression pattern of these areas from infected pigs was compared to healthy lung tissue from un-infected pigs. Transcription of selected...... genes important in the innate defence response were further analysed by quantitative realtime reverse-transcriptase PCR. A clear correlation was observed between the number of differentially expressed genes as well as the magnitude of their induction and the sampling location in the infected lung...

  20. Differential transcription profiles in Aedes aegypti detoxification genes following temephos selection

    OpenAIRE

    Saavedra-Rodriguez, Karla; Strode, Clare; FLORES, ADRIANA E.; Garcia-Luna, Selene; Reyes-Solis, Guadalupe; Ranson, Hilary; Hemingway, Janet; Black, William C.

    2013-01-01

    The mosquito Aedes aegypti is the main vector of Dengue and Yellow Fever flaviviruses. The organophosphate insecticide temephos is a larvicide that is used globally to control Ae. aegypti populations; many of which have in turn evolved resistance. Target site alteration in the acetylcholine esterase of this species has not being identified. Instead, we tracked changes in transcription of metabolic detoxification genes using the Ae. aegypti ‘Detox Chip’ microarray during five generations of te...

  1. Transcript profiling reveals expression differences in wild-type and glabrous soybean lines

    OpenAIRE

    Stromvik Martina; Kaur Navneet; Hunt Matt; Vodkin Lila

    2011-01-01

    Abstract Background Trichome hairs affect diverse agronomic characters such as seed weight and yield, prevent insect damage and reduce loss of water but their molecular control has not been extensively studied in soybean. Several detailed models for trichome development have been proposed for Arabidopsis thaliana, but their applicability to important crops such as cotton and soybean is not fully known. Results Two high throughput transcript sequencing methods, Digital Gene Expression (DGE) Ta...

  2. Identification and Expression Profiles of Six Transcripts Encoding Carboxylesterase Protein in Vitis flexuosa Infected with Pathogens

    Science.gov (United States)

    Islam, Md. Zaherul; Yun, Hae Keun

    2016-01-01

    Plants protect themselves from pathogen attacks via several mechanisms, including hypersensitive cell death. Recognition of pathogen attack by the plant resistance gene triggers expression of carboxylesterase genes associated with hypersensitive response. We identified six transcripts of carboxylesterase genes, Vitis flexuosa carboxylesterase 5585 (VfCXE5585), VfCXE12827, VfCXE13132, VfCXE17159, VfCXE18231, and VfCXE47674, which showed different expression patterns upon transcriptome analysis of V. flexuosa inoculated with Elsinoe ampelina. The lengths of genes ranged from 1,098 to 1,629 bp, and their encoded proteins consisted of 309 to 335 amino acids. The predicted amino acid sequences showed hydrolase like domains in all six transcripts and contained two conserved motifs, GXSXG of serine hydrolase characteristics and HGGGF related to the carboxylesterase family. The deduced amino acid sequence also contained a potential catalytic triad consisted of serine, aspartic acid and histidine. Of the six transcripts, VfCXE12827 showed upregulated expression against E. ampelina at all time points. Three genes (VfCXE5585, VfCXE12827, and VfCXE13132) showed upregulation, while others (VfCXE17159, VfCXE18231, and VfCXE47674) were down regulated in grapevines infected with Botrytis cinerea. All transcripts showed upregulated expression against Rhizobium vitis at early and later time points except VfCXE12827, and were downregulated for up to 48 hours post inoculation (hpi) after upregulation at 1 hpi in response to R. vitis infection. All tested genes showed high and differential expression in response to pathogens, indicating that they all may play a role in defense pathways during pathogen infection in grapevines. PMID:27493610

  3. Transcriptional and Proteomic Profiling of Aspergillus flavipes in Response to Sulfur Starvation.

    Directory of Open Access Journals (Sweden)

    Ashraf S A El-Sayed

    Full Text Available Aspergillus flavipes has received considerable interest due to its potential to produce therapeutic enzymes involved in sulfur amino acid metabolism. In natural habitats, A. flavipes survives under sulfur limitations by mobilizing endogenous and exogenous sulfur to operate diverse cellular processes. Sulfur limitation affects virulence and pathogenicity, and modulates proteome of sulfur assimilating enzymes of several fungi. However, there are no previous reports aimed at exploring effects of sulfur limitation on the regulation of A. flavipes sulfur metabolism enzymes at the transcriptional, post-transcriptional and proteomic levels. In this report, we show that sulfur limitation affects morphological and physiological responses of A. flavipes. Transcription and enzymatic activities of several key sulfur metabolism genes, ATP-sulfurylase, sulfite reductase, methionine permease, cysteine synthase, cystathionine β- and γ-lyase, glutathione reductase and glutathione peroxidase were increased under sulfur starvation conditions. A 50 kDa protein band was strongly induced by sulfur starvation, and the proteomic analyses of this protein band using LC-MS/MS revealed similarity to many proteins involved in the sulfur metabolism pathway.

  4. Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling

    Science.gov (United States)

    Zur, Hadas; Aviner, Ranen; Tuller, Tamir

    2016-01-01

    Two novel approaches were recently suggested for genome-wide identification of protein aspects synthesized at a given time. Ribo-Seq is based on sequencing all the ribosome protected mRNA fragments in a cell, while PUNCH-P is based on mass-spectrometric analysis of only newly synthesized proteins. Here we describe the first Ribo-Seq/PUNCH-P comparison via the analysis of mammalian cells during the cell-cycle for detecting relevant differentially expressed genes between G1 and M phase. Our analyses suggest that the two approaches significantly overlap with each other. However, we demonstrate that there are biologically meaningful proteins/genes that can be detected to be post-transcriptionally regulated during the mammalian cell cycle only by each of the approaches, or their consolidation. Such gene sets are enriched with proteins known to be related to intra-cellular signalling pathways such as central cell cycle processes, central gene expression regulation processes, processes related to chromosome segregation, DNA damage, and replication, that are post-transcriptionally regulated during the mammalian cell cycle. Moreover, we show that combining the approaches better predicts steady state changes in protein abundance. The results reported here support the conjecture that for gaining a full post-transcriptional regulation picture one should integrate the two approaches. PMID:26898226

  5. Transcriptional profiling of the soil invertebrate Folsomia candida in pentachlorophenol-contaminated soil.

    Science.gov (United States)

    Qiao, Min; Wang, Guang-Peng; Zhang, Cai; Roelofs, Dick; van Straalen, Nico M; Zhu, Yong-Guan

    2015-06-01

    Pentachlorophenol (PCP), a widely used pesticide, is considered to be an endocrine disruptor. The molecular effects of chemicals with endocrine-disrupting potential on soil invertebrates are largely unknown. In the present study, the authors explored the transcriptional expression changes of collembola (Folsomia candida) in response to PCP contamination. A total of 92 genes were significantly differentially expressed at all exposure times, and the majority of them were found to be downregulated. In addition to the transcripts encoding cytochrome P450s and transferase enzymes, chitin-binding protein was also identified in the list of common differentially expressed genes. Analyses of gene ontology annotation and enrichment revealed that cell cycle-related transcripts were significantly induced by PCP, indicating that PCP can stimulate cell proliferation in springtail, as has been reported in human breast cancer cells. Enrichment of functional terms related to steroid receptors was observed, particularly in 20 significant differentially expressed genes involved in chitin metabolism in response to PCP exposure. Combined with confirmation by quantitative polymerase chain reaction, the results indicate that the adverse effects on reproduction of springtails after exposure to PCP can be attributed to a chemical-induced delay in the molting cycle and that molting-associated genes may serve as possible biomarkers for assessing toxicological effects. PMID:25703271

  6. Transcript levels of major interleukins in relation to the clinicopathological profile of patients with tuberculous intervertebral discs and healthy controls.

    Directory of Open Access Journals (Sweden)

    Chong Liu

    Full Text Available The purpose of the present study was to simultaneously examine the transcript levels of a large number of interleukins (ILs; IL-9, IL-10, IL-12, IL-13, IL-16, IL-17, IL-18, IL-26, and IL-27 and investigate their correlation with the clinicopathological profiles of patients with tuberculous intervertebral discs.Clinical data were collected from 150 patients participating in the study from January 2013 to December 2013. mRNA expression levels in 70 tuberculous, 70 herniated, and 10 control intervertebral disc specimens were determined by real-time polymerase chain reaction.IL-10, IL-16, IL-17, IL-18, and IL-27 displayed stronger expression in tuberculous spinal disc tissue than in normal intervertebral disc tissue (P<0.05. Our results illustrated multiple correlations among IL-10, IL-16, IL-17, IL-18, and IL-27 mRNA expression in tuberculous samples. Smoking habits were found to have a positive correlation with IL-17 transcript levels and a negative correlation with IL-10 transcript levels (P<0.05. Pain intensity, symptom duration, C-reactive protein levels, and the erythrocyte sedimentation rate exhibited multiple correlations with the transcript levels of several ILs (P<0.05.The experimental data imply a double-sided effect on the activity of ILs in tuberculous spinal intervertebral discs, suggesting that they may be involved in intervertebral discs destruction. Our findings also suggest that smoking may affect the intervertebral discs destruction process of spinal tuberculosis. However, further studies are necessary to elucidate the exact role of ILs in the intervertebral discs destruction process of spinal tuberculosis.

  7. Transcriptional profiling of tissue plasticity: Role of shifts in gene expression and technical limitations

    NARCIS (Netherlands)

    Flück, Martin; Däpp, Christoph; Schmutz, Silvia; Wit, Ernst; Hoppeler, Hans

    2005-01-01

    Reprogramming of gene expression has been recognized as a main instructive modality for the adjustments of tissues to various kinds of stress. The recent application of gene expression profiling has provided a powerful tool to elucidate the molecular pathways underlying such tissue remodeling. Howev

  8. Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis.

    Directory of Open Access Journals (Sweden)

    Randy J Hempel

    Full Text Available Johne's disease is a chronic infection of the small intestine caused by Mycobacterium avium subspecies paratuberculosis (MAP, an intracellular bacterium. The events of pathogen survival within the host cell(s, chronic inflammation and the progression from asymptomatic subclinical stage to an advanced clinical stage of infection, are poorly understood. This study examines gene expression in the ileocecal valve (ICV of Holstein dairy cows at different stages of MAP infection. The ICV is known to be a primary site of MAP colonization and provides an ideal location to identify genes that are relevant to the progression of this disease. RNA was prepared from ICV tissues and RNA-Seq was used to compare gene transcription between clinical, subclinical, and uninfected control animals. Interpretation of the gene expression data was performed using pathway analysis and gene ontology categories containing multiple differentially expressed genes. Results demonstrated that many of the pathways that had strong differential gene expression between uninfected control and clinical cows were related to the immune system, such as the T- and B-cell receptor signaling, apoptosis, NOD-like receptor signaling, and leukocyte transendothelial migration pathways. In contrast, the comparison of gene transcription between control and subclinical cows identified pathways that were primarily involved in metabolism. The results from the comparison between clinical and subclinical animals indicate recruitment of neutrophils, up regulation of lysosomal peptidases, increase in immune cell transendothelial migration, and modifications of the extracelluar matrix. This study provides important insight into how cattle respond to a natural MAP infection at the gene transcription level within a key target tissue for infection.

  9. Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis.

    Science.gov (United States)

    Hempel, Randy J; Bannantine, John P; Stabel, Judith R

    2016-01-01

    Johne's disease is a chronic infection of the small intestine caused by Mycobacterium avium subspecies paratuberculosis (MAP), an intracellular bacterium. The events of pathogen survival within the host cell(s), chronic inflammation and the progression from asymptomatic subclinical stage to an advanced clinical stage of infection, are poorly understood. This study examines gene expression in the ileocecal valve (ICV) of Holstein dairy cows at different stages of MAP infection. The ICV is known to be a primary site of MAP colonization and provides an ideal location to identify genes that are relevant to the progression of this disease. RNA was prepared from ICV tissues and RNA-Seq was used to compare gene transcription between clinical, subclinical, and uninfected control animals. Interpretation of the gene expression data was performed using pathway analysis and gene ontology categories containing multiple differentially expressed genes. Results demonstrated that many of the pathways that had strong differential gene expression between uninfected control and clinical cows were related to the immune system, such as the T- and B-cell receptor signaling, apoptosis, NOD-like receptor signaling, and leukocyte transendothelial migration pathways. In contrast, the comparison of gene transcription between control and subclinical cows identified pathways that were primarily involved in metabolism. The results from the comparison between clinical and subclinical animals indicate recruitment of neutrophils, up regulation of lysosomal peptidases, increase in immune cell transendothelial migration, and modifications of the extracelluar matrix. This study provides important insight into how cattle respond to a natural MAP infection at the gene transcription level within a key target tissue for infection.

  10. Transcript profiling of individual twin blastomeres derived by splitting two-cell stage murine embryos.

    Science.gov (United States)

    Roberts, R Michael; Katayama, Mika; Magnuson, Scott R; Falduto, Michael T; Torres, Karen E O

    2011-03-01

    In invertebrates and amphibians, informational macromolecules in egg cytoplasm are organized to provide direction to the formation of embryonic lineages, but it is unclear whether vestiges of such prepatterning exist in mammals. Here we examined whether twin blastomeres from 2-cell stage mouse embryos differ in mRNA content. mRNA from 26 blastomeres derived from 13 embryos approximately mid-way through their second cell cycle was subjected to amplification. Twenty amplified samples were hybridized to arrays. Of those samples that hybridized successfully, 12 samples in six pairs were used in the final analysis. Probes displaying normalized values >0.25 (n = 4573) were examined for consistent bias in expression within blastomere pairs. Although transcript content varied between both individual embryos and twin blastomeres, no consistent asymmetries were observed for the majority of genes, with only 178 genes displaying a >1.4-fold difference in expression across all six pairs. Although class discovery clustering showed that blastomere pairs separated into two distinct groups in terms of their differentially expressed genes, when the data were tested for significance of asymmetrical expression, only 39 genes with >1.4-fold change ratios in six of six blastomere pairs passed the two-sample t-test (P < 0.05). Transcripts encoding proteins implicated in RNA processing and cytoskeletal organization were among the most abundant, differentially distributed mRNA, suggesting that a stochastically based lack of synchrony in cell cycle progression between the two cells might explain at least some and possibly all of the asymmetries in transcript composition.

  11. Global transcriptional profiling of the toxic dinoflagellate Alexandrium fundyense using Massively Parallel Signature Sequencing

    Directory of Open Access Journals (Sweden)

    Anderson Donald M

    2006-04-01

    duplication in dinoflagellates, which would contribute to the transcriptional complexity of these organisms. The MPSS data also demonstrate that a significant number of dinoflagellate mRNAs are transcriptionally regulated, indicating that dinoflagellates commonly employ transcriptional gene regulation along with the post-transcriptional regulation that has been well documented in these organisms.

  12. Transcriptional profiling of summer wheat, grown under different realistic UV-B irradiation regimes.

    Science.gov (United States)

    Zinser, Christian; Seidlitz, Harald K; Welzl, Gerhard; Sandermann, Heinrich; Heller, Werner; Ernst, Dieter; Rau, Werner

    2007-07-01

    There is limited information on the impact of present-day ultraviolet-B (UV-B) radiation on a reprogramming of gene expression in crops. Summer wheat was cultivated in controlled environmental facilities under simulated realistic climatic conditions. We investigated the effect of different regimes of UV-B radiation on summer wheat (Triticum aestivum L.) cultivars Nandu, Star and Turbo. Until recently, these were most important in Bavaria. Different cultivars of crops often show great differences in their sensitivity towards UV-B radiation. To identify genes that might be involved in UV-B defence mechanisms, we first analyzed selected genes known to be involved in plant defence mechanisms. RNA gel blot analysis of RNA isolated from the flag leaf of 84-day-old plants showed differences in transcript levels among the cultivars. Flag leaves are known to be important for grain development, which was completed at 84 days post-anthesis. Catalase 2 (Cat2) transcripts were elevated by increased UV irradiation in all cultivars with highest levels in cv. Nandu. Pathogenesis-related protein 1 (PR1) transcripts were elevated only in cv. Star. A minor influence on transcripts for phenylalanine ammonia-lyase (PAL) was observed in all three cultivars. This indicates different levels of acclimation to UV-B radiation in the wheat cultivars studied. To analyze these responses in more detail, UV-B-exposed flag leaves of 84-day-old wheat (cv. Nandu) were pooled to isolate cDNAs of induced genes by suppression-subtractive hybridization (SSH). Among the initially isolated cDNA clones, 13 were verified by RNA gel blot analysis showing an up-regulation at elevated levels of UV-B radiation. Functional classification revealed genes encoding proteins associated with protein assembly, chaperonins, programmed cell death and signal transduction. We also studied growth, flowering time, ear development and yield as more typical agricultural parameters. Plant growth of young plants was reduced at

  13. Transcriptional profiles of chicken embryo cell cultures following infection with infectious bursal disease virus

    DEFF Research Database (Denmark)

    Li, Yiping; Handberg, K.J.; Juul-Madsen, H.R.;

    2007-01-01

    Infectious bursal disease virus (IBDV) is the causative agent of infectious bursal disease in chickens and causes a significant economic loss for the poultry industry. Little is understood about the mechanism involved in the host responses to IBDV infection. For better understanding the IBDV......-host interaction, we measured steady-state levels of transcripts from 28 cellular genes of chicken embryo (CE) cell cultures infected with IBDV vaccine stain Bursine-2 during a 7-day infection course by use of the quantitative real-time RT-PCR SYBR green method. Of the genes tested, 21 genes (IRF-1, IFN 1...

  14. Transcript Profile of Flowering Regulatory Genes in VcFT-Overexpressing Blueberry Plants

    Science.gov (United States)

    Walworth, Aaron E.; Chai, Benli; Song, Guo-qing

    2016-01-01

    In order to identify genetic components in flowering pathways of highbush blueberry (Vaccinium corymbosum L.), a transcriptome reference composed of 254,396 transcripts and 179,853 gene contigs was developed by assembly of 72.7 million reads using Trinity. Using this transcriptome reference and a query of flowering pathway genes of herbaceous plants, we identified potential flowering pathway genes/transcripts of blueberry. Transcriptome analysis of flowering pathway genes was then conducted on leaf tissue samples of transgenic blueberry cv. Aurora (‘VcFT-Aurora’), which overexpresses a blueberry FLOWERING LOCUS T-like gene (VcFT). Sixty-one blueberry transcripts of 40 genes showed high similarities to 33 known flowering-related genes of herbaceous plants, of which 17 down-regulated and 16 up-regulated genes were identified in ‘VcFT-Aurora’. All down-regulated genes encoded transcription factors/enzymes upstream in the signaling pathway containing VcFT. A blueberry CONSTANS-LIKE 5-like (VcCOL5) gene was down-regulated and associated with five other differentially expressed (DE) genes in the photoperiod-mediated flowering pathway. Three down-regulated genes, i.e., a MADS-AFFECTING FLOWERING 2-like gene (VcMAF2), a MADS-AFFECTING FLOWERING 5-like gene (VcMAF5), and a VERNALIZATION1-like gene (VcVRN1), may function as integrators in place of FLOWERING LOCUS C (FLC) in the vernalization pathway. Because no CONSTAN1-like or FLOWERING LOCUS C-like genes were found in blueberry, VcCOL5 and VcMAF2/VcMAF5 or VRN1 might be the major integrator(s) in the photoperiod- and vernalization-mediated flowering pathway, respectively. The major down-stream genes of VcFT, i.e., SUPPRESSOR of Overexpression of Constans 1-like (VcSOC1), LEAFY-like (VcLFY), APETALA1-like (VcAP1), CAULIFLOWER 1-like (VcCAL1), and FRUITFULL-like (VcFUL) genes were present and showed high similarity to their orthologues in herbaceous plants. Moreover, overexpression of VcFT promoted expression of all

  15. Transcriptional profiling of MHC class I genes in rainbow trout infected with infectious hematopoietic necrosis virus

    Science.gov (United States)

    Landis, E.D.; Purcell, M.K.; Thorgaard, G.H.; Wheeler, P.A.; Hansen, J.D.

    2008-01-01

    Major histocompatibility complex (MHC) molecules are important mediators of cell-mediated immunity in vertebrates. MHC class IA molecules are important for host anti-viral immunity as they present intracellular antigens and regulate natural killer cell (NK) activity. MHC class Ib molecules on the other hand are less understood and have demonstrated diverse immune and non-immune functions in mammals. Rainbow trout possess a single classical MHC IA locus (Onmy-UBA) that is believed to function similar to that of mammalian MHC class Ia. Numerous MHC class Ib genes with undetermined functions have also been described in trout. Here we utilize quantitative reverse transcriptase PCR (qRT-PCR) techniques to survey the levels of basal and inducible transcription for selected trout MHC class Ib genes, sIgM and sentinels of IFN induction in response to viral infection. Basal transcription of all the class Ib genes examined in this study was lower than Onmy-UBA in nai??ve fish. UBA, along with all of the non-classical genes were induced in fish infected with virus but not in control fish. Our results support a non-classical designation for the majority of the class IB genes surveyed in this study based upon expression levels while also indicating that they may play an important role in anti-viral immunity in trout.

  16. Soybean roots grown under heat stress show global changes in their transcriptional and proteomic profiles

    Directory of Open Access Journals (Sweden)

    Oswaldo eValdes-Lopez

    2016-04-01

    Full Text Available Heat stress is likely to be a key factor in the negative impact of climate change on crop production. Heat stress significantly influences the functions of roots, which provide support, water and nutrients to other plant organs. Likewise, roots play an important role in the establishment of symbiotic associations with different microorganisms. Despite the physiological relevance of roots, few studies have examined their response to heat stress. In this study, we performed genome-wide transcriptomic and proteomic analyses on isolated root hairs, which are a single, epidermal cell type, and compared their response to stripped roots. On average, we identified 1,849 and 3,091 genes differentially regulated in root hairs and stripped roots, respectively, in response to heat stress. Our gene regulatory module analysis identified ten key modules that might control the majority of the transcriptional response to heat stress. We also conducted proteomic analysis on membrane fractions isolated from root hairs and compared these responses to stripped roots. These experiments identified a variety of proteins whose expression changed within 3 hours of application of heat stress. Most of these proteins were predicted to play a significant role in thermo-tolerance, as well as in chromatin remodeling and post-transcriptional regulation. The data presented represent an in-depth analysis of the heat stress response of a single cell type in soybean.

  17. Comparative Analysis of the Chrysanthemum Leaf Transcript Profiling in Response to Salt Stress

    Science.gov (United States)

    Wu, Yin-Huan; Wang, Tong; Wang, Ke; Liang, Qian-Yu; Bai, Zhen-Yu; Liu, Qing-Lin; Pan, Yuan-Zhi; Jiang, Bei-Bei; Zhang, Lei

    2016-01-01

    Salt stress has some remarkable influence on chrysanthemum growth and productivity. To understand the molecular mechanisms associated with salt stress and identify genes of potential importance in cultivated chrysanthemum, we carried out transcriptome sequencing of chrysanthemum. Two cDNA libraries were generated from the control and salt-treated samples (Sample_0510_control and Sample_0510_treat) of leaves. By using the Illumina Solexa RNA sequencing technology, 94 million high quality sequencing reads and 161,522 unigenes were generated and then we annotated unigenes through comparing these sequences to diverse protein databases. A total of 126,646 differentially expressed transcripts (DETs) were identified in leaf. Plant hormones, amino acid metabolism, photosynthesis and secondary metabolism were all changed under salt stress after the complete list of GO term and KEGG enrichment analysis. The hormone biosynthesis changing and oxidative hurt decreasing appeared to be significantly related to salt tolerance of chrysanthemum. Important protein kinases and major transcription factor families involved in abiotic stress were differentially expressed, such as MAPKs, CDPKs, MYB, WRKY, AP2 and HD-zip. In general, these results can help us to confirm the molecular regulation mechanism and also provide us a comprehensive resource of chrysanthemum under salt stress. PMID:27447718

  18. Blood Genome-Wide Transcriptional Profiles of HER2 Negative Breast Cancers Patients

    Directory of Open Access Journals (Sweden)

    Ovidiu Balacescu

    2016-01-01

    Full Text Available Tumors act systemically to sustain cancer progression, affecting the physiological processes in the host and triggering responses in the blood circulating cells. In this study, we explored blood transcriptional patterns of patients with two subtypes of HER2 negative breast cancers, with different prognosis and therapeutic outcome. Peripheral blood samples from seven healthy female donors and 29 women with breast cancer including 14 triple-negative breast cancers and 15 hormone-dependent breast cancers were evaluated by microarray. We also evaluated the stroma in primary tumors. Transcriptional analysis revealed distinct molecular signatures in the blood of HER2− breast cancer patients according to ER/PR status. Our data showed the implication of immune signaling in both breast cancer subtypes with an enrichment of these processes in the blood of TNBC patients. We observed a significant alteration of “chemokine signaling,” “IL-8 signaling,” and “communication between innate and adaptive immune cells” pathways in the blood of TNBC patients correlated with an increased inflammation and necrosis in their primary tumors. Overall, our data indicate that the presence of triple-negative breast cancer is associated with an enrichment of altered systemic immune-related pathways, suggesting that immunotherapy could possibly be synergistic to the chemotherapy, to improve the clinical outcome of these patients.

  19. Reference Genes in the Pathosystem Phakopsora pachyrhizi/ Soybean Suitable for Normalization in Transcript Profiling

    Directory of Open Access Journals (Sweden)

    Daniela Hirschburger

    2015-09-01

    Full Text Available Phakopsora pachyrhizi is a devastating pathogen on soybean, endangering soybean production worldwide. Use of Host Induced Gene Silencing (HIGS and the study of effector proteins could provide novel strategies for pathogen control. For both approaches quantification of transcript abundance by RT-qPCR is essential. Suitable stable reference genes for normalization are indispensable to obtain accurate RT-qPCR results. According to the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE guidelines and using algorithms geNorm and NormFinder we tested candidate reference genes from P. pachyrhizi and Glycine max for their suitability in normalization of transcript levels throughout the infection process. For P. pachyrhizi we recommend a combination of CytB and PDK or GAPDH for in planta experiments. Gene expression during in vitro stages and over the whole infection process was found to be highly unstable. Here, RPS14 and UbcE2 are ranked best by geNorm and NormFinder. Alternatively CytB that has the smallest Cq range (Cq: quantification cycle could be used. We recommend specification of gene expression relative to the germ tube stage rather than to the resting urediospore stage. For studies omitting the resting spore and the appressorium stages a combination of Elf3 and RPS9, or PKD and GAPDH should be used. For normalization of soybean genes during rust infection Ukn2 and cons7 are recommended.

  20. Effects of wildfire on sea otter (Enhydra lutris) gene transcript profiles

    Science.gov (United States)

    Bowen, Lizabeth; Miles, A. Keith; Kolden, Crystal A.; Saarinen, Justin A.; Bodkin, James L.; Murray, Michael J.; Tinker, M. Tim

    2015-01-01

    Wildfires have been shown to impact terrestrial species over a range of temporal scales. Little is known, however, about the more subtle toxicological effects of wildfires, particularly in downstream marine or downwind locations from the wildfire perimeter. These down-current effects may be just as substantial as those effects within the perimeter. We used gene transcription technology, a sensitive indicator of immunological perturbation, to study the effects of the 2008 Basin Complex Fire on the California coast on a sentinel marine species, the sea otter (Enhydra lutris). We captured sea otters in 2008 (3 mo after the Basin Complex Fire was controlled) and 2009 (15 mo after the Basin Complex Fire was controlled) in the adjacent nearshore environment near Big Sur, California. Gene responses were distinctly different between Big Sur temporal groups, signifying detoxification of PAHs, possible associated response to potential malignant transformation, and suppression of immune function as the primary responses of sea otters to fire in 2008 compared to those captured in 2009. In general, gene transcription patterns in the 2008 sea otters were indicative of molecular reactions to organic exposure, malignant transformation, and decreased ability to respond to pathogens that seemed to consistent with short-term hydrocarbon exposure.

  1. Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles

    Energy Technology Data Exchange (ETDEWEB)

    Valdes-Lopez, Oswaldo; Batek Rios, Josef M.; Gomez-Hernandez, Nicolas; Nguyen, Cuong T.; Isidra-Arellano, Mariel C.; Zhang, Ning; Joshi, Trupti; Xu, Dong; Hixson, Kim K.; Weitz, Karl K.; Aldrich, Joshua T.; Pasa-Tolic, Ljiljana; Stacey, Gary

    2016-04-25

    Heat stress is likely to be a key factor in the negative impact of climate change on crop production. Roots provide support, water and nutrients to other plant organs. Likewise, roots play an important role in the establishment of symbiotic associations with different microorganisms. Despite the physiological relevance of roots, few studies have examined the response of these plant organs to heat stress. In this study, we performed genome-wide transcriptomic and proteomic analyses on isolated root hairs, which are a single, epidermal cell type, and compared their response to whole roots. We identified 2,013 genes differentially regulated in root hairs in response to heat stress. Our gene regulatory module analysis identified ten, key modules that controlled the majority of the transcriptional response to heat stress. We also conducted proteomic analysis on membrane fractions isolated from roots and root hairs. These experiments identified a variety of proteins whose expression changed within 3 hours of application of heat stress. Most of these proteins were predicted to play a role in thermotolerance, as well as in chromatin remodeling and post-transcriptional regulation. The data presented represent an in-depth analysis of the heat stress response of a single cell type in soybean.

  2. Comparative transcriptional profiling identifies takeout as a gene that regulates life span

    OpenAIRE

    Bauer, Johannes; Antosh, Michael; Chang, Chengyi; Schorl, Christoph; Kolli, Santharam; Neretti, Nicola; HELFAND, STEPHEN L.

    2010-01-01

    A major challenge in translating the positive effects of dietary restriction (DR) for the improvement of human health is the development of therapeutic mimics. One approach to finding DR mimics is based upon identification of the proximal effectors of DR life span extension. Whole genome profiling of DR in Drosophila shows a large number of changes in gene expression, making it difficult to establish which changes are involved in life span determination as opposed to other unrelated physiolog...

  3. Transcriptional Profile of Ki-Ras-Induced Transformation of Thyroid Cells

    DEFF Research Database (Denmark)

    Visconti, Roberta; Federico, Antonella; Coppola, Valeria;

    2007-01-01

    Abstract In the last years, an increasing number of experiments has provided compelling evidence for a casual role of Ras protein mutations, resulting in their constitutive activation, in thyroid carcinogenesis. However, despite the clear involvement of Ras proteins in thyroid carcinogenesis, the...... in human thyroid carcinoma cell lines and tumor samples, our results, therefore, providing a new molecular profile of the genes involved in thyroid neoplastic transformation....

  4. Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study

    OpenAIRE

    Williams Adam R; Mondala Tony S; Robison Elizabeth H; Head Steven R; Salomon Daniel R; Kurian Sunil M

    2009-01-01

    Abstract Background Whole genome gene expression profiling has revolutionized research in the past decade especially with the advent of microarrays. Recently, there have been significant improvements in whole blood RNA isolation techniques which, through stabilization of RNA at the time of sample collection, avoid bias and artifacts introduced during sample handling. Despite these improvements, current human whole blood RNA stabilization/isolation kits are limited by the requirement of a veno...

  5. Transcript Profiling Distinguishes Complete Treatment Responders With Locally Advanced Cervical Cancer

    Directory of Open Access Journals (Sweden)

    Jorge Fernandez-Retana

    2015-04-01

    Full Text Available Cervical cancer (CC mortality is a major public health concern since it is the second cause of cancer-related deaths among women. Patients diagnosed with locally advanced CC (LACC have an important rate of recurrence and treatment failure. Conventional treatment for LACC is based on chemotherapy and radiotherapy; however, up to 40% of patients will not respond to conventional treatment; hence, we searched for a prognostic gene signature able to discriminate patients who do not respond to the conventional treatment employed to treat LACC. Tumor biopsies were profiled with genome-wide high-density expression microarrays. Class prediction was performed in tumor tissues and the resultant gene signature was validated by quantitative reverse transcription–polymerase chain reaction. A 27-predictive gene profile was identified through its association with pathologic response. The 27-gene profile was validated in an independent set of patients and was able to distinguish between patients diagnosed as no response versus complete response. Gene expression analysis revealed two distinct groups of tumors diagnosed as LACC. Our findings could provide a strategy to select patients who would benefit from neoadjuvant radiochemotherapy-based treatment.

  6. Transcript Profiling Distinguishes Complete Treatment Responders With Locally Advanced Cervical Cancer1234

    Science.gov (United States)

    Fernandez-Retana, Jorge; Lasa-Gonsebatt, Federico; Lopez-Urrutia, Eduardo; Coronel-Martínez, Jaime; Cantu De Leon, David; Jacobo-Herrera, Nadia; Peralta-Zaragoza, Oscar; Perez-Montiel, Delia; Reynoso-Noveron, Nancy; Vazquez-Romo, Rafael; Perez-Plasencia, Carlos

    2015-01-01

    Cervical cancer (CC) mortality is a major public health concern since it is the second cause of cancer-related deaths among women. Patients diagnosed with locally advanced CC (LACC) have an important rate of recurrence and treatment failure. Conventional treatment for LACC is based on chemotherapy and radiotherapy; however, up to 40% of patients will not respond to conventional treatment; hence, we searched for a prognostic gene signature able to discriminate patients who do not respond to the conventional treatment employed to treat LACC. Tumor biopsies were profiled with genome-wide high-density expression microarrays. Class prediction was performed in tumor tissues and the resultant gene signature was validated by quantitative reverse transcription–polymerase chain reaction. A 27-predictive gene profile was identified through its association with pathologic response. The 27-gene profile was validated in an independent set of patients and was able to distinguish between patients diagnosed as no response versus complete response. Gene expression analysis revealed two distinct groups of tumors diagnosed as LACC. Our findings could provide a strategy to select patients who would benefit from neoadjuvant radiochemotherapy-based treatment. PMID:25926073

  7. Expression profile of G-protein βγ subunit gene transcripts in the mouse olfactory sensory epithelia

    Directory of Open Access Journals (Sweden)

    Aaron eSathyanesan

    2013-06-01

    Full Text Available Heterotrimeric G-proteins mediate a variety of cellular functions, including signal transduction in sensory neurons of the olfactory system. Whereas the Gα subunits in these neurons are well characterized, the gene transcript expression profile of Gβγ subunits is largely missing. Here we report our comprehensive expression analysis to identify Gβ and Gγ subunit gene transcripts in the mouse main olfactory epithelium (MOE and the vomeronasal organ (VNO. Our reverse transcriptase PCR (RT-PCR and realtime qPCR analyses of all known Gβ(β1,2,3,4,5 and Gγ(γ1,2,2t,3,4,5,7,8,10,11,12,13 subunits indicate presence of multiple Gβ and Gγ subunit gene transcripts in the MOE and the VNO at various expression levels. These results are supported by our RNA in situ hybridization (RISH experiments, which reveal the expression patterns of two Gβ subunits and four Gγ subunits in the MOE as well as one Gβ and four Gγ subunits in the VNO. Using double-probe fluorescence RISH and line intensity scan analysis of the RISH signals of two dominant Gβγ subunits, we show that Gγ13 is expressed in mature olfactory sensory neurons (OSNs, while Gβ1 is present in both mature and immature OSNs. Interestingly, we also found Gβ1 to be the dominant Gβsubunit in the VNO and present throughout the sensory epithelium. In contrast, we found diverse expression of Gγ subunit gene transcripts with Gγ2, Gγ3 and Gγ13 in the Gαi2-expressing neuronal population, while Gγ8 is expressed in both layers. Further, we determined the expression of these Gβγ gene transcripts in three post-natal developmental stages (p0, 7 and 14 and found their cell-type specific expression remains largely unchanged, except the transient expression of Gγ2 in a single basal layer of cells in the MOE during P7 and P14. Taken together, our comprehensive expression analyses reveal cell-type specific gene expression of multiple Gβ and Gγ in sensory neurons of the olfactory system.

  8. Unique transcriptional profile of sustained ligand-activated preconditioning in pre- and post-ischemic myocardium.

    Directory of Open Access Journals (Sweden)

    Kevin J Ashton

    Full Text Available BACKGROUND: Opioidergic SLP (sustained ligand-activated preconditioning induced by 3-5 days of opioid receptor (OR agonism induces persistent protection against ischemia-reperfusion (I-R injury in young and aged hearts, and is mechanistically distinct from conventional preconditioning responses. We thus applied unbiased gene-array interrogation to identify molecular effects of SLP in pre- and post-ischemic myocardium. METHODOLOGY/PRINCIPAL FINDINGS: Male C57Bl/6 mice were implanted with 75 mg morphine or placebo pellets for 5 days. Resultant SLP did not modify cardiac function, and markedly reduced dysfunction and injury in perfused hearts subjected to 25 min ischemia/45 min reperfusion. Microarray analysis identified 14 up- and 86 down-regulated genes in normoxic hearts from SLP mice (≥1.3-fold change, FDR≤5%. Induced genes encoded sarcomeric/contractile proteins (Myh7, Mybpc3,Myom2,Des, natriuretic peptides (Nppa,Nppb and stress-signaling elements (Csda,Ptgds. Highly repressed genes primarily encoded chemokines (Ccl2,Ccl4,Ccl7,Ccl9,Ccl13,Ccl3l3,Cxcl3, cytokines (Il1b,Il6,Tnf and other proteins involved in inflammation/immunity (C3,Cd74,Cd83, Cd86,Hla-dbq1,Hla-drb1,Saa1,Selp,Serpina3, together with endoplasmic stress proteins (known: Dnajb1,Herpud1,Socs3; putative: Il6, Gadd45g,Rcan1 and transcriptional controllers (Egr2,Egr3, Fos,Hmox1,Nfkbid. Biological themes modified thus related to inflammation/immunity, together with cellular/cardiovascular movement and development. SLP also modified the transcriptional response to I-R (46 genes uniquely altered post-ischemia, which may influence later infarction/remodeling. This included up-regulated determinants of cellular resistance to oxidant (Mgst3,Gstm1,Gstm2 and other forms of stress (Xirp1,Ankrd1,Clu, and repression of stress-response genes (Hspa1a,Hspd1,Hsp90aa,Hsph1,Serpinh1 and Txnip. CONCLUSIONS: Protection via SLP is associated with transcriptional repression of inflammation/immunity, up

  9. Transcriptional profiling of ectoderm specification to keratinocyte fate in human embryonic stem cells.

    Science.gov (United States)

    Tadeu, Ana Mafalda Baptista; Lin, Samantha; Hou, Lin; Chung, Lisa; Zhong, Mei; Zhao, Hongyu; Horsley, Valerie

    2015-01-01

    In recent years, several studies have shed light into the processes that regulate epidermal specification and homeostasis. We previously showed that a broad-spectrum γ-secretase inhibitor DAPT promoted early keratinocyte specification in human embryonic stem cells triggered to undergo ectoderm specification. Here, we show that DAPT accelerates human embryonic stem cell differentiation and induces expression of the ectoderm protein AP2. Furthermore, we utilize RNA sequencing to identify several candidate regulators of ectoderm specification including those involved in epithelial and epidermal development in human embryonic stem cells. Genes associated with transcriptional regulation and growth factor activity are significantly enriched upon DAPT treatment during specification of human embryonic stem cells to the ectoderm lineage. The human ectoderm cell signature identified in this study contains several genes expressed in ectodermal and epithelial tissues. Importantly, these genes are also associated with skin disorders and ectodermal defects, providing a platform for understanding the biology of human epidermal keratinocyte development under diseased and homeostatic conditions.

  10. PCBs are associated with altered gene transcript profiles in arctic Beluga Whales (Delphinapterus leucas).

    Science.gov (United States)

    Noël, Marie; Loseto, Lisa L; Helbing, Caren C; Veldhoen, Nik; Dangerfield, Neil J; Ross, Peter S

    2014-01-01

    High trophic level arctic beluga whales (Delphinapterus leucas) are exposed to persistent organic pollutants (POP) originating primarily from southern latitudes. We collected samples from 43 male beluga harvested by Inuvialuit hunters (2008-2010) in the Beaufort Sea to evaluate the effects of POPs on the levels of 13 health-related gene transcripts using quantitative real-time polymerase chain reaction. Consistent with their role in detoxification, the aryl hydrocarbon receptor (Ahr) (r(2) = 0.18, p = 0.045 for 2008 and 2009) and cytochrome P450 1A1 (Cyp1a1) (r(2) = 0.20, p whales during these two years. While this provides insight into the legacy of PCBs in a remote environment, the possible impacts of a changing ice climate on the health of beluga underscores the need for long-term studies. PMID:24490950

  11. Transcriptional profiling of cattle infected with Trypanosoma congolense highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility

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    Naessens Jan

    2009-05-01

    Full Text Available Abstract Background African animal trypanosomiasis (AAT caused by tsetse fly-transmitted protozoa of the genus Trypanosoma is a major constraint on livestock and agricultural production in Africa and is among the top ten global cattle diseases impacting on the poor. Here we show that a functional genomics approach can be used to identify temporal changes in host peripheral blood mononuclear cell (PBMC gene expression due to disease progression. We also show that major gene expression differences exist between cattle from trypanotolerant and trypanosusceptible breeds. Using bovine long oligonucleotide microarrays and real time quantitative reverse transcription PCR (qRT-PCR validation we analysed PBMC gene expression in naïve trypanotolerant and trypanosusceptible cattle experimentally challenged with Trypanosoma congolense across a 34-day infection time course. Results Trypanotolerant N'Dama cattle displayed a rapid and distinct transcriptional response to infection, with a ten-fold higher number of genes differentially expressed at day 14 post-infection compared to trypanosusceptible Boran cattle. These analyses identified coordinated temporal gene expression changes for both breeds in response to trypanosome infection. In addition, a panel of genes were identified that showed pronounced differences in gene expression between the two breeds, which may underlie the phenomena of trypanotolerance and trypanosusceptibility. Gene ontology (GO analysis demonstrate that the products of these genes may contribute to increased mitochondrial mRNA translational efficiency, a more pronounced B cell response, an elevated activation status and a heightened response to stress in trypanotolerant cattle. Conclusion This study has revealed an extensive and diverse range of cellular processes that are altered temporally in response to trypanosome infection in African cattle. Results indicate that the trypanotolerant N'Dama cattle respond more rapidly and with a

  12. Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling.

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    Mónica Sebastiana

    Full Text Available Ectomycorrhizal symbiosis is essential for the life and health of trees in temperate and boreal forests where it plays a major role in nutrient cycling and in functioning of the forest ecosystem. Trees with ectomycorrhizal root tips are more tolerant to environmental stresses, such as drought, and biotic stresses such as root pathogens. Detailed information on these molecular processes is essential for the understanding of symbiotic tissue development in order to optimize the benefits of this natural phenomenon. Next generation sequencing tools allow the analysis of non model ectomycorrhizal plant-fungal interactions that can contribute to find the "symbiosis toolkits" and better define the role of each partner in the mutualistic interaction. By using 454 pyrosequencing we compared ectomycorrhizal cork oak roots with non-symbiotic roots. From the two cDNA libraries sequenced, over 2 million reads were obtained that generated 19,552 cork oak root unique transcripts. A total of 2238 transcripts were found to be differentially expressed when ECM roots were compared with non-symbiotic roots. Identification of up- and down-regulated gens in ectomycorrhizal roots lead to a number of insights into the molecular mechanisms governing this important symbiosis. In cork oak roots, ectomycorrhizal colonization resulted in extensive cell wall remodelling, activation of the secretory pathway, alterations in flavonoid biosynthesis, and expression of genes involved in the recognition of fungal effectors. In addition, we identified genes with putative roles in symbiotic processes such as nutrient exchange with the fungal partner, lateral root formation or root hair decay. These findings provide a global overview of the transcriptome of an ectomycorrhizal host root, and constitute a foundation for future studies on the molecular events controlling this important symbiosis.

  13. Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling.

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    Sebastiana, Mónica; Vieira, Bruno; Lino-Neto, Teresa; Monteiro, Filipa; Figueiredo, Andreia; Sousa, Lisete; Pais, Maria Salomé; Tavares, Rui; Paulo, Octávio S

    2014-01-01

    Ectomycorrhizal symbiosis is essential for the life and health of trees in temperate and boreal forests where it plays a major role in nutrient cycling and in functioning of the forest ecosystem. Trees with ectomycorrhizal root tips are more tolerant to environmental stresses, such as drought, and biotic stresses such as root pathogens. Detailed information on these molecular processes is essential for the understanding of symbiotic tissue development in order to optimize the benefits of this natural phenomenon. Next generation sequencing tools allow the analysis of non model ectomycorrhizal plant-fungal interactions that can contribute to find the "symbiosis toolkits" and better define the role of each partner in the mutualistic interaction. By using 454 pyrosequencing we compared ectomycorrhizal cork oak roots with non-symbiotic roots. From the two cDNA libraries sequenced, over 2 million reads were obtained that generated 19,552 cork oak root unique transcripts. A total of 2238 transcripts were found to be differentially expressed when ECM roots were compared with non-symbiotic roots. Identification of up- and down-regulated gens in ectomycorrhizal roots lead to a number of insights into the molecular mechanisms governing this important symbiosis. In cork oak roots, ectomycorrhizal colonization resulted in extensive cell wall remodelling, activation of the secretory pathway, alterations in flavonoid biosynthesis, and expression of genes involved in the recognition of fungal effectors. In addition, we identified genes with putative roles in symbiotic processes such as nutrient exchange with the fungal partner, lateral root formation or root hair decay. These findings provide a global overview of the transcriptome of an ectomycorrhizal host root, and constitute a foundation for future studies on the molecular events controlling this important symbiosis.

