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  1. Functional and comparative analysis of expressed sequences from ...

    African Journals Online (AJOL)

    Functional and comparative analysis of expressed sequences from Diuraphis noxia infested wheat obtained utilizing the conserved Nucleotide Binding Site. Lynelle Lacock, Chantal van Niekerk, Shilo Loots, Franco du Preez, Anna-Maria Botha ...

  2. A comparative analysis of biclustering algorithms for gene expression data.

    Science.gov (United States)

    Eren, Kemal; Deveci, Mehmet; Küçüktunç, Onur; Çatalyürek, Ümit V

    2013-05-01

    The need to analyze high-dimension biological data is driving the development of new data mining methods. Biclustering algorithms have been successfully applied to gene expression data to discover local patterns, in which a subset of genes exhibit similar expression levels over a subset of conditions. However, it is not clear which algorithms are best suited for this task. Many algorithms have been published in the past decade, most of which have been compared only to a small number of algorithms. Surveys and comparisons exist in the literature, but because of the large number and variety of biclustering algorithms, they are quickly outdated. In this article we partially address this problem of evaluating the strengths and weaknesses of existing biclustering methods. We used the BiBench package to compare 12 algorithms, many of which were recently published or have not been extensively studied. The algorithms were tested on a suite of synthetic data sets to measure their performance on data with varying conditions, such as different bicluster models, varying noise, varying numbers of biclusters and overlapping biclusters. The algorithms were also tested on eight large gene expression data sets obtained from the Gene Expression Omnibus. Gene Ontology enrichment analysis was performed on the resulting biclusters, and the best enrichment terms are reported. Our analyses show that the biclustering method and its parameters should be selected based on the desired model, whether that model allows overlapping biclusters, and its robustness to noise. In addition, we observe that the biclustering algorithms capable of finding more than one model are more successful at capturing biologically relevant clusters.

  3. Comparative expression pathway analysis of human and canine mammary tumors

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    Marconato Laura

    2009-03-01

    Full Text Available Abstract Background Spontaneous tumors in dog have been demonstrated to share many features with their human counterparts, including relevant molecular targets, histological appearance, genetics, biological behavior and response to conventional treatments. Mammary tumors in dog therefore provide an attractive alternative to more classical mouse models, such as transgenics or xenografts, where the tumour is artificially induced. To assess the extent to which dog tumors represent clinically significant human phenotypes, we performed the first genome-wide comparative analysis of transcriptional changes occurring in mammary tumors of the two species, with particular focus on the molecular pathways involved. Results We analyzed human and dog gene expression data derived from both tumor and normal mammary samples. By analyzing the expression levels of about ten thousand dog/human orthologous genes we observed a significant overlap of genes deregulated in the mammary tumor samples, as compared to their normal counterparts. Pathway analysis of gene expression data revealed a great degree of similarity in the perturbation of many cancer-related pathways, including the 'PI3K/AKT', 'KRAS', 'PTEN', 'WNT-beta catenin' and 'MAPK cascade'. Moreover, we show that the transcriptional relationships between different gene signatures observed in human breast cancer are largely maintained in the canine model, suggesting a close interspecies similarity in the network of cancer signalling circuitries. Conclusion Our data confirm and further strengthen the value of the canine mammary cancer model and open up new perspectives for the evaluation of novel cancer therapeutics and the development of prognostic and diagnostic biomarkers to be used in clinical studies.