  14. A Brassica exon array for whole-transcript gene expression profiling.

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    Christopher G Love

    Full Text Available Affymetrix GeneChip® arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip® arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip® arrays whose probes are localised primarily in 3' exons. Plant whole-transcript (WT GeneChip® arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip® Brassica Exon 1.0 ST Array is a 5 µM feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E(-5, with ≤98% sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18, and categorisation by Gene Ontologies (GO based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/index.html.

  15. Transcriptional profiling of the effect of lipopolysaccharide (LPS) pretreatment in blood from probiotics-treated dairy cows.

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    Adjei-Fremah, Sarah; Ekwemalor, Kingsley; Asiamah, Emmanuel; Ismail, Hamid; Worku, Mulumebet

    2016-12-01

    Probiotic supplements are beneficial for animal health and rumen function; and lipopolysaccharides (LPS) from gram negative bacteria have been associated with inflammatory diseases. In this study the transcriptional profile in whole blood collected from probiotics-treated cows was investigated in response to stimulation with lipopolysaccharides (LPS) in vitro. Microarray experiment was performed between LPS-treated and control samples using the Agilent one-color bovine v2 bovine (v2) 4x44K array slides. Global gene expression analysis identified 13,658 differentially expressed genes (fold change cutoff ≥ 2, P probiotics may stimulate the innate immune response of animal against parasitic and bacterial infections. We have provided a detailed description of the experimental design, microarray experiment and normalization and analysis of data which have been deposited into NCBI Gene Expression Omnibus (GEO): GSE75240. PMID:27656413

  16. An inducible HSP70 gene from the midge Chironomus dilutus: Characterization and transcription profile under environmental stress

    Science.gov (United States)

    Karouna-Renier, N. K.; Rao, K.R.

    2009-01-01

    In the present study, we identified and characterized an inducible heat shock protein 70 (HSP70) from the midge Chironomus dilutus and investigated the transcriptional profile of the gene under baseline and environmentally stressful conditions. Using real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR), we observed increased expression of CD-HSP70-1 in response to both heat shock and copper stress. We also investigated the expression of this gene during midge development. All C. dilutus developmental stages expressed CD-HSP70-1 under normal conditions, although at extremely low levels. Phylogenetic analysis of the amino acid sequence demonstrated distinct clustering of this gene with inducible HSP70s from other insect species. ?? 2008 The Authors.

  17. Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq

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    Hui eWei

    2014-04-01

    Full Text Available The anaerobic, thermophilic bacterium, Clostridium thermocellum, secretes multi-protein enzyme complexes, termed cellulosomes, which synergistically interact with the microbial cell surface and efficiently disassemble plant cell wall biomass. C. thermocellum has also been considered a potential consolidated bioprocessing (CBP organism due to its ability to produce the biofuel products, hydrogen and ethanol. We found that C. thermocellum fermentation of pretreated yellow poplar (PYP produced 30% and 39% of ethanol and hydrogen product concentrations, respectively, compared to fermentation of cellobiose. RNA-seq was used to analyze the transcriptional profiles of these cells. The PYP-grown cells taken for analysis at the late stationary phase showed 1211 genes up-regulated and 314 down-regulated by more than 2-fold compared to the cellobiose-grown cells. These affected genes cover a broad spectrum of specific functional categories. The transcriptional analysis was further validated by sub-proteomics data taken from the literature; as well as by quantitative reverse transcription-PCR (qRT-PCR analyses of selected genes. Specifically, 47 cellulosomal protein-encoding genes, genes for 4 pairs of SigI-RsgI for polysaccharide sensing, 7 cellodextrin ABC transporter genes, and a set of NAD(PH hydogenase and alcohol dehydrogenase genes were up-regulated for cells growing on PYP compared to cellobiose. These genes could be potential candidates for future studies aimed at gaining insight into the regulatory mechanism of this organism as well as for improvement of C. thermocellum in its role as a CBP organism.

  18. A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing.

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    Marc W Schmid

    Full Text Available The acquisition of distinct cell fates is central to the development of multicellular organisms and is largely mediated by gene expression patterns specific to individual cells and tissues. A spatially and temporally resolved analysis of gene expression facilitates the elucidation of transcriptional networks linked to cellular identity and function. We present an approach that allows cell type-specific transcriptional profiling of distinct target cells, which are rare and difficult to access, with unprecedented sensitivity and resolution. We combined laser-assisted microdissection (LAM, linear amplification starting from <1 ng of total RNA, and RNA-sequencing (RNA-Seq. As a model we used the central cell of the Arabidopsis thaliana female gametophyte, one of the female gametes harbored in the reproductive organs of the flower. We estimated the number of expressed genes to be more than twice the number reported previously in a study using LAM and ATH1 microarrays, and identified several classes of genes that were systematically underrepresented in the transcriptome measured with the ATH1 microarray. Among them are many genes that are likely to be important for developmental processes and specific cellular functions. In addition, we identified several intergenic regions, which are likely to be transcribed, and describe a considerable fraction of reads mapping to introns and regions flanking annotated loci, which may represent alternative transcript isoforms. Finally, we performed a de novo assembly of the transcriptome and show that the method is suitable for studying individual cell types of organisms lacking reference sequence information, demonstrating that this approach can be applied to most eukaryotic organisms.

  19. Transcription profiling of immune genes during parasite infection in susceptible and resistant strains of the flour beetles (Tribolium castaneum).

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    Zhong, Daibin; Wang, Mei-Hui; Pai, Aditi; Yan, Guiyun

    2013-05-01

    The flour beetle, Tribolium castaneum, is an intermediate host for the tapeworm Hymenolepis diminuta and has become an important genetic model to explore immune responses to parasite infection in insect hosts. The present study examined the immune responses to tapeworm infection in resistant (TIW1) and susceptible (cSM) strains of the red flour beetle, T. castaneum, using real-time quantitative reverse transcription PCR on 29 immunity-related genes that exhibit antimicrobial properties. Thirteen of the 29 genes showed constitutive differences in expression between the two strains. Fourteen to fifteen of the 29 genes exhibited significant differences in transcription levels when beetles were challenged with tapeworm parasite in the resistant and susceptible strains. Nine genes (GNBP3, cSPH2, lysozyme4, defensin1, PGRP-SA, defensin2, coleoptericin1, attacin2 and serpin29) in cSM and 13 genes (lysozyme2, proPO1, GNBP3, cSPH2, lysozyme4, defensin1, PGRP-SA, defensin2, coleoptericin1, attacin2, proPO2/3, PGRP-LE and PGRP-SB) in TIW1 were up-regulated by infections or showed parasite infection-induced expression. Seven genes (attacin2, coleoptericin1, defensin1, defensin2, lysozyme2, PGRP-SA and PGRP-SB) were more than 10 folds higher in the resistant TIW1 strain than in the susceptible cSM strain after exposure to tapeworm parasites. This study demonstrated the effects of genetic background, the transcription profile to parasite infection, and identified the immunity-related genes that were significantly regulated by the infection of tapeworms in Tribolium beetles.

  20. PCB related effects thresholds as derived through gene transcript profiles in locally contaminated ringed seals (Pusa hispida).

    Science.gov (United States)

    Brown, Tanya M; Ross, Peter S; Reimer, Ken J; Veldhoen, Nik; Dangerfield, Neil J; Fisk, Aaron T; Helbing, Caren C

    2014-11-01

    Causal evidence linking toxic injury to polychlorinated biphenyl (PCB) exposure is typically confounded by the complexity of real-world contaminant mixtures to which aquatic wildlife are exposed. A local PCB "hotspot" on the Labrador coast provided a rare opportunity to evaluate the effects of PCBs on the health of a marine mammal as this chemical dominated their persistent organic pollutant (POP) burdens. The release of approximately 260 kg of PCBs by a military radar facility over a 30 year period (1970-2000) contaminated some local marine biota, including the ringed seal (Pusa hispida). The abundance profiles of eight health-related gene transcripts were evaluated in liver samples collected from 43 ringed seals in the affected area. The mRNA transcript levels of five gene targets, including aryl hydrocarbon receptor (Ahr), interleukin-1 β (Il1b), estrogen receptor α (Esr1), insulin like growth factor receptor 1 (Igf1), and glucocorticoid receptor α (Nr3c1) correlated with increasing levels of blubber PCBs. PCB threshold values calculated using best-fit hockey-stick regression models for these five genes averaged 1,680±206 ng/g lw, with the lowest, most conservative, being 1,370 ng/g lw for Il1b. Approximately 14% of the seals in the region exceeded this threshold. The dominance of PCBs in the seals studied enabled an assessment of the effects of this chemical on gene transcripts involved in regulating the health of a highly mobile predator, something that is rarely possible in the world of complex mixtures. PMID:25286162

  1. Genomic analyses and transcriptional profiles of the glycoside hydrolase family 18 genes of the entomopathogenic fungus Metarhizium anisopliae.

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    Ângela Junges

    Full Text Available Fungal chitin metabolism involves diverse processes such as metabolically active cell wall maintenance, basic nutrition, and different aspects of virulence. Chitinases are enzymes belonging to the glycoside hydrolase family 18 (GH18 and 19 (GH19 and are responsible for the hydrolysis of β-1,4-linkages in chitin. This linear homopolymer of N-acetyl-β-D-glucosamine is an essential constituent of fungal cell walls and arthropod exoskeletons. Several chitinases have been directly implicated in structural, morphogenetic, autolytic and nutritional activities of fungal cells. In the entomopathogen Metarhizium anisopliae, chitinases are also involved in virulence. Filamentous fungi genomes exhibit a higher number of chitinase-coding genes than bacteria or yeasts. The survey performed in the M. anisopliae genome has successfully identified 24 genes belonging to glycoside hydrolase family 18, including three previously experimentally determined chitinase-coding genes named chit1, chi2 and chi3. These putative chitinases were classified based on domain organization and phylogenetic analysis into the previously described A, B and C chitinase subgroups, and into a new subgroup D. Moreover, three GH18 proteins could be classified as putative endo-N-acetyl-β-D-glucosaminidases, enzymes that are associated with deglycosylation and were therefore assigned to a new subgroup E. The transcriptional profile of the GH18 genes was evaluated by qPCR with RNA extracted from eight culture conditions, representing different stages of development or different nutritional states. The transcripts from the GH18 genes were detected in at least one of the different M. anisopliae developmental stages, thus validating the proposed genes. Moreover, not all members from the same chitinase subgroup presented equal patterns of transcript expression under the eight distinct conditions studied. The determination of M. anisopliae chitinases and ENGases and a more detailed study

  2. Global transcriptional profiles of beating clusters derived from human induced pluripotent stem cells and embryonic stem cells are highly similar

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    Gupta Manoj K

    2010-09-01

    Full Text Available Abstract Background Functional and molecular integrity of cardiomyocytes (CMs derived from induced pluripotent stem (iPS cells is essential for their use in tissue repair, disease modelling and drug screening. In this study we compared global transcriptomes of beating clusters (BCs microdissected from differentiating human iPS cells and embryonic stem (ES cells. Results Hierarchical clustering and principal component analysis revealed that iPS-BCs and ES-BCs cluster together, are similarly enriched for cardiospecific genes and differ in expression of only 1.9% of present transcripts. Similarly, sarcomeric organization, electrophysiological properties and calcium handling of iPS-CMs were indistinguishable from those of ES-CMs. Gene ontology analysis revealed that among 204 genes that were upregulated in iPS-BCs vs ES-BCs the processes related to extracellular matrix, cell adhesion and tissue development were overrepresented. Interestingly, 47 of 106 genes that were upregulated in undifferentiated iPS vs ES cells remained enriched in iPS-BCs vs ES-BCs. Most of these genes were found to be highly expressed in fibroblasts used for reprogramming and 34% overlapped with the recently reported iPS cell-enriched genes. Conclusions These data suggest that iPS-BCs are transcriptionally highly similar to ES-BCs. However, iPS-BCs appear to share some somatic cell signature with undifferentiated iPS cells. Thus, iPS-BCs may not be perfectly identical to ES-BCs. These minor differences in the expression profiles may occur due to differential cellular composition of iPS-BCs and ES-BCs, due to retention of some genetic profile of somatic cells in differentiated iPS cell-derivatives, or both.

  3. Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans

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    Schaller Martin

    2008-10-01

    Full Text Available Abstract Background Invasion of host tissue by the human fungal pathogen Candida albicans is an important step during the development of candidosis. However, not all C. albicans strains possess the same invasive and virulence properties. For example, the two clinical isolates SC5314 and ATCC10231 differ in their ability to invade host tissue and cause experimental infections. Strain SC5314 is invasive whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence compared to SC5314. In this study we compare the in vitro phenotypic, transcriptional and genomic profiles of these two widely used laboratory strains in order to determine the principal biological and genetic properties responsible for their differential virulence. Results In all media tested, the two strains showed the same metabolic flexibility, stress resistance, adhesion properties and hydrolytic enzyme secretion in vitro. However, differences were observed in response to cell-surface disturbing agents and alkaline pH. Furthermore, reduced hyphal formation in strain ATCC10231 under certain conditions correlated with reduced invasive properties in an in vitro invasion assay and a reduced ability to invade epithelial tissue. Despite these diverse phenotypic properties, no substantial genomic differences were detected by comparative genome hybridisation within the open reading frames. However, in vitro transcriptional profiling displayed major differences in the gene expression of these two strains, even under normal in vitro growth conditions. Conclusion Our data suggest that the reason for differential virulence of C. albicans strains is not due to the absence of specific genes, but rather due to differences in the expression, function or activity of common genes.

  4. The colitis-associated transcriptional profile of commensal Bacteroides thetaiotaomicron enhances adaptive immune responses to a bacterial antigen.

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    Jonathan J Hansen

    Full Text Available BACKGROUND: Inflammatory bowel diseases (IBD may be caused in part by aberrant immune responses to commensal intestinal microbes including the well-characterized anaerobic gut commensal Bacteroides thetaiotaomicron (B. theta. Healthy, germ-free HLA-B27 transgenic (Tg rats develop chronic colitis when colonized with complex gut commensal bacteria whereas non-transgenic (nTg rats remain disease-free. However, the role of B. theta in causing disease in Tg rats is unknown nor is much known about how gut microbes respond to host inflammation. METHODS: Tg and nTg rats were monoassociated with a human isolate of B. theta. Colonic inflammation was assessed by histologic scoring and tissue pro-inflammatory cytokine measurement. Whole genome transcriptional profiling of B. theta recovered from ceca was performed using custom GeneChips and data analyzed using dChip, Significance Analysis of Microarrays, and Gene Set Enrichment Analysis (GSEA software. Western Blots were used to determine adaptive immune responses to a differentially expressed B. theta gene. RESULTS: B. theta monoassociated Tg rats, but not nTg or germ-free controls, developed chronic colitis. Transcriptional profiles of cecal B. theta were significantly different in Tg vs. nTg rats. GSEA revealed that genes in KEGG canonical pathways involved in bacterial growth and metabolism were downregulated in B. theta from Tg rats with colitis though luminal bacterial concentrations were unaffected. Bacterial genes in the Gene Ontology molecular function "receptor activity", most of which encode nutrient binding proteins, were significantly upregulated in B. theta from Tg rats and include a SusC homolog that induces adaptive immune responses in Tg rats. CONCLUSIONS: B. theta induces colitis in HLA-B27 Tg rats, which is associated with regulation of bacterial genes in metabolic and nutrient binding pathways that may affect host immune responses. These studies of the host-microbial dialogue may lead to

  5. Transcriptional profiling of human brain endothelial cells reveals key properties crucial for predictive in vitro blood-brain barrier models.

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    Eduard Urich

    Full Text Available Brain microvascular endothelial cells (BEC constitute the blood-brain barrier (BBB which forms a dynamic interface between the blood and the central nervous system (CNS. This highly specialized interface restricts paracellular diffusion of fluids and solutes including chemicals, toxins and drugs from entering the brain. In this study we compared the transcriptome profiles of the human immortalized brain endothelial cell line hCMEC/D3 and human primary BEC. We identified transcriptional differences in immune response genes which are directly related to the immortalization procedure of the hCMEC/D3 cells. Interestingly, astrocytic co-culturing reduced cell adhesion and migration molecules in both BECs, which possibly could be related to regulation of immune surveillance of the CNS controlled by astrocytic cells within the neurovascular unit. By matching the transcriptome data from these two cell lines with published transcriptional data from freshly isolated mouse BECs, we discovered striking differences that could explain some of the limitations of using cultured BECs to study BBB properties. Key protein classes such as tight junction proteins, transporters and cell surface receptors show differing expression profiles. For example, the claudin-5, occludin and JAM2 expression is dramatically reduced in the two human BEC lines, which likely explains their low transcellular electric resistance and paracellular leakiness. In addition, the human BEC lines express low levels of unique brain endothelial transporters such as Glut1 and Pgp. Cell surface receptors such as LRP1, RAGE and the insulin receptor that are involved in receptor-mediated transport are also expressed at very low levels. Taken together, these data illustrate that BECs lose their unique protein expression pattern outside of their native environment and display a more generic endothelial cell phenotype. A collection of key genes that seems to be highly regulated by the local

  6. Transcriptional profiling of suberoylanilide hydroxamic acid (SAHA regulated genes in mineralizing dental pulp cells at early and late time points

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    Henry F. Duncan

    2015-09-01

    Full Text Available Dental pulp tissue can be damaged by a range of irritants, however, if the irritation is removed and/or the tooth is adequately restored, pulp regeneration is possible (Mjör and Tronstad, 1974 [1]. At present, dental restorative materials limit healing by impairing mineralization and repair processes and as a result new biologically-based materials are being developed (Ferracane et al., 2010 [2]. Previous studies have highlighted the benefit of epigenetic modification by histone deacetylase inhibitor (HDACi application to dental pulp cells (DPCs, which induces changes to chromatin architecture, promoting gene expression and cellular-reparative events (Duncan et al., 2013 [3]; Paino et al., 2014 [4]. In this study a genome-wide transcription profiling in epigenetically-modified mineralizing primary DPC cultures was performed, at relatively early and late time-points, to identify differentially regulated transcripts that may provide novel therapeutic targets for use in restorative dentistry. Here we provide detailed methods and analysis on these microarray data which has been deposited in Gene Expression Omnibus (GEO: GSE67175.

  7. Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages.

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    Ludovic Tailleux

    Full Text Available BACKGROUND: Transcriptional profiling using microarrays provides a unique opportunity to decipher host pathogen cross-talk on the global level. Here, for the first time, we have been able to investigate gene expression changes in both Mycobacterium tuberculosis, a major human pathogen, and its human host cells, macrophages and dendritic cells. METHODOLOGY/PRINCIPAL FINDINGS: In addition to common responses, we could identify eukaryotic and microbial transcriptional signatures that are specific to the cell type involved in the infection process. In particular M. tuberculosis shows a marked stress response when inside dendritic cells, which is in accordance with the low permissivity of these specialized phagocytes to the tubercle bacillus and to other pathogens. In contrast, the mycobacterial transcriptome inside macrophages reflects that of replicating bacteria. On the host cell side, differential responses to infection in macrophages and dendritic cells were identified in genes involved in oxidative stress, intracellular vesicle trafficking and phagosome acidification. CONCLUSIONS/SIGNIFICANCE: This study provides the proof of principle that probing the host and the microbe transcriptomes simultaneously is a valuable means to accessing unique information on host pathogen interactions. Our results also underline the extraordinary plasticity of host cell and pathogen responses to infection, and provide a solid framework to further understand the complex mechanisms involved in immunity to M. tuberculosis and in mycobacterial adaptation to different intracellular environments.

  8. Regulatory features underlying pollination-dependent and -independent tomato fruit set revealed by transcript and primary metabolite profiling.

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    Wang, Hua; Schauer, Nicolas; Usadel, Bjoern; Frasse, Pierre; Zouine, Mohamed; Hernould, Michel; Latché, Alain; Pech, Jean-Claude; Fernie, Alisdair R; Bouzayen, Mondher

    2009-05-01

    Indole Acetic Acid 9 (IAA9) is a negative auxin response regulator belonging to the Aux/IAA transcription factor gene family whose downregulation triggers fruit set before pollination, thus giving rise to parthenocarpy. In situ hybridization experiments revealed that a tissue-specific gradient of IAA9 expression is established during flower development, the release of which upon pollination triggers the initiation of fruit development. Comparative transcriptome and targeted metabolome analysis uncovered important features of the molecular events underlying pollination-induced and pollination-independent fruit set. Comprehensive transcriptomic profiling identified a high number of genes common to both types of fruit set, among which only a small subset are dependent on IAA9 regulation. The fine-tuning of Aux/IAA and ARF genes and the downregulation of TAG1 and TAGL6 MADS box genes are instrumental in triggering the fruit set program. Auxin and ethylene emerged as the most active signaling hormones involved in the flower-to-fruit transition. However, while these hormones affected only a small number of transcriptional events, dramatic shifts were observed at the metabolic and developmental levels. The activation of photosynthesis and sucrose metabolism-related genes is an integral regulatory component of fruit set process. The combined results allow a far greater comprehension of the regulatory and metabolic events controlling early fruit development both in the presence and absence of pollination/fertilization. PMID:19435935

  9. Transcriptional profiling of rats subjected to gestational undernourishment: implications for the developmental variations in metabolic traits.

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    Tiffany J Morris

    Full Text Available A link has been established between prenatal nutrition and the development of metabolic and cardiovascular diseases later in life, a process referred to as developmental programming. It has been suggested that the trajectory of development is shifted by alterations in the maternal nutritional state leading to changes in developmental plasticity, in part underpinned by epigenetic changes in gene regulation. However, to date, only candidate gene approaches have been used to assess expression and molecular changes in the offspring of maternally undernourished animals. Furthermore, most work has focused on animals at an age where the programmed phenotype is already manifest and little is known about changes in gene expression in the offspring prior to development of obesity and related metabolic disorders. Gene expression profiles of liver, retroperitoneal white adipose fat, and biceps femoris skeletal muscle tissue from young adult male rats (55 days old in which nutritional status had been manipulated in utero by maternal undernutrition (UN were compared to the profiles of offspring of ad libitum fed mothers serving as the control group (AD (8 offspring/group. The expression profiles were determined using the Illumina RatRef-12 BeadChip. No significant changes in expression were identified for skeletal muscle or white adipose tissue. However, studies of liver tissue showed 249 differentially expressed genes (143 up regulated, 106 down regulated. Although the animals at day 55 have yet to develop obesity they already show biochemical abnormalities and by day 110 express a phenotype characterized by increased adiposity and altered insulin sensitivity. An analysis of pathways affected suggests that intrauterine programming of UN animals to favor fat as an energy source results in mitochondrial dysfunction which initially affects the postnatal hepatic function and subsequently, via the resultant metabolic changes in other organs leads to the evolution

  10. Transcriptional profiling of rats subjected to gestational undernourishment: implications for the developmental variations in metabolic traits.

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    Morris, Tiffany J; Vickers, Mark; Gluckman, Peter; Gilmour, Stewart; Affara, Nabeel

    2009-09-29

    A link has been established between prenatal nutrition and the development of metabolic and cardiovascular diseases later in life, a process referred to as developmental programming. It has been suggested that the trajectory of development is shifted by alterations in the maternal nutritional state leading to changes in developmental plasticity, in part underpinned by epigenetic changes in gene regulation. However, to date, only candidate gene approaches have been used to assess expression and molecular changes in the offspring of maternally undernourished animals. Furthermore, most work has focused on animals at an age where the programmed phenotype is already manifest and little is known about changes in gene expression in the offspring prior to development of obesity and related metabolic disorders. Gene expression profiles of liver, retroperitoneal white adipose fat, and biceps femoris skeletal muscle tissue from young adult male rats (55 days old) in which nutritional status had been manipulated in utero by maternal undernutrition (UN) were compared to the profiles of offspring of ad libitum fed mothers serving as the control group (AD) (8 offspring/group). The expression profiles were determined using the Illumina RatRef-12 BeadChip. No significant changes in expression were identified for skeletal muscle or white adipose tissue. However, studies of liver tissue showed 249 differentially expressed genes (143 up regulated, 106 down regulated). Although the animals at day 55 have yet to develop obesity they already show biochemical abnormalities and by day 110 express a phenotype characterized by increased adiposity and altered insulin sensitivity. An analysis of pathways affected suggests that intrauterine programming of UN animals to favor fat as an energy source results in mitochondrial dysfunction which initially affects the postnatal hepatic function and subsequently, via the resultant metabolic changes in other organs leads to the evolution of a phenotype

  11. AFLP genetic polymorphism in wild barley (Hordeum spontaneum) populations in Israel.

    Science.gov (United States)

    Turpeinen, T; Vanhala, T; Nevo, E; Nissilä, E

    2003-05-01

    The genetic diversity produced by the amplified fragment length polymorphism (AFLP) method was studied in 94 genotypes of wild barley, Hordeum spontaneum (C. Koch) Thell., originating from ten ecologically and geographically different locations in Israel. Eight primer pairs produced 204 discernible loci of which 189 (93%) were polymorphic. Each genotype had a unique banding profile and the genetic similarity coefficient varied between 0.74 and 0.98. The phenogram generated from these similarities by the UPGMA method did not group genotypes strictly according to their geographical origin, which pattern was also seen in the principal coordinate (PCO) plot. Genetic diversity was larger within (69%) than among (31%) populations. Associations between ecogeographical variables and the mean gene diversity were found at one primer pair. The results are discussed and compared with data obtained by the simple sequence repeat (SSR) method. PMID:12748785

  12. Transcriptional profiling of thymidine-producing strain recombineered from Escherichia coli BL21

    Directory of Open Access Journals (Sweden)

    Jin-Sook Kim

    2015-12-01

    Full Text Available DNA microarrays were used to compare the expression profiles of a thymidine overproducing strain (BLT013 and its isogenic parent, Escherichia coli BL21(DE3, when each was grown under well-defined thymidine production conditions with glycerol as carbon source. Here we describe the experimental procedures and methods in detail to reproduce the results and provide resource to be applied to similar engineering approach (available at Gene Expression Omnibus database under GSE69963. Taken together, the microarray data provide a basis for new testable hypotheses regarding enhancement of thymidine productivity and attaining a more complete understanding of nucleotide metabolism in bacteria.

  13. Transcript profiling reveals auxin and cytokinin signaling pathways and transcription regulation during in vitro organogenesis of Ramie (Boehmeria nivea L. Gaud.

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    Xing Huang

    Full Text Available In vitro organogenesis, one of the most common pathways leading to in vitro plant regeneration, is widely used in biotechnology and the fundamental study of plant biology. Although previous studies have constructed a complex regulatory network model for Arabidopsis in vitro organogenesis, no related study has been reported in ramie. To generate more complete observations of transcriptome content and dynamics during ramie in vitro organogenesis, we constructed a reference transcriptome library and ten digital gene expression (DGE libraries for illumina sequencing. Approximately 111.34 million clean reads were obtained for transcriptome and the DGE libraries generated between 13.5 and 18.8 million clean reads. De novo assembly produced 43,222 unigenes and a total of 5,760 differentially expressed genes (DEGs were filtered. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database, 26 auxin related and 11 cytokinin related DEGs were selected for qRT-PCR validation of two ramie cultivars, which had high (Huazhu No. 5 or extremely low (Dazhuhuangbaima shoot regeneration abilities. The results revealed differing regulation patterns of auxin and cytokinin in different genotypes. Here we report the first genome-wide gene expression profiling of in vitro organogenesis in ramie and provide an overview of transcription and phytohormone regulation during the process. Furthermore, the auxin and cytokinin related genes have distinct expression patterns in two ramie cultivars with high or extremely low shoot regeneration ability, which has given us a better understanding of the in vitro organogenesis mechanism. This result will provide a foundation for future phytohormone research and lead to improvements of the ramie regeneration system.

  14. Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program.

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    Dunja Knapp

    Full Text Available Understanding how the limb blastema is established after the initial wound healing response is an important aspect of regeneration research. Here we performed parallel expression profile time courses of healing lateral wounds versus amputated limbs in axolotl. This comparison between wound healing and regeneration allowed us to identify amputation-specific genes. By clustering the expression profiles of these samples, we could detect three distinguishable phases of gene expression - early wound healing followed by a transition-phase leading to establishment of the limb development program, which correspond to the three phases of limb regeneration that had been defined by morphological criteria. By focusing on the transition-phase, we identified 93 strictly amputation-associated genes many of which are implicated in oxidative-stress response, chromatin modification, epithelial development or limb development. We further classified the genes based on whether they were or were not significantly expressed in the developing limb bud. The specific localization of 53 selected candidates within the blastema was investigated by in situ hybridization. In summary, we identified a set of genes that are expressed specifically during regeneration and are therefore, likely candidates for the regulation of blastema formation.

  15. Transcript profile of the response of two soybean genotypes to potassium deficiency.

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    Cheng Wang

    Full Text Available The macronutrient potassium (K is essential to plant growth and development. Crop yield potential is often affected by lack of soluble K. The molecular regulation mechanism of physiological and biochemical responses to K starvation in soybean roots and shoots is not fully understood. In the present study, two soybean varieties were subjected to low-K stress conditions: a low-K-tolerant variety (You06-71 and a low-K-sensitive variety (HengChun04-11. Eight libraries were generated for analysis: 2 genotypes ×2 tissues (roots and shoots ×2 time periods [short term (0.5 to 12 h and long term (3 to 12 d]. RNA derived from the roots and shoots of these two varieties across two periods (short term and long term were sequenced and the transcriptomes were compared using high-throughput tag-sequencing. To this end, a large number of clean tags (tags used for analysis after removal of dirty tags corresponding to distinct tags (all types of clean tags were identified in eight libraries (L1, You06-71-root short term; L2, HengChun04-11-root short term; L3, You06-71-shoot short term; L4, HengChun04-11-shoot short term; L5, You06-71-root long term; L6, HengChun04-11-root long term; L7, You06-71-shoot long term; L8, HengChun04-11-shoot long term. All clean tags were mapped to the available soybean (Glycine max transcript database (http://www.soybase.org. Many genes showed substantial differences in expression across the libraries. In total, 5,440 transcripts involved in 118 KEGG pathways were either up- or down-regulated. Fifteen genes were randomly selected and their expression levels were confirmed using quantitative RT-PCR. Our results provide preliminary information on the molecular mechanism of potassium absorption and transport under low-K stress conditions in different soybean tissues.

  16. Comparative transcriptional profiling of Bacillus cereus sensu lato strains during growth in CO2-bicarbonate and aerobic atmospheres.

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    Karla D Passalacqua

    Full Text Available BACKGROUND: Bacillus species are spore-forming bacteria that are ubiquitous in the environment and display a range of virulent and avirulent phenotypes. This range is particularly evident in the Bacillus cereus sensu lato group; where closely related strains cause anthrax, food-borne illnesses, and pneumonia, but can also be non-pathogenic. Although much of this phenotypic range can be attributed to the presence or absence of a few key virulence factors, there are other virulence-associated loci that are conserved throughout the B. cereus group, and we hypothesized that these genes may be regulated differently in pathogenic and non-pathogenic strains. METHODOLOGY/PRINCIPAL FINDINGS: Here we report transcriptional profiles of three closely related but phenotypically unique members of the Bacillus cereus group--a pneumonia-causing B. cereus strain (G9241, an attenuated strain of B. anthracis (Sterne 34F(2, and an avirulent B. cereus strain (10987--during exponential growth in two distinct atmospheric environments: 14% CO(2/bicarbonate and ambient air. We show that the disease-causing Bacillus strains undergo more distinctive transcriptional changes between the two environments, and that the expression of plasmid-encoded virulence genes was increased exclusively in the CO(2 environment. We observed a core of conserved metabolic genes that were differentially expressed in all three strains in both conditions. Additionally, the expression profiles of putative virulence genes in G9241 suggest that this strain, unlike Bacillus anthracis, may regulate gene expression with both PlcR and AtxA transcriptional regulators, each acting in a different environment. CONCLUSIONS/SIGNIFICANCE: We have shown that homologous and even identical genes within the genomes of three closely related members of the B. cereus sensu lato group are in some instances regulated very differently, and that these differences can have important implications for virulence. This study

  17. Genetic diversity of Cuban pineapple germplasm assessed by AFLP Markers

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    Ermis Yanes Paz

    2012-01-01

    Full Text Available The Cuban pineapple germplasm collection represents the genetic diversity of pineapple cultivated in that country and includes other important genotypes obtained from the germplasm collections in Brazil and Martinique. The collection has previously been characterized with morphological descriptors but a molecular characterization has been lacking. With this aim, 56 six genotypes of A. comosus and one of Bromelia pinguin were analyzed with a total of 191 AFLP markers. A dendrogram that represents the genetic relationships between these samples based on the AFLP results showed a low level of diversity in the Cuban pineapple collection. All Ananas comosus accessions, being the majority obtained from farmers in different regions in Cuba, are grouped at distances lower than 0.20. Molecular characterization was in line with morphological characterization. These results are useful for breeding and conservation purposes.

  18. The molecular characterization of maize B chromosome specific AFLPs

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The origin and evolution of B chromosomes could be explained by the specific DNA sequence on them.But the specific sequences known were quite limited. To investigate maize B chromosome sqicific DNA sequeces, maize genomes with and without B chromosomes were analyzed by AFLP. Only 5 markers were found specific to genomes with B chromosomes among about 2000 AFLP markers. Southern hybridization and sequence analysis revealed that only the sequence of M8-2D was a B chromosome specific sequence.This sequence contained the telomeric repeat unit AGGGTTT conserved in plant chromosome telomeres.In addition, the sequence of M8-2D shared low homology to clones from maize chromosome 4 centromere as well. M8-2D were localized to B chromosome centromeric and telomeric regions.

  19. Transcriptional profiling of the parr-smolt transformation in Atlantic salmon

    Science.gov (United States)

    Robertson, Laura S.; McCormick, Stephen D.

    2012-01-01

    The parr–smolt transformation in Atlantic salmon (Salmo salar) is a complex developmental process that culminates in the ability to migrate to and live in seawater. We used GRASP 16K cDNA microarrays to identify genes that are differentially expressed in the liver, gill, hypothalamus, pituitary, and olfactory rosettes of smolts compared to parr. Smolts had higher levels of gill Na+/K+-ATPase activity, plasma cortisol and plasma thyroid hormones relative to parr. Across all five tissues, stringent microarray analyses identified 48 features that were differentially expressed in smolts compared to parr. Using a less stringent method we found 477 features that were differentially expressed at least 1.2-fold in smolts, including 172 features in the gill. Smolts had higher mRNA levels of genes involved in transcription, protein biosynthesis and folding, electron transport, oxygen transport, and sensory perception and lower mRNA levels for genes involved in proteolysis. Quantitative RT-PCR was used to confirm differential expression in select genes identified by microarray analyses and to quantify expression of other genes known to be involved in smolting. This study expands our understanding of the molecular processes that underlie smolting in Atlantic salmon and identifies genes for further investigation.

  20. Differential transcription profiles in Aedes aegypti detoxification genes after temephos selection.

    Science.gov (United States)

    Saavedra-Rodriguez, K; Strode, C; Flores, A E; Garcia-Luna, S; Reyes-Solis, G; Ranson, H; Hemingway, J; Black, W C

    2014-04-01

    The mosquito Aedes aegypti is the main vector of Dengue and Yellow Fever flaviviruses. The organophosphate insecticide temephos is a larvicide that is used globally to control Ae. aegypti populations; many of which have in turn evolved resistance. Target site alteration in the acetylcholine esterase of this species has not being identified. Instead, we tracked changes in transcription of metabolic detoxification genes using the Ae. aegypti 'Detox Chip' microarray during five generations of temephos selection. We selected for temephos resistance in three replicates in each of six collections, five from Mexico, and one from Peru. The response to selection was tracked in terms of lethal concentrations. Uniform upregulation was seen in the epsilon class glutathione-S-transferase (eGST) genes in strains from Mexico prior to laboratory selection, while eGSTs in the Iquitos Peru strain became upregulated after five generations of temephos selection. While expression of many carboxyl/cholinesterase esterase (CCE) genes increased with selection, no single esterase was consistently upregulated and this same pattern was noted in the cytochrome P450 monooxygenase (CYP) genes and in other genes involved in reduction or oxidation of xenobiotics. Bioassays using glutathione-S-transferase (GST), CCE and CYP inhibitors suggest that various CCEs instead of GSTs are the main metabolic mechanism conferring resistance to temephos. We show that temephos-selected strains show no cross resistance to permethrin and that genes associated with temephos selection are largely independent of those selected with permethrin in a previous study. PMID:24299217

  1. Comparative serial analysis of gene expression of transcript profiles of tomato roots infected with cyst nematode.

    Science.gov (United States)

    Uehara, Taketo; Sugiyama, Shunpei; Masuta, Chikara

    2007-01-01

    We analyzed global transcripts for tomato roots infected with the cyst nematode Globodera rostochiensis using serial analysis of gene expression (SAGE). SAGE libraries were made from nematode-infected roots and uninfected roots at 14 days after inoculation, and the clones including SAGE tags were sequenced. Genes were identified by matching the SAGE tags to tomato expressed sequence tags and cDNA databases. We then compiled a list of numerous genes according to the mRNA levels that were altered after cyst nematode infection. Our SAGE results showed significant changes in expression of many unreported genes involved in nematode infection. Of these, for discussion we selected five SAGE tags of RSI-1, BURP domain-containing protein, hexose transporter, P-rich protein, and PHAP2A that were activated by cyst nematode infection. Over 20% of the tags that were upregulated in the infected root have unknown functions (non-annotated), suggesting that we can obtain information on previously unreported and uncharacterized genes by SAGE. We can also obtain information on previously reported genes involved in nematode infection (e.g., multicystatin, peroxidase, catalase, pectin esterase, and S-adenosylmethionine transferase). To evaluate the validity of our SAGE results, seven genes were further analyzed by semiquantitative reverse transcriptase-polymerase chain reaction and Northern blot hybridization; the results agreed well with the SAGE data. PMID:16983456

  2. Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles.

    Directory of Open Access Journals (Sweden)

    Raúl Castanera

    2016-06-01

    Full Text Available Transposable elements (TEs are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation.

  3. Differential transcription profiles in Aedes aegypti detoxification genes after temephos selection.

    Science.gov (United States)

    Saavedra-Rodriguez, K; Strode, C; Flores, A E; Garcia-Luna, S; Reyes-Solis, G; Ranson, H; Hemingway, J; Black, W C

    2014-04-01

    The mosquito Aedes aegypti is the main vector of Dengue and Yellow Fever flaviviruses. The organophosphate insecticide temephos is a larvicide that is used globally to control Ae. aegypti populations; many of which have in turn evolved resistance. Target site alteration in the acetylcholine esterase of this species has not being identified. Instead, we tracked changes in transcription of metabolic detoxification genes using the Ae. aegypti 'Detox Chip' microarray during five generations of temephos selection. We selected for temephos resistance in three replicates in each of six collections, five from Mexico, and one from Peru. The response to selection was tracked in terms of lethal concentrations. Uniform upregulation was seen in the epsilon class glutathione-S-transferase (eGST) genes in strains from Mexico prior to laboratory selection, while eGSTs in the Iquitos Peru strain became upregulated after five generations of temephos selection. While expression of many carboxyl/cholinesterase esterase (CCE) genes increased with selection, no single esterase was consistently upregulated and this same pattern was noted in the cytochrome P450 monooxygenase (CYP) genes and in other genes involved in reduction or oxidation of xenobiotics. Bioassays using glutathione-S-transferase (GST), CCE and CYP inhibitors suggest that various CCEs instead of GSTs are the main metabolic mechanism conferring resistance to temephos. We show that temephos-selected strains show no cross resistance to permethrin and that genes associated with temephos selection are largely independent of those selected with permethrin in a previous study.

  4. Transcriptome-Wide Identification and Expression Profiling Analysis of Chrysanthemum Trihelix Transcription Factors

    Directory of Open Access Journals (Sweden)

    Aiping Song

    2016-02-01

    Full Text Available Trihelix transcription factors are thought to feature a typical DNA-binding trihelix (helix-loop-helix-loop-helix domain that binds specifically to the GT motif, a light-responsive DNA element. Members of the trihelix family are known to function in a number of processes in plants. Here, we characterize 20 trihelix family genes in the important ornamental plant chrysanthemum (Chrysanthemum morifolium. Based on transcriptomic data, 20 distinct sequences distributed across four of five groups revealed by a phylogenetic tree were isolated and amplified. The phylogenetic analysis also identified four pairs of orthologous proteins shared by Arabidopsis and chrysanthemum and five pairs of paralogous proteins in chrysanthemum. Conserved motifs in the trihelix proteins shared by Arabidopsis and chrysanthemum were analyzed using MEME, and further bioinformatic analysis revealed that 16 CmTHs can be targeted by 20 miRNA families and that miR414 can target 9 CmTHs. qPCR results displayed that most chrysanthemum trihelix genes were highly expressed in inflorescences, while 20 CmTH genes were in response to phytohormone treatments and abiotic stresses. This work improves our understanding of the various functions of trihelix gene family members in response to hormonal stimuli and stress.

  5. Transcriptome-Wide Identification and Expression Profiling Analysis of Chrysanthemum Trihelix Transcription Factors.

    Science.gov (United States)

    Song, Aiping; Wu, Dan; Fan, Qingqing; Tian, Chang; Chen, Sumei; Guan, Zhiyong; Xin, Jingjing; Zhao, Kunkun; Chen, Fadi

    2016-01-01

    Trihelix transcription factors are thought to feature a typical DNA-binding trihelix (helix-loop-helix-loop-helix) domain that binds specifically to the GT motif, a light-responsive DNA element. Members of the trihelix family are known to function in a number of processes in plants. Here, we characterize 20 trihelix family genes in the important ornamental plant chrysanthemum (Chrysanthemum morifolium). Based on transcriptomic data, 20 distinct sequences distributed across four of five groups revealed by a phylogenetic tree were isolated and amplified. The phylogenetic analysis also identified four pairs of orthologous proteins shared by Arabidopsis and chrysanthemum and five pairs of paralogous proteins in chrysanthemum. Conserved motifs in the trihelix proteins shared by Arabidopsis and chrysanthemum were analyzed using MEME, and further bioinformatic analysis revealed that 16 CmTHs can be targeted by 20 miRNA families and that miR414 can target 9 CmTHs. qPCR results displayed that most chrysanthemum trihelix genes were highly expressed in inflorescences, while 20 CmTH genes were in response to phytohormone treatments and abiotic stresses. This work improves our understanding of the various functions of trihelix gene family members in response to hormonal stimuli and stress. PMID:26848650

  6. Transcriptional Profiling of Hydrogen Production Metabolism of Rhodobacter capsulatus under Temperature Stress by Microarray Analysis

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    Muazzez Gürgan

    2015-06-01

    Full Text Available Biohydrogen is a clean and renewable form of hydrogen, which can be produced by photosynthetic bacteria in outdoor large-scale photobioreactors using sunlight. In this study, the transcriptional response of Rhodobacter capsulatus to cold (4 °C and heat (42 °C stress was studied using microarrays. Bacteria were grown in 30/2 acetate/glutamate medium at 30 °C for 48 h under continuous illumination. Then, cold and heat stresses were applied for two and six hours. Growth and hydrogen production were impaired under both stress conditions. Microarray chips for R. capsulatus were custom designed by Affymetrix (GeneChip®. TR_RCH2a520699F. The numbers of significantly changed genes were 328 and 293 out of 3685 genes under cold and heat stress, respectively. Our results indicate that temperature stress greatly affects the hydrogen production metabolisms of R. capsulatus. Specifically, the expression of genes that participate in nitrogen metabolism, photosynthesis and the electron transport system were induced by cold stress, while decreased by heat stress. Heat stress also resulted in down regulation of genes related to cell envelope, transporter and binding proteins. Transcriptome analysis and physiological results were consistent with each other. The results presented here may aid clarification of the genetic mechanisms for hydrogen production in purple non-sulfur (PNS bacteria under temperature stress.

  7. Comparative Transcriptional Profiling of Two Contrasting Barley Genotypes under Salinity Stress during the Seedling Stage

    Directory of Open Access Journals (Sweden)

    Runhong Gao

    2013-01-01

    Full Text Available Salinity is one of the major abiotic stresses that affect crop productivity. Identification of the potential novel genes responsible for salt tolerance in barley will contribute to understanding the molecular mechanism of barley responses to salt stress. We compared changes in transcriptome between Hua 11 (a salt-tolerant genotype and Hua 30 (a salt sensitive genotype in response to salt stress at the seedling stage using barley cDNA microarrays. In total, 557 and 247 salt-responsive genes were expressed exclusively in the shoot and root tissue of the salt-tolerant genotype, respectively. Among these genes, a number of signal-related genes, transcription factors and compatible solutes were identified and some of these genes were carefully discussed. Notably, a LysM RLK was firstly found involved in salt stress response. Moreover, key enzymes in the pathways of jasmonic acid biosynthesis, lipid metabolism and indole-3-acetic acid homeostasis were specifically affected by salt stress in salt tolerance genotype. These salt-responsive genes and biochemical pathways identified in this study could provide further information for understanding the mechanisms of salt tolerance in barley.