  4. Canine Mammary Carcinomas: A Comparative Analysis of Altered Gene Expression

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    Farruk M. Lutful Kabir

    2015-12-01

    Full Text Available Breast cancer represents the second most frequent neoplasm in humans and sexually intact female dogs after lung and skin cancers, respectively. Many similar features in human and dog cancers including, spontaneous development, clinical presentation, tumor heterogeneity, disease progression and response to conventional therapies have supported development of this comparative model as an alternative to mice. The highly conserved similarities between canine and human genomes are also key to this comparative analysis, especially when compared to the murine genome. Studies with canine mammary tumor (CMT models have shown a strong genetic correlation with their human counterparts, particularly in terms of altered expression profiles of cell cycle regulatory genes, tumor suppressor and oncogenes and also a large group of non-coding RNAs or microRNAs (miRNAs. Because CMTs are considered predictive intermediate models for human breast cancer, similarities in genetic alterations and cancer predisposition between humans and dogs have raised further interest. Many cancer-associated genetic defects critical to mammary tumor development and oncogenic determinants of metastasis have been reported and appear to be similar in both species. Comparative analysis of deregulated gene sets or cancer signaling pathways has shown that a significant proportion of orthologous genes are comparably up- or down-regulated in both human and dog breast tumors. Particularly, a group of cell cycle regulators called cyclin-dependent kinase inhibitors (CKIs acting as potent tumor suppressors are frequently defective in CMTs. Interestingly, comparative analysis of coding sequences has also shown that these genes are highly conserved in mammals in terms of their evolutionary divergence from a common ancestor. Moreover, co-deletion and/or homozygous loss of the INK4A/ARF/INK4B (CDKN2A/B locus, encoding three members of the CKI tumor suppressor gene families (p16/INK4A, p14ARF and p15

  5. Comparative gene expression analysis of murine retina and brain.

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    Hackam, Abigail S; Qian, Jiang; Liu, Dongmei; Gunatilaka, Tushara; Farkas, Ronald H; Chowers, Itay; Kageyama, Masaaki; Parmigiani, Giovanni; Zack, Donald J

    2004-08-31

    Several high-throughput studies have described gene expression in the central nervous system (CNS), and recently there has been increasing interest in analyzing how gene expression compares in different regions of the CNS. As the retina is often used as a model system to study CNS development and function, we compared retina and brain gene expression using microarray analyses. Mouse retina, brain and liver RNA was hybridized to a custom cDNA microarray containing 5,376 genes and ESTs, and the data from the quantified scanned images were analyzed using Bioconductor and SAM. Preferential retina expression was confirmed by real-time PCR. The cellular distribution of genes newly identified as retina enriched genes was determined by immunohistochemistry. Using stringent statistical analyses we identified 733 genes that were preferentially expressed in retina and 389 in brain. The retina-liver hybridizations identified an additional 837 retina enriched genes. The cellular distribution in the retina was determined for two genes that had not previously been reported to be expressed in the retina, the transcription regulatory proteins EWS and PCPB1. Both proteins were found primarily in the inner nuclear layer. Finally, a comparison of the microarray data to publicly available SAGE and EST library databases demonstrated only limited overlap of the sets of retina enriched genes identified by the different methodologies. The preferential retinal expression of a subset of genes from the microarray, which were not identified as differentially expressed by other methods, was confirmed by quantitative PCR. The finding of differences in the groups of identified retina enriched genes from the various profiling techniques supports the use of multiple approaches to obtain a more complete description of retinal gene expression. Characterization of gene expression profiles of retina and brain may facilitate the understanding of the processes that underlie differences between the retina

  6. Comparative analysis of gene expression profiles of OPN signalling ...

    Indian Academy of Sciences (India)

    The results showed that 23, 33, 59 and 74 genes were significantly changed in the above four kinds of liver diseases, respectively. H-clustering analysis showed that the expression profiles of OPN signalling-related genes were notably different in four kinds of liver diseases. Subsequently, a total of above-mentioned 147 ...

  7. Comparative gene expression profile analysis between native human odontoblasts and pulp tissue.

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    Pääkkönen, V; Vuoristo, J T; Salo, T; Tjäderhane, L

    2008-02-01

    To undertake a large-scale analysis of the expression profiles of native human pulp tissue and odontoblasts, and search for genes expressed only in odontoblasts. Microarray was performed to pooled pulp and odontoblasts of native human third molars and to pooled +/- TGF-beta1 cultured pulps and odontoblasts (137 teeth). The repeatability of microarray analysis was estimated by comparing the experimental pulp samples with expression profiles of two pulp samples downloaded from the GEO database. The genes expressed only in the experimental pulp samples or in odontoblasts were divided into categories, and the expression of selected odontoblast-specific genes of extracellular matrix (ECM) organization and biogenesis category was confirmed with RT-PCR and Western blot. A 85.3% repeatability was observed between pulp microarrays, demonstrating the high reliability of the technique. Overall 1595 probe sets were positive only in pulp and 904 only in odontoblasts. Sixteen expressed sequence tags (ESTs), which represent transcribed sequences encoding possibly unknown genes, were detected only in odontoblasts; two consistently expressed in all odontoblast samples. Matrilin 4 (MATN4) was the only ECM biogenesis and organization related gene detected in odontoblasts but not in pulp by microarray and RT-PCR. MATN4 protein expression only in odontoblasts was confirmed by Western blot. Pulp tissue and odontoblast gene expression profiling provides basic data for further, more detailed protein analysis. In addition, MATN4 and the two ESTs could serve as an odontoblast differentiation marker, e.g. in odontoblast stem cell research.

  8. Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides

    Energy Technology Data Exchange (ETDEWEB)

    Pena-Castillo, Lourdes; Mercer, Ryan; Gurinovich, Anastasia; Callister, Stephen J.; Wright, Aaron T.; Westbye, Alexander; Beatty, J. T.; Lang, Andrew S.

    2014-08-28

    The genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of two Rhodobacter species, R. capsulatus and R. sphaeroides, have had their genomes fully sequenced and both have been the subject of transcriptional profiling studies. Gene co-expression networks can be used to identify modules of genes with similar expression profiles. Functional analysis of gene modules can then associate co-expressed genes with biological pathways, and network statistics can determine the degree of module preservation in related networks. In this paper, we constructed an R. capsulatus gene co-expression network, performed functional analysis of identified gene modules, and investigated preservation of these modules in R. capsulatus proteomics data and in R. sphaeroides transcriptomics data. Results: The analysis identified 40 gene co-expression modules in R. capsulatus. Investigation of the module gene contents and expression profiles revealed patterns that were validated based on previous studies supporting the biological relevance of these modules. We identified two R. capsulatus gene modules preserved in the protein abundance data. We also identified several gene modules preserved between both Rhodobacter species, which indicate that these cellular processes are conserved between the species and are candidates for functional information transfer between species. Many gene modules were non-preserved, providing insight into processes that differentiate the two species. In addition, using Local Network Similarity (LNS), a recently proposed metric for expression divergence, we assessed the expression conservation of between-species pairs of orthologs, and within-species gene-protein expression profiles. Conclusions: Our analyses provide new sources of information for functional annotation in R. capsulatus because uncharacterized genes in modules are now connected with groups of genes that constitute a joint functional

  9. Carotenoid biosynthetic genes in Brassica rapa: comparative genomic analysis, phylogenetic analysis, and expression profiling.

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    Li, Peirong; Zhang, Shujiang; Zhang, Shifan; Li, Fei; Zhang, Hui; Cheng, Feng; Wu, Jian; Wang, Xiaowu; Sun, Rifei

    2015-07-03

    Carotenoids are isoprenoid compounds synthesized by all photosynthetic organisms. Despite much research on carotenoid biosynthesis in the model plant Arabidopsis thaliana, there is a lack of information on the carotenoid pathway in Brassica rapa. To better understand its carotenoid biosynthetic pathway, we performed a systematic analysis of carotenoid biosynthetic genes at the genome level in B. rapa. We identified 67 carotenoid biosynthetic genes in B. rapa, which were orthologs of the 47 carotenoid genes in A. thaliana. A high level of synteny was observed for carotenoid biosynthetic genes between A. thaliana and B. rapa. Out of 47 carotenoid biosynthetic genes in A. thaliana, 46 were successfully mapped to the 10 B. rapa chromosomes, and most of the genes retained more than one copy in B. rapa. The gene expansion was caused by the whole-genome triplication (WGT) event experienced by Brassica species. An expression analysis of the carotenoid biosynthetic genes suggested that their expression levels differed in root, stem, leaf, flower, callus, and silique tissues. Additionally, the paralogs of each carotenoid biosynthetic gene, which were generated from the WGT in B. rapa, showed significantly different expression levels among tissues, suggesting differentiated functions for these multi-copy genes in the carotenoid pathway. This first systematic study of carotenoid biosynthetic genes in B. rapa provides insights into the carotenoid metabolic mechanisms of Brassica crops. In addition, a better understanding of carotenoid biosynthetic genes in B. rapa will contribute to the development of conventional and transgenic B. rapa cultivars with enriched carotenoid levels in the future.