  8. Molecular variation of Trypanosoma brucei subspecies as revealed by AFLP fingerprinting

    OpenAIRE

    Agbo, E.E.C.; Majiwa, P.A.O.; Claassen, H.J.H.M.; Pas, te, M.F.W.

    2002-01-01

    Genetic analysis of Trypanosoma spp. depends on the detection of variation between strains. We have used the amplified fragment length polymorphism (AFLP) technique to develop a convenient and reliable method for genetic characterization of Trypanosome (sub)species. AFLP accesses multiple independent sites within the genome and would allow a better definition of the relatedness of different Trypanosome (sub)species. Nine isolates (3 from each T. brucei subspecies) were tested with 40 AFLP pri...

  9. Transcriptional profiles of glutathione-S-Transferase isoforms, Cyp, and AOE genes in atrazine-exposed zebrafish embryos.

    Science.gov (United States)

    Glisic, Branka; Hrubik, Jelena; Fa, Svetlana; Dopudj, Nela; Kovacevic, Radmila; Andric, Nebojsa

    2016-02-01

    Glutathione-S-transferase (GST) superfamily consists of multiple members involved in xenobiotic metabolism. Expressional pattern of the GST isoforms in adult fish has been used as a biomarker of exposure to environmental chemicals. However, GST transcriptional responses vary across organs, thus requiring a cross-tissue examination of multiple mRNAs for GST profiling in an animal after chemical exposure. Zebrafish embryos express all GST isoforms as adult fish and could therefore represent an alternative model for identification of biomarkers of exposure. To evaluate such a possibility, we studied a set of cytosolic and microsomal GST isoform-specific expression profiles in the zebrafish embryos after exposure to atrazine, a widely used herbicide. Expression of the GST isoforms was compared with that of CYP genes involved in the phase I of xenobiotic metabolism and antioxidant enzyme (AOE) genes. Using quantitative real-time PCR, we showed dynamic changes in the expressional pattern of twenty GST isoforms, cyp1a, cyp3a65, ahr2, and four AOEs in early development of zebrafish. Acute (48 and 72 h) exposure of 24 h-old embryos to atrazine, from environmentally relevant (0.005 mg/L) to high (40 mg/L) concentrations, caused a variety of transient, albeit minor changes (atrazine (5 and 40 mg/L). In summary, an analysis of the response of multiple systems in the zebrafish embryos provided a comprehensive understanding of atrazine toxicity and its potential impact on biological processes.

  10. Development of a fluorescent microsphere-based multiplexed high-throughput assay system for profiling of transcription factor activation.

    Science.gov (United States)

    Yaoi, Takuro; Jiang, Xin; Li, Xianqiang

    2006-06-01

    Transcription factors (TFs), which play crucial roles in the regulation of gene expression in the human genome, are highly regulated by a variety of mechanisms. A single extracellular stimulus can trigger multiple signaling pathways, and these in turn can activate multiple TFs to mediate the inducible expression of target genes. Alterations in the activities of TFs are often associated with human diseases, such as altered activating factor 1, estrogen receptor, and p53 function in cancer, nuclear factor kappaB in inflammatory diseases, and peroxisome proliferator-activated receptor gamma in obesity. A systematic assay for profiling the activation of TFs will aid in elucidating the mechanisms of TF activation, reveal altered TFs associated with human diseases, and aid in developing assays for drug discovery. Here, we developed a 24-plex fluorescent microsphere-based TF activation assay system with a 96-well plate format. The assay system enabled high-throughput profiling of the DNA binding activity of TFs in multiple samples with high sensitivity. PMID:16834534

  11. Integrative miRNA-mRNA profiling of adipose tissue unravels transcriptional circuits induced by sleep fragmentation.

    Directory of Open Access Journals (Sweden)

    Sina A Gharib

    Full Text Available Obstructive sleep apnea (OSA is a prevalent condition and strongly associated with metabolic disorders. Sleep fragmentation (SF is a major consequence of OSA, but its contribution to OSA-related morbidities is not known. We hypothesized that SF causes specific perturbations in transcriptional networks of visceral fat cells, leading to systemic metabolic disturbances. We simultaneously profiled visceral adipose tissue mRNA and miRNA expression in mice exposed to 6 hours of SF during sleep, and developed a new computational framework based on gene set enrichment and network analyses to merge these data. This approach leverages known gene product interactions and biologic pathways to interrogate large-scale gene expression profiling data. We found that SF induced the activation of several distinct pathways, including those involved in insulin regulation and diabetes. Our integrative methodology identified putative controllers and regulators of the metabolic response during SF. We functionally validated our findings by demonstrating altered glucose and lipid homeostasis in sleep-fragmented mice. This is the first study to link sleep fragmentation with widespread disruptions in visceral adipose tissue transcriptome, and presents a generalizable approach to integrate mRNA-miRNA information for systematic mapping of regulatory networks.

  12. Single-cell transcript profiling of barley attacked by the powdery mildew fungus

    DEFF Research Database (Denmark)

    Gjetting, Torben; Hagedorn, Peter; Schweizer, Patrick;

    2007-01-01

    attacked at the same time may resist fungal penetration. To date, the mixed cellular responses seen even in susceptible host leaves have made it difficult to relate induced changes in gene expression to resistance or susceptibility in bulk leaf samples. By microextraction of cell-specific m......RNA and subsequent cDNA array analysis, we have successfully obtained separate gene expression profiles for specific mildew-resistant and -infected barley cells. Thus, for the first time, it is possible to identify genes that are specifically regulated in infected cells and, presumably, involved in fungal...... establishment. Further, although much is understood about the genetic basis of effective papilla resistance associated with mutant mlo barley, we provide here the first evidence for gene regulation associated with effective papilla-based nonspecific resistance expressed in nominally "susceptible" wild...

  13. Evidence for diversity in transcriptional profiles of single hematopoietic stem cells.

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    Carlos A Ramos

    2006-09-01

    Full Text Available Hematopoietic stem cells replenish all the cells of the blood throughout the lifetime of an animal. Although thousands of stem cells reside in the bone marrow, only a few contribute to blood production at any given time. Nothing is known about the differences between individual stem cells that dictate their particular state of activation readiness. To examine such differences between individual stem cells, we determined the global gene expression profile of 12 single stem cells using microarrays. We showed that at least half of the genetic expression variability between 12 single cells profiled was due to biological variation in 44% of the genes analyzed. We also identified specific genes with high biological variance that are candidates for influencing the state of readiness of individual hematopoietic stem cells, and confirmed the variability of a subset of these genes using single-cell real-time PCR. Because apparent variation of some genes is likely due to technical factors, we estimated the degree of biological versus technical variation for each gene using identical RNA samples containing an RNA amount equivalent to that of single cells. This enabled us to identify a large cohort of genes with low technical variability whose expression can be reliably measured on the arrays at the single-cell level. These data have established that gene expression of individual stem cells varies widely, despite extremely high phenotypic homogeneity. Some of this variation is in key regulators of stem cell activity, which could account for the differential responses of particular stem cells to exogenous stimuli. The capacity to accurately interrogate individual cells for global gene expression will facilitate a systems approach to biological processes at a single-cell level.

  14. Genetic Relationships among Prunus mume var. pendula Using AFLP Markers

    Institute of Scientific and Technical Information of China (English)

    Ming Jun; Zhang Qixiang; Ru Guangxin; Mao Qingshan; Yan Xiaolan; Lan Yanping

    2003-01-01

    Genetic relationships among Prunus mume var. pendula were studied by using AFLP markers. 18 accessions representing 14 cultivars ofPrunus murne var. pendula were selected from the germplasm collection at the Research Center of China Mci Flower. Seven Mse I-EcoR I AFLP primer combinations revealed 450 legible bands, and 269 of which were polymorphic markers. A similarity matrix was prepared using the simple matching coefficient of similarity and Nei's (72) distance coefficient. A UPGMA dendrogram demonstrated the genetic relationships of the cultivars. The information given by AFLP markers was basically consistent with the morphological classification and the evolutionary history of the morphotypes, and roughly supported the new revised classification system for Chinese Mci Cultivars. But there were still several exceptions: 1) the 'Guhong Chuizhi' inserted between the 'Tiaoxue Chuizhi' and the 'Danfen Chuizhi'; 2) the 'Wufu Chuizhi' kept off the Pink Pendant Form, and the 'Moshan Chuizhi' was removed from Viridiflora Pendant Form; 3) the 'Danbi Chuizhi' and the 'Shuangbi Chuizhi' of Viridiflora Pendant Form got together well but fell within the Pink Pendant Form.

  15. Multiparametric analysis, sorting, and transcriptional profiling of plant protoplasts and nuclei according to cell type.

    Science.gov (United States)

    Galbraith, David W; Janda, Jaroslav; Lambert, Georgina M

    2011-01-01

    Flow cytometry has been employed for the analysis of higher plants for approximately the last 30 years. For the angiosperms, ∼500,000 species, itself a daunting number, parametric measurements enabled through the use of flow cytometers started with basic descriptors of the individual cells and their contents, and have both inspired the development of novel cytometric methods that subsequently have been applied to organisms within other kingdoms of life, and adopted cytometric methods devised for other species, particularly mammals. Higher plants offer unique challenges in terms of flow cytometric analysis, notably the facts that their organs and tissues are complex three-dimensional assemblies of different cell types, and that their individual cells are, in general, larger than those of mammals.This chapter provides an overview of the general types of parametric measurement that have been applied to plants, and provides detailed methods for selected examples based on the plant model Arabidopsis thaliana. These illustrate the use of flow cytometry for the analysis of protoplasts and nuclear DNA contents (genome size and the cell cycle). These are further integrated with measurements focusing on specific cell types, based on transgenic expression of Fluorescent Proteins (FPs), and on analysis of the spectrum of transcripts found within protoplasts and nuclei. These measurements were chosen in particular to illustrate, respectively, the issues encountered in the flow analysis and sorting of large biological cells, typified by protoplasts; how to handle flow analyses under conditions that require processing of large numbers of samples in which the individual samples contain only a very small minority of objects of interest; and how to deal with exceptionally small amounts of RNA within the sorted samples.

  16. cDNA-AFLP analysis of Rhizoctonia solani AG1-lA-induced maize differential gene expression%利用cDNA-AFLP分析纹枯病菌诱导的玉米差异表达基因

    Institute of Scientific and Technical Information of China (English)

    刘丽; 马永毅; 张志明; 潘光堂; 赵茂俊

    2009-01-01

    cDNA amplified fragment length polymorphisms(cDNA-AFLP) was used to analyze gene expression profile in high tolerance maize inbreed lines R15 induced by AGl-IA (Rhizoctonia solani). At the jointing stage, the seedlings were inoculated and sampled at 12, 24, 36, 48 and 60 h and the untreated seedlings were used as control. Gene expression profile was tested by cDNA-AFLP. From the obtained 87 differential fragments, eliminating the false positive, 18 transcript-derived fragments (TDFs) were cloned. The sequences were then analyzed through bioinformatical methods, 13 of them had significant homology sequence with that in GenBank database and their function were as follows: signal transduction (two sequences), resistance and defense (two sequences), transcription and regulation (two sequences), energy metabolism (two sequences) etc. 13 differential expression fragments were confirmed by semi-quantitive RT-PCR at different inoculating times.%以纹枯病菌AGl-IA(Rhizoctonia solani)诱导玉米高耐纹枯病自交系R15,采用cDNA-AFLP技术分析其基因差异表达谱.在拔节期对R15幼苗进行接菌处理,12、24、36、48、60 h分别取材,以不接菌为对照.用56对AFLP选扩增引物对处理和对照的cDNA进行AFLP分析,得到87个差异片段,回收并剔除假阳性,克隆获得18条阳性差异条带(TDFs).BLASTn比对结果表明,其中可以找到同源序列的有13个TDFs,按其功能可分为信号传导(2个)、抗病与防御基因(2个)、转录凋控(2个)、能量代谢(2个)等.对13个TDFs基因进行了半定量RT-PCR分析,结果表明13个差异片段在对照与处理,或是处理的不同时段存在着表达量的差异.

  17. Variabilidade genética de Colletotrichum guaranicola usando marcadores AFLP Variability of Colletotrichum guaranicola using AFLP markers

    Directory of Open Access Journals (Sweden)

    Jânia Lilia da Silva Bentes

    2011-01-01

    Full Text Available Foi detectada a variabilidade genética de vinte isolados de Colletotrichum guaranicola (Albuq. provenientes de diferentes localidades produtoras de guaraná no Amazonas, utilizando-se marcadores moleculares AFLP. Foi possível separar os isolados em dois grupos. O coeficiente de variação genética entre os isolados foi de 0,0216 e a similaridade genética foi de 94,95%, confirmando que os isolados pertencem à mesma espécie, no entanto, foi observada variabilidade intra-específica.The genetic variability of twenty Colletotrichum guaranicola (Albuq. isolates from different fields of guarana in Amazonas, was studied using molecular AFLP markers. The isolates were separated into two groups. The genetic variability coefficient was 0.0216 and the genetic similarity was 94.5%, confirming that the isolates belongs to the same species, however, an intra-specific variability was observed.

  18. Gene expression and metabolite profiling of developing highbush blueberry fruit indicates transcriptional regulation of flavonoid metabolism and activation of abscisic acid metabolism.

    Science.gov (United States)

    Zifkin, Michael; Jin, Alena; Ozga, Jocelyn A; Zaharia, L Irina; Schernthaner, Johann P; Gesell, Andreas; Abrams, Suzanne R; Kennedy, James A; Constabel, C Peter

    2012-01-01

    Highbush blueberry (Vaccinium corymbosum) fruits contain substantial quantities of flavonoids, which are implicated in a wide range of health benefits. Although the flavonoid constituents of ripe blueberries are known, the molecular genetics underlying their biosynthesis, localization, and changes that occur during development have not been investigated. Two expressed sequence tag libraries from ripening blueberry fruit were constructed as a resource for gene identification and quantitative real-time reverse transcription-polymerase chain reaction primer design. Gene expression profiling by quantitative real-time reverse transcription-polymerase chain reaction showed that flavonoid biosynthetic transcript abundance followed a tightly regulated biphasic pattern, and transcript profiles were consistent with the abundance of the three major classes of flavonoids. Proanthocyanidins (PAs) and corresponding biosynthetic transcripts encoding anthocyanidin reductase and leucoanthocyanidin reductase were most concentrated in young fruit and localized predominantly to the inner fruit tissue containing the seeds and placentae. Mean PA polymer length was seven to 8.5 subunits, linked predominantly via B-type linkages, and was relatively constant throughout development. Flavonol accumulation and localization patterns were similar to those of the PAs, and the B-ring hydroxylation pattern of both was correlated with flavonoid-3'-hydroxylase transcript abundance. By contrast, anthocyanins accumulated late in maturation, which coincided with a peak in flavonoid-3-O-glycosyltransferase and flavonoid-3'5'-hydroxylase transcripts. Transcripts of VcMYBPA1, which likely encodes an R2R3-MYB transcriptional regulator of PA synthesis, were prominent in both phases of development. Furthermore, the initiation of ripening was accompanied by a substantial rise in abscisic acid, a growth regulator that may be an important component of the ripening process and contribute to the regulation of

  19. Gene expression and metabolite profiling of developing highbush blueberry fruit indicates transcriptional regulation of flavonoid metabolism and activation of abscisic acid metabolism.

    Science.gov (United States)

    Zifkin, Michael; Jin, Alena; Ozga, Jocelyn A; Zaharia, L Irina; Schernthaner, Johann P; Gesell, Andreas; Abrams, Suzanne R; Kennedy, James A; Constabel, C Peter

    2012-01-01

    Highbush blueberry (Vaccinium corymbosum) fruits contain substantial quantities of flavonoids, which are implicated in a wide range of health benefits. Although the flavonoid constituents of ripe blueberries are known, the molecular genetics underlying their biosynthesis, localization, and changes that occur during development have not been investigated. Two expressed sequence tag libraries from ripening blueberry fruit were constructed as a resource for gene identification and quantitative real-time reverse transcription-polymerase chain reaction primer design. Gene expression profiling by quantitative real-time reverse transcription-polymerase chain reaction showed that flavonoid biosynthetic transcript abundance followed a tightly regulated biphasic pattern, and transcript profiles were consistent with the abundance of the three major classes of flavonoids. Proanthocyanidins (PAs) and corresponding biosynthetic transcripts encoding anthocyanidin reductase and leucoanthocyanidin reductase were most concentrated in young fruit and localized predominantly to the inner fruit tissue containing the seeds and placentae. Mean PA polymer length was seven to 8.5 subunits, linked predominantly via B-type linkages, and was relatively constant throughout development. Flavonol accumulation and localization patterns were similar to those of the PAs, and the B-ring hydroxylation pattern of both was correlated with flavonoid-3'-hydroxylase transcript abundance. By contrast, anthocyanins accumulated late in maturation, which coincided with a peak in flavonoid-3-O-glycosyltransferase and flavonoid-3'5'-hydroxylase transcripts. Transcripts of VcMYBPA1, which likely encodes an R2R3-MYB transcriptional regulator of PA synthesis, were prominent in both phases of development. Furthermore, the initiation of ripening was accompanied by a substantial rise in abscisic acid, a growth regulator that may be an important component of the ripening process and contribute to the regulation of

  20. Transcriptional Profiles Uncover Aspergillus flavus-Induced Resistance in Maize Kernels

    Science.gov (United States)

    Luo, Meng; Brown, Robert L.; Chen, Zhi-Yuan; Menkir, Abebe; Yu, Jiujiang; Bhatnagar, Deepak

    2011-01-01

    Aflatoxin contamination caused by the opportunistic pathogen A. flavus is a major concern in maize production prior to harvest and through storage. Previous studies have highlighted the constitutive production of proteins involved in maize kernel resistance against A. flavus’ infection. However, little is known about induced resistance nor about defense gene expression and regulation in kernels. In this study, maize oligonucleotide arrays and a pair of closely-related maize lines varying in aflatoxin accumulation were used to reveal the gene expression network in imbibed mature kernels in response to A. flavus’ challenge. Inoculated kernels were incubated 72 h via the laboratory-based Kernel Screening Assay (KSA), which highlights kernel responses to fungal challenge. Gene expression profiling detected 6955 genes in resistant and 6565 genes in susceptible controls; 214 genes induced in resistant and 2159 genes induced in susceptible inoculated kernels. Defense related and regulation related genes were identified in both treatments. Comparisons between the resistant and susceptible lines indicate differences in the gene expression network which may enhance our understanding of the maize-A. flavus interaction. PMID:22069739

  1. Transcriptional profiles uncover Aspergillus flavus-induced resistance in maize kernels.

    Science.gov (United States)

    Luo, Meng; Brown, Robert L; Chen, Zhi-Yuan; Menkir, Abebe; Yu, Jiujiang; Bhatnagar, Deepak

    2011-07-01

    Aflatoxin contamination caused by the opportunistic pathogen A. flavus is a major concern in maize production prior to harvest and through storage. Previous studies have highlighted the constitutive production of proteins involved in maize kernel resistance against A. flavus' infection. However, little is known about induced resistance nor about defense gene expression and regulation in kernels. In this study, maize oligonucleotide arrays and a pair of closely-related maize lines varying in aflatoxin accumulation were used to reveal the gene expression network in imbibed mature kernels in response to A. flavus' challenge. Inoculated kernels were incubated 72 h via the laboratory-based Kernel Screening Assay (KSA), which highlights kernel responses to fungal challenge. Gene expression profiling detected 6955 genes in resistant and 6565 genes in susceptible controls; 214 genes induced in resistant and 2159 genes induced in susceptible inoculated kernels. Defense related and regulation related genes were identified in both treatments. Comparisons between the resistant and susceptible lines indicate differences in the gene expression network which may enhance our understanding of the maize-A. flavus interaction. PMID:22069739

  2. Transcriptional Profiling of Cutaneous MRGPRD Free Nerve Endings and C-LTMRs

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    Ana Reynders

    2015-02-01

    Full Text Available Cutaneous C-unmyelinated MRGPRD+ free nerve endings and C-LTMRs innervating hair follicles convey two opposite aspects of touch sensation: a sensation of pain and a sensation of pleasant touch. The molecular mechanisms underlying these diametrically opposite functions are unknown. Here, we used a mouse model that genetically marks C-LTMRs and MRGPRD+ neurons in combination with fluorescent cell surface labeling, flow cytometry, and RNA deep-sequencing technology (RNA-seq. Cluster analysis of RNA-seq profiles of the purified neuronal subsets revealed 486 and 549 genes differentially expressed in MRGPRD-expressing neurons and C-LTMRs, respectively. We validated 48 MRGPD- and 68 C-LTMRs-enriched genes using a triple-staining approach, and the Cav3.3 channel, found to be exclusively expressed in C-LTMRs, was validated using electrophysiology. Our study greatly expands the molecular characterization of C-LTMRs and suggests that this particular population of neurons shares some molecular features with Aβ and Aδ low-threshold mechanoreceptors.

  3. Identification of plant defence regulators through transcriptional profiling of Arabidopsis thaliana cdd1 mutant

    Indian Academy of Sciences (India)

    Swadhin Swain; Nidhi Singh; Ashis Kumar Nandi

    2015-03-01

    A sustainable balance between defence and growth is essential for optimal fitness under pathogen stress. Plants activate immune response at the cost of normal metabolic requirements. Thus, plants that constitutively activate defence are deprived of growth. Arabidopsis thaliana mutant constitutive defence without defect in growth and development1 (cdd1) is an exception. The cdd1 mutant is constitutive for salicylic acid accumulation, signalling, and defence against biotrophic and hemibiotrophic pathogens, without having much impact on growth. Thus, cdd1 offers an ideal genetic background to identify novel regulators of plant defence. Here we report the differential gene expression profile between cdd1 and wild-type plants as obtained by microarray hybridization. Expression of several defence-related genes also supports constitutive activation of defence in cdd1. We screened T-DNA insertion mutant lines of selected genes, for resistance against virulent bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Through bacterial resistance, callose deposition and pathogenesis-associated expression analyses, we identified four novel regulators of plant defence. Resistance levels in the mutants suggest that At2g19810 and [rom] At5g05790 are positive regulators, whereas At1g61370 and At3g42790 are negative regulators of plant defence against bacterial pathogens.

  4. Explore Small Molecule-induced Genome-wide Transcriptional Profiles for Novel Inflammatory Bowel Disease Drug

    Science.gov (United States)

    Cai, Xiaoshu; Chen, Yang; Gao, Zhen; Xu, Rong

    2016-01-01

    Abstract Inflammatory Bowel Disease (IBD) is a chronic and relapsing disorder, which affects millions people worldwide. Current drug options cannot cure the disease and may cause severe side effects. We developed a systematic framework to identify novel IBD drugs exploiting millions of genomic signatures for chemical compounds. Specifically, we searched all FDA-approved drugs for candidates that share similar genomic profiles with IBD. In the evaluation experiments, our approach ranked approved IBD drugs averagely within top 26% among 858 candidates, significantly outperforming a state-of-art genomics-based drug repositioning method (p-value < e-8). Our approach also achieved significantly higher average precision than the state-of-art approach in predicting potential IBD drugs from clinical trials (0.072 vs. 0.043, p<0.1) and off-label IBD drugs (0.198 vs. 0.138, p<0.1). Furthermore, we found evidences supporting the therapeutic potential of the top-ranked drugs, such as Naloxone, in literature and through analyzing target genes and pathways. PMID:27570643

  5. Dynamic changes of transcript profiles after fertilization are associated with de novo transcription and maternal elimination in tobacco zygote, and mark the onset of the maternal-to-zygotic transition.

    Science.gov (United States)

    Zhao, Jing; Xin, Haiping; Qu, Lianghuan; Ning, Jue; Peng, Xiongbo; Yan, Tingting; Ma, Ligang; Li, Shisheng; Sun, Meng-Xiang

    2011-01-01

    The maternal-to-zygotic transition (MZT) is characterized by the turnover of zygote development from maternal to zygotic control, and has been extensively studied in animals. A majority of studies have suggested that early embryogenesis is maternally controlled and that the zygotic genome remains transcriptionally inactive prior to the MZT. However, little is known about the MZT in higher plants, and its timing and impact remain uncharacterized. Here, we constructed cDNA libraries from tobacco (Nicotiana tabacum) egg cells, zygotes and two-celled embryos for gene expression profiling analysis, followed by RT-PCR confirmation. These analyses, together with experiments using zygote microculture coupled with transcription inhibition, revealed that a marked change in transcript profiles occurs approximately 50 h after fertilization, and that the MZT is initiated prior to zygotic division in tobacco. Although maternal transcripts deposited in egg cells support several early developmental processes, they appear to be insufficient for zygotic polar growth and subsequent cell divisions. Thus, we propose that de novo transcripts are probably required to trigger embryogenesis in later zygotes in tobacco. PMID:21175896

  6. cDNA-AFLP analysis reveals differential gene expression in incompatible interaction between infected non-heading Chinese cabbage and Hyaloperonospora parasitica.

    Science.gov (United States)

    Xiao, Dong; Liu, Shi-Tuo; Wei, Yan-Ping; Zhou, Dao-Yun; Hou, Xi-Lin; Li, Ying; Hu, Chun-Mei

    2016-01-01

    Non-heading Chinese cabbage (Brassica rapa ssp. chinensis) is one of the main green leafy vegetables in the world, especially in China, with significant economic value. Hyaloperonospora parasitica is a fungal pathogen responsible for causing downy mildew disease in Chinese cabbage, which greatly affects its production. The objective of this study was to identify transcriptionally regulated genes during incompatible interactions between non-heading Chinese cabbage and H. parasitica using complementary DNA-amplified fragment length polymorphism (cDNA-AFLP). We obtained 129 reliable differential transcript-derived fragments (TDFs) in a resistant line 'Suzhou Qing'. Among them, 121 upregulated TDFs displayed an expression peak at 24-48 h post inoculation (h.p.i.). Fifteen genes were further selected for validation of cDNA-AFLP expression patterns using quantitative reverse transcription PCR. Results confirmed the altered expression patterns of 13 genes (86.7%) revealed by the cDNA-AFLP. We identified four TDFs related to fungal resistance among the 15 TDFs. Furthermore, comparative analysis of four TDFs between resistant line 'Suzhou Qing' and susceptible line 'Aijiao Huang' showed that transcript levels of TDF14 (BcLIK1_A01) peaked at 48 h.p.i. and 25.1-fold increased in the resistant line compared with the susceptible line. Similarly, transcript levels of the other three genes, TDF42 (BcCAT3_A07), TDF75 (BcAAE3_A06) and TDF88 (BcAMT2_A05) peaked at 24, 48 and 24 h.p.i. with 25.1-, 100- and 15.8-fold increases, respectively. The results suggested that the resistance genes tended to transcribe at higher levels in the resistance line than in the susceptible line, which may provide resistance against pathogen infections. The present study might facilitate elucidating the molecular basis of the infection process and identifying candidate genes for resistance improvement of susceptible cultivars. PMID:27602230

  7. Erratum: Transcript and Metabolite Profiling for the Evaluation of Tobacco Tree and Poplar as Feedstock for the Bio-based Industry.

    Science.gov (United States)

    2016-01-01

    A correction was made to: Transcript and Metabolite Profiling for the Evaluation of Tobacco Tree and Poplar as Feedstock for the Bio-based Industry. There was a spelling error in one of the authors' surname. The author's name was corrected from: Juan Pedro Navarro to: Juan Navarro-Aviñó. PMID:27387492

  8. Within and between whorls: comparative transcriptional profiling of Aquilegia and Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Claudia Voelckel

    Full Text Available BACKGROUND: The genus Aquilegia is an emerging model system in plant evolutionary biology predominantly because of its wide variation in floral traits and associated floral ecology. The anatomy of the Aquilegia flower is also very distinct. There are two whorls of petaloid organs, the outer whorl of sepals and the second whorl of petals that form nectar spurs, as well as a recently evolved fifth whorl of staminodia inserted between stamens and carpels. METHODOLOGY/PRINCIPAL FINDINGS: We designed an oligonucleotide microarray based on EST sequences from a mixed tissue, normalized cDNA library of an A. formosa x A. pubescens F2 population representing 17,246 unigenes. We then used this array to analyze floral gene expression in late pre-anthesis stage floral organs from a natural A. formosa population. In particular, we tested for gene expression patterns specific to each floral whorl and to combinations of whorls that correspond to traditional and modified ABC model groupings. Similar analyses were performed on gene expression data of Arabidopsis thaliana whorls previously obtained using the Ath1 gene chips (data available through The Arabidopsis Information Resource. CONCLUSIONS/SIGNIFICANCE: Our comparative gene expression analyses suggest that 1 petaloid sepals and petals of A. formosa share gene expression patterns more than either have organ-specific patterns, 2 petals of A. formosa and A. thaliana may be independently derived, 3 staminodia express B and C genes similar to stamens but the staminodium genetic program has also converged on aspects of the carpel program and 4 staminodia have unique up-regulation of regulatory genes and genes that have been implicated with defense against microbial infection and herbivory. Our study also highlights the value of comparative gene expression profiling and the Aquilegia microarray in particular for the study of floral evolution and ecology.

  9. Transcriptional profiling of mammary gland in Holstein cows with extremely different milk protein and fat percentage using RNA sequencing

    Science.gov (United States)

    2014-01-01

    Background Recently, RNA sequencing (RNA-seq) has rapidly emerged as a major transcriptome profiling system. Elucidation of the bovine mammary gland transcriptome by RNA-seq is essential for identifying candidate genes that contribute to milk composition traits in dairy cattle. Results We used massive, parallel, high-throughput, RNA-seq to generate the bovine transcriptome from the mammary glands of four lactating Holstein cows with extremely high and low phenotypic values of milk protein and fat percentage. In total, we obtained 48,967,376–75,572,578 uniquely mapped reads that covered 82.25% of the current annotated transcripts, which represented 15549 mRNA transcripts, across all the four mammary gland samples. Among them, 31 differentially expressed genes (p < 0.05, false discovery rate q < 0.05) between the high and low groups of cows were revealed. Gene ontology and pathway analysis demonstrated that the 31 differently expressed genes were enriched in specific biological processes with regard to protein metabolism, fat metabolism, and mammary gland development (p < 0.05). Integrated analysis of differential gene expression, previously reported quantitative trait loci, and genome-wide association studies indicated that TRIB3, SAA (SAA1, SAA3, and M-SAA3.2), VEGFA, PTHLH, and RPL23A were the most promising candidate genes affecting milk protein and fat percentage. Conclusions This study investigated the complexity of the mammary gland transcriptome in dairy cattle using RNA-seq. Integrated analysis of differential gene expression and the reported quantitative trait loci and genome-wide association study data permitted the identification of candidate key genes for milk composition traits. PMID:24655368

  10. Transcriptional profiles of mating-responsive genes from testes and male accessory glands of the Mediterranean fruit fly, Ceratitis capitata.

    Directory of Open Access Journals (Sweden)

    Francesca Scolari

    Full Text Available BACKGROUND: Insect seminal fluid is a complex mixture of proteins, carbohydrates and lipids, produced in the male reproductive tract. This seminal fluid is transferred together with the spermatozoa during mating and induces post-mating changes in the female. Molecular characterization of seminal fluid proteins in the Mediterranean fruit fly, Ceratitis capitata, is limited, although studies suggest that some of these proteins are biologically active. METHODOLOGY/PRINCIPAL FINDINGS: We report on the functional annotation of 5914 high quality expressed sequence tags (ESTs from the testes and male accessory glands, to identify transcripts encoding putative secreted peptides that might elicit post-mating responses in females. The ESTs were assembled into 3344 contigs, of which over 33% produced no hits against the nr database, and thus may represent novel or rapidly evolving sequences. Extraction of the coding sequences resulted in a total of 3371 putative peptides. The annotated dataset is available as a hyperlinked spreadsheet. Four hundred peptides were identified with putative secretory activity, including odorant binding proteins, protease inhibitor domain-containing peptides, antigen 5 proteins, mucins, and immunity-related sequences. Quantitative RT-PCR-based analyses of a subset of putative secretory protein-encoding transcripts from accessory glands indicated changes in their abundance after one or more copulations when compared to virgin males of the same age. These changes in abundance, particularly evident after the third mating, may be related to the requirement to replenish proteins to be transferred to the female. CONCLUSIONS/SIGNIFICANCE: We have developed the first large-scale dataset for novel studies on functions and processes associated with the reproductive biology of Ceratitis capitata. The identified genes may help study genome evolution, in light of the high adaptive potential of the medfly. In addition, studies of male

  11. Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study

    Directory of Open Access Journals (Sweden)

    Williams Adam R

    2009-12-01

    Full Text Available Abstract Background Whole genome gene expression profiling has revolutionized research in the past decade especially with the advent of microarrays. Recently, there have been significant improvements in whole blood RNA isolation techniques which, through stabilization of RNA at the time of sample collection, avoid bias and artifacts introduced during sample handling. Despite these improvements, current human whole blood RNA stabilization/isolation kits are limited by the requirement of a venous blood sample of at least 2.5 mL. While fingerstick blood collection has been used for many different assays, there has yet to be a kit developed to isolate high quality RNA for use in gene expression studies from such small human samples. The clinical and field testing advantages of obtaining reliable and reproducible gene expression data from a fingerstick are many; it is less invasive, time saving, more mobile, and eliminates the need of a trained phlebotomist. Furthermore, this method could also be employed in small animal studies, i.e. mice, where larger sample collections often require sacrificing the animal. In this study, we offer a rapid and simple method to extract sufficient amounts of high quality total RNA from approximately 70 μl of whole blood collected via a fingerstick using a modified protocol of the commercially available Qiagen PAXgene RNA Blood Kit. Results From two sets of fingerstick collections, about 70 uL whole blood collected via finger lancet and capillary tube, we recovered an average of 252.6 ng total RNA with an average RIN of 9.3. The post-amplification yields for 50 ng of total RNA averaged at 7.0 ug cDNA. The cDNA hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips had an average % Present call of 52.5%. Both fingerstick collections were highly correlated with r2 values ranging from 0.94 to 0.97. Similarly both fingerstick collections were highly correlated to the venous collection with r2 values ranging from 0.88 to 0

  12. Transcript profiles in longissimus dorsi muscle and subcutaneous adipose tissue: a comparison of pigs with different postweaning growth rates.

    Science.gov (United States)

    Pilcher, C M; Jones, C K; Schroyen, M; Severin, A J; Patience, J F; Tuggle, C K; Koltes, J E

    2015-05-01

    Although most pigs recover rapidly from stresses associated with the transition of weaning, a portion of the population lags behind their contemporaries in growth performance. The underlying biological and molecular mechanisms involved in postweaning differences in growth performance are poorly understood. The objective of this experiment was to use transcriptional profiling of skeletal muscle and adipose tissue to develop a better understanding of the metabolic basis for poor weaned-pig transition. A total of 1,054 pigs was reared in commercial conditions and weighed at birth, weaning, and 3 wk postweaning. Transition ADG (tADG) was calculated as the ADG for the 3-wk period postweaning. Nine pigs from both the lowest 10th percentile (low tADG) and the 60th to 70th percentile (high tADG) were harvested at 3 wk postweaning. Differential expression analysis was conducted in longissimus dorsi muscle (LM) and subcutaneous adipose tissue using RNA-Seq methodology. In LM, 768 transcripts were differentially expressed (DE), 327 with higher expression in low tADG and 441 with higher expression in high tADG pigs (q adipose tissue. To identify biological functions potentially underlying the effects of tADG on skeletal muscle metabolism and physiology, functional annotation analysis of the DE transcripts was conducted using DAVID and Pathway Studio analytic tools. The group of DE genes with lower expression in LM of low tADG pigs was enriched in genes with functions related to muscle contraction, glucose metabolism, cytoskeleton organization, muscle development, and response to hormone stimulus (enrichment score > 1.3). The list of DE genes with higher expression in low tADG LM was enriched in genes with functions related to protein catabolism (enrichment score > 1.3). Analysis of known gene-gene interactions identified possible regulators of these differences in gene expression in LM of high and low tADG pigs; these include forkhead box O1 (FOXO1), growth hormone (GH1), and

  13. ASGR1 and ASGR2, the Genes that Encode the Asialoglycoprotein Receptor (Ashwell Receptor, Are Expressed in Peripheral Blood Monocytes and Show Interindividual Differences in Transcript Profile

    Directory of Open Access Journals (Sweden)

    Rebecca Louise Harris

    2012-01-01

    Full Text Available Background. The asialoglycoprotein receptor (ASGPR is a hepatic receptor that mediates removal of potentially hazardous glycoconjugates from blood in health and disease. The receptor comprises two proteins, asialoglycoprotein receptor 1 and 2 (ASGR1 and ASGR2, encoded by the genes ASGR1 and ASGR2. Design and Methods. Using reverse transcription amplification (RT-PCR, expression of ASGR1 and ASGR2 was investigated in human peripheral blood monocytes. Results. Monocytes were found to express ASGR1 and ASGR2 transcripts. Correctly spliced transcript variants encoding different isoforms of ASGR1 and ASGR2 were present in monocytes. The profile of transcript variants from both ASGR1 and ASGR2 differed among individuals. Transcript expression levels were compared with the hepatocyte cell line HepG2 which produces high levels of ASGPR. Monocyte transcripts were 4 to 6 orders of magnitude less than in HepG2 but nonetheless readily detectable using standard RT-PCR. The monocyte cell line THP1 gave similar results to monocytes harvested from peripheral blood, indicating it may provide a suitable model system for studying ASGPR function in this cell type. Conclusions. Monocytes transcribe and correctly process transcripts encoding the constituent proteins of the ASGPR. Monocytes may therefore represent a mobile pool of the receptor, capable of reaching sites remote from the liver.

  14. Imaging brain gene expression profiles by antipsychotics: region-specific action of amisulpride on postsynaptic density transcripts compared to haloperidol.

    Science.gov (United States)

    de Bartolomeis, Andrea; Marmo, Federica; Buonaguro, Elisabetta Filomena; Rossi, Rodolfo; Tomasetti, Carmine; Iasevoli, Felice

    2013-11-01

    Induction of motor disorders is considered the clinical landmark differentiating typical from atypical antipsychotics, and has been mainly correlated to dopamine D2 receptors blockade in striatum. This view is challenged by benzamides, such as amisulpride, which display low liability for motor side effects despite being D2/D3 receptors high-affinity blocking agents. These effects have been explained with the prominent presynaptic action of amisulpride or with the fast dissociation at D2 receptors, but there is scarce information on the effects of amisulpride on postsynaptic signaling. We carried out a molecular imaging study of gene expression after acute administration of haloperidol (0.8 mg/kg), amisulpride (10 or 35 mg/kg), or vehicle, focusing on postsynaptic genes that are key regulators of synaptic plasticity, such as Arc, c-fos, Zif-268, Norbin, Homer. The last one has been associated to schizophrenia both in clinical and preclinical studies, and is differentially induced by antipsychotics with different D2 receptors affinity. Topography of gene expression revealed that amisulpride, unlike haloperidol, triggers transcripts expression peak in medial striatal regions. Correlation analysis of gene expression revealed a prevalent correlated gene induction within motor corticostriatal regions by haloperidol and a more balanced gene induction within limbic and motor corticostriatal regions by amisulpride. Despite the selective dopaminergic profile of both compounds, our results demonstrated a differential modulation of postsynaptic molecules by amisulpride and haloperidol, the former impacting preferentially medial regions of striatum whereas the latter inducing strong gene expression in lateral regions. Thus, we provided a possible molecular profile of amisulpride, putatively explaining its "atypical atypicality".

  15. Transcriptional profiles of glutathione-S-Transferase isoforms, Cyp, and AOE genes in atrazine-exposed zebrafish embryos.

    Science.gov (United States)

    Glisic, Branka; Hrubik, Jelena; Fa, Svetlana; Dopudj, Nela; Kovacevic, Radmila; Andric, Nebojsa

    2016-02-01

    Glutathione-S-transferase (GST) superfamily consists of multiple members involved in xenobiotic metabolism. Expressional pattern of the GST isoforms in adult fish has been used as a biomarker of exposure to environmental chemicals. However, GST transcriptional responses vary across organs, thus requiring a cross-tissue examination of multiple mRNAs for GST profiling in an animal after chemical exposure. Zebrafish embryos express all GST isoforms as adult fish and could therefore represent an alternative model for identification of biomarkers of exposure. To evaluate such a possibility, we studied a set of cytosolic and microsomal GST isoform-specific expression profiles in the zebrafish embryos after exposure to atrazine, a widely used herbicide. Expression of the GST isoforms was compared with that of CYP genes involved in the phase I of xenobiotic metabolism and antioxidant enzyme (AOE) genes. Using quantitative real-time PCR, we showed dynamic changes in the expressional pattern of twenty GST isoforms, cyp1a, cyp3a65, ahr2, and four AOEs in early development of zebrafish. Acute (48 and 72 h) exposure of 24 h-old embryos to atrazine, from environmentally relevant (0.005 mg/L) to high (40 mg/L) concentrations, caused a variety of transient, albeit minor changes (GST isoforms, ahr2 and AOE genes response. However, expression of cyp1a and cyp3a65 mRNA was markedly and consistently induced by high doses of atrazine (5 and 40 mg/L). In summary, an analysis of the response of multiple systems in the zebrafish embryos provided a comprehensive understanding of atrazine toxicity and its potential impact on biological processes. PMID:25158112

  16. Transcriptional profiling of cortical versus cancellous bone from mechanically-loaded murine tibiae reveals differential gene expression.

    Science.gov (United States)

    Kelly, Natalie H; Schimenti, John C; Ross, F Patrick; van der Meulen, Marjolein C H

    2016-05-01

    Mechanical loading is an anabolic stimulus that increases bone mass, and thus a promising method to counteract osteoporosis-related bone loss. The mechanism of this anabolism remains unclear, and needs to be established for both cortical and cancellous envelopes individually. We hypothesized that cortical and cancellous bone display different gene expression profiles at baseline and in response to mechanical loading. To test this hypothesis, the left tibiae of 10-week-old female C57Bl/6 mice were subjected to one session of axial tibial compression (9N, 1200cycles, 4Hz triangle waveform) and euthanized 3 and 24h following loading. The right limb served as the contralateral control. We performed RNA-seq on marrow-free metaphyseal samples from the cortical shell and the cancellous core to determine differential gene expression at baseline (control limb) and in response to load. Differential expression was verified with qPCR. Cortical and cancellous bone exhibited distinctly different transcriptional profiles basally and in response to mechanical loading. More genes were differentially expressed with loading at 24h with more genes downregulated at 24h than at 3h in both tissues. Enhanced Wnt signaling dominated the response in cortical bone at 3 and 24h, but in cancellous bone only at 3h. In cancellous bone at 24h many muscle-related genes were downregulated. These findings reveal key differences between cortical and cancellous genetic regulation in response to mechanical loading. Future studies at different time points and multiple loading sessions will add to our knowledge of cortical and cancellous mechanotransduction with the potential to identify new targets for mouse genetic knockout studies and drugs to treat osteoporosis. PMID:26876048

  17. Comparative transcripts profiling of fruit mesocarp and endocarp relevant to secondary metabolism by suppression subtractive hybridization in Azadirachta indica (neem).

    Science.gov (United States)

    Narnoliya, Lokesh K; Rajakani, Raja; Sangwan, Neelam S; Gupta, Vikrant; Sangwan, Rajender S

    2014-05-01

    Azadirachta indica (neem) is a medicinally important plant that is valued for its bioactive secondary metabolites. Higher levels of the bioactive phytochemicals are accumulated in fruits than in other tissues. In the present study, a total of 387 and 512 ESTs, respectively, from endocarp and mesocarp of neem fruits were isolated and analyzed. Out of them 318 ESTs (82.17%) clones from endocarp and 418 ESTs (81.64%) from mesocarp encoded putative proteins that could be classified into three major gene ontology categories: biological process, molecular function and cellular component. From the analyses of contigs, 73 unigenes from the forward subtracted library and 35 unigenes from the reverse subtracted library were obtained. The ESTs from mesocarp encoded cytochrome P450 enzymes, which indicated hydroxylation to be a major metabolic event and that biogeneration of hydroxylated neem fruit phytochemicals was differentially regulated with developmental stage-specificity of synthesis. Through this study, we present the first report of any gene expression data in neem tissues. Neem hydroxy-methyl glutaryl-coenzyme A reductase (NHMGR) gene was used as expressing control vis-a-vis subtracted tissues. NHMGR was present in fruit, endocarp and mesocarp tissues, but absent in subtractive libraries, revealing that it was successfully eliminated during subtraction. Eight genes of interest from subtracted libraries were profiled for their expression in fruit, mesocarp and endocarp. Expression profiles validated the quality of the libraries and functional diversity of the tissues. The subtractive cDNA library and EST database described in this study represent a valuable transcript sequence resource for future research aimed at improving the economically important medicinal plant.

  18. Comparative transcripts profiling of fruit mesocarp and endocarp relevant to secondary metabolism by suppression subtractive hybridization in Azadirachta indica (neem).