  10. Comparative gene-expression analysis of the dental follicle and periodontal ligament in humans.

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    Hyo-Seol Lee

    Full Text Available The human dental follicle partially differentiates into the periodontal ligament (PDL, but their biological functions are different. The gene-expression profiles of the dental follicle and PDL were compared using the cDNA microarray technique. Microarray analysis identified 490 genes with a twofold or greater difference in expression, 365 and 125 of which were more abundant in the dental follicle and PDL, respectively. The most strongly expressed genes in the dental follicle were those related to bone development and remodeling (EGFL6, MMP8, FRZB, and NELL1, apoptosis and chemotaxis (Nox4, CXCL13, and CCL2, and tooth and embryo development (WNT2, PAX3, FGF7, AMBN, AMTN, and SLC4A4, while in the PDL it was the tumor-suppressor gene WIF1. Genes related to bone development and remodeling (STMN2, IBSP, BMP8A, BGLAP, ACP5, OPN, BMP3, and TM7SF4 and wound healing (IL1, IL8, MMP3, and MMP9 were also more strongly expressed in the PDL than in the dental follicle. In selected genes, a comparison among cDNA microarray, real-time reverse-transcription polymerase chain reaction, and immunohistochemical staining confirmed similar relative gene expressions. The gene-expression profiles presented here identify candidate genes that may enable differentiation between the dental follicle and PDL.

  11. Comparative gene expression analysis of the human periodontal ligament in deciduous and permanent teeth.

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    Je Seon Song

    Full Text Available There are histological and functional differences between human deciduous and permanent periodontal ligament (PDL tissues. The aim of this study was to determine the differences between these two types of tissue at the molecular level by comparing their gene expression patterns. PDL samples were obtained from permanent premolars (n = 38 and anterior deciduous teeth (n = 31 extracted from 40 healthy persons. Comparative cDNA microarray analysis revealed several differences in gene expression between the deciduous and permanent PDL tissues. These findings were verified by qRT-PCR (quantitative reverse-transcription-polymerase chain reaction analysis, and the areas where genes are expressed were revealed by immunohistochemical staining. The expressions of 21 genes were up-regulated in deciduous relative to PDL tissues, and those of 30 genes were up-regulated in permanent relative to deciduous PDL tissues. The genes that were up-regulated in deciduous PDL tissues were those involved in the formation of the extracellular matrix (LAMC2, LAMB3, and COMP, tissue development (IGF2BP, MAB21L2, and PAX3, and inflammatory or immune reactions leading to tissue degradation (IL1A, CCL21, and CCL18. The up-regulated genes in permanent PDL tissues were related to tissue degradation (IL6 and ADAMTS18, myocontraction (PDE3B, CASQ2, and MYH10, and neurological responses (FOS, NCAM2, SYT1, SLC22A3, DOCK3, LRRTM1, LRRTM3, PRSS12, and ARPP21. The analysis of differential gene expressions between deciduous and permanent PDL tissues aids our understanding of histological and functional differences between them at the molecular level.

  12. Comparative analysis of weighted gene co-expression networks in human and mouse.

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    Eidsaa, Marius; Stubbs, Lisa; Almaas, Eivind

    2017-01-01

    The application of complex network modeling to analyze large co-expression data sets has gained traction during the last decade. In particular, the use of the weighted gene co-expression network analysis framework has allowed an unbiased and systems-level investigation of genotype-phenotype relationships in a wide range of systems. Since mouse is an important model organism for biomedical research on human disease, it is of great interest to identify similarities and differences in the functional roles of human and mouse orthologous genes. Here, we develop a novel network comparison approach which we demonstrate by comparing two gene-expression data sets from a large number of human and mouse tissues. The method uses weighted topological overlap alongside the recently developed network-decomposition method of s-core analysis, which is suitable for making gene-centrality rankings for weighted networks. The aim is to identify globally central genes separately in the human and mouse networks. By comparing the ranked gene lists, we identify genes that display conserved or diverged centrality-characteristics across the networks. This framework only assumes a single threshold value that is chosen from a statistical analysis, and it may be applied to arbitrary network structures and edge-weight distributions, also outside the context of biology. When conducting the comparative network analysis, both within and across the two species, we find a clear pattern of enrichment of transcription factors, for the homeobox domain in particular, among the globally central genes. We also perform gene-ontology term enrichment analysis and look at disease-related genes for the separate networks as well as the network comparisons. We find that gene ontology terms related to regulation and development are generally enriched across the networks. In particular, the genes FOXE3, RHO, RUNX2, ALX3 and RARA, which are disease genes in either human or mouse, are on the top-10 list of globally