    Science.gov (United States)

    Narnoliya, Lokesh K; Rajakani, Raja; Sangwan, Neelam S; Gupta, Vikrant; Sangwan, Rajender S

    2014-05-01

    Azadirachta indica (neem) is a medicinally important plant that is valued for its bioactive secondary metabolites. Higher levels of the bioactive phytochemicals are accumulated in fruits than in other tissues. In the present study, a total of 387 and 512 ESTs, respectively, from endocarp and mesocarp of neem fruits were isolated and analyzed. Out of them 318 ESTs (82.17%) clones from endocarp and 418 ESTs (81.64%) from mesocarp encoded putative proteins that could be classified into three major gene ontology categories: biological process, molecular function and cellular component. From the analyses of contigs, 73 unigenes from the forward subtracted library and 35 unigenes from the reverse subtracted library were obtained. The ESTs from mesocarp encoded cytochrome P450 enzymes, which indicated hydroxylation to be a major metabolic event and that biogeneration of hydroxylated neem fruit phytochemicals was differentially regulated with developmental stage-specificity of synthesis. Through this study, we present the first report of any gene expression data in neem tissues. Neem hydroxy-methyl glutaryl-coenzyme A reductase (NHMGR) gene was used as expressing control vis-a-vis subtracted tissues. NHMGR was present in fruit, endocarp and mesocarp tissues, but absent in subtractive libraries, revealing that it was successfully eliminated during subtraction. Eight genes of interest from subtracted libraries were profiled for their expression in fruit, mesocarp and endocarp. Expression profiles validated the quality of the libraries and functional diversity of the tissues. The subtractive cDNA library and EST database described in this study represent a valuable transcript sequence resource for future research aimed at improving the economically important medicinal plant. PMID:24477588

  19. Transcriptional profiling of Bordetella pertussis reveals requirement of RNA chaperone Hfq for Type III secretion system functionality.

    Science.gov (United States)

    Bibova, Ilona; Hot, David; Keidel, Kristina; Amman, Fabian; Slupek, Stephanie; Cerny, Ondrej; Gross, Roy; Vecerek, Branislav

    2015-01-01

    Bordetella pertussis, the causative agent of human whooping cough (pertussis) produces a complex array of virulence factors in order to establish efficient infection in the host. The RNA chaperone Hfq and small regulatory RNAs are key players in posttranscriptional regulation in bacteria and have been shown to play an essential role in virulence of a broad spectrum of bacterial pathogens. This study represents the first attempt to characterize the Hfq regulon of the human pathogen B. pertussis under laboratory conditions as well as upon passage in the host and indicates that loss of Hfq has a profound effect on gene expression in B. pertussis. Comparative transcriptional profiling revealed that Hfq is required for expression of several virulence factors in B. pertussis cells including the Type III secretion system (T3SS). In striking contrast to the wt strain, T3SS did not become operational in the hfq mutant passaged either through mice or macrophages thereby proving that Hfq is required for the functionality of the B. pertussis T3SS. Likewise, expression of virulence factors vag8 and tcfA encoding autotransporter and tracheal colonization factor, respectively, was strongly reduced in the hfq mutant. Importantly, for the first time we demonstrate that B. pertussis T3SS can be activated upon contact with macrophage cells in vitro.

  20. Gene Structures, Evolution and Transcriptional Profiling of the WRKY Gene Family in Castor Bean (Ricinus communis L.).

    Science.gov (United States)

    Zou, Zhi; Yang, Lifu; Wang, Danhua; Huang, Qixing; Mo, Yeyong; Xie, Guishui

    2016-01-01

    WRKY proteins comprise one of the largest transcription factor families in plants and form key regulators of many plant processes. This study presents the characterization of 58 WRKY genes from the castor bean (Ricinus communis L., Euphorbiaceae) genome. Compared with the automatic genome annotation, one more WRKY-encoding locus was identified and 20 out of the 57 predicted gene models were manually corrected. All RcWRKY genes were shown to contain at least one intron in their coding sequences. According to the structural features of the present WRKY domains, the identified RcWRKY genes were assigned to three previously defined groups (I-III). Although castor bean underwent no recent whole-genome duplication event like physic nut (Jatropha curcas L., Euphorbiaceae), comparative genomics analysis indicated that one gene loss, one intron loss and one recent proximal duplication occurred in the RcWRKY gene family. The expression of all 58 RcWRKY genes was supported by ESTs and/or RNA sequencing reads derived from roots, leaves, flowers, seeds and endosperms. Further global expression profiles with RNA sequencing data revealed diverse expression patterns among various tissues. Results obtained from this study not only provide valuable information for future functional analysis and utilization of the castor bean WRKY genes, but also provide a useful reference to investigate the gene family expansion and evolution in Euphorbiaceus plants. PMID:26849139

  1. RNA-seq dependent transcriptional analysis unveils gene expression profile in the intestine of sea cucumber Apostichopus japonicus during aestivation.

    Science.gov (United States)

    Zhao, Ye; Yang, Hongsheng; Storey, Kenneth B; Chen, Muyan

    2014-06-01

    The seasonal marine, the sea cucumber Apostichopus japonicus (Selenka, 1867), cycles annually between periods of torpor when water temperature is above about 25°C in summer and active life when temperature is below about 18°C. This species is a good candidate model organism for studies of environmentally-induced aestivation in marine invertebrates. Previous studies have examined various aspects of aestivation of A. japonicus, however, knowledge of the molecular regulation underpinning these events is still fragmentary. In the present study, we constructed a global gene expression profile of the intestine tissue of A. japonicus using RNA-seq to identify transcriptional responses associated with transitions between different states: non-aestivation (NA), deep-aestivation (DA), and arousal from aestivation (AA). The analysis identified 1245 differentially expressed genes (DEGs) between DA vs. NA states, 1338 DEGs between AA vs. DA, and 1321 DEGs between AA vs. NA using the criteria |Log2Ratio|≥1 and FDR≤0.001. Of these, 25 of the most significant DEGs were verified by real-time PCR, showing trends in expression patterns that were almost in full concordance between the two techniques. GO analysis revealed that for DA vs. NA, 24 metabolic associated processes were highly enriched (corrected p valuejaponicus and identifies a series of candidate genes and pathways for further research on the molecular mechanisms of aestivation. PMID:24713300

  2. Effects of phenol on metabolic activities and transcription profiles of cytochrome P450 enzymes in Chironomus kiinensis larvae.

    Science.gov (United States)

    Cao, C W; Sun, L L; Niu, F; Liu, P; Chu, D; Wang, Z Y

    2016-02-01

    Phenol, also known as carbolic acid or phenic acid, is a priority pollutant in aquatic ecosystems. The present study has investigated metabolic activities and transcription profiles of cytochrome P450 enzymes in Chironomus kiinensis under phenol stress. Exposure of C. kiinensis larvae to three sublethal doses of phenol (1, 10 and 100 µM) inhibited cytochrome P450 enzyme activity during the 96 h exposure period. The P450 activity measured after the 24 h exposure to phenol stress could be used to assess the level (low or high) of phenol contamination in the environment. To investigate the potential of cytochrome P450 genes as molecular biomarkers to monitor phenol contamination, the cDNA of ten CYP6 genes from the transcriptome of C. kiinensis were identified and sequenced. The open reading frames of the CYP6 genes ranged from 1266 to 1587 bp, encoding deduced polypeptides composed of between 421 and 528 amino acids, with predicted molecular masses from 49.01 to 61.94 kDa and isoelectric points (PI) from 6.01 to 8.89. Among the CYP6 genes, the mRNA expression levels of the CYP6EW3, CYP6EV9, CYP6FV1 and CYP6FV2 genes significantly altered in response to phenol exposure; therefore, these genes could potentially serve as biomarkers in the environment. This study shows that P450 activity combined with one or multiple CYP6 genes could be used to monitor phenol pollution.

  3. Gene Structures, Evolution and Transcriptional Profiling of the WRKY Gene Family in Castor Bean (Ricinus communis L.).

    Science.gov (United States)

    Zou, Zhi; Yang, Lifu; Wang, Danhua; Huang, Qixing; Mo, Yeyong; Xie, Guishui

    2016-01-01

    WRKY proteins comprise one of the largest transcription factor families in plants and form key regulators of many plant processes. This study presents the characterization of 58 WRKY genes from the castor bean (Ricinus communis L., Euphorbiaceae) genome. Compared with the automatic genome annotation, one more WRKY-encoding locus was identified and 20 out of the 57 predicted gene models were manually corrected. All RcWRKY genes were shown to contain at least one intron in their coding sequences. According to the structural features of the present WRKY domains, the identified RcWRKY genes were assigned to three previously defined groups (I-III). Although castor bean underwent no recent whole-genome duplication event like physic nut (Jatropha curcas L., Euphorbiaceae), comparative genomics analysis indicated that one gene loss, one intron loss and one recent proximal duplication occurred in the RcWRKY gene family. The expression of all 58 RcWRKY genes was supported by ESTs and/or RNA sequencing reads derived from roots, leaves, flowers, seeds and endosperms. Further global expression profiles with RNA sequencing data revealed diverse expression patterns among various tissues. Results obtained from this study not only provide valuable information for future functional analysis and utilization of the castor bean WRKY genes, but also provide a useful reference to investigate the gene family expansion and evolution in Euphorbiaceus plants.

  4. Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling

    Science.gov (United States)

    Jahn, Martin T.; Markert, Sebastian M.; Ryu, Taewoo; Ravasi, Timothy; Stigloher, Christian; Hentschel, Ute; Moitinho-Silva, Lucas

    2016-01-01

    Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal. Cellular 3D reconstructions revealed bipolar, spherical granules of low electron density, which likely represent carbon reserves. Poribacterial activity profiles were retrieved from prokaryotic enriched sponge metatranscriptomes using simulation-based optimised mapping. We observed high transcriptional activity for proteins related to bacterial microcompartments (BMC) and we resolved their subcellular localisation by combining FISH-CLEM with immunohistochemistry (IHC) on ultra-thin sponge tissue sections. In terms of functional relevance, we propose that the BMC-A region may be involved in 1,2-propanediol degradation. The FISH-IHC-CLEM approach was proven an effective toolkit to combine -omics approaches with functional studies and it should be widely applicable in environmental microbiology. PMID:27796326

  5. Molecular variation of Trypanosoma brucei subspecies as revealed by AFLP fingerprinting

    NARCIS (Netherlands)

    Agbo, E.E.C.; Majiwa, P.A.O.; Claassen, H.J.H.M.; Pas, te M.F.W.

    2002-01-01

    Genetic analysis of Trypanosoma spp. depends on the detection of variation between strains. We have used the amplified fragment length polymorphism (AFLP) technique to develop a convenient and reliable method for genetic characterization of Trypanosome (sub)species. AFLP accesses multiple independen

  6. The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling

    Directory of Open Access Journals (Sweden)

    Hernando-Amado Sara

    2012-11-01

    Full Text Available Abstract Background Transcription factors (TFs are proteins that have played a central role both in evolution and in domestication, and are major regulators of development in living organisms. Plant genome sequences reveal that approximately 7% of all genes encode putative TFs. The DOF (DNA binding with One Finger TF family has been associated with vital processes exclusive to higher plants and to their close ancestors (algae, mosses and ferns. These are seed maturation and germination, light-mediated regulation, phytohormone and plant responses to biotic and abiotic stresses, etc. In Hordeum vulgare and Oryza sativa, 26 and 30 different Dof genes, respectively, have been annotated. Brachypodium distachyon has been the first Pooideae grass to be sequenced and, due to its genomic, morphological and physiological characteristics, has emerged as the model system for temperate cereals, such as wheat and barley. Results Through searches in the B. distachyon genome, 27 Dof genes have been identified and a phylogenetic comparison with the Oryza sativa and the Hordeum vulgare DOFs has been performed. To explore the evolutionary relationship among these DOF proteins, a combined phylogenetic tree has been constructed with the Brachypodium DOFs and those from rice and barley. This phylogenetic analysis has classified the DOF proteins into four Major Cluster of Orthologous Groups (MCOGs. Using RT-qPCR analysis the expression profiles of the annotated BdDof genes across four organs (leaves, roots, spikes and seeds has been investigated. These results have led to a classification of the BdDof genes into two groups, according to their expression levels. The genes highly or preferentially expressed in seeds have been subjected to a more detailed expression analysis (maturation, dry stage and germination. Conclusions Comparison of the expression profiles of the Brachypodium Dof genes with the published functions of closely related DOF sequences from the cereal

  7. Methodological comparison of DNA extraction from Holcocerrus hippophaecolus (Lepidoptera: Cossidae) for AFLP analysis

    Institute of Scientific and Technical Information of China (English)

    CHEN Min; ZHU Yang-yu; TAO Jing; Luo You-qing

    2008-01-01

    Amplified fragment length polymorphism (AFLP) is a powerful DNA fingerprinting technique for studying genetic rela-tionships and genetic diversity in insects. However, the crucial prerequisite for AFLP analysis is to extract DNA of high quality. In this study, we evaluate four different protocols (SDS method, improved SDS method, CTAB method and a complex method with SDS and CTAB) for isolating DNA from the seabuckthorn carpenter moth (Holcocerrus hippophaecolus (Lepidoptera: Cossidae)). The results indicate that the CTAB method does not produce DNA suitable for AFLP analysis. The SDS method and the complex method with SDS and CTAB are comparatively time-consuming and resulted in low yields of DNA and were therefore not used for AFLP assay. The improved SDS method is recommended for preparing DNA templates from H. hippophaecolus for AFLP analysis.

  8. Transcriptional profiling induced by pesticides employed in organic agriculture in a wild population of Chironomus riparius under laboratory conditions.

    Science.gov (United States)

    Lencioni, Valeria; Grazioli, Valentina; Rossaro, Bruno; Bernabò, Paola

    2016-07-01

    Copper (Cu) and azadirachtin (AZA-A+B) are pesticides allowed in organic agriculture whose environmental risk and toxicity for aquatic wildlife is only partially known. Reverse Transcription Polymerase Chain Reaction was used to assess the molecular effect of acute and short-term exposure (3, 24h) of Cu (0.01, 0.05, 1, 10, 25mgl(-1)) and AZA-A+B (0.2, 0.3, 0.4, 0.5, 1mgl(-1)) on the expression of five candidate genes (hsp70, hsc70, hsp40, hsp10 and cyP450) in a non-target species, Chironomus riparius. Fourth-instar larvae were collected from a mountain stream polluted by agricultural land run-off. All genes were responsive to both pesticides but each gene had a specific response to the different experimental concentrations and exposure times. A few similarities in transcriptional profiling were observed, such as a linear concentration-dependent response of hsp70 after 24h of exposure (at ≥1mgl(-1) of Cu and ≥0.2mgl(-1) of AZA-A+B) and an up-regulation regardless of the concentration of hsc70 after 24h of exposure (at ≥0mgl(-1) of Cu and ≥0.2mgl(-1) of AZA-A+B and the up-regulation of hsp70 after 3h of exposure at ~LC50 (Cu-LC50=26.1±2.5mgl(-1), AZA-A+B-LC50=1.1±0.2mgl(-1)). According to the results, hsp40, hsp10 and cyP450 may be defined as pesticide-dependent (i.e., hsp40 and hsp10 seemed to responded mainly to AZA-A+B and cyP450 to Cu), while hsc70 as time-dependent regardless of the pesticide (i.e., hsc70 responded only after 24h of treatment with Cu and AZA-A+B). This study gives new insights on the potential role of the C. riparius's hsps and cyP450 genes as sensitive biomarkers for freshwater monitoring. PMID:26994805

  9. Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice

    Directory of Open Access Journals (Sweden)

    Van Anh Le Thi

    2011-08-01

    Full Text Available Abstract Background In rice, the major part of the post-embryonic root system is made of stem-derived roots named crown roots (CR. Among the few characterized rice mutants affected in root development, crown rootless1 mutant is unable to initiate crown root primordia. CROWN ROOTLESS1 (CRL1 is induced by auxin and encodes an AS2/LOB-domain transcription factor that acts upstream of the gene regulatory network controlling CR development. Results To identify genes involved in CR development, we compared global gene expression profile in stem bases of crl1 mutant and wild-type (WT plants. Our analysis revealed that 250 and 236 genes are down- and up-regulated respectively in the crl1 mutant. Auxin induces CRL1 expression and consequently it is expected that auxin also alters the expression of genes that are early regulated by CRL1. To identify genes under the early control of CRL1, we monitored the expression kinetics of a selected subset of genes, mainly chosen among those exhibiting differential expression, in crl1 and WT following exogenous auxin treatment. This analysis revealed that most of these genes, mainly related to hormone, water and nutrient, development and homeostasis, were likely not regulated directly by CRL1. We hypothesized that the differential expression for these genes observed in the crl1 mutant is likely a consequence of the absence of CR formation. Otherwise, three CRL1-dependent auxin-responsive genes: FSM (FLATENNED SHOOT MERISTEM/FAS1 (FASCIATA1, GTE4 (GENERAL TRANSCRIPTION FACTOR GROUP E4 and MAP (MICROTUBULE-ASSOCIATED PROTEIN were identified. FSM/FAS1 and GTE4 are known in rice and Arabidopsis to be involved in the maintenance of root meristem through chromatin remodelling and cell cycle regulation respectively. Conclusion Our data showed that the differential regulation of most genes in crl1 versus WT may be an indirect consequence of CRL1 inactivation resulting from the absence of CR in the crl1 mutant. Nevertheless

  10. Effect of Dietary Restriction and Subsequent Re-Alimentation on the Transcriptional Profile of Bovine Skeletal Muscle.

    Science.gov (United States)

    Keogh, Kate; Kenny, David A; Cormican, Paul; McCabe, Matthew S; Kelly, Alan K; Waters, Sinead M

    2016-01-01

    Compensatory growth (CG), an accelerated growth phenomenon which occurs following a period of dietary restriction is exploited worldwide in animal production systems as a method to lower feed costs. However the molecular mechanisms regulated CG expression remain to be elucidated fully. This study aimed to uncover the underlying biology regulating CG in cattle, through an examination of skeletal muscle transcriptional profiles utilising next generation mRNA sequencing technology. Twenty Holstein Friesian bulls were fed either a restricted diet for 125 days, with a target growth rate of 0.6 kg/day (Period 1), following which they were allowed feed ad libitum for a further 55 days (Period 2) or fed ad libitum for the entirety of the trial. M. longissimus dorsi biopsies were harvested from all bulls on days 120 and 15 of periods 1 and 2 respectively and RNAseq analysis was performed. During re-alimentation in Period 2, previously restricted animals displayed CG, growing at 1.8 times the rate of the ad libitum control animals. Compensating animals were also more feed efficient during re-alimentation and compensated for 48% of their previous dietary restriction. 1,430 and 940 genes were identified as significantly differentially expressed (Benjamini Hochberg adjusted P < 0.1) in periods 1 and 2 respectively. Additionally, 2,237 genes were differentially expressed in animals undergoing CG relative to dietary restriction. Dietary restriction in Period 1 was associated with altered expression of genes involved in lipid metabolism and energy production. CG expression in Period 2 occurred in association with greater expression of genes involved in cellular function and organisation. This study highlights some of the molecular mechanisms regulating CG in cattle. Differentially expressed genes identified are potential candidate genes for the identification of biomarkers for CG and feed efficiency, which may be incorporated into future breeding programmes. PMID:26871690

  11. Effect of Dietary Restriction and Subsequent Re-Alimentation on the Transcriptional Profile of Bovine Skeletal Muscle.

    Directory of Open Access Journals (Sweden)

    Kate Keogh

    Full Text Available Compensatory growth (CG, an accelerated growth phenomenon which occurs following a period of dietary restriction is exploited worldwide in animal production systems as a method to lower feed costs. However the molecular mechanisms regulated CG expression remain to be elucidated fully. This study aimed to uncover the underlying biology regulating CG in cattle, through an examination of skeletal muscle transcriptional profiles utilising next generation mRNA sequencing technology. Twenty Holstein Friesian bulls were fed either a restricted diet for 125 days, with a target growth rate of 0.6 kg/day (Period 1, following which they were allowed feed ad libitum for a further 55 days (Period 2 or fed ad libitum for the entirety of the trial. M. longissimus dorsi biopsies were harvested from all bulls on days 120 and 15 of periods 1 and 2 respectively and RNAseq analysis was performed. During re-alimentation in Period 2, previously restricted animals displayed CG, growing at 1.8 times the rate of the ad libitum control animals. Compensating animals were also more feed efficient during re-alimentation and compensated for 48% of their previous dietary restriction. 1,430 and 940 genes were identified as significantly differentially expressed (Benjamini Hochberg adjusted P < 0.1 in periods 1 and 2 respectively. Additionally, 2,237 genes were differentially expressed in animals undergoing CG relative to dietary restriction. Dietary restriction in Period 1 was associated with altered expression of genes involved in lipid metabolism and energy production. CG expression in Period 2 occurred in association with greater expression of genes involved in cellular function and organisation. This study highlights some of the molecular mechanisms regulating CG in cattle. Differentially expressed genes identified are potential candidate genes for the identification of biomarkers for CG and feed efficiency, which may be incorporated into future breeding programmes.

  12. Transcriptional profiling of rat white adipose tissue response to 2,3,7,8-tetrachlorodibenzo-ρ-dioxin.

    Science.gov (United States)

    Houlahan, Kathleen E; Prokopec, Stephenie D; Sun, Ren X; Moffat, Ivy D; Lindén, Jere; Lensu, Sanna; Okey, Allan B; Pohjanvirta, Raimo; Boutros, Paul C

    2015-10-15

    Polychlorinated dibenzodioxins are environmental contaminants commonly produced as a by-product of industrial processes. The most potent of these, 2,3,7,8-tetrachlorodibenzo-ρ-dioxin (TCDD), is highly lipophilic, leading to bioaccumulation. White adipose tissue (WAT) is a major site for energy storage, and is one of the organs in which TCDD accumulates. In laboratory animals, exposure to TCDD causes numerous metabolic abnormalities, including a wasting syndrome. We therefore investigated the molecular effects of TCDD exposure on WAT by profiling the transcriptomic response of WAT to 100μg/kg of TCDD at 1 or 4days in TCDD-sensitive Long-Evans (Turku/AB; L-E) rats. A comparative analysis was conducted simultaneously in identically treated TCDD-resistant Han/Wistar (Kuopio; H/W) rats one day after exposure to the same dose. We sought to identify transcriptomic changes coinciding with the onset of toxicity, while gaining additional insight into later responses. More transcriptional responses to TCDD were observed at 4days than at 1day post-exposure, suggesting WAT shows mostly secondary responses. Two classic AHR-regulated genes, Cyp1a1 and Nqo1, were significantly induced by TCDD in both strains, while several genes involved in the immune response, including Ms4a7 and F13a1 were altered in L-E rats alone. We compared genes affected by TCDD in rat WAT and human adipose cells, and observed little overlap. Interestingly, very few genes involved in lipid metabolism exhibited altered expression levels despite the pronounced lipid mobilization from peripheral fat pads by TCDD in L-E rats. Of these genes, the lipolysis-associated Lpin1 was induced slightly over 2-fold in L-E rat WAT on day 4.

  13. Expression Profiles and RNAi Silencing of Inhibitor of Apoptosis Transcripts in Aedes, Anopheles, and Culex Mosquitoes (Diptera: Culicidae).

    Science.gov (United States)

    Puglise, Jason M; Estep, Alden S; Becnel, James J

    2016-03-01

    Effective mosquito control is vital to curtail the devastating health effects of many vectored diseases. RNA interference (RNAi)-mediated control of mosquitoes is an attractive alternative to conventional chemical pesticides. Previous studies have suggested that transcripts for inhibitors of apoptosis (IAPs) may be good RNAi targets. To revisit and extend previous reports, we examined the expression of Aedes aegypti (L.) IAPs (AaeIAPs) 1, 2, 5, 6, 9, and a viral IAP-associated factor (vIAF) as well as Anopheles quadrimaculatus Say and Culex quinquefasciatus Say IAP1 homologs (AquIAP1 and CquIAP1) in adult females. Expression profiles of IAPs suggested that some older female mosquitoes had significantly higher IAP mRNA levels when compared to the youngest ones. Minor differences in expression of AaeIAPs were observed in mosquitoes that imbibed a bloodmeal, but the majority of the time points (up to 48 h) were not significantly different. Although in vitro experiments with the Ae. aegypti Aag-2 cell line demonstrated that the various AaeIAPs could be effectively knocked down within one day after dsRNA treatment, only Aag-2 cells treated with dsIAP1 displayed apoptotic morphology. Gene silencing and mortality were also evaluated after topical application and microinjection of the same dsRNAs into female Ae. aegypti. In contrast to previous reports, topical administration of dsRNA against AaeIAP1 did not yield a significant reduction in gene expression or increased mortality. Knockdown of IAP1 and other IAPs by microinjection did not result in significant mortality. In toto, our findings suggest that IAPs may not be suitable RNAi targets for controlling adult mosquito populations.

  14. Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds

    OpenAIRE

    Weissgerber, Thomas; Dobler, Nadine; Polen, Tino; Latus, Jeanette; Stockdreher, Yvonne; Dahl, Christiane

    2013-01-01

    The purple sulfur bacterium Allochromatium vinosum DSM 180T is one of the best-studied sulfur-oxidizing anoxygenic phototrophic bacteria, and it has been developed into a model organism for laboratory-based studies of oxidative sulfur metabolism. Here, we took advantage of the organism's high metabolic versatility and performed whole-genome transcriptional profiling to investigate the response of A. vinosum cells upon exposure to sulfide, thiosulfate, elemental sulfur, or sulfite compared to ...

  15. Transcriptional profiles of hybrid Eucalyptus genotypes with contrasting lignin content reveal that monolignol biosynthesis-related genes regulate wood composition

    Directory of Open Access Journals (Sweden)

    Tomotaka eShinya

    2016-04-01

    Full Text Available Eucalyptus species constitutes the most widely planted hardwood trees in temperate and subtropical regions. In this study, we compared the transcript levels of genes involved in lignocellulose formation such as cellulose, hemicellulose and lignin biosynthesis in two selected three-year old hybrid Eucalyptus (Eucalyptus urophylla x E. grandis genotypes (AM063 and AM380 that have different lignin content. AM063 and AM380 had 20.2 and 35.5% of Klason lignin content and 59.0% and 48.2%, -cellulose contents, respectively. We investigated the correlation between wood properties and transcript levels of wood formation-related genes using RNA-seq with total RNAs extracted from developing xylem tissues at a breast height. Transcript levels of cell wall construction genes such as cellulose synthase (CesA and sucrose synthase (SUSY were almost the same in both genotypes. However, AM063 exhibited higher transcript levels of UDP-glucose pyrophosphorylase (UGP and xyloglucan endotransglucoxylase (XTH than those in AM380. Most monolignol biosynthesis- related isozyme genes showed higher transcript levels in AM380. These results indicate monolignol biosynthesis-related genes may regulate wood composition in Eucalyptus. Flavonoids contents were also observed at much higher levels in AM380 as a result of the elevated transcript levels of common phenylpropanoid pathway genes, phenylalanine ammonium lyase (PAL, cinnamate-4-hydroxylase (C4H and 4-coumarate-CoA ligase (4CL. Secondary plant cell wall formation is regulated by many transcription factors. We analyzed genes encoding NAC, WRKY, AP2/ERF and KNOX transcription factors and found higher transcript levels of these genes in AM380. We also observed increased transcription of some MYB and LIM domain transcription factors in AM380 compared to AM063. All these results show that genes related to monolignol biosynthesis may regulate the wood composition and help maintain the ratio of cellulose and lignin contents

  16. AFLP marker linked to water-stress-tolerant bulks in barley (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    A. Altinkut

    2003-01-01

    Full Text Available The amplified fragment length polymorphism (AFLP assay is an efficient method for the identification of molecular markers, useful in the improvement of numerous crop species. Bulked Segregant Analysis (BSA was used to identify AFLP markers associated with water-stress tolerance in barley, as this would permit rapid selection of water-stress tolerant genotypes in breeding programs. AFLP markers linked to water-stress tolerance was identified in two DNA pools (tolerant and sensitive, which were established using selected F2 individuals resulting from a cross between water-stress-tolerant and sensitive barley parental genotypes, based on their paraquat (PQ tolerance, leaf size, and relative water content (RWC. All these three traits were previously shown to be associated with water-stress tolerance in segregating F2 progeny of the barley cross used in a previous study. AFLP analysis was then performed on these DNA pools, using 40 primer pairs to detect AFLP fragments that are present/absent, respectively, in the two pools and their parental lines. One separate AFLP fragment, which was present in the tolerant parent and in the tolerant bulk, but absent in the sensitive parent and in the sensitive bulk, was identified. Polymorphism of the AFLP marker was tested among tolerant and sensitive F2 individuals. The presence of this marker that is associated with water-stress tolerance will greatly enhance selection for paraquat and water-stress tolerant genotypes in future breeding programs.

  17. Chinese Cabbage-pak-choi Transcriptome Map Construction with cDNA-AFLP Techniques

    Institute of Scientific and Technical Information of China (English)

    FAN Shu-ying; LE Jian-gang; CHENG Guang-jie; WU Cai-jun

    2008-01-01

    Chinese cabbage-pak-choi (Brassica campestris L. ssp. chinensis Makino) transcriptome map with cDNA-APLP techniques was constructed. The inbred line Aijiaohuang 97-3-2, the inbred line Baimanjing 001-24 of turnip [B. campestris ssp. rapifera (Matzg.) Sinsk] and 183 F6 (recombinant inbred population) plants were used as experimental materials. cDNAs were synthesized from total RNA extracted from young leaves at rosette stage. 256 pairs of cDNA-AFLP primers were used to detect the polymorphisms between parents Aijiaohuang 97-3-2 and Baimanjing 001-24. 56 pairs of cDNA-AFLP primers with high polymorphisms were screened from 256 pairs of primer by DNA-AFLP techniques. The genetic diversity of parents and 183 F6 progenies was detected by 56 pairs of cDNA-AFLP primers. The segregation and distribution of cDNA-AFLPs molecular marker were analyzed to construct transcriptome map amongst parents and F6 plants. A total of 164 cDNA-AFLPs marker loci were mapped into 13 linkage groups which covered 1 401.2 cM with an average distance of 9.7 cM. It was the first transcriptome map of Chinese cabbage using cDNA-AFLP technique.

  18. Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes

    Directory of Open Access Journals (Sweden)

    Jung Hans-Joachim G

    2010-05-01

    Full Text Available Abstract Background The GeneChip® Medicago Genome Array, developed for Medicago truncatula, is a suitable platform for transcript profiling in tetraploid alfalfa [Medicago sativa (L. subsp. sativa]. However, previous research involving cross-species hybridization (CSH has shown that sequence variation between two species can bias transcript profiling by decreasing sensitivity (number of expressed genes detected and the accuracy of measuring fold-differences in gene expression. Results Transcript profiling using the Medicago GeneChip® was conducted with elongating stem (ES and post-elongation stem (PES internodes from alfalfa genotypes 252 and 1283 that differ in stem cell wall concentrations of cellulose and lignin. A protocol was developed that masked probes targeting inter-species variable (ISV regions of alfalfa transcripts. A probe signal intensity threshold was selected that optimized both sensitivity and accuracy. After masking for both ISV regions and previously identified single-feature polymorphisms (SFPs, the number of differentially expressed genes between the two genotypes in both ES and PES internodes was approximately 2-fold greater than the number detected prior to masking. Regulatory genes, including transcription factor and receptor kinase genes that may play a role in development of secondary xylem, were significantly over-represented among genes up-regulated in 252 PES internodes compared to 1283 PES internodes. Several cell wall-related genes were also up-regulated in genotype 252 PES internodes. Real-time quantitative RT-PCR of differentially expressed regulatory and cell wall-related genes demonstrated increased sensitivity and accuracy after masking for both ISV regions and SFPs. Over 1,000 genes that were differentially expressed in ES and PES internodes of genotypes 252 and 1283 were mapped onto putative orthologous loci on M. truncatula chromosomes. Clustering simulation analysis of the differentially expressed genes

  19. Study on the sex-related AFLP marker of the Yangtze finless porpoise

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The sex-related molecular marker of the Yangtze finless porpoise was screened using Amplified Fragment Length Polymorphism (AFLP) technique combined with the bulked segregant analysis. Totally 36 AFLP primer combinations were used to detect the genome DNA bulks of the female and male porpoises, and one sex-related AFLP marker was finally obtained. The marker can be applied to sex identification, and provides a base for further cloning of sex-related genes and analyzing of Y chromosome haplotypes of the Yangtze finless porpoise.

  20. Genetic diversity among some currants (Ribes spp.) cultivars as assessed by AFLP markers

    International Nuclear Information System (INIS)

    Currants cultivation has increased its popularity in Turkey due to the use of more currants in Turkish cuisine. To provide farmers with well adapted currants cultivars, some currants cultivars have been planted in various geographical regions of Turkey. In this study, genetic diversity among some of these currants cultivars has been analyzed using AFLP markers. Our results indicated that red and black currants genotypes are genetically distinct, sharing very small proportion of AFLP markers. Selected currants genotypes from Turkey shared all AFLP markers suggesting that they might be the same genotype. (author)

  1. Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L..

    Directory of Open Access Journals (Sweden)

    Charu Lata

    Full Text Available The APETALA2/ethylene-responsive element binding factor (AP2/ERF family is one of the largest transcription factor (TF families in plants that includes four major sub-families, namely AP2, DREB (dehydration responsive element binding, ERF (ethylene responsive factors and RAV (Related to ABI3/VP. AP2/ERFs are known to play significant roles in various plant processes including growth and development and biotic and abiotic stress responses. Considering this, a comprehensive genome-wide study was conducted in foxtail millet (Setaria italica L.. A total of 171 AP2/ERF genes were identified by systematic sequence analysis and were physically mapped onto nine chromosomes. Phylogenetic analysis grouped AP2/ERF genes into six classes (I to VI. Duplication analysis revealed that 12 (∼7% SiAP2/ERF genes were tandem repeated and 22 (∼13% were segmentally duplicated. Comparative physical mapping between foxtail millet AP2/ERF genes and its orthologs of sorghum (18 genes, maize (14 genes, rice (9 genes and Brachypodium (6 genes showed the evolutionary insights of AP2/ERF gene family and also the decrease in orthology with increase in phylogenetic distance. The evolutionary significance in terms of gene-duplication and divergence was analyzed by estimating synonymous and non-synonymous substitution rates. Expression profiling of candidate AP2/ERF genes against drought, salt and phytohormones revealed insights into their precise and/or overlapping expression patterns which could be responsible for their functional divergence in foxtail millet. The study showed that the genes SiAP2/ERF-069, SiAP2/ERF-103 and SiAP2/ERF-120 may be considered as potential candidate genes for further functional validation as well for utilization in crop improvement programs for stress resistance since these genes were up-regulated under drought and salinity stresses in ABA dependent manner. Altogether the present study provides new insights into evolution, divergence and

  2. Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.).

    Science.gov (United States)

    Lata, Charu; Mishra, Awdhesh Kumar; Muthamilarasan, Mehanathan; Bonthala, Venkata Suresh; Khan, Yusuf; Prasad, Manoj

    2014-01-01

    The APETALA2/ethylene-responsive element binding factor (AP2/ERF) family is one of the largest transcription factor (TF) families in plants that includes four major sub-families, namely AP2, DREB (dehydration responsive element binding), ERF (ethylene responsive factors) and RAV (Related to ABI3/VP). AP2/ERFs are known to play significant roles in various plant processes including growth and development and biotic and abiotic stress responses. Considering this, a comprehensive genome-wide study was conducted in foxtail millet (Setaria italica L.). A total of 171 AP2/ERF genes were identified by systematic sequence analysis and were physically mapped onto nine chromosomes. Phylogenetic analysis grouped AP2/ERF genes into six classes (I to VI). Duplication analysis revealed that 12 (∼7%) SiAP2/ERF genes were tandem repeated and 22 (∼13%) were segmentally duplicated. Comparative physical mapping between foxtail millet AP2/ERF genes and its orthologs of sorghum (18 genes), maize (14 genes), rice (9 genes) and Brachypodium (6 genes) showed the evolutionary insights of AP2/ERF gene family and also the decrease in orthology with increase in phylogenetic distance. The evolutionary significance in terms of gene-duplication and divergence was analyzed by estimating synonymous and non-synonymous substitution rates. Expression profiling of candidate AP2/ERF genes against drought, salt and phytohormones revealed insights into their precise and/or overlapping expression patterns which could be responsible for their functional divergence in foxtail millet. The study showed that the genes SiAP2/ERF-069, SiAP2/ERF-103 and SiAP2/ERF-120 may be considered as potential candidate genes for further functional validation as well for utilization in crop improvement programs for stress resistance since these genes were up-regulated under drought and salinity stresses in ABA dependent manner. Altogether the present study provides new insights into evolution, divergence and systematic

  3. Alteration of the exopolysaccharide production and the transcriptional profile of free-living Frankia strain CcI3 under nitrogen-fixing conditions.

    Science.gov (United States)

    Lee, Hae-In; Donati, Andrew J; Hahn, Dittmar; Tisa, Louis S; Chang, Woo-Suk

    2013-12-01

    We investigated the effect of different nitrogen (N) sources on exopolysaccharide (EPS) production and composition by Frankia strain CcI3, a N2-fixing actinomycete that forms root nodules with Casuarina species. Frankia cells grown in the absence of NH4Cl (i.e., under N2-fixing conditions) produced 1.7-fold more EPS, with lower galactose (45.1 vs. 54.7 mol%) and higher mannose (17.3 vs. 9.7 mol%) contents than those grown in the presence of NH4Cl as a combined N-source. In the absence of the combined N-source, terminally linked and branched residue contents were nearly twice as high with 32.8 vs. 15.1 mol% and 15.1 vs. 8.7 mol%, respectively, than in its presence, while the content of linearly linked residues was lower with 52.1 mol% compared to 76.2 mol%. To find out clues for the altered EPS production at the transcriptional level, we performed whole-gene expression profiling using quantitative reverse transcription PCR and microarray technology. The transcription profiles of Frankia strain CcI3 grown in the absence of NH4Cl revealed up to 2 orders of magnitude higher transcription of nitrogen fixation-related genes compared to those of CcI3 cells grown in the presence of NH4Cl. Unexpectedly, microarray data did not provide evidence for transcriptional regulation as a mechanism for differences in EPS production. These findings indicate effects of nitrogen fixation on the production and composition of EPS in Frankia strain CcI3 and suggest posttranscriptional regulation of enhanced EPS production in the absence of the combined N-source. PMID:24097014

  4. Simultaneous host and parasite expression profiling identifies tissue-specific transcriptional programs associated with susceptibility or resistance to experimental cerebral malaria

    Directory of Open Access Journals (Sweden)

    Liles W Conrad

    2006-11-01

    Full Text Available Abstract Background The development and outcome of cerebral malaria (CM reflects a complex interplay between parasite-expressed virulence factors and host response to infection. The murine CM model, Plasmodium berghei ANKA (PbA, which simulates many of the features of human CM, provides an excellent system to study this host/parasite interface. We designed "combination" microarrays that concurrently detect genome-wide transcripts of both PbA and mouse, and examined parasite and host transcriptional programs during infection of CM-susceptible (C57BL/6 and CM-resistant (BALB/c mice. Results Analysis of expression data from brain, lung, liver, and spleen of PbA infected mice showed that both host and parasite gene expression can be examined using a single microarray, and parasite transcripts can be detected within whole organs at a time when peripheral blood parasitemia is low. Parasites display a unique transcriptional signature in each tissue, and lung appears to be a large reservoir for metabolically active parasites. In comparisons of susceptible versus resistant animals, both host and parasite display distinct, organ-specific transcriptional profiles. Differentially expressed mouse genes were related to humoral immune response, complement activation, or cell-cell interactions. PbA displayed differential expression of genes related to biosynthetic activities. Conclusion These data show that host and parasite gene expression profiles can be simultaneously analysed using a single "combination" microarray, and that both the mouse and malaria parasite display distinct tissue- and strain-specific responses during infection. This technology facilitates the dissection of host-pathogen interactions in experimental cerebral malaria and could be extended to other disease models.

  5. cDNA-AFLP analysis reveals differential gene expression in compatible interaction of wheat challenged with Puccinia striiformis f. sp. tritici

    Directory of Open Access Journals (Sweden)

    Huang Lili

    2009-06-01

    Full Text Available Abstract Background Puccinia striiformis f. sp. tritici is a fungal pathogen causing stripe rust, one of the most important wheat diseases worldwide. The fungus is strictly biotrophic and thus, completely dependent on living host cells for its reproduction, which makes it difficult to study genes of the pathogen. In spite of its economic importance, little is known about the molecular basis of compatible interaction between the pathogen and wheat host. In this study, we identified wheat and P. striiformis genes associated with the infection process by conducting a large-scale transcriptomic analysis using cDNA-AFLP. Results Of the total 54,912 transcript derived fragments (TDFs obtained using cDNA-AFLP with 64 primer pairs, 2,306 (4.2% displayed altered expression patterns after inoculation, of which 966 showed up-regulated and 1,340 down-regulated. 186 TDFs produced reliable sequences after sequencing of 208 TDFs selected, of which 74 (40% had known functions through BLAST searching the GenBank database. Majority of the latter group had predicted gene products involved in energy (13%, signal transduction (5.4%, disease/defence (5.9% and metabolism (5% of the sequenced TDFs. BLAST searching of the wheat stem rust fungus genome database identified 18 TDFs possibly from the stripe rust pathogen, of which 9 were validated of the pathogen origin using PCR-based assays followed by sequencing confirmation. Of the 186 reliable TDFs, 29 homologous to genes known to play a role in disease/defense, signal transduction or uncharacterized genes were further selected for validation of cDNA-AFLP expression patterns using qRT-PCR analyses. Results confirmed the altered expression patterns of 28 (96.5% genes revealed by the cDNA-AFLP technique. Conclusion The results show that cDNA-AFLP is a reliable technique for studying expression patterns of genes involved in the wheat-stripe rust interactions. Genes involved in compatible interactions between wheat and the

  6. Lung transcriptional profiling: insights into the mechanisms of ozone-induced pulmonary injury in Wistar Kyoto rats

    Science.gov (United States)

    Acute ozone-induced pulmonary injury and inflammation are well characterized in rats; however, mechanistic understanding of the pathways involved is limited. We hypothesized that acute exposure of healthy rats to ozone will cause transcriptional alterations, and comprehensive ana...

  7. Gene transcription profiles, global DNA methylation and potential transgenerational epigenetic effects related to Zn exposure history in Daphnia magna

    International Nuclear Information System (INIS)

    A reduced level of DNA methylation has recently been described in both Zn-exposed and non-exposed offspring of Daphnia magna exposed to Zn. The hypothesis examined in this study is that DNA hypomethylation has an effect on gene transcription. A second hypothesis is that accumulative epigenetic effects can affect gene transcription in non-exposed offspring from parents with an exposure history of more than one generation. Transcriptional gene regulation was studied with a cDNA microarray. In the exposed and non-exposed hypomethylated daphnids, a large proportion of common genes were similarly up- or down-regulated, indicating a possible effect of the DNA hypomethylation. Two of these genes can be mechanistically involved in DNA methylation reduction. The similar transcriptional regulation of two and three genes in the F0 and F1 exposed daphnids on one hand and their non-exposed offspring on the other hand, could be the result of a one-generation temporary transgenerational epigenetic effect, which was not accumulative. - Zn-induced DNA hypomethylation is related to gene transcription in Daphnia magna and Zn exposure potentially induced limited temporary transgenerational effects on gene transcription.

  8. Gene transcription profiles, global DNA methylation and potential transgenerational epigenetic effects related to Zn exposure history in Daphnia magna

    Energy Technology Data Exchange (ETDEWEB)

    Vandegehuchte, Michiel B., E-mail: michiel.vandegehuchte@ugent.b [Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, J. Plateaustraat 22, B-9000 Ghent (Belgium); De Coninck, Dieter [Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, J. Plateaustraat 22, B-9000 Ghent (Belgium); Vandenbrouck, Tine; De Coen, Wim M. [Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Janssen, Colin R. [Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, J. Plateaustraat 22, B-9000 Ghent (Belgium)

    2010-10-15

    A reduced level of DNA methylation has recently been described in both Zn-exposed and non-exposed offspring of Daphnia magna exposed to Zn. The hypothesis examined in this study is that DNA hypomethylation has an effect on gene transcription. A second hypothesis is that accumulative epigenetic effects can affect gene transcription in non-exposed offspring from parents with an exposure history of more than one generation. Transcriptional gene regulation was studied with a cDNA microarray. In the exposed and non-exposed hypomethylated daphnids, a large proportion of common genes were similarly up- or down-regulated, indicating a possible effect of the DNA hypomethylation. Two of these genes can be mechanistically involved in DNA methylation reduction. The similar transcriptional regulation of two and three genes in the F{sub 0} and F{sub 1} exposed daphnids on one hand and their non-exposed offspring on the other hand, could be the result of a one-generation temporary transgenerational epigenetic effect, which was not accumulative. - Zn-induced DNA hypomethylation is related to gene transcription in Daphnia magna and Zn exposure potentially induced limited temporary transgenerational effects on gene transcription.

  9. Use of AFLP for differentiation of Metschnikowia pulcherrima strains for postharvest disease biological control.

    Science.gov (United States)

    Spadaro, D; Sabetta, W; Acquadro, A; Portis, E; Garibaldi, A; Gullino, M L

    2008-01-01

    Metschnikowia pulcherrima occurs naturally on fruits, buds and floral parts of apple trees. Some strains are effective as biocontrol agents against postharvest decay of apples and other fruits. The usefulness of the amplified fragment length polymorphism (AFLP) technique was evaluated for the genetic analysis of 26 strains of M. pulcherrima, isolated from different sources in different geographical regions. With six AFLP primer pairs, 729 polymorphic bands were scored. The technique showed a high discriminatory power. Genetic relationships between strains were also estimated using AFLP. All the isolates from the carposphere of apple, previously tested as biocontrol agents, were grouped in a single cluster with a high bootstrap value (97), indicating robustness and reproducibility. AFLP patterns could clearly distinguish the different strains and research is in progress to use some putative specific bands for single tag sequence (STS) conversion to develop isolate-specific markers.

  10. Assessment of the Genetic Diversity of Pummelo Germplasms Using AFLP and SSR Markers

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The genetic diversities of 110 pummelo germplasms and 12 of their relatives were analyzed by SSR and AFLP methods. Approximately 99.1% of the 335 SSR loci were polymorphic, and 9.85 alleles per SSR locus were identified. The gene diversity values changed from 0.1939 to 0.9073, and 46 SSR polymorphic bands were scored. 72% of the 343 AFLP loci were polymorphic, and 82 polymorphic loci per AFLP were identified. Heterozygosity changed from 0.21863 to 0.28445,and 44 AFLP polymorphic bands were scored. The UPGMA result showed that 122 pummelo genotypes and their relatives could be divided into eight groups, and the pummelo genotypes composed mainly of Shatian pummelo varieties group,Wendan pummelo vareties group and a huge hybrid pummelo varieties group. The classification result was expected to widen the genetic background of pummelos using various target varieties.

  11. Veronaea botryosa: molecular identification with amplified fragment length polymorphism (AFLP) and in vitro antifungal susceptibility

    NARCIS (Netherlands)

    H. Badali; S.A. Yazdanparast; A. Bonifaz; B. Mousavi; G.S. de Hoog; C.H.W. Klaassen; J.F. Meis

    2013-01-01

    Inter- and intraspecific genomic variability of 18 isolates of Veronaea botryosa originating from clinical and environmental sources was studied using amplified fragment length polymorphism (AFLP). The species was originally described from the environment, but several severe cases of disseminated in

  12. Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport

    OpenAIRE

    Phirke, Prasad; Efimenko, Evgeni; Mohan, Swetha; Burghoorn, Jan; Crona, Filip; Bakhoum, Mathieu W.; Trieb, Maria; Schuske, Kim; Erik M. Jorgensen; Piasecki, Brian P.; Leroux, Michel R.; Swoboda, Peter

    2011-01-01

    Cilia are ubiquitous cell surface projections that mediate various sensory- and motility-based processes and are implicated in a growing number of multi-organ genetic disorders termed ciliopathies. To identify new components required for cilium biogenesis and function, we sought to further define and validate the transcriptional targets of DAF-19, the ciliogenic C. elegans RFX transcription factor. Transcriptional profiling of daf-19 mutants (which do not form cilia) and wild-type animals was...

  13. Genomic variations of Mycoplasma capricolum subsp capripneumoniae detected by amplified fragment length polymorphism (AFLP) analysis

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Bolske, G.; Ahrens, Peter;

    2000-01-01

    The genetic diversity of Mycoplasma capricolum subsp. capripneumoniae strains based on determination of amplified fragment length polymorphisms (AFLP) is described. AFLP fingerprints of 38 strains derived from different countries in Africa and the Middle East consisted of over 100 bands in the size...... found by 16S rDNA analysis. The present data support previous observations regarding genetic homogeneity of M. capricolum subsp. capripneumoniae, and confirm the two evolutionary lines of descent found by analysis of 16S rRNA genes....

  14. RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis.

    Science.gov (United States)

    Handa, Yoshihiro; Nishide, Hiroyo; Takeda, Naoya; Suzuki, Yutaka; Kawaguchi, Masayoshi; Saito, Katsuharu

    2015-08-01

    Gene expression during arbuscular mycorrhizal development is highly orchestrated in both plants and arbuscular mycorrhizal fungi. To elucidate the gene expression profiles of the symbiotic association, we performed a digital gene expression analysis of Lotus japonicus and Rhizophagus irregularis using a HiSeq 2000 next-generation sequencer with a Cufflinks assembly and de novo transcriptome assembly. There were 3,641 genes differentially expressed during arbuscular mycorrhizal development in L. japonicus, approximately 80% of which were up-regulated. The up-regulated genes included secreted proteins, transporters, proteins involved in lipid and amino acid metabolism, ribosomes and histones. We also detected many genes that were differentially expressed in small-secreted peptides and transcription factors, which may be involved in signal transduction or transcription regulation during symbiosis. Co-regulated genes between arbuscular mycorrhizal and root nodule symbiosis were not particularly abundant, but transcripts encoding for membrane traffic-related proteins, transporters and iron transport-related proteins were found to be highly co-up-regulated. In transcripts of arbuscular mycorrhizal fungi, expansion of cytochrome P450 was observed, which may contribute to various metabolic pathways required to accommodate roots and soil. The comprehensive gene expression data of both plants and arbuscular mycorrhizal fungi provide a powerful platform for investigating the functional and molecular mechanisms underlying arbuscular mycorrhizal symbiosis.

  15. Transcriptome Profiling of Tomato Fruit Development Reveals Transcription Factors Associated with Ascorbic Acid, Carotenoid and Flavonoid Biosynthesis.

    Science.gov (United States)

    Ye, Jie; Hu, Tixu; Yang, Congmei; Li, Hanxia; Yang, Mingze; Ijaz, Raina; Ye, Zhibiao; Zhang, Yuyang

    2015-01-01

    Tomato (Solanum lycopersicum) serves as a research model for fruit development; however, while it is an important dietary source of antioxidant nutrients, the transcriptional regulation of genes that determine nutrient levels remains poorly understood. Here, the transcriptomes of fruit at seven developmental stages (7, 14, 21, 28, 35, 42 and 49 days after flowering) from two tomato cultivars (Ailsa Craig and HG6-61) were evaluated using the Illumina sequencing platform. A total of 26,397 genes, which were expressed in at least one developmental stage, were detected in the two cultivars, and the expression patterns of those genes could be divided into 20 groups using a K-mean cluster analysis. Gene Ontology term enrichment analysis indicated that genes involved in RNA regulation, secondary metabolism, hormone metabolism and cell wall metabolism were the most highly differentially expressed genes during fruit development and ripening. A co-expression analysis revealed several transcription factors whose expression patterns correlated with those of genes associated with ascorbic acid, carotenoid and flavonoid biosynthesis. This transcriptional correlation was confirmed by agroinfiltration mediated transient expression, which showed that most of the enzymatic genes in the ascorbic acid biosynthesis were regulated by the overexpression of each of the three transcription factors that were tested. The metabolic dynamics of ascorbic acid, carotenoid and flavonoid were investigated during fruit development and ripening, and some selected transcription factors showed transcriptional correlation with the accumulation of ascorbic acid, carotenoid and flavonoid. This transcriptome study provides insight into the regulatory mechanism of fruit development and presents candidate transcription factors involved in secondary metabolism.

  16. Transcriptome Profiling of Tomato Fruit Development Reveals Transcription Factors Associated with Ascorbic Acid, Carotenoid and Flavonoid Biosynthesis.

    Directory of Open Access Journals (Sweden)

    Jie Ye

    Full Text Available Tomato (Solanum lycopersicum serves as a research model for fruit development; however, while it is an important dietary source of antioxidant nutrients, the transcriptional regulation of genes that determine nutrient levels remains poorly understood. Here, the transcriptomes of fruit at seven developmental stages (7, 14, 21, 28, 35, 42 and 49 days after flowering from two tomato cultivars (Ailsa Craig and HG6-61 were evaluated using the Illumina sequencing platform. A total of 26,397 genes, which were expressed in at least one developmental stage, were detected in the two cultivars, and the expression patterns of those genes could be divided into 20 groups using a K-mean cluster analysis. Gene Ontology term enrichment analysis indicated that genes involved in RNA regulation, secondary metabolism, hormone metabolism and cell wall metabolism were the most highly differentially expressed genes during fruit development and ripening. A co-expression analysis revealed several transcription factors whose expression patterns correlated with those of genes associated with ascorbic acid, carotenoid and flavonoid biosynthesis. This transcriptional correlation was confirmed by agroinfiltration mediated transient expression, which showed that most of the enzymatic genes in the ascorbic acid biosynthesis were regulated by the overexpression of each of the three transcription factors that were tested. The metabolic dynamics of ascorbic acid, carotenoid and flavonoid were investigated during fruit development and ripening, and some selected transcription factors showed transcriptional correlation with the accumulation of ascorbic acid, carotenoid and flavonoid. This transcriptome study provides insight into the regulatory mechanism of fruit development and presents candidate transcription factors involved in secondary metabolism.

  17. Identification of AFLP and STS markers closely linked to the def locus in pea.

    Science.gov (United States)

    von Stackelberg, M; Lindemann, S; Menke, M; Riesselmann, S; Jacobsen, H-J

    2003-05-01

    The recessive mutation of the def gene of pea (Pisum sativum L.) leads to the loss of the hilum, the abscission zone between the seed and the pod. Thereby, it reduces the free dispersal of the seeds through pod shattering. As a prerequisite for a gene isolation via a map-based cloning approach, bulked segregant analysis followed by single plant analyses of over 200 homozygous individuals of a population of 476 F2 plants derived from a cross between 'DGV' (def wild-type) and 'PF' (def mutant), were used to detect markers closely linked to the def locus. The AFLP technique in combination with silver staining was used to maximize numbers of reproducible marker loci. Fifteen AFLP loci showed a genetic distance less than 5 and two of them less than 1 centiMorgans (cM) to the gene of interest. AFLPs were converted into sequence tagged sites (STSs) and into a newly refined AFLP-based single locus marker named the 'sequence specified AFLP' (ssAFLP).

  18. Diversidade genética em maracujazeiro-amarelo utilizando marcadores moleculares fAFLP Genetic diversity in yellow passion fruit utilizing fAFLP molecular markers

    OpenAIRE

    Rita Maria Devós Ganga; Carlos Ruggiero; Eliana Gertrudes de Macedo Lemos; Gisele Ventura Garcia Grili; Michele Mantovani Gonçalves; Edvan Alves Chagas; Ester Wickert

    2004-01-01

    Marcadores moleculares fAFLP foram utilizados para estimar a diversidade genética entre 36 acessos de maracujá-amarelo (Passiflora edulis f. flavicarpa Deg.) coletados em 18 estados do Brasil. Os resultados obtidos permitiram concluir que os marcadores fAFLP se mostraram consistentes na avaliação da variabilidade genética, detectando e quantificando a ampla divergência genética entre os 36 acessos analisados, bem como a não-formação de estruturação geográfica. Tais resultados podem auxiliar n...

  19. Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes

    Directory of Open Access Journals (Sweden)

    Killick Kate E

    2011-12-01

    study demonstrates that genome-wide transcriptional profiling of PBL can distinguish active M. bovis-infected animals from control non-infected animals. Furthermore, the results obtained support previous investigations demonstrating that mycobacterial infection is associated with host transcriptional suppression. These data support the use of transcriptomic technologies to enable the identification of robust, reliable transcriptional markers of active M. bovis infection.

  20. Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection

    Directory of Open Access Journals (Sweden)

    Cho Won

    2012-05-01

    Full Text Available Abstract Background Fusarium graminearum virus 1 strain-DK21 (FgV1-DK21 is a mycovirus that confers hypovirulence to F. graminearum, which is the primary phytopathogenic fungus that causes Fusarium head blight (FHB disease in many cereals. Understanding the interaction between mycoviruses and plant pathogenic fungi is necessary for preventing damage caused by F. graminearum. Therefore, we investigated important cellular regulatory processes in a host containing FgV1-DK21 as compared to an uninfected parent using a transcriptional approach. Results Using a 3′-tiling microarray covering all known F. graminearum genes, we carried out genome-wide expression analyses of F. graminearum at two different time points. At the early point of growth of an infected strain as compared to an uninfected strain, genes associated with protein synthesis, including ribosome assembly, nucleolus, and ribosomal RNA processing, were significantly up-regulated. In addition, genes required for transcription and signal transduction, including fungal-specific transcription factors and cAMP signaling, respectively, were actively up-regulated. In contrast, genes involved in various metabolic pathways, particularly in producing carboxylic acids, aromatic amino acids, nitrogen compounds, and polyamines, showed dramatic down-regulation at the early time point. Moreover, genes associated with transport systems localizing to transmembranes were down-regulated at both time points. Conclusion This is the first report of global change in the prominent cellular pathways in the Fusarium host containing FgV1-DK21. The significant increase in transcripts for transcription and translation machinery in fungal host cells seems to be related to virus replication. In addition, significant down-regulation of genes required for metabolism and transporting systems in a fungal host containing the virus appears to be related to the host defense mechanism and fungal virulence. Taken together

  1. Identification and transcript profiles of citrus growth-regulating factor genes involved in the regulation of leaf and fruit development.

    Science.gov (United States)

    Liu, Xiao; Guo, Ling-Xia; Jin, Long-Fei; Liu, Yong-Zhong; Liu, Tao; Fan, Yu-Hua; Peng, Shu-Ang

    2016-10-01

    Growth-regulating factor (GRF) is an important protein in GA-mediated response, with key roles in plant growth and development. However, it is not known whether or how the GRF proteins in citrus to regulate organ size. In this study, nine citrus GRF genes (CsGRF1-9) were validated from the 'Anliu' sweet orange (AL, Citrus sinensis cv. Anliu) by PCR amplification. They all contain two conserved motifs (QLQ and WRC) and have 3-4 exons. The transcript levels of genes were detected by qRT-PCR. Transcript analysis showed that (1) CsGRF 1, 2, 5, 6, 7, and 9 expressed predominantly in young leaf, CsGRF 3 and 4 expressed predominantly in fruit immature juice sacs and CsGRF 8 expressed predominantly in root; (2) all citrus GRF genes had significantly higher expression in young leaves than mature leaf; (3) in juice sacs, the transcript levels of CsGRF1, 4, 5, 6, and 8 increased significantly while the transcript levels of CsGRF2, 3, 7, and 9 had no significant change from 80 DAF to 100 DAF. Besides, GA3 treatment did not affect the transcript levels of CsGRF5 and CsGRF6 but significantly increased the transcript levels of the other seven CsGRF genes in young leaves. These results suggested that all CsGRF genes involve in the leaf development, CsGRF1, 4, 5, 6, and 8 act developmentally whilst CsGRF2, 3, 7, and 9 play fundamental roles in fruit cell enlargement, which may be through GA pathway or GA-independent pathway.

  2. Transcriptional profiling of the bovine hepatic response to experimentally induced E. coli mastitis

    DEFF Research Database (Denmark)

    Jørgensen, Hanne Birgitte Hede; Buitenhuis, Bart; Røntved, Christine Maria;

    2012-01-01

    The mammalian liver works to keep the body in a state of homeostasis and plays an important role in systemic acute phase response to infections. In this study we investigated the bovine hepatic acute phase response at the gene transcription level in dairy cows with experimentally E. coli-induced ......The mammalian liver works to keep the body in a state of homeostasis and plays an important role in systemic acute phase response to infections. In this study we investigated the bovine hepatic acute phase response at the gene transcription level in dairy cows with experimentally E. coli...

  3. Transcriptional profile of genes involved in ascorbate glutathione cycle in senescing leaves for an early senescence leaf (esl) rice mutant.

    Science.gov (United States)

    Li, Zhaowei; Su, Da; Lei, Bingting; Wang, Fubiao; Geng, Wei; Pan, Gang; Cheng, Fangmin

    2015-03-15

    To clarify the complex relationship between ascorbate-glutathione (AsA-GSH) cycle and H2O2-induced leaf senescence, the genotype-dependent difference in some senescence-related physiological parameters and the transcript levels and the temporal patterns of genes involved in the AsA-GSH cycle during leaf senescence were investigated using two rice genotypes, namely, the early senescence leaf (esl) mutant and its wild type. Meanwhile, the triggering effect of exogenous H2O2 on the expression of OsAPX genes was examined using detached leaves. The results showed that the esl mutant had higher H2O2 level than its wild type at the initial stage of leaf senescence. At transcriptional level, the association of expression of various genes involved in the AsA-GSH cycle with leaf senescence was isoform dependent. For OsAPXs, the transcripts of two cytosolic OsAPX genes (OsAPX1 and OsAPX2), thylakoid-bound OsAPX8, chloroplastic OsAPX7 and peroxisomal OsAPX4 exhibited remarkable genotype-dependent variation in their expression levels and temporal patterns during leaf senescence, there were significantly increasing transcripts of OsAXP1 and OsAPX7, severely repressed transcripts of OsAPX4 and OsAPX8 for the esl rice at the initial leaf senescence. In contrast, the repressing transcript of OsAPX8 was highly sensitive to the increasing H2O2 level in the senescing rice leaves, while higher H2O2 concentration resulted in the enhancing transcripts of two cytosolic OsAPX genes, OsAPX7 transcript was greatly variable with different H2O2 concentrations and incubating duration, suggesting that the different OsAPXs isoforms played a complementary role in perceiving and scavenging H2O2 accumulation at various H2O2 concentrations during leaf senescence. Higher H2O2 level, increased AsA level, higher activities of APX and glutathione reductase (GR), and relatively stable GSH content during the entire sampling period in the leaves of esl mutant implied that a close interrelationship existed

  4. Profiling of histone H3 lysine 9 trimethylation levels predicts transcription factor activity and survival in acute myeloid leukemia

    DEFF Research Database (Denmark)

    Müller-Tidow, Carsten; Klein, Hans-Ulrich; Hascher, Antje;

    2010-01-01

    . The altered genomic regions showed an overrepresentation of cis-binding sites for ets and c-AMP response elements (CREs) for transcription factors of the CREB/CREM/ATF1 family. The decrease in H3K9me3 levels at CREs was associated with increased CRE-driven promoter activity in AML blasts in vivo. AML......Acute Myeloid Leukemia (AML) is commonly associated with alterations in transcription factors due to altered expression or gene mutations. These changes might induce leukemia- specific patterns of histone modifications. We used ChIP-Chip to analyze histone H3 Lysine 9 trimethylation (H3K9me3...

  5. Transcriptional profiling of myotubes from patients with type 2 diabetes: no evidence for a primary defect in oxidative phosphorylation genes

    DEFF Research Database (Denmark)

    Frederiksen, C M; Højlund, K; Hansen, L;

    2008-01-01

    . It is unknown whether reduced mitochondrial biogenesis or other transcriptional alterations co-exist with impaired insulin responsiveness in primary human muscle cells from patients with type 2 diabetes. METHODS: Using cDNA microarray technology and global pathway analysis with the Gene Map Annotator...

  6. Transcriptional profiling in C. elegans suggests DNA damage dependent apoptosis as an ancient function of the p53 family

    NARCIS (Netherlands)

    S. Greiss (Sebastian); B. Schumacher (Björn); K. Grandien (Kaj); J. Rothblatt (Jonathan); A. Gartner (Anton)

    2008-01-01

    textabstractBackground: In contrast to the three mammalian p53 family members, p53, which is generally involved in DNA damage responses, and p63 and p73 which are primarily needed for developmental regulation, cep-1 encodes for the single C. elegans p53-like gene. cep-1 acts as a transcription activ

  7. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

    DEFF Research Database (Denmark)

    Bryne, J.C.; Valen, E.; Tang, M.H.E.;

    2008-01-01

    JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR...

  8. Organ-specific phosphorus-allocation patterns and transcript profiles linked to phosphorus efficiency in two contrasting wheat genotypes.

    Science.gov (United States)

    Aziz, Tariq; Finnegan, Patrick M; Lambers, Hans; Jost, Ricarda

    2014-04-01

    Recent studies have identified genotypic variation in phosphorus (P) efficiency, but rarely have the underlying mechanisms been described at the molecular level. We demonstrate that the highly P-efficient wheat (Triticum aestivum L.) cultivar Chinese 80-55 maintains higher inorganic phosphate (Pi ) concentrations in all organs upon Pi withdrawal in combination with higher Pi acquisition in the presence of Pi when compared with the less-efficient cultivar Machete. These findings correlated with differential organ-specific expression of Pi transporters TaPHT1;2, TaPHT1;5, TaPHT1;8, TaPHT2;1 and H(+) -ATPase TaHa1. Observed transcript level differences between the cultivars suggest that higher de novo phospholipid biosynthetic activities in Pi -limited elongating basal leaf sections are another crucial adaptation in Chinese 80-55 for sustaining growth upon Pi withdrawal. These activities may be supported through enhanced breakdown of starch in Chinese 80-55 stems as suggested by higher TaGPho1 transcript levels. Chinese 80-55 fine roots on the other hand show strong suppression of transcripts involved in glycolysis, transcriptional regulation and ribosomal activities. Our work reveals major differences in the way the two contrasting cultivars allocate Pi and organic P compounds between source and sink tissues and in the acclimation of their metabolism to changes in Pi availability.

  9. Intergenic transcription, cell-cycle and the developmentally regulated epigenetic profile of the human beta-globin locus.

    Directory of Open Access Journals (Sweden)

    Joanne Miles

    Full Text Available Several lines of evidence have established strong links between transcriptional activity and specific post-translation modifications of histones. Here we show using RNA FISH that in erythroid cells, intergenic transcription in the human beta-globin locus occurs over a region of greater than 250 kb including several genes in the nearby olfactory receptor gene cluster. This entire region is transcribed during S phase of the cell cycle. However, within this region there are approximately 20 kb sub-domains of high intergenic transcription that occurs outside of S phase. These sub-domains are developmentally regulated and enriched with high levels of active modifications primarily to histone H3. The sub-domains correspond to the beta-globin locus control region, which is active at all developmental stages in erythroid cells, and the region flanking the developmentally regulated, active globin genes. These results correlate high levels of non-S phase intergenic transcription with domain-wide active histone modifications to histone H3.

  10. Genome-wide profiling of transcription factor binding and epigenetic marks in adipocytes by ChIP-seq

    DEFF Research Database (Denmark)

    Nielsen, Ronni; Mandrup, Susanne

    2014-01-01

    of the most widely used of these technologies. Using these methods, association of transcription factors, cofactors, and epigenetic marks can be mapped to DNA in a genome-wide manner. Here, we provide a detailed protocol for performing ChIP-seq analyses in preadipocytes and adipocytes. We have focused mainly...

  11. Transcriptional profiling of an Fd-GOGAT1/GLU1 mutant in Arabidopsis thaliana reveals a multiple stress response and extensive reprogramming of the transcriptome

    Directory of Open Access Journals (Sweden)

    Størseth Trond R

    2010-03-01

    Full Text Available Abstract Background Glutamate plays a central position in the synthesis of a variety of organic molecules in plants and is synthesised from nitrate through a series of enzymatic reactions. Glutamate synthases catalyse the last step in this pathway and two types are present in plants: NADH- or ferredoxin-dependent. Here we report a genome wide microarray analysis of the transcriptional reprogramming that occurs in leaves and roots of the A. thaliana mutant glu1-2 knocked-down in the expression of Fd-GOGAT1 (GLU1; At5g04140, one of the two genes of A. thaliana encoding ferredoxin-dependent glutamate synthase. Results Transcriptional profiling of glu1-2 revealed extensive changes with the expression of more than 5500 genes significantly affected in leaves and nearly 700 in roots. Both genes involved in glutamate biosynthesis and transformation are affected, leading to changes in amino acid compositions as revealed by NMR metabolome analysis. An elevated glutamine level in the glu1-2 mutant was the most prominent of these changes. An unbiased analysis of the gene expression datasets allowed us to identify the pathways that constitute the secondary response of an FdGOGAT1/GLU1 knock-down. Among the most significantly affected pathways, photosynthesis, photorespiratory cycle and chlorophyll biosynthesis show an overall downregulation in glu1-2 leaves. This is in accordance with their slight chlorotic phenotype. Another characteristic of the glu1-2 transcriptional profile is the activation of multiple stress responses, mimicking cold, heat, drought and oxidative stress. The change in expression of genes involved in flavonoid biosynthesis is also revealed. The expression of a substantial number of genes encoding stress-related transcription factors, cytochrome P450 monooxygenases, glutathione S-transferases and UDP-glycosyltransferases is affected in the glu1-2 mutant. This may indicate an induction of the detoxification of secondary metabolites in the

  12. Genome-wide screening and transcriptional profile analysis of desaturase genes in the European corn borer moth

    Institute of Scientific and Technical Information of China (English)

    Bingye Xue; Alejandro P. Rooney; Wendell L. Roelofs

    2012-01-01

    Acyl-coenzyme A (Acyl-CoA) desaturases play a key role in the biosynthesis of female moth sex pheromones.Desaturase genes are encoded by a large multigene family,and they have been divided into five subgroups on the basis of biochemical functionality and phylogenetic affinity.In this study both copy numbers and transcriptional levels of desaturase genes in the European corn borer (ECB),Ostrinia nubilalis,were investigated.The results from genome-wide screening of ECB bacterial artificial chromosome (BAC)library indicated there are many copies of some desaturase genes in the genome.An open reading frame (ORF) has been isolated for the novel desaturase gene ECB ezi-△11β from ECB gland complementary DNA and its functionality has been analyzed by two yeast expression systems.No functional activities have been detected for it.The expression levels of the four desaturase genes both in the pheromone gland and fat body of ECB and Asian corn borer (ACB),O.furnacalis,were determined by real-time polymerase chain reaction.In the ECB gland,△ 11 is the most abundant,although the amount of △14 is also considerable.In the ACB gland,△14 is the most abundant and is 100 times more abundant than all the other three combined.The results from the analysis of evolution of desaturase gene transcription in the ECB,ACB and other moths indicate that the pattern of △ 11 gene transcription is significantly different from the transcriptional patterns of other desaturase genes and this difference is tied to the underlying nucleotide composition bias of the genome.

  13. Transcriptional profile of isoproterenol-induced cardiomyopathy and comparison to exercise-induced cardiac hypertrophy and human cardiac failure

    Directory of Open Access Journals (Sweden)

    McIver Lauren J

    2009-12-01

    Full Text Available Abstract Background Isoproterenol-induced cardiac hypertrophy in mice has been used in a number of studies to model human cardiac disease. In this study, we compared the transcriptional response of the heart in this model to other animal models of heart failure, as well as to the transcriptional response of human hearts suffering heart failure. Results We performed microarray analyses on RNA from mice with isoproterenol-induced cardiac hypertrophy and mice with exercise-induced physiological hypertrophy and identified 865 and 2,534 genes that were significantly altered in pathological and physiological cardiac hypertrophy models, respectively. We compared our results to 18 different microarray data sets (318 individual arrays representing various other animal models and four human cardiac diseases and identified a canonical set of 64 genes that are generally altered in failing hearts. We also produced a pairwise similarity matrix to illustrate relatedness of animal models with human heart disease and identified ischemia as the human condition that most resembles isoproterenol treatment. Conclusion The overall patterns of gene expression are consistent with observed structural and molecular differences between normal and maladaptive cardiac hypertrophy and support a role for the immune system (or immune cell infiltration in the pathology of stress-induced hypertrophy. Cross-study comparisons such as the results presented here provide targets for further research of cardiac disease that might generally apply to maladaptive cardiac stresses and are also a means of identifying which animal models best recapitulate human disease at the transcriptional level.

  14. Genome-wide profiling of AP-1-regulated transcription provides insights into the invasiveness of triple-negative breast cancer.

    Science.gov (United States)

    Zhao, Chunyan; Qiao, Yichun; Jonsson, Philip; Wang, Jian; Xu, Li; Rouhi, Pegah; Sinha, Indranil; Cao, Yihai; Williams, Cecilia; Dahlman-Wright, Karin

    2014-07-15

    Triple-negative breast cancer (TNBC) is an aggressive clinical subtype accounting for up to 20% of all breast cancers, but its malignant determinants remain largely undefined. Here, we show that in TNBC the overexpression of Fra-1, a component of the transcription factor AP-1, offers prognostic potential. Fra-1 depletion or its heterodimeric partner c-Jun inhibits the proliferative and invasive phenotypes of TNBC cells in vitro. Similarly, RNAi-mediated attenuation of Fra-1 or c-Jun reduced cellular invasion in vivo in a zebrafish tumor xenograft model. Exploring the AP-1 cistrome and the AP-1-regulated transcriptome, we obtained insights into the transcriptional regulatory networks of AP-1 in TNBC cells. Among the direct targets identified for Fra-1/c-Jun involved in proliferation, adhesion, and cell-cell contact, we found that AP-1 repressed the expression of E-cadherin by transcriptional upregulation of ZEB2 to stimulate cell invasion. Overall, this work illuminates the pathways through which TNBC cells acquire invasive and proliferative properties.

  15. Genetic diversity revealed by AFLP markers in Albanian goat breeds

    Directory of Open Access Journals (Sweden)

    Hoda Anila

    2012-01-01

    Full Text Available The amplified fragment length polymorphism (AFLP technique with three EcoRI/TaqI primer combinations was used in 185 unrelated individuals, representative of 6 local goat breeds of Albania, and 107 markers were generated. The mean Nei’s expected heterozygosity value for the whole population was 0.199 and the mean Shannon index was 0.249, indicating a high level of within-breed diversity. Wright’s FST index, Nei’s unbiased genetic distance and Reynolds’ genetic distance were calculated. Pairwise Fst values among the populations ranged from 0.019 to 0.047. A highly significant average FST of 0.031 was estimated, showing a low level of breed subdivision. Most of the variation is accounted for by differences among individuals. Cluster analysis based on Reynolds’ genetic distance between breeds and PCA were performed. An individual UPGMA tree based on Jaccard’s similarity index showed clusters with individuals from all goat breeds. Analysis of population structure points to a high level of admixture among breeds.

  16. Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds.

    Science.gov (United States)

    Weissgerber, Thomas; Dobler, Nadine; Polen, Tino; Latus, Jeanette; Stockdreher, Yvonne; Dahl, Christiane

    2013-09-01

    The purple sulfur bacterium Allochromatium vinosum DSM 180(T) is one of the best-studied sulfur-oxidizing anoxygenic phototrophic bacteria, and it has been developed into a model organism for laboratory-based studies of oxidative sulfur metabolism. Here, we took advantage of the organism's high metabolic versatility and performed whole-genome transcriptional profiling to investigate the response of A. vinosum cells upon exposure to sulfide, thiosulfate, elemental sulfur, or sulfite compared to photoorganoheterotrophic growth on malate. Differential expression of 1,178 genes was observed, corresponding to 30% of the A. vinosum genome. Relative transcription of 551 genes increased significantly during growth on one of the different sulfur sources, while the relative transcript abundance of 627 genes decreased. A significant number of genes that revealed strongly enhanced relative transcription levels have documented sulfur metabolism-related functions. Among these are the dsr genes, including dsrAB for dissimilatory sulfite reductase, and the sgp genes for the proteins of the sulfur globule envelope, thus confirming former results. In addition, we identified new genes encoding proteins with appropriate subcellular localization and properties to participate in oxidative dissimilatory sulfur metabolism. Those four genes for hypothetical proteins that exhibited the strongest increases of mRNA levels on sulfide and elemental sulfur, respectively, were chosen for inactivation and phenotypic analyses of the respective mutant strains. This approach verified the importance of the encoded proteins for sulfur globule formation during the oxidation of sulfide and thiosulfate and thereby also documented the suitability of comparative transcriptomics for the identification of new sulfur-related genes in anoxygenic phototrophic sulfur bacteria. PMID:23873913

  17. A Reliable Method for the Selection of Exploitable Melanoma Archival Paraffin Embedded Tissues for Transcript Biomarker Profiling

    OpenAIRE

    Celeste Lebbe; Mickael Guedj; Nicole Basset-Seguin; Marie Pierre Podgorniak; Suzanne Menashi; Anne Janin; Samia Mourah

    2012-01-01

    The source tissue for biomarkers mRNA expression profiling of tumors has traditionally been fresh-frozen tissue. The adaptation of formalin-fixed, paraffin-embedded (FFPE) tissues for routine mRNA profiling would however be invaluable in view of their abundance and the clinical information related to them. However, their use in the clinic remains a challenge due to the poor quality of RNA extracted from such tissues. Here, we developed a method for the selection of melanoma archival paraffin-...

  18. Simulated Microgravity Regulates Gene Transcript Profiles of 2T3 Preosteoblasts: Comparison of the Random Positioning Machine and the Rotating Wall Vessel Bioreactor

    Science.gov (United States)

    Patel, Mamta J.; Liu, Wenbin; Sykes, Michelle C.; Ward, Nancy E.; Risin, Semyon A.; Risin, Diana; Hanjoong, Jo

    2007-01-01

    Microgravity of spaceflight induces bone loss due in part to decreased bone formation by osteoblasts. We have previously examined the microgravity-induced changes in gene expression profiles in 2T3 preosteoblasts using the Random Positioning Machine (RPM) to simulate microgravity conditions. Here, we hypothesized that exposure of preosteoblasts to an independent microgravity simulator, the Rotating Wall Vessel (RWV), induces similar changes in differentiation and gene transcript profiles, resulting in a more confined list of gravi-sensitive genes that may play a role in bone formation. In comparison to static 1g controls, exposure of 2T3 cells to RWV for 3 days inhibited alkaline phosphatase activity, a marker of differentiation, and downregulated 61 genes and upregulated 45 genes by more than two-fold as shown by microarray analysis. The microarray results were confirmed with real time PCR for downregulated genes osteomodulin, bone morphogenic protein 4 (BMP4), runx2, and parathyroid hormone receptor 1. Western blot analysis validated the expression of three downregulated genes, BMP4, peroxiredoxin IV, and osteoglycin, and one upregulated gene peroxiredoxin I. Comparison of the microarrays from the RPM and the RWV studies identified 14 gravi-sensitive genes that changed in the same direction in both systems. Further comparison of our results to a published database showing gene transcript profiles of mechanically loaded mouse tibiae revealed 16 genes upregulated by the loading that were shown to be downregulated by RWV and RPM. These mechanosensitive genes identified by the comparative studies may provide novel insights into understanding the mechanisms regulating bone formation and potential targets of countermeasure against decreased bone formation both in astronauts and in general patients with musculoskeletal disorders.

  19. Molecular interaction of a kinase inhibitor midostaurin with anticancer drug targets, S100A8 and EGFR: transcriptional profiling and molecular docking study for kidney cancer therapeutics.

    Directory of Open Access Journals (Sweden)

    Zeenat Mirza

    Full Text Available The S100A8 and epidermal growth factor receptor (EGFR proteins are proto-oncogenes that are strongly expressed in a number of cancer types. EGFR promotes cellular proliferation, differentiation, migration and survival by activating molecular pathways. Involvement of proinflammatory S100A8 in tumor cell differentiation and progression is largely unclear and not studied in kidney cancer (KC. S100A8 and EGFR are potential therapeutic biomarkers and anticancer drug targets for KC. In this study, we explored molecular mechanisms of interaction profiles of both molecules with potential anticancer drugs. We undertook transcriptional profiling in Saudi KCs using Affymetrix HuGene 1.0 ST arrays. We identified 1478 significantly expressed genes, including S100A8 and EGFR overexpression, using cut-off p value <0.05 and fold change ≥2. Additionally, we compared and confirmed our findings with expression data available at NCBI's GEO database. A significant number of genes associated with cancer showed involvement in cell cycle progression, DNA repair, tumor morphology, tissue development, and cell survival. Atherosclerosis signaling, leukocyte extravasation signaling, notch signaling, and IL-12 signaling were the most significantly disrupted signaling pathways. The present study provides an initial transcriptional profiling of Saudi KC patients. Our analysis suggests distinct transcriptomic signatures and pathways underlying molecular mechanisms of KC progression. Molecular docking analysis revealed that the kinase inhibitor "midostaurin" has amongst the selected drug targets, the best ligand properties to S100A8 and EGFR, with the implication that its binding inhibits downstream signaling in KC. This is the first structure-based docking study for the selected protein targets and anticancer drug, and the results indicate S100A8 and EGFR as attractive anticancer targets and midostaurin with effective drug properties for therapeutic intervention in KC.

  20. Outcrossing rate between 'Haden' and 'Tommy Atkins' mangoes estimated using microsatellite and AFLP markers

    Directory of Open Access Journals (Sweden)

    Carlos Antonio Fernandes Santos

    2011-08-01

    Full Text Available The objective of this work was to estimate outcrossing rates between Haden and Tommy Atkins mango cultivars, using AFLP and microsatellite markers. Progenies of an isolated 'Haden' plant, identified in a 'Tommy Atkins' commercial orchard, in Petrolina, PE, Brazil, were analyzed. Total DNA was isolated from the progeny leaves and used for AFLP and microsatellite reactions. Multilocus outcrossing rates (t m were estimated by direct count of AFLP or microsatellite markers and by the mLTR software. Outcrossing rates ranged from 0.85 to 0.87 with the analysis based on seven AFLP markers, and from 0.83 to 0.91 based on three microsatellite primers. No unexpected band patterns were observed for 'Haden' and 'Tommy Atkins'. The estimates obtained with the mLTR software were close to those obtained by direct AFLP and microsatellite allele counting, which indicates that the multilocus model was appropriate for this kind of study. The microsatellites mMiCIR005, mMiCIR030, and mMiCIR036 can be used to elucidate the origin of 'Haden' and 'Tommy Atkins' seedlings.

  1. cDNA-AFLP analysis of differential gene expression related to cell chemotactic and encystment of Azospirillum brasilense.

    Science.gov (United States)

    Li, Huamin; Cui, Yanhua; Wu, Lixian; Tu, Ran; Chen, Sanfeng

    2011-12-20

    Our previous study indicated org35 was involved in chemotaxis and interacted with nitrogen fixation transcriptional activator NifA via PAS domain. In order to reveal the role of org35 in nitrogen regulation, the downstream target genes of org35 were identified. We here report differentially expressed genes in org35 mutants comparing with wild type Sp7 by means of cDNA-AFLP. Four up-regulated transcript-derived fragments (TDFs) homologues of chemotaxis transduction proteins were found, including CheW, methyl-accepting chemotaxis protein and response regulator CheY-like receiver. Three distinct TDFs (AB46, AB58 and AB63) were similar to PHB de-polymerase C-terminus, cell shape-determining protein and flagellin domain protein. And 11 TDFs showed similarities with signal transduction proteins, including homologous protein of the nitrogen regulation protein NtrY and nitrate/nitrite response regulator protein NarL. These data suggested that the Azospirillum brasilense org35 was a multi-effecter and involved in chemotaxis, cyst development and regulation of nitrogen fixation.

  2. Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds

    NARCIS (Netherlands)

    Scheublin, T.R.; Deusch, S.; Moreno-Forero, S.K.; Müller, J.A.; van der Meer, J.R.; Leveau, J.H.J.

    2014-01-01

    Arthrobacter chlorophenolicus A6 is a Gram-positive, 4-chlorophenol degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome-wide expression profile of A.

  3. Transcriptional profiling of human familial longevity indicates a role for ASF1A and IL7R

    NARCIS (Netherlands)

    Passtoors, W.M.; Boer, J.M.; Goeman, J.G.; Van den Akker, E.B.; Deelen, J.; Zwaan, B.J.; Scarborough, A.; Van der Breggen, R.; Vossen, R.H.A.M.; et al.

    2012-01-01

    The Leiden Longevity Study consists of families that express extended survival across generations, decreased morbidity in middle-age, and beneficial metabolic profiles. To identify which pathways drive this complex phenotype of familial longevity and healthy aging, we performed a genome-wide gene ex

  4. Changes in the transcriptional profile of transporters in the intestine along the anterior-posterior and crypt-villus axes

    Directory of Open Access Journals (Sweden)

    Delorenzi Mauro

    2005-05-01

    Full Text Available Abstract Background The purpose of this work was to characterize the expression of drug and nutrient carriers along the anterior-posterior and crypt-villus axes of the intestinal epithelium and to study the validity of utilizing whole gut tissue rather than purified epithelial cells to examine regional variations in gene expression. Results We have characterized the mRNA expression profiles of 76 % of all currently known transporters along the anterior-posterior axis of the gut. This is the first study to describe the expression profiles of the majority of all known transporters in the intestine. The expression profiles of transporters, as defined according to the Gene Ontology consortium, were measured in whole tissue of the murine duodenum, jejunum, ileum and colon using high-density microarrays. For nine transporters (Abca1, Abcc1, Abcc3, Abcg8, Slc10a2, Slc28a2, Slc2a1, Slc34a2 and Slc5a8, the mRNA profiles were further measured by RT-PCR in laser micro-dissected crypt and villus epithelial cells corresponding to the aforementioned intestinal regions. With respect to differentially regulated transporters, the colon had a distinct expression profile from small intestinal segments. The majority (59 % for p cutoff ≤ 0.05 of transporter mRNA levels were constant across the intestinal sections studied. For the transporter subclass "carrier activity", which contains the majority of known carriers for biologically active compounds, a significant change (p ≤ 0.05 along the anterior-posterior axis was observed. Conclusion All nine transporters examined in laser-dissected material demonstrated good replication of the region-specific profiles revealed by microarray. Furthermore, we suggest that the distribution characteristics of Slc5a8 along the intestinal tract render it a suitable candidate carrier for monocarboxylate drugs in the posterior portion of the intestine. Our findings also predict that there is a significant difference in the

  5. Utility of in vivo transcription profiling for identifying Pseudomonas aeruginosa genes needed for gastrointestinal colonization and dissemination

    DEFF Research Database (Denmark)

    Koh, Andrew Y; Mikkelsen, Per J; Smith, Roger S;

    2010-01-01

    mutants and WT P. aeruginosa PA14. To evaluate T3SS factors, we tested GI colonization and neutropenia-induced dissemination of both deletional (PAO1 and PAK) and insertional (PA14) mutants in four genes in the P. aeruginosa T3SS, exoS or exoU, exoT, and popB. There were no significant differences in GI......, increased transcription of genes during in vivo murine GI colonization is not predictive of an essential role for the gene product in either colonization or overall survival following induction of neutropenia....

  6. Genetic structure in cultivated and wild carrots (¤Daucus carota¤ L.) revealed by AFLP analysis

    DEFF Research Database (Denmark)

    Shim, S.I.; Bagger Jørgensen, Rikke

    2000-01-01

    Genetic variation within and among five Danish populations of wild carrot and five cultivated varieties was investigated using amplified fragment length polymorphism (AFLP). Ten AFLP primer combinations produced 116 polymorphic bands. Based on the marker data an UPGMA-cluster analysis and principal...... markers specific to the cultivated carrot makes it possible to detect introgression from cultivated to wild types....

  7. Optimization of AFLP fingerprinting of organisms with a large-sized genome: a study on Alstroemeria spp

    NARCIS (Netherlands)

    Han, T.H.; Eck, van H.J.; Jeu, de M.J.; Jacobsen, E.

    1999-01-01

    The recently introduced PCR-based DNA fingerprinting technique AFLP (amplified fragment length polymorphism) allows the selective amplification of subsets of genomic restriction fragments. AFLP has been used for multiple purposes such as the construction of linkage maps, marker saturation at specifi

  8. Genome-Wide Transcriptional Profile Analysis of Prunus persica in Response to Low Sink Demand after Fruit Removal.

    Science.gov (United States)

    Duan, Wei; Xu, Hongguo; Liu, Guotian; Fan, Peige; Liang, Zhenchang; Li, Shaohua

    2016-01-01

    Prunus persica fruits were removed from 1-year-old shoots to analysis photosynthesis, chlorophyll fluorescence and genes changes in leaves to low sink demand caused by fruit removal (-fruit) during the final stage of rapid fruit growth. A decline in net photosynthesis rate was observed, accompanied with a decrease in stomatal conductance. The intercellular CO2 concentrations and leaf temperature increased as compared with a normal fruit load (+fruit). Moreover, low sink demand significantly inhibited the donor side and the reaction center of photosystem II. 382 genes in leaf with an absolute fold change ≥1 change in expression level, representing 116 up- and 266 down-regulated genes except for unknown transcripts. Among these, 25 genes for photosynthesis were down-regulated, 69 stress and 19 redox related genes up-regulated under the low sink demand. These studies revealed high leaf temperature may result in a decline of net photosynthesis rate through down-regulation in photosynthetic related genes and up-regulation in redox and stress related genes, especially heat shock proteins genes. The complex changes in genes at the transcriptional level under low sink demand provided useful starting points for in-depth analyses of source-sink relationship in P. persica.

  9. Characterization and Transcriptional Profile of Genes Involved in Glycoalkaloid Biosynthesis in New Varieties of Solanum tuberosum L.

    Science.gov (United States)

    Mariot, Roberta Fogliatto; de Oliveira, Luisa Abruzzi; Voorhuijzen, Marleen M; Staats, Martijn; Hutten, Ronald C B; van Dijk, Jeroen P; Kok, Esther J; Frazzon, Jeverson

    2016-02-01

    Before commercial release, new potato (Solanum tuberosum) varieties must be evaluated for content of toxic compounds such as glycoalkaloids (GAs), which are potent poisons. GA biosynthesis proceeds via the cholesterol pathway to α-chaconine and α-solanine. The goal of this study was to evaluate the relationship between total glycoalkaloid (TGA) content and the expression of GAME, SGT1, and SGT3 genes in potato tubers. TGA content was measured by HPLC-MS, and reverse transcription quantitative polymerase chain reactions were performed to determine the relative expression of GAME, SGT1, and SGT3 genes. We searched for cis-elements of the transcription start site using the PlantPAN database. There was a relationship between TGA content and the relative expression of GAME, SGT1, and SGT3 genes in potato tubers. Putative promoter regions showed the presence of several cis-elements related to biotic and abiotic stresses and light. These findings provide an important step toward understanding TGA regulation and variation in potato tubers.

  10. Transcriptional profiling of immortalized and K-ras-transformed mouse fibroblasts upon PKA stimulation by forskolin in low glucose availability.

    Science.gov (United States)

    Chiaradonna, Ferdinando; Pirola, Yuri; Ricciardiello, Francesca; Palorini, Roberta

    2016-09-01

    Forskolin (FSK) induces activation of protein kinase A (PKA). This activation protects specifically some cancer cells from death induced by glucose starvation. Cell effects upon FSK treatment prompted us to investigate in detail the physiological role of PKA in the activation of pro-survival mechanisms in glucose starvation. In this regard we performed a microarray analysis of normal NIH3T3 and transformed NIH3T3-K-ras mouse fibroblasts cultured at 1 mM glucose and daily treated or not with 10 μM FSK until 72 h of growth, when the samples were collected. The microarray is deposited into Gene Expression Omnibus under Series GSE68266. The microarray data revealed that the activation of PKA regulates the expression of genes involved in metabolic, stress-response and pro-survival processes, like glutamine metabolism, autophagy and unfolded protein response, preventing cancer cell death in glucose starvation. Altogether these findings suggest that PKA activation, by inducing a complex transcriptional program, leads to cancer survival in nutrient stress, a typical feature of developing tumor. These transcriptional data, identifying this important role of PKA, will be useful to identify novel target in cancer therapy. PMID:27486565

  11. Global expression profiling of transcription factor genes provides new insights into pathogenicity and stress responses in the rice blast fungus.

    Directory of Open Access Journals (Sweden)

    Sook-Young Park

    Full Text Available Because most efforts to understand the molecular mechanisms underpinning fungal pathogenicity have focused on studying the function and role of individual genes, relatively little is known about how transcriptional machineries globally regulate and coordinate the expression of a large group of genes involved in pathogenesis. Using quantitative real-time PCR, we analyzed the expression patterns of 206 transcription factor (TF genes in the rice blast fungus Magnaporthe oryzae under 32 conditions, including multiple infection-related developmental stages and various abiotic stresses. The resulting data, which are publicly available via an online platform, provided new insights into how these TFs are regulated and potentially work together to control cellular responses to a diverse array of stimuli. High degrees of differential TF expression were observed under the conditions tested. More than 50% of the 206 TF genes were up-regulated during conidiation and/or in conidia. Mutations in ten conidiation-specific TF genes caused defects in conidiation. Expression patterns in planta were similar to those under oxidative stress conditions. Mutants of in planta inducible genes not only exhibited sensitive to oxidative stress but also failed to infect rice. These experimental validations clearly demonstrated the value of TF expression patterns in predicting the function of individual TF genes. The regulatory network of TF genes revealed by this study provides a solid foundation for elucidating how M. oryzae regulates its pathogenesis, development, and stress responses.

  12. Transcriptome-wide analysis of WRKY transcription factors in wheat and their leaf rust responsive expression profiling.

    Science.gov (United States)

    Satapathy, Lopamudra; Singh, Dharmendra; Ranjan, Prashant; Kumar, Dhananjay; Kumar, Manish; Prabhu, Kumble Vinod; Mukhopadhyay, Kunal

    2014-12-01

    WRKY, a plant-specific transcription factor family, has important roles in pathogen defense, abiotic cues and phytohormone signaling, yet little is known about their roles and molecular mechanism of function in response to rust diseases in wheat. We identified 100 TaWRKY sequences using wheat Expressed Sequence Tag database of which 22 WRKY sequences were novel. Identified proteins were characterized based on their zinc finger motifs and phylogenetic analysis clustered them into six clades consisting of class IIc and class III WRKY proteins. Functional annotation revealed major functions in metabolic and cellular processes in control plants; whereas response to stimuli, signaling and defense in pathogen inoculated plants, their major molecular function being binding to DNA. Tag-based expression analysis of the identified genes revealed differential expression between mock and Puccinia triticina inoculated wheat near isogenic lines. Gene expression was also performed with six rust-related microarray experiments at Gene Expression Omnibus database. TaWRKY10, 15, 17 and 56 were common in both tag-based and microarray-based differential expression analysis and could be representing rust specific WRKY genes. The obtained results will bestow insight into the functional characterization of WRKY transcription factors responsive to leaf rust pathogenesis that can be used as candidate genes in molecular breeding programs to improve biotic stress tolerance in wheat.

  13. Jasmonic acid-isoleucine formation in grapevine (Vitis vinifera L.) by two enzymes with distinct transcription profiles

    Institute of Scientific and Technical Information of China (English)

    Christine Böttcher; Crista A. Burbidge; Valentina di Rienzo; PauLK. Boss; Christopher Davies

    2015-01-01

    The plant hormone jasmonic acid (JA) is essential for stress responses and the formation of reproductive organs, but its role in fruit development and ripening is unclear. Conjugation of JA to isoleucine is a crucial step in the JA signaling pathway since only JA-Ile is recognized by the jasmonate receptor. The conjugation reaction is catalyzed by JA-amido synthetases, belonging to the family of Gretchen Hagen3 (GH3) proteins. Here, in vitro studies of two grapevine (Vitis vinifera L. cv Shiraz) GH3 enzymes, VvGH3-7 and VvGH3-9, demonstrated JA-conjugating activ-ities with an overlapping range of amino acid substrates, including isoleucine. Expression studies of the correspond-ing genes in grape berries combined with JA and JA-Ile measurements suggested a primary role for JA signaling in fruit set and cell division and did not support an involvement of JA in the ripening process. In response to methyl JA (MeJA) treatment, and in wounded and unwounded (distal) leaves, VvGH3-9 transcripts accumulated, indicating a participation in the JA response. In contrast, VvGH3-7 was unresponsive to MeJA and local wounding, demonstrating a differential transcriptional regulation of VvGH3-7 and VvGH3-9. The transient induction of VvGH3-7 in unwounded, distal leaves was suggestive of the involvement of an unknown mobile wound signal.

  14. Expression profiles and transactivation analysis of a novel ethylene-responsive transcription factor gene GhERF5 from cotton

    Institute of Scientific and Technical Information of China (English)

    Longguo Jin; Bo Huang; Hui Li; Jinyuan Liu

    2009-01-01

    Plant AP2/EREBP transcription factors play important roles in plant development and in plant responses to biotic and abiotic stresses.A novel gene for ethylene-responsive element binding protein (EREBP),designated GhERF5,which encodes a protein of 255 amino acids,was isolated by RACE-PCR from cotton (Gossypium hirsutum) seedlings.Sequence alignment revealed that GhERF5 contains a typical AP2/ERF domain,and belongs to the B3 subgroup of the ERF subfamily.Particle bombardment assay showed that GhERF5 functions as an in vivo transcription activator in tobacco cells,and it is located in the nuclei of onion epidermis cells.Semi-quantitative RT-PCR revealed that the expression of GhERF5 was highly and rapidly induced when plants were treated with exogenous ethylene,abscisic acid (ABA),salt,cold and drought.Promoter analysis indicated that there are conserved cis-acting elements induced by these stresses in the 5'-upstream region of the GhERF5 gene.These results suggest that the GhERF5 gene might play an important role in cotton response to ethylene,ABA and environmental stresses.(C)2008 National Natural Science Foundation of China and Chinese Academy of Sciences.Published by Elsevier Limited and Science in China Press.All rights reserved.

  15. 利用cDNA-AFLP分析内生解淀粉芽胞杆菌Fy11诱导辣椒差异表达基因%cDNA-AFLP Analysis of Differential Gene Expression in Pepper Inoculated with Endophytic Bacillus amyloliquefaciens Fy11

    Institute of Scientific and Technical Information of China (English)

    杨瑞先; 范晓静; 邱思鑫; 蔡学清; 胡方平

    2013-01-01

    [目的]分析内生解淀粉芽胞杆菌(Bacillus amyloliquefaciens)Fy11诱导辣椒(Capsicum annuum)幼苗差异表达基因,了解辣椒与内生芽胞杆菌互作的分子机制.[方法]利用cDNA-AFLP技术,采用256对引物,分析辣椒幼苗接种内生解淀粉芽胞杆菌Fy11后5个时间点的基因表达谱;利用qRT-PCR分析差异基因表达模式,验证cDNA-AFLP表达谱.[结果]256对引物共产生18620个转录本(TDF),筛选获得353条差异表达条带,占扩增条带总数的1.89%.经克隆、测序分析,最终获得257个差异TDF,聚类分析得到229个独立基因(EST,unigenes),其中144个基因上调表达,85个基因下调表达.经Blastx比对和功能分类分析,其中65条EST(28.38%)未找到同源性匹配,8条(3.49%)与未知功能蛋白同源性较高.其余156条EST主要涉及基础代谢基因(10.92%);与能量和抗病与防御类相关基因,各占8.73%;信号转导基因占7.42%;转运子或转座子基因占6.99%;与细胞结构相关基因占6.55%;参与转录调控基因占5.68%;细胞生长类基因占3.93%;参与蛋白质运输和储存有8个基因,占3.49%;蛋白质合成类基因占2.18%;次生代谢类和胞间运输类基因,其数量相对较少,各占1.75%.选取与抗病防御、转录调控及信号转导类等相关的10个差异基因,qRT-PCR分析结果显示其表达模式符合cDNA-AFLP表达谱.[结论]内生细菌与植物互作的分子机制涉及植物多方面生理生化反应,包括抗病防御、转录调控、蛋白质代谢、信号转导、以及非生物胁迫等多种途径相关基因的协同控制.%[Objective] The objective of this study is to analyze extensive transcription profiling of pepper seedlings inoculated with an endophytic bacterial strain,Bacillus amyloliquefaciens Fyl l,and elucidate the molecular mechanism of endophytic Bacillus and plant interaction.[Method] cDNA-AFLP technique was used to conduct transcription profiling of

  16. Isolation, cloning and sequencing of AFLP markers related to disease-resistance traits in Fenneropenaeus chinensis

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Amplified fragment length polymorphisms (AFLP) technique was used to analyze the fingerprinting of four successive generations of Fenneropenaeus chinensis to reveal their disease-resistance traits. Some loci showed quite different genetic frequencies due to artificial selection, which implied that these fragments were putative markers related to the disease-resistance trait. We developed a simple and effective method to further characterize these AFLP fragments. Specific AFLP bands were cut directly from polyacrylamide gels,re-amplified, cloned and sequenced. Eight putative genetic markers were sequenced and their sizes ranged from 63 to 209 bp. The sequences were submitted to dbGSS (database of Genome Sequence Survey); and the BLAST analysis showed low similarity to the function genes, indicating these markers were tightly linked to a disease-resistance trait but were not functional genes.

  17. Genetic diversity of Chilean and Brazilian alstroemeria species assessed by AFLP analysis.

    Science.gov (United States)

    Han, T H; de Jeu, M; van Eck, H; Jacobsen, E

    2000-05-01

    One to three accessions of 22 Alstroemeria species, an interspecific hybrid (A. aurea x A. inodora), and single accessions of Bomarea salsilla and Leontochir ovallei were evaluated using the AFLP-marker technique to estimate the genetic diversity within the genus Alstroemeria. Three primer combinations generated 716 markers and discriminated all Alstroemeria species. The dendrogram inferred from the AFLP fingerprints supported the conjecture of the generic separation of the Chilean and Brazilian Alstroemeria species. The principal co-ordinate plot showed the separate allocation of the A. ligtu group and the allocation of A. aurea, which has a wide range of geographical distribution and genetic variation, in the middle of other Alstroemeria species. The genetic distances, based on AFLP markers, determined the genomic contribution of the parents to the interspecific hybrid. PMID:10849081

  18. Low level of genetic variation within Melica transsilvanica populations from the Kraków-Częstochowa Upland and the Pieniny Mts revealed by AFLPs analysis

    Directory of Open Access Journals (Sweden)

    Magdalena Szczepaniak

    2011-04-01

    Full Text Available Fragmented distribution, the breeding system and effects of genetic drift in small-size populations occurring at edge of the species range play an important role in shaping genetic diversity of such a species. Melica transsilvanica is a plant rare in the flora of Poland, where it reaches the northern limit of its continuous range. Amplified Fragment Length Polymorphism (AFLP DNA profiling method was applied to measure genetic diversity among and within populations of M. transsilvanica. Additionally, genetic relationships between M. transsilvanica and Melica ciliata, two closely related species, were explored. A total of 68 plants from 7 populations of M. transsilvanica and 24 plants from 2 populations of M. ciliata, collected in Poland and outside it, were analyzed. Using 294 AFLP fragments from 3 primer combinations, accessions were grouped into two major clusters associating with M. ciliata and M. transsilvanica, respectively. Further, two subclusters, corresponding to the samples collected from the Pieniny Mts and from the Kraków - Częstochowa Upland were clearly distinguished within the M. transsilvanica group. The hierarchical AMOVA exhibited significant genetic distinction between these geographic regions (60.89%, p < 0.001. The obtained results showed that the most genetic diversity resided between the populations of M. transsilvanica (86.03% while considerably lower genetic variation was found within the populations (13.97%, which is consistent with the results reported for self-plants. The low level of AFLP genetic variation of M. transsilvanica can be caused by the geographic isolation of populations, which preserves the dominant self-mating breeding system of the species. Individual populations of M. transsilvanica are characterized by isolated gene pools differing by a small number of loci.

  19. Gene expression profiling reveals the heterogeneous transcriptional activity of Oct3/4 and its possible interaction with Gli2 in mouse embryonic stem cells.

    Science.gov (United States)

    Li, Yanzhen; Drnevich, Jenny; Akraiko, Tatiana; Band, Mark; Li, Dong; Wang, Fei; Matoba, Ryo; Tanaka, Tetsuya S

    2013-01-01

    We examined the transcriptional activity of Oct3/4 (Pou5f1) in mouse embryonic stem cells (mESCs) maintained under standard culture conditions to gain a better understanding of self-renewal in mESCs. First, we built an expression vector in which the Oct3/4 promoter drives the monocistronic transcription of Venus and a puromycin-resistant gene via the foot-and-mouth disease virus self-cleaving peptide T2A. Then, a genetically-engineered mESC line with the stable integration of this vector was isolated and cultured in the presence or absence of puromycin. The cultures were subsequently subjected to Illumina expression microarray analysis. We identified approximately 4600 probes with statistically significant differential expression. The genes involved in nucleic acid synthesis were overrepresented in the probe set associated with mESCs maintained in the presence of puromycin. In contrast, the genes involved in cell differentiation were overrepresented in the probe set associated with mESCs maintained in the absence of puromycin. Therefore, it is suggested with these data that the transcriptional activity of Oct3/4 fluctuates in mESCs and that Oct3/4 plays an essential role in sustaining the basal transcriptional activities required for cell duplication in populations with equal differentiation potential. Heterogeneity in the transcriptional activity of Oct3/4 was dynamic. Interestingly, we found that genes involved in the hedgehog signaling pathway showed unique expression profiles in mESCs and validated this observation by RT-PCR analysis. The expression of Gli2, Ptch1 and Smo was consistently detected in other types of pluripotent stem cells examined in this study. Furthermore, the Gli2 protein was heterogeneously detected in mESC nuclei by immunofluorescence microscopy and this result correlated with the detection of the Oct3/4 protein. Finally, forced activation of Gli2 in mESCs increased their proliferation rate. Collectively, it is suggested with these results

  20. Transcriptional profiling of nitrogen fixation and the role of NifA in the diazotrophic endophyte Azoarcus sp. strain BH72.

    Directory of Open Access Journals (Sweden)

    Abhijit Sarkar

    Full Text Available BACKGROUND: The model endophyte Azoarcus sp. strain BH72 is known to contribute fixed nitrogen to its host Kallar grass and also expresses nitrogenase genes endophytically in rice seedlings. Availability of nitrogen is a signal regulating the transcription of nitrogenase genes. Therefore, we analysed global transcription in response to differences in the nitrogen source. METHODOLOGY/PRINCIPAL FINDINGS: A DNA microarray, comprising 70-mer oligonucleotides representing 3989 open reading frames of the genome of strain BH72, was used for transcriptome studies. Transcription profiles of cells grown microaerobically on N2 versus ammonium were compared. Expression of 7.2% of the genes was significantly up-regulated, and 5.8% down-regulated upon N2 fixation, respectively. A parallel genome-wide prediction of σ(54-type promoter elements mapped to the upstream region of 38 sequences of which 36 were modulated under the N2 response. In addition to modulation of genes related to N2 fixation, the expressions of gene clusters that might be related to plant-microbe interaction and of several transcription factors were significantly enhanced. While comparing under N2-fixation conditions the transcriptome of wild type with a nifLA(- insertion mutant, NifA being the essential transcriptional activator for nif genes, 24.5% of the genome was found to be affected in expression. A genome-wide prediction of 29 NifA binding sequences matched to 25 of the target genes whose expression was differential during microarray analysis, some of which were putatively negatively regulated by NifA. For selected genes, differential expression was corroborated by real time RT-PCR studies. CONCLUSION/SIGNIFICANCE: Our data suggest that life under conditions of nitrogen fixation is an important part of the lifestyle of strain BH72 in roots, as a wide range of genes far beyond the nif regulon is modulated. Moreover, the NifA regulon in strain BH72 appears to encompass a wider range of

  1. [Use of AFLP analysis for the molecular biological fine typing of Campylobacter jejuni strains from turkey flocks].

    Science.gov (United States)

    Alter, Thomas; Fehlhaber, Karsten

    2003-01-01

    One of the most promising genotyping methods for microorganisms is the AFLP (amplified fragment length polymorphism)-analysis, originally developed to genotype plants. The AFLP method has a high discriminatory power and an excellent reproducibility. Thus it is suitable for solving taxonomic and epidemiological questions. AFLP analysis was used to reveal the genetic diversity of Campylobacter (C.) jejuni strains from turkeys. The aim was to detect and genotype C. jejuni strains on individual turkeys throughout the complete slaughter process. A broad spectrum of genotypes was detectable on the turkey skin at the beginning of the slaughter line. At the end of the slaughter process-after chilling, only a diminished spectrum of genotypes was detectable by AFLP-analysis, suggesting, that slaughter specific environmental stressors may exert a selective pressure on the strain diversity. Our results proved, that AFLP analysis is an excellent tool for subtyping large numbers of Campylobacter strains. PMID:14655622

  2. The transcriptional profile of mesenchymal stem cell populations in primary osteoporosis is distinct and shows overexpression of osteogenic inhibitors.

    Directory of Open Access Journals (Sweden)

    Peggy Benisch

    Full Text Available Primary osteoporosis is an age-related disease characterized by an imbalance in bone homeostasis. While the resorptive aspect of the disease has been studied intensely, less is known about the anabolic part of the syndrome or presumptive deficiencies in bone regeneration. Multipotent mesenchymal stem cells (MSC are the primary source of osteogenic regeneration. In the present study we aimed to unravel whether MSC biology is directly involved in the pathophysiology of the disease and therefore performed microarray analyses of hMSC of elderly patients (79-94 years old suffering from osteoporosis (hMSC-OP. In comparison to age-matched controls we detected profound changes in the transcriptome in hMSC-OP, e.g. enhanced mRNA expression of known osteoporosis-associated genes (LRP5, RUNX2, COL1A1 and of genes involved in osteoclastogenesis (CSF1, PTH1R, but most notably of genes coding for inhibitors of WNT and BMP signaling, such as Sclerostin and MAB21L2. These candidate genes indicate intrinsic deficiencies in self-renewal and differentiation potential in osteoporotic stem cells. We also compared both hMSC-OP and non-osteoporotic hMSC-old of elderly donors to hMSC of ∼30 years younger donors and found that the transcriptional changes acquired between the sixth and the ninth decade of life differed widely between osteoporotic and non-osteoporotic stem cells. In addition, we compared the osteoporotic transcriptome to long term-cultivated, senescent hMSC and detected some signs for pre-senescence in hMSC-OP.Our results suggest that in primary osteoporosis the transcriptomes of hMSC populations show distinct signatures and little overlap with non-osteoporotic aging, although we detected some hints for senescence-associated changes. While there are remarkable inter-individual variations as expected for polygenetic diseases, we could identify many susceptibility genes for osteoporosis known from genetic studies. We also found new candidates, e.g. MAB21L

  3. Comparative profiling of the transcriptional response to iron restriction in six serotypes of Actinobacillus pleuropneumoniae with different virulence potential

    DEFF Research Database (Denmark)

    Schou, Kirstine Klitgaard; Friis, Carsten; Angen, Øystein;

    2011-01-01

    receptor of Neisseria meningitidis, a possible virulence factor which contributes to bacterial survival in rats. Conclusions By comparative analysis of gene expression among 6 different serotypes of A. pleuropneumoniae we identified a common set of presumably essential core genes, involved in iron......Background Comparative analysis of gene expression among serotypes within a species can provide valuable information on important differences between related genomes. For the pig lung pathogen Actinobacillus pleuropneumoniae, 15 serotypes with a considerable variation in virulence potential and...... virulence genes. We used a pan-genomic microarray to study the transcriptional response to iron restriction in vitro in six serotypes of A. pleuropneumoniae (1, 2, 3, 5b, 6, and 7), representing at least two levels of virulence. Results In total, 45 genes were significantly (p <0.0001) up-regulated and 67...

  4. Genome-Wide Identification and Expression Profile of Dof Transcription Factor Gene Family in Pepper (Capsicum annuum L.)

    Science.gov (United States)

    Wu, Zhiming; Cheng, Jiaowen; Cui, Junjie; Xu, Xiaowan; Liang, Guansheng; Luo, Xirong; Chen, Xiaocui; Tang, Xiangqun; Hu, Kailin; Qin, Cheng

    2016-01-01

    Dof (DNA-binding One Zinc Finger) transcription factor family is unique to plants and has diverse roles associated with plant-specific phenomena, such as light, phytohormone and defense responses as well as seed development and germination. Although, genome-wide analysis of this family has been performed in many species, information regarding Dof genes in the pepper, Capsicum annuum L., is extremely limited. In this study, exhaustive searches of pepper genome revealed 33 potential CaDofs that were phylogenetically clustered into four subgroups. Twenty-nine of the 33 Dof genes could be mapped on 11 chromosomes, except for chromosome 7. The intron/exon organizations and conserved motif compositions of these genes were also analyzed. Additionally, phylogenetic analysis and classification of the Dof transcription factor family in eight plant species revealed that S. lycopersicum and C. annuum as well as O. sativa and S. bicolor Dof proteins may have evolved conservatively. Moreover, comprehensive expression analysis of CaDofs using a RNA-seq atlas and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that these genes exhibit a variety of expression patterns. Most of the CaDofs were expressed in at least one of the tissues tested, whereas several genes were identified as being highly responsive to heat and salt stresses. Overall, this study describes the first genome-wide analysis of the pepper Dof family, whose genes exhibited different expression patterns in all primary fruit developmental stages and tissue types, as in response to abiotic stress. In particular, some Dof genes might be used as biomarkers for heat and salt stress. The results could expand our understanding of the roles of Dof genes in pepper. PMID:27200047

  5. Host response transcriptional profiling reveals extracellular components and ABC (ATP-binding cassette transporters gene enrichment in typhoid fever-infected Nigerian children

    Directory of Open Access Journals (Sweden)

    Resau James H

    2011-09-01

    Full Text Available Abstract Background Salmonella enterica serovar Typhi (S. Typhi is a human-specific pathogen that causes typhoid fever, and remains a global health problem especially in developing countries. Its pathogenesis is complex and host response is poorly understood. In Africa, typhoid fever can be a major cause of morbidity in young infected children. The onset of the illness is insidious and clinical diagnosis is often unreliable. Gold standard blood culture diagnostic services are limited, thus rapid, sensitive, and affordable diagnostic test is essential in poor-resourced clinical settings. Routine typhoid fever vaccination is highly recommended but currently licensed vaccines provide only 55-75% protection. Recent epidemiological studies also show the rapid emergence of multi-drug resistant S. Typhi strains. High-throughput molecular technologies, such as microarrays, can dissect the molecular mechanisms of host responses which are S. Typhi-specific to provide a comprehensive genomic component of immunological responses and suggest new insights for diagnosis and treatment. Methods Global transcriptional profiles of S. Typhi-infected young Nigerian children were obtained from their peripheral blood and compared with that of other bacteremic infections using Agilent gene expression microarrays. The host-response profiles of the same patients in acute vs. convalescent phases were also determined. The top 96-100 differentially-expressed genes were identified and four genes were validated by quantitative real-time PCR. Gene clusters were obtained and functional pathways were predicted by DAVID (Database for Annotation, Visualization and Integrated Discovery. Results Transcriptional profiles from S. Typhi-infected children could be distinguished from those of other bacteremic infections. Enriched gene clusters included genes associated with extracellular peptides/components such as lipocalin (LCN2 and systemic immune response which is atypical in

  6. Transcriptional profiling of type 1 diabetes genes on chromosome 21 in a rat beta-cell line and human pancreatic islets

    DEFF Research Database (Denmark)

    Bergholdt, R.; Karlsen, A.E.; Hagedorn, Peter;

    2007-01-01

    likely candidate genes influencing beta-cell function in this region. Two array-based approaches were used, a rat insulinoma cell line (INS-1alphabeta) overexpressing pancreatic duodenum homeobox 1 (pdx-1) and treated with interleukin 1beta (IL-1beta) as well as human pancreatic islets stimulated...... with a mixture of cytokines. Several candidate genes with likely functional significance in T1D were identified. Genes showing differential expression in the two approaches were highly similar, supporting the role of these specific gene products in cytokine-induced beta-cell damage. These were genes involved...... in cytokine signaling, oxidative phosphorylation, defense responses and apoptosis. The analyses, furthermore, revealed several transcription factor binding sites shared by the differentially expressed genes and by genes demonstrating highly similar expression profiles with these genes. Comparable findings...

  7. A Genetic Linkage Map of Brassica rapa Based on AFLP Markers

    Institute of Scientific and Technical Information of China (English)

    ZHAO Jian-jun; WANG Xiao-wu; Guusje Bonnema; SUN Ri-fei; XU Ze-yong; Dick Vreugdenhi; Maarten Koornneef

    2005-01-01

    A F2 mapping population was developed by crossing a Chinese cabbage-pe-tsai variety CC156 and an oil type Rapid cycling RC144 which were different from each other in morphology, maturity, self-compatibility, plant height, etc. Using 244 AFLP markers a map was constructed containing 10 main linkage groups covering a total distance of 857 cM,corresponding to 3.5 cM per marker. Length of linkage groups varied from 43 to 125 cM and the number of AFLP markers linkage to each group ranged from 7 to 41.

  8. Comparison of hepatic transcription profiles of locked ribonucleic acid antisense oligonucleotides: evidence of distinct pathways contributing to non-target mediated toxicity in mice.

    Science.gov (United States)

    Kakiuchi-Kiyota, Satoko; Koza-Taylor, Petra H; Mantena, Srinivasa R; Nelms, Linda F; Enayetallah, Ahmed E; Hollingshead, Brett D; Burdick, Andrew D; Reed, Lori A; Warneke, James A; Whiteley, Lawrence O; Ryan, Anne M; Mathialagan, Nagappan

    2014-03-01

    Development of LNA gapmers, antisense oligonucleotides used for efficient inhibition of target RNA expression, is limited by non-target mediated hepatotoxicity issues. In the present study, we investigated hepatic transcription profiles of mice administered non-toxic and toxic LNA gapmers. After repeated administration, a toxic LNA gapmer (TS-2), but not a non-toxic LNA gapmer (NTS-1), caused hepatocyte necrosis and increased serum alanine aminotransferase levels. Microarray data revealed that, in addition to gene expression patterns consistent with hepatotoxicity, 17 genes in the clathrin-mediated endocytosis (CME) pathway were altered in the TS-2 group. TS-2 significantly down-regulated myosin 1E (Myo1E), which is involved in release of clathrin-coated pits from plasma membranes. To map the earliest transcription changes associated with LNA gapmer-induced hepatotoxicity, a second microarray analysis was performed using NTS-1, TS-2, and a severely toxic LNA gapmer (HTS-3) at 8, 16, and 72 h following a single administration in mice. The only histopathological change observed was minor hepatic hypertrophy in all LNA groups across time points. NTS-1, but not 2 toxic LNA gapmers, increased immune response genes at 8 and 16 h but not at 72 h. TS-2 significantly perturbed the CME pathway only at 72 h, while Myo1E levels were decreased at all time points. In contrast, HTS-3 modulated DNA damage pathway genes at 8 and 16 h and also modulated the CME pathway genes (but not Myo1E) at 16 h. Our results may suggest that different LNAs modulate distinct transcriptional genes and pathways contributing to non-target mediated hepatotoxicity in mice.

  9. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling.

    Directory of Open Access Journals (Sweden)

    Kristofer Davie

    2015-02-01

    Full Text Available Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs. When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling

  10. Human CD117 (cKit+ innate lymphoid cells have a discrete transcriptional profile at homeostasis and are expanded during filarial infection.

    Directory of Open Access Journals (Sweden)

    Alexis Boyd

    Full Text Available Since innate lymphoid cells (ILCs have been found to play a role in the immune response to helminth parasites in rodents, we sought to determine their role in human helminth infection. By developing multicolor flow cytometry-based methods to identify and enumerate circulating ILCs and their subsets, we were able to identify a subset of cKit+ ILCs defined as Lineage (Lin-/CD45+/cKit+/CD127+ that were significantly expanded in the filarial-infected individuals (p=0.0473 as were those cKit+ ILCs that produced IL-13. Additionally, the frequency of these cKit+ ILCs correlated with the frequency of IL-17 producing CD4+ T cells (Th17 cells; p=0.025. To investigate the function of cKit+ ILCs, sorted, highly purified human ILCs were subjected to transcriptional profiling by RNAseq and compared to appropriate control cells. These cKit+ ILCs expressed TLRs, a broad range of cytokines/cytokine receptors and MHC Class II molecules suggesting that these ILCs sense pathogens independent of other cell types. Functional analysis revealed expanded cKit+ ILC-specific transcription and ILC-specific microRNA precursors.

  11. Whole Blood Transcriptional Profiling of Interferon-Inducible Genes Identifies Highly Upregulated IFI27 in Primary Myelofibrosis

    DEFF Research Database (Denmark)

    Skov, Vibe; Larsen, Thomas Stauffer; Thomassen, Mads;

    2011-01-01

    Gene expression profiling studies have unraveled deregulation of several genes that might be of pathogenetic importance for the development and phenotype of the Philadelphia-negative chronic myeloproliferative neoplasms. In the context of interferon-alpha2 as a promising therapeutic agent, we foc...... myelofibrosis as the burn-out phase of chronic inflammation which ultimately elicits clonal evolution and expansion owing to an exaggerated but incompetent antitumor immune response. Finally, IFI27 may be a novel biomarker of disease activity and tumor burden in patients with CMPNs....

  12. Whole-blood transcriptional profiling of interferon-inducible genes identifies highly upregulated IFI27 in primary myelofibrosis

    DEFF Research Database (Denmark)

    Skov, Vibe; Larsen, Thomas Stauffer; Thomassen, Mads;

    2011-01-01

    Gene expression profiling studies have unraveled deregulation of several genes that might be of pathogenetic importance for the development and phenotype of the Philadelphia-negative chronic myeloproliferative neoplasms. In the context of interferon-alpha2 as a promising therapeutic agent, we foc...... myelofibrosis as the burn-out phase of chronic inflammation which ultimately elicits clonal evolution and expansion owing to an exaggerated but incompetent antitumor immune response. Finally, IFI27 may be a novel biomarker of disease activity and tumor burden in patients with CMPNs....

  13. Transcript profiling of cytokinin action in Arabidopsis roots and shoots discovers largely similar but also organ-specific responses

    Directory of Open Access Journals (Sweden)

    Brenner Wolfram G

    2012-07-01

    Full Text Available Abstract Background The plant hormone cytokinin regulates growth and development of roots and shoots in opposite ways. In shoots it is a positive growth regulator whereas it inhibits growth in roots. It may be assumed that organ-specific regulation of gene expression is involved in these differential activities, but little is known about it. To get more insight into the transcriptional events triggered by cytokinin in roots and shoots, we studied genome-wide gene expression in cytokinin-treated and cytokinin-deficient roots and shoots. Results It was found by principal component analysis of the transcriptomic data that the immediate-early response to a cytokinin stimulus differs from the later response, and that the transcriptome of cytokinin-deficient plants is different from both the early and the late cytokinin induction response. A higher cytokinin status in the roots activated the expression of numerous genes normally expressed predominantly in the shoot, while a lower cytokinin status in the shoot reduced the expression of genes normally more active in the shoot to a more root-like level. This shift predominantly affected nuclear genes encoding plastid proteins. An organ-specific regulation was assigned to a number of genes previously known to react to a cytokinin signal, including root-specificity for the cytokinin hydroxylase gene CYP735A2 and shoot specificity for the cell cycle regulator gene CDKA;1. Numerous cytokinin-regulated genes were newly discovered or confirmed, including the meristem regulator genes SHEPHERD and CLAVATA1, auxin-related genes (IAA7, IAA13, AXR1, PIN2, PID, several genes involved in brassinosteroid (CYP710A1, CYP710A2, DIM/DWF and flavonol (MYB12, CHS, FLS1 synthesis, various transporter genes (e.g. HKT1, numerous members of the AP2/ERF transcription factor gene family, genes involved in light signalling (PhyA, COP1, SPA1, and more than 80 ribosomal genes. However, contrasting with the fundamental difference of

  14. 辣椒 AFLP 反应体系的优化与建立%Optimization and Establishment of AFLP Analysis System in Hot Pepper (Capsicum annuum L.)

    Institute of Scientific and Technical Information of China (English)

    徐明磊; 詹玉丝; 陈晓; 樊红杰

    2008-01-01

    以5个辣椒(Capsicum annuum L.)材料为研究对象,对 AFLP 反应体系中的 DNA 用量、酶切连接时间、预扩增产物的稀释倍数等关键因素进行优化分析,建立了适宜辣椒作物的 AFLP 反应体系.研究结果:酶切连接反应中,基因组 DNA 适宜用量为100 ng,反应时间是6h最为合适,预扩增产物适宜稀释倍数在30~50倍时较为理想.

  15. Transcript profiles uncover temporal and stress-induced changes of metabolic pathways in germinating sugar beet seeds

    Directory of Open Access Journals (Sweden)

    Windhövel Andrea

    2008-12-01

    Full Text Available Abstract Background With a cultivation area of 1.75 Mio ha and sugar yield of 16.7 Mio tons in 2006, sugar beet is a crop of great economic importance in Europe. The productivity of sugar beet is determined significantly by seed vigour and field emergence potential; however, little is known about the molecular mechanisms underlying these traits. Both traits exhibit large variations within sugar beet germplasm that have been difficult to ascribe to either environmental or genetic causes. Among potential targets for trait improvement, an enhancement of stress tolerance is considered because of the high negative influence of environmental stresses on trait parameters. Extending our knowledge of genetic and molecular determinants of sugar beet germination, stress response and adaptation mechanisms would facilitate the detection of new targets for breeding crop with an enhanced field emergence potential. Results To gain insight into the sugar beet germination we initiated an analysis of gene expression in a well emerging sugar beet hybrid showing high germination potential under various environmental conditions. A total of 2,784 ESTs representing 2,251 'unigenes' was generated from dry mature and germinating seeds. Analysis of the temporal expression of these genes during germination under non-stress conditions uncovered drastic transcriptional changes accompanying a shift from quiescent to metabolically active stages of the plant life cycle. Assay of germination under stressful conditions revealed 157 genes showing significantly different expression patterns in response to stress. As deduced from transcriptome data, stress adaptation mechanisms included an alteration in reserve mobilization pathways, an accumulation of the osmoprotectant glycine betaine, late embryogenesis abundant proteins and detoxification enzymes. The observed transcriptional changes are supposed to be regulated by ABA-dependent signal transduction pathway. Conclusion This study

  16. Identification of stable endogenous control genes for transcriptional profiling of photon, proton and carbon-ion irradiated cells

    Directory of Open Access Journals (Sweden)

    Sharungbam Geeta D

    2012-05-01

    Full Text Available Abstract Background Quantitative analysis of transcriptional regulation of genes is a prerequisite for a better understanding of the molecular mechanisms of action of different radiation qualities such as photon, proton or carbon ion irradiation. Microarrays and real-time quantitative RT-PCR (qRT-PCR are considered the two cornerstones of gene expression analysis. In interpreting these results it is critical to normalize the expression levels of the target genes by that of appropriately selected endogenous control genes (ECGs or housekeeping genes. We sought to systematically investigate common ECG candidates for their stability after different radiation modalities in different human cell lines by qRT-PCR. We aimed to identify the most robust set of ECGs or housekeeping genes for transcriptional analysis in irradiation studies. Methods We tested the expression stability of 32 ECGs in three human cancer cell lines. The epidermoid carcinoma cells (A431, the non small cell lung carcinoma cells (A549 and the pancreatic adenocarincoma cells (BxPC3 were irradiated with photon, proton and carbon ions. Expression Heat maps, clustering and statistic algorithms were employed using SUMO software package. The expression stability was evaluated by computing: mean, standard deviation, ANOVA, coefficient of variation and the stability measure (M given by the geNorm algorithm. Results Expression analysis revealed significant cell type specific regulation of 18 out of 32 ECGs (p 18S, one of the most frequently used ECG, was differentially regulated as the function of different radiation qualities (p ≤ 0.01. A comprehensive search for the most stable ECGs using the geNorm algorithm identified 3 ECGs for A431 and BxPC3 to be sufficient for normalization. In contrast, 6 ECGs were required to properly normalize expression data in the more variable A549 cells. Considering both variables tested, i.e. cell type and radiation qualities, 5 genes-- RPLP0, UBC

  17. Identification of stable endogenous control genes for transcriptional profiling of photon, proton and carbon-ion irradiated cells

    International Nuclear Information System (INIS)

    Quantitative analysis of transcriptional regulation of genes is a prerequisite for a better understanding of the molecular mechanisms of action of different radiation qualities such as photon, proton or carbon ion irradiation. Microarrays and real-time quantitative RT-PCR (qRT-PCR) are considered the two cornerstones of gene expression analysis. In interpreting these results it is critical to normalize the expression levels of the target genes by that of appropriately selected endogenous control genes (ECGs) or housekeeping genes. We sought to systematically investigate common ECG candidates for their stability after different radiation modalities in different human cell lines by qRT-PCR. We aimed to identify the most robust set of ECGs or housekeeping genes for transcriptional analysis in irradiation studies. We tested the expression stability of 32 ECGs in three human cancer cell lines. The epidermoid carcinoma cells (A431), the non small cell lung carcinoma cells (A549) and the pancreatic adenocarincoma cells (BxPC3) were irradiated with photon, proton and carbon ions. Expression Heat maps, clustering and statistic algorithms were employed using SUMO software package. The expression stability was evaluated by computing: mean, standard deviation, ANOVA, coefficient of variation and the stability measure (M) given by the geNorm algorithm. Expression analysis revealed significant cell type specific regulation of 18 out of 32 ECGs (p < 0.05). A549 and A431 cells shared a similar pattern of ECG expression as the function of different radiation qualities as compared to BxPC3. Of note, the ribosomal protein 18S, one of the most frequently used ECG, was differentially regulated as the function of different radiation qualities (p ≤ 0.01). A comprehensive search for the most stable ECGs using the geNorm algorithm identified 3 ECGs for A431 and BxPC3 to be sufficient for normalization. In contrast, 6 ECGs were required to properly normalize expression data in the more

  18. Genome wide transcription profiling of the effects of overexpression of Spc1 and its kinase dead mutant in Schizosaccharomyces pombe

    Directory of Open Access Journals (Sweden)

    Madhurima Paul

    2015-12-01

    Full Text Available The Mitogen Activated Protein Kinase Spc1 (p38 homolog is a major player in stress responses of the unicellular fission yeast Schizosaccharomyces pombe. This pathway is therefore also known as the SAPK or Stress Activated Protein Kinase pathway. Spc1 is a known activator of transcription factors that control gene expression in response to extracellular stimuli and is also known to interact with the translation machinery [1–8]. Spc1 has also been implicated in cell cycle regulation and meiosis in S. pombe [1,2,9,10]. Given its documented role in modulating gene expression, we performed a microarray based identification of genes whose expression in unperturbed cells (absence of stress stimuli is dependent on Spc1. For this we overexpressed Spc1 in S. pombe. Additionally we also overexpressed Spc1K49R (a kinase dead mutant of Spc1 to understand the contribution of Spc1's kinase activity towards the observed gene expression changes. The microarray data are available at NCBI's Gene Expression Omnibus (GEO Series (accession number GSE73618. Here we report the annotation of the genes whose expression get altered by Spc1/Spc1K49R overexpression and also provide details related to sample processing and statistical analysis of our microarray data.

  19. In Vivo T-Box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuromesodermal Bipotency

    Directory of Open Access Journals (Sweden)

    George E. Gentsch

    2013-09-01

    Full Text Available The design of effective cell replacement therapies requires detailed knowledge of how embryonic stem cells form primary tissues, such as mesoderm or neurectoderm that later become skeletal muscle or nervous system. Members of the T-box transcription factor family are key in the formation of these primary tissues, but their underlying molecular activities are poorly understood. Here, we define in vivo genome-wide regulatory inputs of the T-box proteins Brachyury, Eomesodermin, and VegT, which together maintain neuromesodermal stem cells and determine their bipotential fates in frog embryos. These T-box proteins are all recruited to the same genomic recognition sites, from where they activate genes involved in stem cell maintenance and mesoderm formation while repressing neurogenic genes. Consequently, their loss causes embryos to form an oversized neural tube with no mesodermal derivatives. This collaboration between T-box family members thus ensures the continuous formation of correctly proportioned neural and mesodermal tissues in vertebrate embryos during axial elongation.

  20. Transcriptome-wide identification and expression profiling of the DOF transcription factor gene family in Chrysanthemum morifolium

    Directory of Open Access Journals (Sweden)

    Aiping eSong

    2016-02-01

    Full Text Available The family of DNA binding with one finger (DOF transcription factors is plant specific, and these proteins contain a highly conserved domain (DOF domain of 50-52 amino acids that includes a C2C2-type zinc finger motif at the N-terminus that is known to function in a number of plant processes. Here, we characterized 20 DOF genes in the important ornamental species chrysanthemum (Chrysanthemum morifolium based on transcriptomic sequences. Phylogenetic analysis identified one pair of putative orthologous proteins in Arabidopsis and chrysanthemum and six pairs of paralogous proteins in chrysanthemum. Conserved motifs in the DOF proteins shared by Arabidopsis and chrysanthemum were analysed using MEME. Bioinformatics analysis revealed that 13 CmDOFs could be targeted by 16 miRNA families. Moreover, we used 5’ RLM-RACE to map the cleavage sites in CmDOF3, 15 and 21. The expression of these 20 genes in response to phytohormone treatments and abiotic stresses was characterized, and the expression patterns of six pairs of paralogous CmDOF genes were found to completely differ from one another, except for CmDOF6 and CmDOF7. This work will promote our research of the various functions of DOF gene family members in plant hormone and stress responses.

  1. Transcriptome-Wide Identification and Expression Profiling of the DOF Transcription Factor Gene Family in Chrysanthemum morifolium.

    Science.gov (United States)

    Song, Aiping; Gao, Tianwei; Li, Peiling; Chen, Sumei; Guan, Zhiyong; Wu, Dan; Xin, Jingjing; Fan, Qingqing; Zhao, Kunkun; Chen, Fadi

    2016-01-01

    The family of DNA binding with one finger (DOF) transcription factors is plant specific, and these proteins contain a highly conserved domain (DOF domain) of 50-52 amino acids that includes a C2C2-type zinc finger motif at the N-terminus that is known to function in a number of plant processes. Here, we characterized 20 DOF genes in the important ornamental species chrysanthemum (Chrysanthemum morifolium) based on transcriptomic sequences. Phylogenetic analysis identified one pair of putative orthologous proteins in Arabidopsis and chrysanthemum and six pairs of paralogous proteins in chrysanthemum. Conserved motifs in the DOF proteins shared by Arabidopsis and chrysanthemum were analyzed using MEME. Bioinformatics analysis revealed that 13 CmDOFs could be targeted by 16 miRNA families. Moreover, we used 5' RLM-RACE to map the cleavage sites in CmDOF3, 15, and 21. The expression of these 20 genes in response to phytohormone treatments and abiotic stresses was characterized, and the expression patterns of six pairs of paralogous CmDOF genes were found to completely differ from one another, except for CmDOF6 and CmDOF7. This work will promote our research of the various functions of DOF gene family members in plant hormone and stress responses. PMID:26941763

  2. An efficient xylose-fermenting recombinant Saccharomyces cerevisiae strain obtained through adaptive evolution and its global transcription profile

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Yu; Chen, Xiao; Peng, Bingyin; Chen, Liyuan; Hou, Jin; Bao, Xiaoming [Shandong Univ., Jinan (China). State Key Lab. of Microbial Technology

    2012-11-15

    Factors related to ethanol production from xylose in engineered Saccharomyces cerevisiae that contain an exogenous initial metabolic pathway are still to be elucidated. In the present study, a strain that expresses the xylose isomerase gene of Piromyces sp. Pi-xylA and overexpresses XKS1, RPE1, RKI1, TAL1, and TKL1, with deleted GRE3 and COX4 genes was constructed. The xylose utilization capacity of the respiratory deficiency strain was poor but improved via adaptive evolution in xylose. The {mu}{sub max} of the evolved strain in 20 gl{sup -1} xylose is 0.11 {+-} 0.00 h{sup -1}, and the evolved strain consumed 17.83 gl{sup -1} xylose within 72 h, with an ethanol yield of 0.43 gg{sup -1} total consumed sugars during glucose-xylose cofermentation. Global transcriptional changes and effect of several specific genes were studied. The result revealed that the increased xylose isomerase activity, the upregulation of enzymes involved in glycolysis and glutamate synthesis, and the downregulation of trehalose and glycogen synthesis, may have contributed to the improved xylose utilization of the strain. Furthermore, the deletion of PHO13 decreased the xylose growth in the respiration deficiency strain although deleting PHO13 can improve the xylose metabolism in other strains. (orig.)

  3. Comparative transcriptional profiling of melatonin synthesis and catabolic genes indicates the possible role of melatonin in developmental and stress responses in rice

    Directory of Open Access Journals (Sweden)

    Yunxie eWei

    2016-05-01

    Full Text Available As a well-known animal hormone, melatonin (N-acetyl-5-methoxytryptamine is also involved in multiple plant biological processes, especially in various stress responses. Rice is one of the most important crops, and melatonin is taken in by many people everyday from rice. However, the transcriptional profiling of melatonin-related genes in rice is largely unknown. In this study, the expression patterns of 11 melatonin related genes in rice in different periods, tissues, in response to different treatments were synthetically analyzed using published microarray data. These results suggest that the melatonin-related genes may play important and dual roles in rice developmental stages. We highlight the commonly regulation of rice melatonin-related genes by abscisic acid (ABA, jasmonic acid (JA, various abiotic stresses and pathogen infection, indicating the possible role of these genes in multiple stress responses and underlying crosstalks of plant hormones, especially ABA and JA. Taken together, this study may provide insight into the association among melatonin biosynthesis and catabolic pathway, plant development and stress responses in rice. The profile analysis identified candidate genes for further functional characterization in circadian rhythm and specific stress responses.

  4. Gene Transcription Profile in Mice Vaccinated with Ultraviolet-attenuated Cercariae of Schistosoma japonicum Reveals Molecules Contributing to Elevated IFN-γLevels

    Institute of Scientific and Technical Information of China (English)

    Xiang ZHU; Feng LIU; Chuan SU; Guan-Ling WU; Zhao-Song ZHANG; Min-Jun JI; Hai-Wei WU; Yong WANG; Xiao-Ping CAI; Lei ZHANG; Shu-Ying HU; Lin-Lin FU

    2005-01-01

    Vaccination with ultraviolet-attenuated cercariae of Schistosoma japonicum induced protective immunity against challenge infection in experimental animal models. Our preliminary study on the transcription levels of IFN-γ and IL-4 in splenic CD4+ T cells revealed that attenuated cercariae elicited predominantly a Thl response in mice at the early stage, whereas normal cercariae stimulated primarily Th2dependent responses. Further analysis on the gene profile of the skin-draining lymph nodes demonstrated that the levels of IFN-γ were significantly higher in vaccinated mice than those in infected mice at day 4, 7 and 14 post-vaccination or post-infection. However, for IL-12 and IL-4, the potent inducers of Th l and Th2 responses, respectively, as well as IL-10, there were no differences over the course of the experiment between the infected and vaccinated mice. To explore the underlying factors that may potentially contribute to elevated IFN-γ in vaccinated mice, the mRNA profiles of the skin-draining lymph nodes at day 4 postexposure were compared using oligonucleotide microarrays. Within the 847 probe sets with increased signal values, we focused on chemokines, cytokines and relevant receptors, which were validated by semi-quantitative RT-PCR. A comprehensive understanding of the immune mechanisms of attenuated cercariae-induced protection may contribute to developing efficient vaccination strategies against S. japonicum, especially during the early stage of infection.

  5. The iron/heme regulated genes of Haemophilus influenzae: comparative transcriptional profiling as a tool to define the species core modulon

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    Morton Daniel J

    2009-01-01

    Full Text Available Abstract Background Haemophilus influenzae requires heme for aerobic growth and possesses multiple mechanisms to obtain this essential nutrient. Although an understanding of the heme acquisition mechanisms of H. influenzae is emerging, significant gaps in our knowledge remain. Unresolved issues include the identities of all genes exhibiting altered transcription in response to iron and heme availability, the fraction of such genes functioning in iron/heme acquisition, and the heterogeneity of this gene set among clinical isolates. Previously we utilized H. influenzae strain Rd KW20 to demonstrate the utility of transcriptional profiling in defining the genes exhibiting altered transcription in response to environmental iron and heme levels. The current study expands upon those observations by determining the iron/heme modulons of two clinical isolates, the type b isolate 10810 and the nontypeable isolate R2866. These data are used to begin to define the core iron/heme modulon of the species. Results Microarray studies were performed to compare gene expression on transition from iron/heme-restricted to iron/heme-replete conditions for each isolate. Of 1820 ORFs on the array corresponding to R2866 genes, 363 were significantly differentially expressed: 233 were maximally transcribed under iron/heme-replete conditions and 130 under iron/heme-restricted conditions. Of the 1883 ORFs representing genes of strain 10810, 353 were significantly differentially transcribed: 150 were preferentially transcribed under iron/heme-replete conditions and 203 under iron/heme-restricted conditions. Comparison of the data sets indicated that 163 genes exhibited similar regulation in both isolates and that 74 of these exhibited similar patterns of regulation in Rd KW20. These comprise the putative core iron/heme modulon. Conclusion This study provides evidence for a conserved core of H. influenzae genes the transcription of which is altered by the availability of

  6. Spatially Resolved Genome-wide Transcriptional Profiling Identifies BMP Signaling as Essential Regulator of Zebrafish Cardiomyocyte Regeneration.

    Science.gov (United States)

    Wu, Chi-Chung; Kruse, Fabian; Vasudevarao, Mohankrishna Dalvoy; Junker, Jan Philipp; Zebrowski, David C; Fischer, Kristin; Noël, Emily S; Grün, Dominic; Berezikov, Eugene; Engel, Felix B; van Oudenaarden, Alexander; Weidinger, Gilbert; Bakkers, Jeroen

    2016-01-11

    In contrast to mammals, zebrafish regenerate heart injuries via proliferation of cardiomyocytes located near the wound border. To identify regulators of cardiomyocyte proliferation, we used spatially resolved RNA sequencing (tomo-seq) and generated a high-resolution genome-wide atlas of gene expression in the regenerating zebrafish heart. Interestingly, we identified two wound border zones with distinct expression profiles, including the re-expression of embryonic cardiac genes and targets of bone morphogenetic protein (BMP) signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast, we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation, ultimately compromising myocardial regeneration, while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non-regenerative hearts.

  7. Transcript profiling of Paoenia ostii during artificial chilling induced dormancy release identifies activation of GA pathway and carbohydrate metabolism.

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    Shupeng Gai

    Full Text Available Endo-dormant flower buds must pass through a period of chilling to reinitiate growth and subsequent flowering, which is a major obstacle to the forcing culture of tree peony in winter. Customized cDNA microarray (8×15 K element was used to investigate gene expression profiling in tree peony 'Feng Dan Bai' buds during 24 d chilling treatment at 0-4°C. According to the morphological changes after the whole plants were transferred to green house, endo-dormancy was released after 18 d chilling treatment, and prolonged chilling treatment increased bud break rate. Pearson correlation hierarchical clustering of sample groups was highly consistent with the dormancy transitions revealed by morphological changes. Totally 3,174 significantly differentially-expressed genes (P<0.05 were observed through endo-dormancy release process, of which the number of up-regulated (1,611 and that of down-regulated (1,563 was almost the same. Functional annotation of differentially-expressed genes revealed that cellular process, metabolic process, response to stimulus, regulation of biological process and development process were well-represented. Hierarchical clustering indicated that activation of genes involved in carbohydrate metabolism (Glycolysis, Citrate cycle and Pentose phosphate pathway, energy metabolism and cell growth. Based on the results of GO analysis, totally 51 probes presented in the microarray were associated with GA response and GA signaling pathway, and 22 of them were differently expressed. The expression profiles also revealed that the genes of GA biosynthesis, signaling and response involved in endo-dormancy release. We hypothesized that activation of GA pathway played a central role in the regulation of dormancy release in tree peony.

  8. Transcription Profiles of Marker Genes Predict The Transdifferentiation Relationship between Eight Types of Liver Cell during Rat Liver Regeneration

    Directory of Open Access Journals (Sweden)

    Xiaguang Chen

    2015-07-01

    Full Text Available Objective: To investigate the transdifferentiation relationship between eight types of liver cell during rat liver regeneration (LR. Materials and Methods: 114 healthy Sprague-Dawley (SD rats were used in this experimental study. Eight types of liver cell were isolated and purified with percoll density gradient centrifugation and immunomagentic bead methods. Marker genes for eight types of cell were obtained by retrieving the relevant references and databases. Expression changes of markers for each cell of the eight cell types were measured using microarray. The relationships between the expression profiles of marker genes and transdifferentiation among liver cells were analyzed using bioinformatics. Liver cell transdifferentiation was predicted by comparing expression profiles of marker genes in different liver cells. Results: During LR hepatocytes (HCs not only express hepatic oval cells (HOC markers (including PROM1, KRT14 and LY6E, but also express biliary epithelial cell (BEC markers (including KRT7 and KRT19; BECs express both HOC markers (including GABRP, PCNA and THY1 and HC markers such as CPS1, TAT, KRT8 and KRT18; both HC markers (KRT18, KRT8 and WT1 and BEC markers (KRT7 and KRT19 were detected in HOCs. Additionally, some HC markers were also significantly upregulated in hepatic stellate cells ( HSCs, sinusoidal endothelial cells (SECs , Kupffer cells (KCs and dendritic cells (DCs, mainly at 6-72 hours post partial hepatectomy (PH. Conclusion: Our findings indicate that there is a mutual transdifferentiation relationship between HC, BEC and HOC during LR, and a tendency for HSCs, SECs, KCs and DCs to transdifferentiate into HCs.

  9. MYB Transcription Factors in Chinese Pear (Pyrus bretschneideri Rehd.: Genome-Wide Identification, Classification and Expression Profiling during Fruit Development

    Directory of Open Access Journals (Sweden)

    Yun Peng eCao

    2016-04-01

    Full Text Available The MYB family is one of the largest families of transcription factors in plants. Although some MYBs have been reported to play roles in secondary metabolism, no comprehensive study of the MYB family in Chinese pear (Pyrus bretschneideri Rehd. has been reported. In the present study, we performed genome-wide analysis of MYB genes in Chinese pear, designated as PbMYBs, including analyses of their phylogenic relationships, structures, chromosomal locations, promoter regions, GO annotations and collinearity. A total of 129 PbMYB genes were identified in the pear genome and were divided into 31 subgroups based on phylogenetic analysis. These PbMYBs were unevenly distributed among 16 chromosomes (total of 17 chromosomes. The occurrence of gene duplication events indicated that whole-genome duplication and segmental duplication likely played key roles in expansion of the PbMYB gene family. Ka/Ks analysis suggested that the duplicated PbMYBs mainly experienced purifying selection with restrictive functional divergence after the duplication events. Interspecies microsynteny analysis revealed maximum orthology between pear and peach, followed by plum and strawberry. Subsequently, the expression patterns of 20 PbMYB genes that may be involved in lignin biosynthesis according to their phylogenetic relationships were examined throughout fruit development. Among the twenty genes examined, PbMYB25 and PbMYB52 exhibited expression patterns consistent with the typical variations in the lignin content previously reported. Moreover, sub-cellular localization analysis revealed that two proteins PbMYB25 and PbMYB52 were localized to the nucleus. All together, PbMYB25 and PbMYB52 were inferred to be candidate genes involved in the regulation of lignin biosynthesis during the development of pear fruit. This study provides useful information for further functional analysis of the MYB gene family in pear.

  10. A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers

    NARCIS (Netherlands)

    Syed, N.; Sorensen, A.P.; Antonise, R.; Wiel, van de C.C.M.; Linden, van der C.G.; Westende, van 't W.P.C.; Hooftman, D.A.P.; Nijs, den H.C.M.; Flavell, A.

    2006-01-01

    Molecular markers based upon a novel lettuce LTR retrotransposon and the nucleotide binding site-leucine-rich repeat (NBS-LRR) family of disease resistance-associated genes have been combined with AFLP markers to generate a 458 locus genetic linkage map for lettuce. A total of 187 retrotransposon-sp

  11. Association of AFLP and SSR markers with agronomic and fibre quality traits in Gossypium hirsutum L.

    Indian Academy of Sciences (India)

    Arunita Rakshit; S. Rakshit; J. Singh; S. K. Chopra; H. S. Balyan; P. K. Gupta; Shripad R. Bhat

    2010-08-01

    Molecular markers linked to QTL contributing to agronomic and fibre quality traits would be useful for cotton improvement. We have attempted to tag yield and fibre quality traits with AFLP and SSR markers using F2 and F3 populations of a cross between two Gossypium hirsutum varieties, PS56-4 and RS2013. Out of 50 AFLP primer combinations and 177 SSR primer pairs tested, 32 AFLP and four SSR primers were chosen for genotyping F2 individuals.Marker-trait associations were studied for eight agronomic and five fibre quality traits through simple and multiple regression analysis (MRA) using a set of 92 AFLP polymorphic loci and four SSR markers. Simple linear regression analysis (SLRA) identified 23 markers for eight different traits whereas multiple regression analysis identified 30 markers for at least one of the 13 traits. SSR marker BNL 3502 was consistently identified to be associated with fibre strength. While all the markers identified in SLRA were also detected in MRA, as many as 16 of the 30 markers were identified to be associated with respective traits in both F2 and F3 generations. The markers explained up to 41 per cent of phenotypic variation for individual traits. A number of markers were found to be associated with multiple traits suggesting clustering of QTLs for fibre quality traits in cotton.

  12. Genetic Relationships of Aglaonema Species and Cultivars Inferred from AFLP Markers

    OpenAIRE

    Chen, Jianjun; DEVANAND, PACHANOOR S.; Norman, David J; HENNY, RICHARD J.; CHAO, CHIH‐CHENG T.

    2004-01-01

    • Background and Aims Aglaonema is an important ornamental foliage plant genus, but genetic relationships among its species and cultivars have not been reported. This study analysed genetic relatedness of 54 cultivars derived from nine species using amplified fragment length polymorphism (AFLP) markers.

  13. Construction of an integrated map of rose with AFLP, SSR, PK, RGA, SCAR and morphological markers

    NARCIS (Netherlands)

    Yan Zifu, Z.; Denneboom, C.; Hattendorf, A.; Dolstra, O.; Debener, T.; Stam, P.; Visser, P.B.

    2005-01-01

    A high-density genetic map with a number of anchor markers has been created to be used as a tool to dissect genetic variation in rose. Linkage maps for the diploid 94/1 population consisting of 88 individuals were constructed using a total of 520 molecular markers including AFLP, SSR, PK, RGA, RFLP,

  14. Analysis of genetic diversity in crocuses with Carpathian Basin origin using AFLP-markers.

    Science.gov (United States)

    Surányi, G; Máthé, C; Mosolygó, Agnes; Borbély, G; Vasas, G

    2010-01-01

    Crocus taxonomy has until now been based primarily on morphology, taking chromosome numbers into consideration. The genetics and genome structure of the genus, the relationships and diversity within the genus are not well known. Amplified fragment length polymorphism (AFLP) is a whole genome approach to study genetic variation that is gaining in popularity for lower-level systematics. The present study employed the AFLP technique for analyzing relationships among taxa of the Crocus genus (particularly the Crocus vernus aggregate) with Carpathian Basin origin. The molecular variance obtained was based on amplification, separation and detection of EcoRI and Tru1I double-digested Crocus spp. genomic DNAs. Our results confirm the relatedness of C. tommasinianus, C. vittatus and C. heuffelianus at the Verni series of the Crocus genus. C. banaticus is taxonomically isolated as the sole member of the subgenus Crociris based on unique morphological features, but the difference is not convincing from AFLP data. The second interesting AFLP analysis result is the position of C. scepusiensis which separated it from the Crocus vernus aggregate. PMID:21565773

  15. The construction of a linkage map of Alstroemeria aurea by AFLP markers

    NARCIS (Netherlands)

    Han, T.H.; Eck, van H.J.; Jeu, de M.J.; Jacobsen, E.

    2002-01-01

    An AFLP based linkage map has been generated for the ornamental cropspecies Alstroemeria aurea. In view of the large genome size of Alstroemeria (25,000 Mb) the number of selective nucleotides for AFLPamplification was increased to EcoRI+4/MseI+4 to generatefingerprints of moderate complexity. In ad

  16. Genetic diversity of Chilean and Brazilian Alstroemeria species assessed by AFLP analysis

    NARCIS (Netherlands)

    Han, T.H.; Jeu, de M.J.; Eck, van H.J.; Jacobsen, E.

    2000-01-01

    One to three accessions of 22 Alstroemeria species, an interspecific hybrid (A. aurea ́ A. inodora), and single accessions of Bomarea salsilla and Leontochir ovallei were evaluated using the AFLP-marker technique to estimate the genetic diversity within the genus Alstroemeria. Three primer combinati

  17. Application of fluorescence-based semi-automated AFLP analysis in barley and wheat

    DEFF Research Database (Denmark)

    Schwarz, G.; Herz, M.; Huang, X.Q.;

    2000-01-01

    of semi-automated codominant analysis for hemizygous AFLP markers in an F-2 population was too low, proposing the use of dominant allele-typing defaults. Nevertheless, the efficiency of genetic mapping, especially of complex plant genomes, will be accelerated by combining the presented genotyping...

  18. AFLP genetic polymorphism in wild barley (Hordeum spontaneum) populations in Israel

    NARCIS (Netherlands)

    Turpeinen, T.; Vanhala, T.; Nevo, E.; Nissila, E.

    2003-01-01

    The genetic diversity produced by the amplified fragment length polymorphism (AFLP) method was studied in 94 genotypes of wild barley, Hordeum spontaneum (C. Koch) Thell., originating from ten ecologically and geographically different locations in Israel. Eight primer pairs produced 204 discernible

  19. Genetic diversity in natural populations of Jacaranda decurrens Cham. determined using RAPD and AFLP markers

    Directory of Open Access Journals (Sweden)

    Bianca W. Bertoni

    2010-01-01

    Full Text Available Jacaranda decurrens (Bignoniaceae is an endemic species of the Cerrado with validated antitumoral activity. The genetic diversity of six populations of J. decurrens located in the State of São Paulo was determined in this study by using molecular markers for randomly amplified polymorphic DNA (RAPD and amplified fragment length polymorphism (AFLP. Following optimization of the amplification reaction, 10 selected primers generated 78 reproducible RAPD fragments that were mostly (69.2% polymorphic. Two hundred and five reproducible AFLP fragments were generated by using four selected primer combinations; 46.3% of these fragments were polymorphic, indicating a considerable level of genetic diversity. Analysis of molecular variance (AMOVA using these two groups of markers indicated that variability was strongly structured amongst populations. The unweighted pair group method with arithmatic mean (UPGMA and Pearson's correlation coefficient (RAPD -0.16, p = 0.2082; AFLP 0.37, p = 0.1006 between genetic matrices and geographic distances suggested that the population structure followed an island model in which a single population of infinite size gave rise to the current populations of J. decurrens, independently of their spatial position. The results of this study indicate that RAPD and AFLP markers were similarly efficient in measuring the genetic variability amongst natural populations of J. decurrens. These data may be useful for developing strategies for the preservation of this medicinal species in the Cerrado.

  20. Bootsie: estimation of coefficient of variation of AFLP data by bootstrap analysis

    Science.gov (United States)

    Bootsie is an English-native replacement for ASG Coelho’s “DBOOT” utility for estimating coefficient of variation of a population of AFLP marker data using bootstrapping. Bootsie improves on DBOOT by supporting batch processing, time-to-completion estimation, built-in graphs, and a suite of export t...

  1. Comparative cDNA-AFLP analysis of Cd-tolerant and -sensitive genotypes derived from crosses between the Cd hyperaccumulator Arabidopsis halleri and Arabidopsis lyrata ssp. petraea.

    Science.gov (United States)

    Craciun, Adrian Radu; Courbot, Mikael; Bourgis, Fabienne; Salis, Pietrino; Saumitou-Laprade, Pierre; Verbruggen, Nathalie

    2006-01-01

    Cadmium (Cd) tolerance seems to be a constitutive species-level trait in Arabidopsis halleri. In order to identify genes potentially implicated in Cd tolerance, a backcross (BC1) segregating population was produced from crosses between A. halleri ssp. halleri and its closest non-tolerant relative A. lyrata ssp. petraea. The most sensitive and tolerant genotypes of the BC1 were analysed on a transcriptome-wide scale by cDNA-amplified fragment length polymorphism (AFLP). A hundred and thirty-four genes expressed more in the root of tolerant genotypes than in sensitive genotypes were identified. Most of the identified genes showed no regulation in their expression when exposed to Cd in a hydroponic culture medium and belonged to diverse functional classes, including reactive oxygen species (ROS) detoxification, cellular repair, metal sequestration, water transport, signal transduction, transcription regulation, and protein degradation, which are discussed. PMID:16916885

  2. Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds.

    Science.gov (United States)

    Scheublin, Tanja R; Deusch, Simon; Moreno-Forero, Silvia K; Müller, Jochen A; van der Meer, Jan Roelof; Leveau, Johan H J

    2014-07-01

    Arthrobacter chlorophenolicus A6 is a Gram-positive, 4-chlorophenol-degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome-wide expression profile of A.chlorophenolicus on leaves of common bean (Phaseolus vulgaris) compared with growth on agar surfaces. In phyllosphere-grown cells, we found elevated expression of several genes known to contribute to epiphytic fitness, for example those involved in nutrient acquisition, attachment, stress response and horizontal gene transfer. A surprising result was the leaf-induced expression of a subset of the so-called cph genes for the degradation of 4-chlorophenol. This subset encodes the conversion of the phenolic compound hydroquinone to 3-oxoadipate, and was shown to be induced not only by 4-chlorophenol but also hydroquinone, its glycosylated derivative arbutin, and phenol. Small amounts of hydroquinone, but not arbutin or phenol, were detected in leaf surface washes of P.vulgaris by gas chromatography-mass spectrometry. Our findings illustrate the utility of genomics approaches for exploration and improved understanding of a microbial habitat. Also, they highlight the potential for phyllosphere-based priming of bacteria to stimulate pollutant degradation, which holds promise for the application of phylloremediation. PMID:24373130

  3. Comparative profiling of the transcriptional response to iron restriction in six serotypes of Actinobacillus pleuropneumoniae with different virulence potential

    Directory of Open Access Journals (Sweden)

    Angen Øystein

    2010-12-01

    Full Text Available Abstract Background Comparative analysis of gene expression among serotypes within a species can provide valuable information on important differences between related genomes. For the pig lung pathogen Actinobacillus pleuropneumoniae, 15 serotypes with a considerable variation in virulence potential and immunogenicity have been identified. This serotypic diversity can only partly be explained by amount of capsule and differences in the RTX toxin genes in their genomes. Iron acquisition in vivo is an important bacterial function and in pathogenic bacteria, iron-limitation is often a signal for the induction of virulence genes. We used a pan-genomic microarray to study the transcriptional response to iron restriction in vitro in six serotypes of A. pleuropneumoniae (1, 2, 3, 5b, 6, and 7, representing at least two levels of virulence. Results In total, 45 genes were significantly (p A. pleuropneumoniae was the up-regulation of a putative cirA-like siderophore in all six serotypes. Three genes, recently described in A. pleuropneumoniae as possibly coding for haemoglobin-haptoglobin binding proteins, displayed significant serotype related up-regulation to iron limitation. For all three genes, the expression appeared at its lowest in serotype 3, which is generally considered one of the least virulent serotypes of A. pleuropneumoniae. The three genes share homology with the hmbR haemoglobin receptor of Neisseria meningitidis, a possible virulence factor which contributes to bacterial survival in rats. Conclusions By comparative analysis of gene expression among 6 different serotypes of A. pleuropneumoniae we identified a common set of presumably essential core genes, involved in iron regulation. The results support and expand previous observations concerning the identification of new potential iron acquisition systems in A. pleuropneumoniae, showing that this bacterium has evolved several strategies for scavenging the limited iron resources of the

  4. Identification and characterization of some aromatic rice mutants using amplified fragment length polymorphism (AFLP) technique

    International Nuclear Information System (INIS)

    Accurate identifying of the genotypes is considered one of the most important mechanisms used in the recording or the protection of plant varieties. The investigation was conducted at the experimental form belonging to the egyptian Atomic Energy Authority, Inshas. The aim was to evaluate grain quality characteristics and molecular genetic variation using Amplified Fragment Length Polymorphism (AFLP) technique among six rice genotypes, Egyptian Jasmine aromatic rice cultivar and five aromatic rice mutants in (M3 mutagenic generation). Two mutation (Egy22 and Egy24) were selected from irradiated Sakha 102 population with 200 and 400Gy of gamma rays in the M2 generation, respectively, and three mutations ( Egy32, Egy33, and Egy34) were selected from irradiated Sakha 103 population with 200, 300, 400Gy of gamma rays in the M2 generation, respectively. The obtained results showed that the strong aroma was obtained for mutant Egy22 as compared with Egyptian Jasmine rice cultivar (moderate aroma). Seven primer combinations were used through six rice genotypes on the molecular level using AFLP marker. The size of AFLP Fragments Were Ranged from 51- 494bp. The total number of amplified bands was 997 band among them 919 polymorphic bans representing 92.2%. The highest similarity index (89%) was observed between Egyptian Jasmine and Egy32 followed by (82%) observed between Egyptian Jasmine and Egy34. On the other hand, the lowest similarity index was (48%) between Egyptian Jasmine and Egy24. In six rice genotypes, Egy24 produced the highest number of the AFLP makers giving 49 unique markers (23 positive and 26 negative), then Egy22 showed 23 unique markers (27 positive and 6 negative) while Egy33 was characterized by 17 unique markers (12 positive and 5 negative). At last Egyptian Jasmine was discriminated by the lowest number of markets, 10 (6 positive and 4 negative). The study further confirmed that AFLP technique was able to differentiate rice genotypes by a higher number

  5. Comparative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers.

    Science.gov (United States)

    Hu, Jihong; Pan, Lei; Liu, Honggao; Wang, Shuzhen; Wu, Zhihua; Ke, Weidong; Ding, Yi

    2012-04-01

    The sacred lotus (Nelumbo nucifera Gaertn.) is an aquatic plant of economic and ornamental importance in China. In this study, we developed twenty novel sacred lotus SSR markers, and used AFLP and SSR markers to investigate the genetic diversity and genetic relationships among 58 accessions of N. nucifera including 15 seed lotus, 12 rhizome lotus, 24 flower lotus and 7 wild lotus. Our results showed that sacred lotus exhibited a low level of genetic diversity, which may attribute to asexual reproduction and long-term artificial selection. A dendrogram based on both AFLP and SSR clustering data showed that: (1) the seed lotus accessions and rhizome lotus accessions were distinctly clustered into different groups, which indicated the significant genetic differentiation between them. This may be attributed to the two modes of reproduction and lack of genetic exchange; (2) the accessions of Thailand wild lotus were separated from other wild lotus accessions. This implied that the Thailand lotus might be genetically differentiated from other wild lotuses. In addition, Mantel test conducted gave highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with the values of r = 0.941 and r = 0.879, respectively, indicating the higher efficiency of the combination of these techniques (AFLP and SSR) in estimation and validation of the genetic diversity among the accession of sacred lotus. This knowledge of the genetic diversity and genetic relatedness of N. nucifera is potentially useful to improve the current strategies in breeding and germplasm conservation to enhance the ornamental and economic value of sacred lotus.

  6. Transcriptional profiling in rat hair follicles following simulated Blast insult: a new diagnostic tool for traumatic brain injury.

    Directory of Open Access Journals (Sweden)

    Jing Zhang

    Full Text Available With wide adoption of explosive-dependent weaponry during military activities, Blast-induced neurotrauma (BINT-induced traumatic brain injury (TBI has become a significant medical issue. Therefore, a robust and accessible biomarker system is in demand for effective and efficient TBI diagnosis. Such systems will also be beneficial to studies of TBI pathology. Here we propose the mammalian hair follicles as a potential candidate. An Advanced Blast Simulator (ABS was developed to generate shock waves simulating traumatic conditions on brains of rat model. Microarray analysis was performed in hair follicles to identify the gene expression profiles that are associated with shock waves. Gene set enrichment analysis (GSEA and sub-network enrichment analysis (SNEA were used to identify cell processes and molecular signaling cascades affected by simulated bomb blasts. Enrichment analyses indicated that genes with altered expression levels were involved in central nervous system (CNS/peripheral nervous system (PNS responses as well as signal transduction including Ca2+, K+-transportation-dependent signaling, Toll-Like Receptor (TLR signaling and Mitogen Activated Protein Kinase (MAPK signaling cascades. Many of the pathways identified as affected by shock waves in the hair follicles have been previously reported to be TBI responsive in other organs such as brain and blood. The results suggest that the hair follicle has some common TBI responsive molecular signatures to other tissues. Moreover, various TBI-associated diseases were identified as preferentially affected using a gene network approach, indicating that the hair follicle may be capable of reflecting comprehensive responses to TBI conditions. Accordingly, the present study demonstrates that the hair follicle is a potentially viable system for rapid and non-invasive TBI diagnosis.

  7. Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening

    Directory of Open Access Journals (Sweden)

    Sansavini Silviero

    2010-10-01

    Full Text Available Abstract Background Fruit development, maturation and ripening consists of a complex series of biochemical and physiological changes that in climacteric fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the functional machinery underlying these processes is of both biological and practical importance. To date many reports have been made on the analysis of gene expression in apple. In this study we focused our investigation on the role of ethylene during apple maturation, specifically comparing transcriptomics of normal ripening with changes resulting from application of the hormone receptor competitor 1-Methylcyclopropene. Results To gain insight into the molecular process regulating ripening in apple, and to compare to tomato (model species for ripening studies, we utilized both homologous and heterologous (tomato microarray to profile transcriptome dynamics of genes involved in fruit development and ripening, emphasizing those which are ethylene regulated. The use of both types of microarrays facilitated transcriptome comparison between apple and tomato (for the later using data previously published and available at the TED: tomato expression database and highlighted genes conserved during ripening of both species, which in turn represent a foundation for further comparative genomic studies. The cross-species analysis had the secondary aim of examining the efficiency of heterologous (specifically tomato microarray hybridization for candidate gene identification as related to the ripening process. The resulting transcriptomics data revealed coordinated gene expression during fruit ripening of a subset of ripening-related and ethylene responsive genes, further facilitating the analysis of ethylene response during fruit maturation and ripening. Conclusion Our combined strategy based on microarray hybridization enabled transcriptome characterization

  8. TCDD-induced transcriptional profiles in different mouse strains that have an identical AhR genotype

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Qing; Suzuki, Junko S.; Tohyama, Chiharu; Ohsako, Seiichiroh [Environmental Health Sciences Division, National Institute for Environmental Studies, Onogawa, Tsukuba (Japan); Takei, Teiji [Environmental Health and Safety Division, Ministry of the Environment, Kasumigaseki, Tokyo (Japan); Lin, Tinmin; Peterson, R.E. [Wisconsin Univ., Wisconsin, MA (United States). School of Pharmacy and Molecular and Environmental Toxicology Center

    2004-09-15

    2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an environmental contaminant that is known to cause hepatotoxicity, teratogenicity and carcinogenicity. A characteristic feature in the toxicity of TCDD is exceptionally large differences in susceptibility among animal species or even strains belonging to the same species. These strain differences in susceptibility to TCDD have now been elucidated to be due to the difference in ligand binding affinity or transcriptional activity of the aryl hydrocarbon receptor (AhR). Actually the C57BL/6 type AhR (AhR{sup b}) showed 6-fold higher ligand binding affinity than the DBA/2 type AhR (AhR{sup d}). The H/W rat AhR has a C-terminal truncation of the transactivating domain compared to the L-E rat AhR. On the other hand, there is considerable species variability in response sensitivity to TCDD that cannot be ascribed simply to polymorphisms of the AhR gene. A non-AhR gene susceptibility loci for hepatic porphyria has been observed in mice treated with iron compounds prior to TCDD injection by using a quantitative trait locus analysis of an F2 intercross between susceptible C57BL/6 and resistant DBA/2 stains. In the rat, a gene B with Han/Wistar type AhR is likely to be involved in resistance to TCDD lethality. These observations suggest that other modulating genes, so-called ''modifier genes'', have profound effects on the AhR-mediated gene expression phenotype. Based on the nucleotide sequence of the AhR coding region, the BALB/c, CBA/J, and C3H/He mouse strains are clustered together on a single branch. In the present study, we try to confirm the existence of modifiers by using microarray analysis to examine hepatic gene expression after TCDD exposure in BALB/c, CBA/J, and C3H/He mice. To recognize the existence of a modifier besides the AhR, it is a prerequisite experimental condition that the analyzed strains have an identical AhR genotype. Therefore, we selected BALB/c, CBA/J, and C3H/He mice as the model

  9. Expression profiling and cross-species RNA interference (RNAi of desiccation-induced transcripts in the anhydrobiotic nematode Aphelenchus avenae

    Directory of Open Access Journals (Sweden)

    Culleton Bridget A

    2010-01-01

    expression profiles of members of the anhydrobiotic gene set in A. avenae. It also demonstrates the potential of RNAi for the analysis of anhydrobiosis and provides the first genetic data to underline the importance of effective antioxidant systems in metazoan desiccation tolerance.

  10. Proteomic profiling of glucocorticoid-exposed myogenic cells: Time series assessment of protein translocation and transcription of inactive mRNAs

    Directory of Open Access Journals (Sweden)

    Hoffman Eric P

    2009-07-01

    approaches of subcellular proteomic profiling and assessment of acute changes on a minute-based time scale. These data expand the current knowledge of acute, non-transcriptional activities of glucocorticoids, including changes in protein subcellular localization, altered translation of quiescent RNA pools, and PKC-mediated cytoskeleton remodeling.

  11. Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

    Directory of Open Access Journals (Sweden)

    Lamb JoAnn FS

    2011-04-01

    Full Text Available Abstract Background Alfalfa, [Medicago sativa (L. sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling. Results Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length were generated from cDNA libraries derived from elongating stem (ES and post-elongation stem (PES internodes of 708 and 773. In addition, 341,984 ESTs were generated from ES and PES internodes of genotype 773 using the GS FLX Titanium platform. The first alfalfa (Medicago sativa gene index (MSGI 1.0 was assembled using the Sanger ESTs available from GenBank, the GS FLX Titanium EST sequences, and the de novo assembled Illumina sequences. MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs, 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1,294 simple sequence repeats (SSR among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs were predicted between the two genotypes. Out of 55 SNPs randomly selected for experimental validation, 47 (85% were polymorphic between the two genotypes. We also identified numerous allelic variations within each genotype. Digital gene expression analysis identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes. Conclusions Our results demonstrate that RNA

  12. Perfil transcricional e resposta à quimioterapia neoadjuvante em câncer de mama Transcriptional profile and response to neoadjuvante chemotherapy in breast cancer

    Directory of Open Access Journals (Sweden)

    Maria Aparecida Azevedo Koike Folgueira

    2011-06-01

    improve the accuracy predictive models of response to neoadjuvante chemotherapy in breast cancer, cDNA microarray technology was used to study tumor transcriptional profile. Gene signatures associated with predicting the response to neoadjuvante chemotherapy are the subject of this review. METHODS: The data base http://www.ncbi.nlm.nih.gov/pubmed/ search was conducted by using the words "breast cancer" AND "neoadjuvante/primary chemotherapy" AND "gene expression profile/microarray". After excluding the repeats and selecting the publications considered most relevant by the authors to be presented, 279 publications were retrieved. RESULTS: The number of publications regarding this subject has been increasing over the years, reaching over 50 in 2010, including the response to different chemotherapeutic drugs, such as anthracyclines and taxanes either alone or in combination. The first studies are from early last decade and used microarray platforms produced by the investigators. Recent studies have used commercial microarray platforms whose data have been stored in public databases, allowing for the analysis of a higher number of samples. Several transcriptional profiles associated with the complete pathological response were identified. Other authors used the clinical response to treatment as an endpoint, and, in this case, a predictive panel of resistance to the chemotherapeutic regimen at issue was determined. This is also a key issue, as it can contribute to individualize treatment, allowing patients resistant to a certain chemotherapeutic agent to be offered another therapeutic regimen. CONCLUSION: Identifying patients responsive to chemotherapy is of essential interest and despite major steps have been taken, the issue warrants further studies in view of its complexity.

  13. Overlaps in the Transcriptional Profiles of Medicago truncatula Roots Inoculated with Two Different Glomus Fungi Provide Insights into the Genetic Program Activated during Arbuscular Mycorrhiza1[w

    Science.gov (United States)

    Hohnjec, Natalija; Vieweg, Martin F.; Pühler, Alfred; Becker, Anke; Küster, Helge

    2005-01-01

    Arbuscular mycorrhiza (AM) is a widespread symbiotic association between plants and fungal microsymbionts that supports plant development under nutrient-limiting and various stress conditions. In this study, we focused on the overlapping genetic program activated by two commonly studied microsymbionts in addition to identifying AM-related genes. We thus applied 16,086 probe microarrays to profile the transcriptome of the model legume Medicago truncatula during interactions with Glomus mosseae and Glomus intraradices and specified a total of 201 plant genes as significantly coinduced at least 2-fold, with more than 160 being reported as AM induced for the first time. Several hundred genes were additionally up-regulated during a sole interaction, indicating that the plant genetic program activated in AM to some extent depends on the colonizing microsymbiont. Genes induced during both interactions specified AM-related nitrate, ion, and sugar transporters, enzymes involved in secondary metabolism, proteases, and Kunitz-type protease inhibitors. Furthermore, coinduced genes encoded receptor kinases and other components of signal transduction pathways as well as AM-induced transcriptional regulators, thus reflecting changes in signaling. By the use of reporter gene expression, we demonstrated that one member of the AM-induced gene family encoding blue copper binding proteins (MtBcp1) was both specifically and strongly up-regulated in arbuscule-containing regions of mycorrhizal roots. A comparison of the AM expression profiles to those of nitrogen-fixing root nodules suggested only a limited overlap between the genetic programs orchestrating root endosymbioses. PMID:15778460

  14. Gene expression profiling identifies microphthalmia-associated transcription factor (MITF and Dickkopf-1 (DKK1 as regulators of microenvironment-driven alterations in melanoma phenotype.

    Directory of Open Access Journals (Sweden)

    Mariusz L Hartman

    Full Text Available BACKGROUND: The diversity of functional phenotypes observed within a tumor does not exclusively result from intratumoral genetic heterogeneity but also from the response of cancer cells to the microenvironment. We have previously demonstrated that the morphological and functional phenotypes of melanoma can be dynamically altered upon external stimuli. FINDINGS: In the present study, transcriptome profiles were generated to explore the molecules governing phenotypes of melanospheres grown in the bFGF(+EGF(+ serum-free cultures and monolayers maintained in the serum-containing medium. Higher expression levels of MITF-dependent genes that are responsible for differentiation, e.g., TYR and MLANA, and stemness-related genes, e.g., ALDH1A1, were detected in melanospheres. These results were supported by the observation that the melanospheres contained more pigmented cells and cells exerting the self-renewal capacity than the monolayers. In addition, the expression of the anti-apoptotic, MITF-dependent genes e.g., BCL2A1 was also higher in the melanospheres. The enhanced activity of MITF in melanospheres, as illustrated by the increased expression of 74 MITF-dependent genes, identified MITF as a central transcriptional regulator in melanospheres. Importantly, several genes including MITF-dependent ones were expressed in melanospheres and original tumors at similar levels. The reduced MITF level in monolayers might be partially explained by suppression of the Wnt/β-catenin pathway, and DKK1, a secreted inhibitor of this pathway, was highly up-regulated in monolayers in comparison to melanospheres and original tumors. Furthermore, the silencing of DKK1 in monolayers increased the percentage of cells with self-renewing capacity. CONCLUSIONS: Our study indicates that melanospheres can be used to unravel the molecular pathways that sustain intratumoral phenotypic heterogeneity. Melanospheres directly derived from tumor specimens more accurately mirrored

  15. Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes

    Directory of Open Access Journals (Sweden)

    Bihoreau Marie-Thérèse

    2009-02-01

    Full Text Available Abstract Background Microarray technologies are widely used to quantify the abundance of transcripts corresponding to thousands of genes. To maximise the robustness of transcriptome results, we have tested the performance and reproducibility of rat and mouse gene expression data obtained with Affymetrix, Illumina and Operon platforms. Results We present a thorough analysis of the degree of reproducibility provided by analysing the transcriptomic profile of the same animals of several experimental groups under different popular microarray technologies in different tissues. Concordant results from inter- and intra-platform comparisons were maximised by testing many popular computational methods for generating fold changes and significances and by only considering oligonucleotides giving high expression levels. The choice of Affymetrix signal extraction technique was shown to have the greatest effect on the concordance across platforms. In both species, when choosing optimal methods, the agreement between data generated on the Affymetrix and Illumina was excellent; this was verified using qRT-PCR on a selection of genes present on all platforms. Conclusion This study provides an extensive assessment of analytical methods best suited for processing data from different microarray technologies and can assist integration of technologically different gene expression datasets in biological systems.

  16. Transcriptional profile of Pseudomonas syringae pv. phaseolicola NPS3121 in response to tissue extracts from a susceptible Phaseolus vulgaris L. cultivar

    Directory of Open Access Journals (Sweden)

    Martínez-Antonio Agustino

    2009-12-01

    Full Text Available Abstract Background Pseudomonas syringae pv. phaseolicola is a Gram-negative plant-pathogenic bacterium that causes "halo blight" disease of beans (Phaseolus vulgaris L.. This disease affects both foliage and pods, and is a major problem in temperate areas of the world. Although several bacterial genes have been determined as participants in pathogenesis, the overall process still remains poorly understood, mainly because the identity and function of many of the genes are largely unknown. In this work, a genomic library of P. syringae pv. phaseolicola NPS3121 was constructed and PCR amplification of individual fragments was carried out in order to print a DNA microarray. This microarray was used to identify genes that are differentially expressed when bean leaf extracts, pod extracts or apoplastic fluid were added to the growth medium. Results Transcription profiles show that 224 genes were differentially expressed, the majority under the effect of bean leaf extract and apoplastic fluid. Some of the induced genes were previously known to be involved in the first stages of the bacterial-plant interaction and virulence. These include genes encoding type III secretion system proteins and genes involved in cell-wall degradation, phaseolotoxin synthesis and aerobic metabolism. On the other hand, most repressed genes were found to be involved in the uptake and metabolism of iron. Conclusion This study furthers the understanding of the mechanisms involved, responses and the metabolic adaptation that occurs during the interaction of P. syringae pv. phaseolicola with a susceptible host plant.

  17. Transcription profile of DNA repair genes and micro RNA in resting human peripheral blood mono nuclear cells exposed to gamma radiation

    International Nuclear Information System (INIS)

    Human genome is constantly under various genotoxic agents including ionizing radiation which may exert multiple cellular and molecular consequences. Ionizing radiation induces a spectrum of DNA damages in human cells that results in activation of various DNA repair pathways to maintain the integrity of the genome. Radiation induced DNA damage response may lead to alteration in expression of gene, protein and microRNA profile in human cells. miRNA are small, non-coding, ssRNA of 20-22 nucleotide in length and regulate gene expression at post-transcriptional level. In the present study, attempts have been made to study the gene expression pattern of selected DNA repair genes and miRNA in resting human peripheral blood mono nuclear cells (PBMC) exposed to gamma radiation. Venous blood samples were collected from 10 volunteers. PBMC were separated and exposed to gamma radiation between 0.1 Gy to 2.0 Gy at a dose rate of 1.0 Gy/min. Total RNA was isolated at 0 h and 4 h post irradiation. Expression profile of p53, ATM (DNA Damage Response), ERCC3, hRad23A, hRad23B (Nucleotide Excision Repair), hMSH2, hMSH6 and hMLH1 (Mis-Match Repair) and miRNA (miR-16, miR-21, miR24 and miR-155) which are known to regulate expression of DNA repair genes was analyzed by real time quantitative PCR. Our results showed significant (P < 0.05) up regulation of p53 at higher doses (1.0 Gy and 2.0 Gy), whereas hRad23A and MLH1 showed significant increase in expression across the doses at 4 h post irradiation. Interestingly, the expression profile of miR155 showed significant (P<0.05) up regulation at 4 h post irradiation across all the doses. The significant up regulation of p53, hRad23A and hMLH1 at mRNA level and significant up regulation of miR-155 perhaps indicates an active role of these genes and miRNA in radiation induced DNA damage and its response in gamma irradiated human PBMC. (author)

  18. 杞柳AFLP反应体系的建立与引物筛选%Establishment of AFLP Reaction System for Salix integra and Primer Selection

    Institute of Scientific and Technical Information of China (English)

    戴晓港; 渠纪腾; 冯凯; 张新叶; 李淑娴

    2012-01-01

    Taking Salix integra F1 progeny as experimental material, the genomic DNA was extracted from the leaves by modified CTAB extraction method. Subsequently, the optimized AFLP experimental protocol was established through enzyme incision, conjunction, pre-amplification and selective amplification. 256 pairs of primer combinations were composed with 16 EcoRI and 16 Msel selective amplification primers respectively. The results showed that clear and repeatable gel profiles could be obtained under the reaction protocol as: 320 ng genomic DNA was digested at 37℃ for 6 hours by 5U of EcoRI and 5U Msel, then conjugated at 20℃ for 12 hours, the ligation products were 10 times diluted, and used as the template for pre-amplification. After pre-amplification, the products were diluted for 15 times, then used as templates for selective amplification. The selective amplification products were detected by ABI -3130 electrophoresis and the clear and repeatable gel profiles were obtained. 98 pairs of primer combinations that yielded high polymorphic bands were selected from the 256 pairs of AFLP primer combinations for AFLP analysis of S. integra.%以杞柳F1群体为试验材料,采用改良的CTAB法提取基因组DNA,经过酶切、连接、预扩增和选择性扩增,建立杞柳AFLP的反应体系,筛选EcoRI和MseI各16条选择性扩增引物组成256对引物组合.结果表明:320ng基因组DNA采用5U EcoRI和MseI 双酶切6h,20℃连接12h,连接产物稀释10倍进行预扩增,预扩增产物稀释15倍进行选择性扩增,选择性扩增产物采用ABI-3130检测,可获得条带清晰的指纹图;从256对引物组合中共筛选出98对多态性较高的引物组合.

  19. High Lycopene AFLP- SCAR Molecular Marker of Fresh Tomato%鲜食番茄茄红素基因的AFLP-SCAR分子标记

    Institute of Scientific and Technical Information of China (English)

    侯丽霞; 刘淑梅; 王施慧; 吕鑫

    2011-01-01

    Lycopene (LYC) is a function of the natural pigment, because of its high antioxidant functions have attracted much attention. For screening high-lycopene varieties of fresh tomatoes to accelerate the process of molecular marker-assisted breeding, AFLP-SCAR marks of high lycopene were studied by using materials high-lycopene selling line F-516F8 and low-lycopene selfing line Nor. Using genetical population of Ft and F2, AFLP and BAS techniques with 64 pairs of E/M primers screening, we obtained one AFLP marker E-AG/M-CAT. Through recovery, and sequencing of idio-fragment, transformation of SCAR, BLAST, marker E-AG/M-CAT was locating on the eighth chromosome. Utilizing SCAR makers can evaluate the content of lycopene at DNA level when the tomato materials are in seedling period, which greatly reducing the workload of field screening. SCAR makers can also be used on molecular marker assisted selection, improving the breeding efficiency.%番茄红素(Lycopene)是功能性天然色素,因其高抗氧化功能而备受关注.为筛选高番茄红素品种,加速鲜食番茄分子标记辅助育种进程,本试验以高茄红素番茄骨干系F-516F8和低茄红素骨干系Nor作为试验材料,研究了鲜食番茄高茄红素基因的AFLP-SCAR分子标记.利用杂交F1代、自交F2代遗传群体,通过64对E/M引物组合的筛选,采用AFLP分析技术和改良BAS法,获得1个与高番茄红素基因连锁的AFLP标记E-AG/M-CAT.通过特异片段回收、测序、SCAR转化、BLAST比对分析,该标记定位在番茄第8染色体.利用SCAR标记可在苗期从DNA水平上对番茄材料的番茄红素含量高低进行鉴定,大大减少了田间筛选工作量,并可用于分子标记辅助育种,提高育种效率.

  20. RNA profiling and chromatin immunoprecipitation-sequencing reveal that PTF1a stabilizes pancreas progenitor identity via the control of MNX1/HLXB9 and a network of other transcription factors

    DEFF Research Database (Denmark)

    Thompson, Nancy; Gésina, Emilie; Scheinert, Peter;

    2012-01-01

    those factors, PTF1a, a basic helix-loop-helix (bHLH) transcription factor which controls pancreas exocrine cell differentiation, maintenance, and functionality, is also needed for the early specification of pancreas progenitors. We used RNA profiling and chromatin immunoprecipitation (ChIP) sequencing...... promoted by PTF1a. These proteins, most of which were previously shown to be necessary for pancreas bud maintenance or formation, form a transcription factor network that allows the maintenance of pancreas progenitors. In addition, we identify Bmp7, Nr5a2, RhoV, and P2rx1 as new targets of PTF1a in...

  1. Characterization and expression profiling of MYB transcription factors against stresses and during male organ development in Chinese cabbage (Brassica rapa ssp. pekinensis).

    Science.gov (United States)

    Saha, Gopal; Park, Jong-In; Ahmed, Nasar Uddin; Kayum, Md Abdul; Kang, Kwon-Kyoo; Nou, Ill-Sup

    2016-07-01

    MYB proteins comprise a large family of plant transcription factors that play regulatory roles in different biological processes such as plant development, metabolism, and defense responses. To gain insight into this gene superfamily and to elucidate its roles in stress resistance, we performed a comprehensive genome-wide identification, characterization, and expression analysis of MYB genes in Chinese cabbage (Brassica rapa ssp. pekinensis). We identified 475 Chinese cabbage MYB genes, among which most were from R2R3-MYB (256 genes) and MYB-related (202) subfamilies. Analysis of sequence characteristics, phylogenetic classification, and protein motif structures confirmed the existence of several categories (1R, 2R, 3R, 4R, and 5R) of Chinese cabbage MYB genes, which is comparable with MYB genes of other crops. An extensive in silico functional analysis, based on established functional properties of MYB genes from different crop species, revealed 11 and four functional clades within the Chinese cabbage R2R3-MYB and MYB-related subfamilies, respectively. In this study, we reported a MYB-like group within the MYB-related subfamily contains 77 MYB genes. Expression analysis using low temperature-treated whole-genome microarray data revealed variable transcript abundance of 1R/2R/3R/4R/5R-MYB genes in 11 clusters between two inbred lines of Chinese cabbage, Chiifu and Kenshin, which differ in cold tolerance. In further validation tests, we used qRT-PCR to examine the cold-responsive expression patterns of 27 BrMYB genes; surprisingly, the MYB-related genes were induced more highly than the R2R3-MYB genes. In addition, we identified 10 genes with corresponsive expression patterns from a set of salt-, drought-, ABA-, JA-, and SA-induced R2R3-MYB genes. We identified 11 R2R3-MYBs functioning in resistance against biotic stress, including 10 against Fusarium oxysporum f.sp. conglutinans and one against Pectobacterium carotovoram subsp. caratovorum. Furthermore, based on

  2. Using AFLP markers and the Geneland program for the inference of population genetic structure

    DEFF Research Database (Denmark)

    Guillot, Gilles; Santos, Filipe

    2010-01-01

    The use of dominant markers such as amplified fragment length polymorphism (AFLP) for population genetics analyses is often impeded by the lack of appropriate computer programs and rarely motivated by objective considerations. The point of the present note is twofold: (i) we describe how the comp......The use of dominant markers such as amplified fragment length polymorphism (AFLP) for population genetics analyses is often impeded by the lack of appropriate computer programs and rarely motivated by objective considerations. The point of the present note is twofold: (i) we describe how...... such as single nucleotide polymorphisms (SNP) markers but this difference becomes negligible for data sets of common size (number of individuals n≥100, number of markers L≥200). The latest Geneland version (3.2.1) handling dominant markers is freely available as an R package with a fully clickable graphical...

  3. Studies on the Primers Screening for AFLP Fingerprints of Rice Cultivars

    Institute of Scientific and Technical Information of China (English)

    ZHANG Chun-qing; JIA Ji-zeng

    2002-01-01

    AFLP(amplified fragment length polymorphism) is a very powerful fingerprinting technology.The key of making variety fingerprints is to select specific powerful primers for each crop. A quick and effective procedure for selecting AFLP primers for rice variety fingerprinting was established as the following: (1)Choose 3 or more group materials that have close genetic relations. (2) Select potential polymorphic primers from primer pairs that are 2 + 2 primer crosses and same at two ends. (3) Recombine the selected potential polymorphic primers and choosing more polymorphic primers. (4) Add one selecting base at one end to become 2 + 3 or 3 + 2primers and further selecting more polymorphic primers. Some primers were selected with this procedure, such as M21Ps7 and M73P17, with which the fingerprints had more polymorphism and high quality.

  4. AFLP fingerprinting of Chinese epidemic strains of Puccinia striiformis f. sp. tritici

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Amplified fragment length polymorphism (AFLP) was used to fingerprint the epidemic strains CY25, CY27, CY28, CY29, CY30, CY31, Hy3, Hy7, Sy13 and a mutant strain WV-4 of P. striiformis f. sp. tritici, the pathogen of wheat stripe rust. The results showed that (i) genetic diversity existed in the pathogen populations, and based on it a dendrogram of these strains was constructed by unweighted pair-group mean average to demonstrate the relationships of the tested strains; (ii) no significant correlation between virulence of the pathogens and the polymorphism of DNA fingerprints was found; ( iii ) AFLP fingerprints showed higher polymorphism than that of the virulence variation; (iv) several new pathotypes identified might evolve independently of the reference strains identified before.

  5. Research of Genetic Diversity in Seven Kobresia by AFLP in Tibetan Plateau

    Institute of Scientific and Technical Information of China (English)

    ZHENG Hong-mei; HU Tian-ming; WANG Quan-zhen; ZHANG Guo-yun; SONG Jiang-hu

    2009-01-01

    This work analyzed the genetic diversity of Kobresia accessions at the molecular level, and further obtained the necessary information for breeding and germplasm evaluation. Genomic DNA of Kobresia was amplified with four E+3 and M+3 primer combinations with AFLP (amplified fragment length polymorphism). AFLP analysis produced 164 scorable bands,of which 154 (93.96%) were polymorphic. The mean Nei's gene diversity index (H) was 0.2430, and the Shannon's information index (I) was 0.4012, indicating the abundant genetic diversity of Kobresia. The 11 Kobresia accessions from Tibetan Plateau, China, can be classified into five groups after cluster analysis based on the UPGMA (unweighted pair group method arithmetic average) method. In general, there was abundant genetic diversity among Kobresia accessions resources, and the genetic coefficient was unrelated to their geographic latitude. Natural habitats influenced genetic differentiation of Kobresia.

  6. Genetic diversity of wild and cultivated Rubus species in Colombia using AFLP and SSR markers

    Directory of Open Access Journals (Sweden)

    Sandra Bibiana Aguilar

    2007-01-01

    Full Text Available The Andean blackberry belongs to the genus Rubus, the largest of the Rosaceae family and one of the mostdiverse of the plant kingdom. In Colombia Rubus glaucus Benth, known as the Andean raspberry or blackberry, is one of thenine edible of the genus out of forty-four reported species. In this study wild and cultivated genotypes, collected in the CentralAndes of Colombia were analyzed by AFLP and SSR markers. Sexual reproduction seems to play an important role inmaintaining the genetic variability in R. glaucus, and the viability of using the SSR of Rubus alceifolius to characterizeColombian Rubus species was clearly demonstrated. All species evaluated produced very specific banding patterns,differentiating them from the others. Both AFLP and SSR produced bands exclusive to each of the following species: R.robustus, R. urticifolius, R. glaucus, and R. rosifolius. The SSR markers differentiated diploid and tetraploid genotypes of R.glaucus.

  7. Transcriptional profiling of Aspergillus niger

    OpenAIRE

    Veen, van der, J.T.

    2009-01-01

    The industrially important fungus Aspergillus niger feeds naturally on decomposing plant material, of which a significant proportion is lipid. Examination of the A. niger genome sequence suggested that all proteins required for metabolic conversion of lipids are present, including 63 predicted lipases. In contrast to polysaccharide-degrading enzyme networks, not much is known about the signaling and regulatory processes that control lipase expression and activity in fungi. This project was ai...

  8. Transcriptional profiling of Aspergillus niger

    NARCIS (Netherlands)

    Veen, van der D.

    2009-01-01

    The industrially important fungus Aspergillus niger feeds naturally on decomposing plant material, of which a significant proportion is lipid. Examination of the A. niger genome sequence suggested that all proteins required for metabolic conversion of lipids are present, including 63 predicted lipas

  9. Phylogenetic Relationships in Genus Arachis Based on SSR and AFLP Markers

    Institute of Scientific and Technical Information of China (English)

    TANG Rong-hua; ZHUANG Wei-jian; GAO Guo-qing; HE Liang-qiong; HAN Zhu-qiang; SHAN Shi-hua; JIANG Jing; LI Yang-rui

    2008-01-01

    Fourteen wild species of different sections in the genus Arachis and 24 accessions of the AABB allotetraploid A. hypogaea (cultivated peanut) from several countries which belong to different botanical varieties, were analyzed by SSR and AFLP marker systems. The assay-units per system needed to distinguish among all the tested accessions were at least five for SSR or two for AFLP. The genetic distance detected by the SSR markers ranged from 0.09 to 0.95, and the mean was 0.73; and the genetic distance detected by the AFLP markers ranged from 0.01 to 0.79 with an average of 0.42. All the tested peanut SSR primer pairs were multilocus ones, and the amplified fragments per SSR marker in each peanut genome ranged from 2 to 15 with the mean of 4.77. The peanut cultivars were closely related to each other, and shared a large numbers of SSR and AFLP fragments. In contrast, the species in the genus Arachis shared few fragments. The results indicated that the cultivated peanut (A. hypogaea L.) varieties could be partitioned into two main groups and four subgroups at the molecular level, and that A. duranensis is one of the wild ancestors of A. hypogaea. The lowest genetic variation was detected between A. cardenasii and A. batizocoi, and the highest was detected between A. pintoi and the species in the section Arachis. The relationships among the botanical varieties in the cultivated peanut (A. hypogaea L.) and among wild species accessions in section Arachis and those in other sections in the genus Arachis were discussed.

  10. Analysis of the Relationship between Genome Diversity and Adult Survive Rate of Botryllus Schlosseri by AFLP

    Institute of Scientific and Technical Information of China (English)

    FENG Xiao-rong; ZHU Jian-zhong; DENG Feng-jiao; Jacob Douek; Baruch Rinkevich

    2004-01-01

    Objective: The self-cross colonial prochordate, Botryllus schlosseri ( B. schlosseri) occupy a key phylogenetic position in the evolution of vertebrates. To clarify the relationship of genome diversity and survive rate, five generations of B.schlosseri was investigated by amplified fragment length polymorphism (AFLP). Methods:AFLP markersare extremely sensitive to even smell sequence variation, using PCR and high-resolution electrophoresis to examine restriction fragments. Results: AFLP polymorphism was high in the parent and lower in its F1, F2, F3 and F4. Each primer combination generated from 80 to more than 120 bands, of which average 25.85% poiymorphic loci in parent, 15.79% polymorphic among F1, 9.16% and 5.58% in F2,F3. The AFLP markers were transmitted from F1 to F2, F3 and F4 and inherited, segregated in expected Mendelian ratio. However, some of the markers were lost in F2, F3 and F4 while it disappeared in their mother. In addition, gene mutation-new loci and lost loci among F1, F2, F3 and F4 were observed. These special fragments were cloned and sequenced. Then, the genomic DNA was analyzed by Southem hybridization with the probes from these specific fragments and the mechanism of gene mutation was clarified. Conclusion:The se results suggest that there are high frequency of polymorphic loci and mutation in genome of B.schlosseri. Gene deletion or iow diversity may be the reason for high rate of death of the offspring of inbred laboratory-reared strains.

  11. AFLP molecular marker and crop improvement%AFLP分子标记与作物改良

    Institute of Scientific and Technical Information of China (English)

    李爱丽; 马峙英

    2001-01-01

    Molecular markers based on DNA play a very important role in crop improvement. Amplified fragment length polymorphism (AFLP) technology is a novel and powerful DNA fingerprinting technique. It is based on the selective amplification of restriction fragments from a total digest of genomic DNA. The AFLP approach is particularly powerful because it requires no prior sequence characterization of the target genome, and it is readily applicable to a wide variety of crops. This paper mainly discussed the application of AFLP in main crops to cultivars identification, genetic map construction, gene location, and assisted selection.%建立于DNA基础之上的分子标记对于作物改良具有重要作用。 AFLP(Amplified fragment length polytism, 简称AFtP)国内译为扩增片段长度多态性,是一种DNA分子标记技术。利用这一方法,在不需要预先知道DNA序列信息的情况下就可以同时进行多数DNA酶切片断的PCR扩增。目前,该技术不仅在小麦、玉米、棉花和大豆等主要农作物上得以应用,而且在蔬菜(番茄、马铃薯、鹰嘴豆等)以及植物基因组研究的模式植物拟南芥上广泛应用。讨论了AFLP在主要作物的品种鉴定、遗传多样性分析、遗传作图、基因定位以及辅助选择等方面的应用进展。

  12. Ochratoxin A producing Penicillium verrucosum isolates from cereals reveal large AFLP fingerprinting variability

    OpenAIRE

    Frisvad, J C; Lund, F; Elmholt, S.

    2005-01-01

    Aims: To examine if molecular amplified fragment length polymorphism (AFLP) fingerprinting of the only ochratoxin A-producing species in European cereals, Penicillium verrucosum, can be used as a method in hazard analysis using critical control points (HACCP). Methods and Results: A total of 321 isolates of P. verrucosum were isolated from ochratoxin A contaminated cereals from Denmark (oats), UK (wheat and barley) and Sweden (wheat). Of these, 236 produced ochratoxin A as determined by t...

  13. Molecular characterization of native potato (Solanum spp. Chungui, Ayacucho, using AFLP

    Directory of Open Access Journals (Sweden)

    Juan C. Gonzales Mamani

    2014-12-01

    Full Text Available Genetic diversity of 25 morphotypes of native potatoes Solanum spp. from Chungui (La Mar, Ayacucho were assess. Morphotypes collected were micropropagated in Murashigue Skoog medium (1962. DNA extraction proceeded using the CTAB method modified from 3 weeks leaves crop, good quality and quantity of DNA was able to use the AFLP. Enzymatic digestion of the DNA was performed using EcoRI and MseI. Three combinations of AFLP primers with three selective nucleotides were used, resulting in a total of 85 clearly discernable bands, of which 63 were polymorphic. The combination E37 – M50 showed the most informative polymorphic index content of 0.43. The presence/absence of polymorphic bands was evaluated using the Simple Matching coefficient similarity and clustering analysis using the UPGMA. The dendrogram produced had a cophenetic correlation coefficient r= 0.7. At the level 0.64 of Simple Matching coefficient similarity, the dendrogram grouped the morphotypes of native potatoes in 4 genetic groups, it not found duplicated morphotypes, despite having some morphotypes very similar. Our results would be showing the highly informative power of AFLP markers for the analysis of genetic diversity of native potatoes.

  14. Molecular Markers for Leaf Rust Resistance Gene Lr45 in Wheat Based on AFLP Analysis

    Institute of Scientific and Technical Information of China (English)

    ZHANG Na; YANG Wen-xiang; YAN Hong-fei; LIU Da-qun; CHU Dong; MENG Qing-fang; ZHANG Ting

    2006-01-01

    Amplified fragment length polymorphism (AFLP) analysis was carried out in Thatcher, near isogenic lines (NILs) carrying different genes conferring resistance against wheat leaf rust, and TcLr45×Thatcher F2 progenies were used to develop markers for Lr45 gene. Sixty AFLP primer combinations were screened and most of them provided clear amplification products, 31 primer combinations displayed polymorphism of TcLr45 in 23 NILs. Two AFLP markers closely linked to the gene Lr45 were acquired: P-AGG/M-GAG261 bp, which was found closely linked to the Lr45 locus at a distance of 0.6 cM on one side, and P-ACA/M-GGT105 bp, which was found at a distance of 1.3 cM on the other side. The specific bands were cloned and subsequently sequenced. The 261-bp fragment produced by P-AGG/M-GAG showed 86% similarity with the sequence of Vulgare Hort Ⅰ gene; the 105-bp fragment produced by P-ACA/M-GGT showed 96% similarity with the phosphatidylserine decarboxylase gene of the Triticum monococcum. Both included an open reading frame (ORF).

  15. Application of AFLP markers for population genetic study on half-smooth tongue sole Cynoglossus semilaevis

    Institute of Scientific and Technical Information of China (English)

    LIU Yunguo; LI Junfeng; YE Naihao

    2011-01-01

    The genetic diversity of wild and hatchery populations of half-smooth tongue sole Cynoglossus semilaevis, based on observation of amplified fragment length polymorphism (AFLP) was described. Two hundred individuals from four wild populations, Laizhou (LZ), Weihai (WH), Qingdao (QD), Rizhao (RZ), and one hatchery population, Mingbo (MB), were screened using eight different AFLP primer combinations. A total of 384 loci were screened in the five studied populations. 48.4%, 51.3%,50.7%, 49.3% and 45.8% of these loci were polymorphic among the individuals tested in the LZ, WH,QD, RZ and MB populations, respectively. The number of polymorphic loci detected by single primer combinations ranged from 17 to 35. The average heterozygosity of the LZ, WH, QD, RZ and MB populations was 0.072, 0.093, 0.092, 0.090 and 0.063, respectively. The WH population showed the highest genetic diversity in terms of total number of AFLP bands, total number of polymorphic bands,average heterozygosity and percentage of low frequency (0-0.2) polymorphic loci among all the populations,while the LZ population was the lowest among the wild populations. Compared with the wild populations,the hatchery population showed a low genetic viability.

  16. Species-specific AFLP markers for identification of Zingiber officinale, Z. montanum and Z. zerumbet (Zingiberaceae).

    Science.gov (United States)

    Ghosh, S; Majumder, P B; Sen Mandi, S

    2011-01-01

    The Zingiber genus, which includes the herbs known as gingers, commonly used in cooking, is well known for its medicinal properties, as described in the Indian pharmacopoeia. Different members of this genus, although somewhat similar in morphology, differ widely in their pharmacological and therapeutic properties. The most important species of this genus, with maximal therapeutic properties, is Zingiber officinale (garden ginger), which is often adulterated with other less-potent Zingiber sp. There is an existing demand in the herbal drug industry for an authentication system for the Zingiber sp in order to facilitate their commercial use as genuine phytoceuticals. To this end, we used amplified fragment length polymorphism (AFLP) to produce DNA fingerprints for three Zingiber species. Sixteen collections (six of Z. officinale, five of Z. montanum, and five of Z. zerumbet) were used in the study. Seven selective primer pairs were found to be useful for all the accessions. A total of 837 fragments were produced by these primer pairs. Species-specific markers were identified for all three Zingiber species (91 for Z. officinale, 82 for Z. montanum, and 55 for Z. zerumbet). The dendogram analysis generated from AFLP patterns showed that Z. montanum and Z. zerumbet are phylogenetically closer to each other than to Z. officinale. The AFLP fingerprints of the Zingiber species could be used to authenticate Zingiber sp-derived drugs and to resolve adulteration-related problems faced by the commercial users of these herbs. PMID:21341214

  17. Extended metAFLP approach in studies of tissue culture induced variation (TCIV) in triticale.

    Science.gov (United States)

    Machczyńska, Joanna; Orłowska, Renata; Zimny, Janusz; Bednarek, Piotr Tomasz

    2014-01-01

    We present the development of the theoretical background of the metAFLP approach which allows for partition of complex variation into sequence changes, de novo methylation and demethylation of the regenerants derived via in vitro tissue culture methods in the case of triticale. It was demonstrated that, independent of whether andro- or embryogenesis was used for plant regeneration, the level of sequence changes identified between regenerants is about 10 %. Moreover, DNA demethylation prevails over de novo methylation of the regenerants compared to the donor plant. The metAFLP approach allows for the evaluation of numerous quantitative characteristics. For instance, one may quantify the number of sites unaffected by tissue culture approaches, global site DNA methylation etc. It is suggested that the approach could be useful for breeders in order to control plant material uniformity or for the evaluation of modified in vitro tissue culture approaches allowing for control of the (epi)mutation level. The extended metAFLP approach presented here delivers sufficient background for the evaluation of software that could facilitate analyses of the tissue culture induced variation. PMID:25242884

  18. Identification of aluminum-regulated genes by cDNA-AFLP analysis of roots in two contrasting genotypes of highbush blueberry (Vaccinium corymbosum L.).

    Science.gov (United States)

    Inostroza-Blancheteau, Claudio; Aquea, Felipe; Reyes-Díaz, Marjorie; Alberdi, Miren; Arce-Johnson, Patricio

    2011-09-01

    To investigate the molecular mechanisms of Al(3+)-stress in blueberry, a cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis was employed to identify Al-regulated genes in roots of contrasting genotypes of highbush blueberry (Brigitta, Al(3+)-resistant and Bluegold, Al(3+)-sensitive). Plants grown in hydroponic culture were treated with 0 and 100 μM Al(3+) and collected at different times over 48 h. Seventy transcript-derived fragments (TDFs) were identified as being Al(3+) responsive, 31 of which showed significant homology to genes with known or putative functions. Twelve TDFs were homologous to uncharacterized genes and 27 did not have significant matches. The expression pattern of several of the genes with known functions in other species was confirmed by quantitative relative real-time RT-PCR. Twelve genes of known or putative function were related to cellular metabolism, nine associated to stress responses and other transcription and transport facilitation processes. Genes involved in signal transduction, photosynthetic and energy processes were also identified, suggesting that a multitude of processes are implicated in the Al(3+)-stress response as reported previously for other species. The Al(3+)-stress response genes identified in this study could be involved in Al(3+)-resistance in woody plants.

  19. Divergência genética entre genótipos de alface por meio de marcadores AFLP Genetics divergence among lettuce genotypes by AFLP markers

    Directory of Open Access Journals (Sweden)

    Cristina Soares de Sousa

    2007-01-01

    Full Text Available Considerando a restrita diversidade de espécies disponíveis para nutrir a carência de vitaminas no Brasil, Kerr e colaboradores, desde 1981, vêm desenvolvendo pesquisas para melhoramento genético de hortaliças ricas em vitamina A. Dentre elas, obtiveram uma cultivar de alface, denominada Uberlândia 10.000 com 10.200 UI de vitamina A em 100 gramas de folha fresca. Este trabalho objetivou comparar o grau de divergência genética entre a cultivar Uberlândia 10.000 e seus parentais para avaliar a eficiência da seleção utilizada, por meio da técnica AFLP. Foram utilizados os seguintes genótipos de alface: Maioba, Salad Bowl-Mimosa, Moreninha-de-Uberlândia, Vitória de Santo Antão, Uberlândia 10.000 lisa 8.ª e 9.ª geração e Uberlândia 10.000 crespa 8.ª e 9.ª geração. A técnica AFLP foi eficiente para identificar genótipos muito próximos e para estudos de progênies em alface. O primer PR15 permitiu a separação da forma lisa e crespa com 1,8% de divergência genética e a oitava da nona geração com apenas 0,71%. Com o estudo da filogenia da cultivar pode-se observar que o programa de melhoramento foi desenvolvido com sucesso, pois a cultivar obtida Uberlândia 10.000 possui alto teor de vitamina A e 92% de similaridade com o parental Vitória de Santo Antão. O primer PR11 conseguiu identificar polimorfismo entre cultivares de alta e baixa resistência à septoriose, sugerindo a possibilidade destas bandas estarem relacionadas à resistência.Considering the restricted diversity of species available to counteract vitamin deficiencies in Brazil, Kerr and coworkers have been engaged since 1981, in developing genetic improved garden vegetables rich in vitamin A. One of these vegetables is the lettuce cultivar Uberlândia 10,000, which contains 10,200 UI of vitamin A per 100 grams of fresh leaves. This study compares the genetic diversity between Uberlândia 10,000 and its parental, evaluating selection efficiency through

  20. Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action

    Directory of Open Access Journals (Sweden)

    Dusica eVidovic

    2014-09-01

    Full Text Available The Library of Integrated Network-based Cellular Signatures (LINCS project is a large-scale coordinated effort to build a comprehensive systems biology reference resource. The goals of the program include the generation of a very large multidimensional data matrix and informatics and computational tools to integrate, analyze, and make the data readily accessible. LINCS data include genome-wide transcriptional signatures, biochemical protein binding profiles, cellular phenotypic response profiles and various other datasets for a wide range of cell model systems and molecular and genetic perturbations. Here we present a partial survey of this data facilitated by data standards and in particular a robust compound standardization workflow; we integrated several types of LINCS signatures and analyzed the results with a focus on mechanism of action and chemical compounds. We illustrate how kinase targets can be related to disease models and relevant drugs. We identified some fundamental trends that appear to link Kinome binding profiles and transcriptional signatures to chemical information and biochemical binding profiles to transcriptional responses independent of chemical similarity. To fill gaps in the datasets we developed and applied predictive models. The results can be interpreted at the systems level as demonstrated based on a large number of signaling pathways. We can identify clear global relationships, suggesting robustness of cellular responses to chemical perturbation. Overall, the results suggest that chemical similarity is a useful measure at the systems level, which would support phenotypic drug optimization efforts. With this study we demonstrate the potential of such integrated analysis approaches and suggest prioritizing further experiments to fill the gaps in the current data.

  1. Transcription profiling of the model cyanobacterium Synechococcus sp. strain PCC 7002 by NextGen (SOLiD™ Sequencing of cDNA

    Directory of Open Access Journals (Sweden)

    Marcus eLudwig

    2011-03-01

    Full Text Available The genome of the unicellular, euryhaline cyanobacterium Synechococcus sp. PCC 7002 encodes about 3200 proteins. Transcripts were detected for nearly all annotated open reading frames by a global transcriptomic analysis by Next-Generation (SOLiDTM sequencing of cDNA. In the cDNA samples sequenced, ~90% of the mapped sequences were derived from the 16S and 23S ribosomal RNAs and ~10% of the sequences were derived from mRNAs. In cells grown photoautotrophically under standard conditions (38 °C, 1% (v/v CO2 in air, 250 µmol photons m-2 s-1, the highest transcript levels (up to 2% of the total mRNA for the most abundantly transcribed genes (e. g., cpcAB, psbA, psaA were generally derived from genes encoding structural components of the photosynthetic apparatus. High light exposure for one hour caused changes in transcript levels for genes encoding proteins of the photosynthetic apparatus, Type-1 NADH dehydrogenase complex and ATP synthase, whereas dark incubation for one hour resulted in a global decrease in transcript levels for photosynthesis-related genes and an increase in transcript levels for genes involved in carbohydrate degradation. Transcript levels for pyruvate kinase and the pyruvate dehydrogenase complex decreased sharply in cells incubated in the dark. Under dark anoxic (fermentative conditions, transcript changes indicated a global decrease in transcripts for respiratory proteins and suggested that cells employ an alternative phosphoenolpyruvate degradation pathway via phosphoenolpyruvate synthase (ppsA and the pyruvate:ferredoxin oxidoreductase (nifJ. Finally, the data suggested that an apparent operon involved in tetrapyrrole biosynthesis and fatty acid desaturation, acsF2-ho2-hemN2-desF, may be regulated by oxygen concentration.

  2. AFLP and RAPD Analysis of the Boer and Indigenous Breeds of the Goat in Jiangsu

    Institute of Scientific and Technical Information of China (English)

    CAO Shao-xian; YANG Li-guo; JIANG Xun-ping; LIU Hong-lin; LU Wei-zhong; XIANG Yang-hai

    2003-01-01

    Blood and tissue samples were collected from 105 goats including 60 Boer goats (30 for eachsex), 30 Xuhuai goats (15 for each sex) and 15 Haimen goats (7 stud and 8 does). DNA was extracted andDNA pools were constructed on the basis of goat breeds. In 36 selective primer combinations, 29 combinationsamplified totally 3 253 markers including 92 polymorphic markers by amplified fragment length polymor-phism (AFLP). On average, 3.17 polymorphic markers were amplified per combination, with a polymorphicfrequency of 2.8%. The primer combinations amplifying more polymorphic markers (showed in brackets)were involved in E00+ACG/M00+CAA (13), E00+ACG/M00+CAG (10), E00+AAC/M00+CAC (8)and E00+AAC/M00+ACT (7). A total of 183 markers including 60 polymorphic markers were amplified byRAPD from the pooled DNA of three breeds using 22 primers with strong polymorphism and high reproduc-ibility selected from 93 RAPD primers. On average, 2.73 polymorphic markers were amplified per primer,with a polymorphic frequency of 32.8%. The results of AFLP and RAPD coincidently suggested that the ge-netic distance is the closest between Xuhuai and Haimen goat, next between Xuhuai and Boer goat, and the far-thest between Haimen and Boer goat. According to the UPGMA method, Haimen and Xuhuai goats can begathered together as a cluster, then Boer goat. Both methods can be used to implicate the genetic difference ofthese three breeds, in particular AFLP has more polymorphic markers.

  3. Assessment of genetic stability in micropropagules of Jatropha curcas genotypes by RAPD and AFLP analysis

    KAUST Repository

    Sharma, Sweta K.

    2011-07-01

    Jatropha curcas (Euphorbiaceae), a drought resistant non edible oil yielding plant, has acquired significant importance as an alternative renewable energy source. Low and inconsistent yields found in field plantations prompted for identification of high yielding clones and their large scale multiplication by vegetative propagation to obtain true to type plants. In the current investigation plantlets of J. curcas generated by axillary bud proliferation (micropropagation) using nodal segments obtained from selected high yielding genotypes were assessed for their genetic stability using Randomly Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) analyses. For RAPD analysis, 21 out of 52 arbitrary decamer primers screened gave clear reproducible bands. In the micropropagated plantlets obtained from the 2nd sub-culture, 4 out of a total of 177 bands scored were polymorphic, but in the 8th and 16th sub-cultures (culture cycle) no polymorphisms were detected. AFLP analysis revealed 0.63%, 0% and 0% polymorphism in the 2nd, 8th and 16th generations, respectively. When different genotypes, viz. IC 56557 16, IC 56557 34 and IC 56557 13, were assessed by AFLP, 0%, 0.31% and 0.47% polymorphisms were found, respectively, indicating a difference in genetic stability among the different genotypes. To the best of our knowledge this is the first report on assessment of genetic stability of micropropagated plantlets in J. curcas and suggests that axillary shoot proliferation can safely be used as an efficient micropropagation method for mass propagation of J. curcas. © 2011 Elsevier B.V.

  4. Molecular mapping of the Pinus monticola Cr2 gene using AFLP and SCAR markers

    Directory of Open Access Journals (Sweden)

    A.K.M. Ekramoddoullah

    2013-12-01

    Full Text Available White pine blister rust (WPBR, caused by Cronartium ribicola, is a devastating disease in five-needle pines. Genetic resistance is an important component of integrated strategies to control WPBR. The major resistance gene Cr2, discovered by Kinloch etal.(1999, is also effective against British Columbia (BC isolates of WPBR (Hunt et al. 2004. Pyramiding Cr2 gene with other resistancegenes is being pursued as a strategy in BC white pine breeding. To facilitate this strategy, we have recently identified a few RAPD markerslinked to Cr2 at one side (Liu et al. 2006. The objective of the present study was to identify amplified fragment length polymorphism(AFLP markers linked to both sides of Cr2 for its more precise apping. Use of the AFLP technique combined with bulked segregant analysis (BSA and haploid segregation analysis allowed the identification of five AFLP markers. Of these five AFLP markers in the Cr2 linkage, markers EacccMccgat-365, EactgMcccac- 290, and EacagEacag-750 werelinked in coupling and EacagMcccag-160r and EacccMccgat-180r in repulsion. Following cloning and sequencing of the AFLP andRAPD markers, specific PCR primers were designed and used in the amplification of sequence characterized amplified region(SCAR markers at both sides of Cr2. EacccMccgat- 365 and RAPD marker U570-843 reported previously were converted into SCARmarkers. These two SCARs segregated in a 1:1 (presence:absence ratio and the scoring cosegregated with their respective AFLP orRAPD marker. The SCAR marker EacccMccgat- 365-scar was positioned at 3.1 Kosambi cM from one side of Cr2 and U570-843-scarlocalized at 1.4 Kosambi cM from other side. Both SCAR markers can be useful in breeding programs with marker-assisted selection procedureto screen for resistance. This study represents the first report of the development of PCR-based sequence-specific markers linkedto blister rust resistance in five-needle pines. These findings may

  5. Genetic variation of space flight carried rice and mutant analysis by AFLP molecular marker

    International Nuclear Information System (INIS)

    Rice seeds were carried by 'Shenzhou No.3' space shuttle, a mutant with golden chaff, stem and leaf was selected and named Golden 1 after the seeds returned to the earth. Except the golden color, other traits of Golden 1 are no obviously different with its original material H9808. Genetic analysis identified that color variation was control by a pair of recessive gene. The DNA fragments of the mutant were compared with its parent by AFLP molecular markers. Five specific bands were found through a serial selection. (authors)

  6. Genetic linkage map of Brassica campestris L. Using AFLP and RAPD markers

    Institute of Scientific and Technical Information of China (English)

    卢钢; 曹家树; 陈杭

    2002-01-01

    A genetic linkage map comprised of 131 loci was constructed with an F2 population derived from an inter-subspecific cross between Brassica 'qisihai'. The genetic map included 93 RAPD loci, 36 AFLP loci and 2 morphological loci organized into 10 main linkage groups (LGs) and 2 small groups, covering 1810.9cM with average distance between adjacent markers being approximately 13.8cM. The map is suitable for identification of molecular markers linked to important agronomic traits, QTL analysis, and even for marker-assisted selection in breeding programs of Chinese cabbage and turnip.

  7. Development of a SCAR marker for male gametophyte of Gracilariopsis lemaneiformis based on AFLP technique

    Science.gov (United States)

    Zhou, Wei; Ding, Hongye; Sui, Zhenghong; Wang, Zhongxia; Wang, Jinguo

    2014-05-01

    The red alga Gracilariopsis lemaneiformis (Bory) is an economically valuable macroalgae. As a means to identify the sex of immature Gracilariopsis lemaneiformis, the amplified fragment length polymorphism (AFLP) technique was used to search for possible sex- or phase-related markers in male gametophytes, female gametophytes, and tetrasporophytes, respectively. Seven AFLP selective amplification primers were used in this study. The primer combination E-TG/M-CCA detected a specific band linked to male gametophytes. The DNA fragment was recovered and a 402-bp fragment was sequenced. However, no DNA sequence match was found in public databases. Sequence characterized amplified region (SCAR) primers were designed from the sequence to test the repeatability of the relationship to the sex, using 69 male gametophytes, 139 female gametophytes, and 47 tetrasporophytes. The test results demonstrate a good linkage and repeatability of the SCAR marker to sex. The SCAR primers developed in this study could reduce the time required for sex identification of Gracilariopsis lemaneiformis by four to six months. This can reduce both the time investment and number of specimens required in breeding experiments.

  8. Sesame mutant induced space flight treatment and analysis of polymorphism by AFLP molecular marker

    International Nuclear Information System (INIS)

    Seeds of two sesame varieties (Yuzhi 8 and H98) were carried by 'Shijian 8' satellite for space treatment. Variants is SP2 and SP1 were observed and the genetic diversity of mutation generation was analyzed using 30 pair of AFLP markers. The results showed that: (1) variants of leaf, plant height, plant characters, floral organs, capsule, fertility, pre-flowering date were observed in SP2 and SP3 of two varieties, variations frequency and variations type of two sesame varieties were significantly different, but only the small capsule variations and tall plant variations could be inherited from SP2 to SP3 generation; (2) AFLP analysis of primers randomly selected to analyze variant plants in SP2 and SP3 generation, showed that multiple sites in sesame genome were induced by space environment and mutation rate was high, while mutation rate was different in molecular level between varieties; (3) variation sites were diverse between different variations types, and mutation sites were also diverse between different plants of same mutation type, this result indicated that variation of sesame genome DNA could not been expressed totally; (4) The same mutant of botany characteristics and the same locus mutation of molecular level were both detected. (authors)

  9. AFLP analysis of genetic diversity and relationship among some Chinese domestic ducks and wild ducks

    Institute of Scientific and Technical Information of China (English)

    YAN Feihuan; ZUO Zhenghong; CHEN Mei; SONG Yueqiang; L(U) Liangju; CHEN Yixin

    2006-01-01

    The amplified fragment length polymorphic(AFLP)technique was used to analyze the genome DNA polymorphism among 8 breeds of domestic ducks and 2 species of wild ducks.Nine of the 17 selected primers pairs gave reproducible polymorphic DNA amplification bands.The amplified bands ranged from 44 to 83 per primer pair.Of the 513 AFLP markers obtained.498 were polymorphic.The proportion of polymorphic loci was 97.1%.The genetic distance(D)and similarity coefficients(GS)were calculated based on the polymorphic data.Between domestic ducks D ranged from 0.331 to 0.589,while between domestic ducks and the wild ducks,it ranged from 0.298 to 0.520(vs.Anas Platyrhynchos)and from 0.316 to 0.522(vs.A.Poecilorhyncha),respectively.The variance analysis showed no significant difference between the two groups of data,which indicated that both mallard and spot-billed ducks made contributions to domestic duck evolution.A dendrogram was constructed according to the D value.

  10. Assessing genetic diversity of wild populations of Japanese flounder using AFLP markers

    Institute of Scientific and Technical Information of China (English)

    XU Xiaofei; ZHANG Quanqi; WANG Zhigang; QI Jie; ZHANG Zhifeng; BAO Zhenmin; Heisuke Nakagawa

    2006-01-01

    Amplified fragment length polymorphism (AFLP) analysis was used to evaluate the genetic diversity of four wild geographical populations of Japanese flounder (Paralichthys olivaceus). A total of 775 loci (58.32% of which was polymorphic) in the range between 100 and 1 300 base pairs were detected from 110 individuals using seven primer combinations. The percentage of polymorphic loci detected by single primer combination for each population was calculated, ranging from 19.59% to 53.33%. Genetic similarities within and among the populations were calculated from the binary matrices of presence - absence. Phylogenetic tree of four populations was constructed by using the UPGMA method using PHYLIP Version 3.5. According to intrapopulation genetic similarities, CW population displayed the highest genetic diversity value and KY population had the lowest genetic diversity value.The distance between CW and CF populations was the farthest, which was possibly resulted from the farthest distance of Weihai of Shandong and Fujian of China compared with the geographical distance between other locations of populations. The subpopulation differentiation value ( Gst ) is 0.356 5, showing a certain extent of differentiation among the four geographical populations. AFLP technology was confirmed to be an effective tool to assess within- and among-population genetic diversity of Japanese flounder. The present survey provided significant insights for research in the Japanese flounder breeding program.

  11. Veronaea botryosa: molecular identification with amplified fragment length polymorphism (AFLP) and in vitro antifungal susceptibility.

    Science.gov (United States)

    Badali, Hamid; Yazdanparast, Seyed Amir; Bonifaz, Alexandro; Mousavi, Bita; de Hoog, G Sybren; Klaassen, Corné H W; Meis, Jacques F

    2013-06-01

    Inter- and intraspecific genomic variability of 18 isolates of Veronaea botryosa originating from clinical and environmental sources was studied using amplified fragment length polymorphism (AFLP). The species was originally described from the environment, but several severe cases of disseminated infection in apparently healthy individuals have been reported worldwide. All tested strains of V. botryosa, identified on the basis of sequencing and phenotypic and physiological criteria prior to our study, were confirmed by AFLP analysis, yielding a clear separation of V. botryosa as a rather homogeneous group from related species. In vitro antifungal susceptibility testing resulted in MIC90s across all strains in increasing order posaconazole (0.25 μg/ml), itraconazole (1 μg/ml), voriconazole (4 μg/ml), terbinafine (4 μg/ml), caspofungin (8 μg/ml), anidulafungin (8 μg/ml), isavuconazole (16 μg/ml), amphotericin B (16 μg/ml), and fluconazole (32 μg/ml). Overall, the isolates showed a uniform pattern of low MICs of itraconazole and posaconazole, but high MICs for remaining agents. The echinocandins (caspofungin and