  13. Comparative analysis of gene expression and regulation of replicative aging associated genes in S. cerevisiae.

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    Dhami, Sukhraj Pal Singh; Mittal, Nitish; Janga, Sarath Chandra; Roy, Nilanjan

    2011-02-01

    Aging is a multi-factorial and complex phenomenon. Saccharomyces cerevisiae is developed as a model of aging and has been widely studied in order to understand the mechanism of lifespan regulation. A large number of high-throughput studies were conducted to identify the genes which modulate lifespan. These studies provide the list of genes that regulates the lifespan in yeast; however the regulation of these aging associated genes had not been fully understood. In this study, we have shown that deletion of the genes which increase the replicative lifespan (RLS) of yeast show discrete expression patterns when compared with the genes that, on deletion, cause a decrease in lifespan. Expression of longlived (LL) genes decreases as the cell progresses from mid log to stationary phase, whereas expression of shortlived (SL) genes remains unchanged. This distinct expression of LL and SL gene-sets suggests their differential gene regulation. Further analysis of transcriptional regulation by transcription factors and epigenetic regulators (acetylation and methylation) suggests that this differential expression of the two gene-sets is due to their differential epigenetic regulations, rather than regulation by transcription factors. These results accentuate the importance of epigenetic modifications in aging. We deduce that future focused studies on epigenetic modification regulation will help lead to a better understanding of the aging process.

  14. Differential gene expression between leaf and rhizome in Atractylodes lancea: a comparative transcriptome analysis

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    Qianqian eHuang

    2016-03-01

    Full Text Available The rhizome of Atractylodes lancea is extensively used in the practice of Traditional Chinese Medicine because of its broad pharmacological activities. This study was designed to characterize the transcriptome profiling of the rhizome and leaf of Atractylodes lancea in an attempt to uncover the molecular mechanisms regulating rhizome formation and growth. Over 270 million clean reads were assembled into 92,366 unigenes, 58% of which are homologous with sequences in public protein databases (NR, Swiss-Prot, GO, and KEGG. Analysis of expression levels showed that genes involved in photosynthesis, stress response, and translation were the most abundant transcripts in the leaf, while transcripts involved in stress response, transcription regulation, translation, and metabolism were dominant in the rhizome. Tissue-specific gene analysis identified distinct gene families active in the leaf and rhizome. Differential gene expression analysis revealed a clear difference in gene expression pattern, identifying 1,518 up-regulated genes and 3,464 down-regulated genes in the rhizome compared with the leaf,, including a series of genes related to signal transduction, primary and secondary metabolism. Transcription factor (TF analysis identified 42 TF families, with 67 and 60 TFs up-regulated in the rhizome and leaf, respectively. A total of 104 unigenes were identified as candidates for regulating rhizome formation and development. These data offer an overview of the gene expression pattern of the rhizome and leaf and provide essential information for future studies on the molecular mechanisms of controlling rhizome formation and growth. The extensive transcriptome data generated in this study will be a valuable resource for further functional genomics studies of A. lancea.

  15. Comparative analysis of HPV16 gene expression profiles in cervical and in oropharyngeal squamous cell carcinoma

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    Cerasuolo, Andrea; Annunziata, Clorinda; Tortora, Marianna; Starita, Noemy; Stellato, Giovanni; Greggi, Stefano; Maglione, Maria Grazia; Ionna, Franco; Losito, Simona; Botti, Gerardo; Buonaguro, Luigi; Buonaguro, Franco M.; Tornesello, Maria Lina

    2017-01-01

    Human papillomavirus type 16 (HPV16) is the major cause of cervical cancer and of a fraction of oropharyngeal carcinoma. Few studies compared the viral expression profiles in the two types of tumor. We analyzed HPV genotypes and viral load as well as early (E2/E4, E5, E6, E6*I, E6*II, E7) and late (L1 and L2) gene expression of HPV16 in cervical and oropharyngeal cancer biopsies. The study included 28 cervical squamous cell carcinoma (SCC) and ten oropharyngeal SCC, along with pair-matched non-tumor tissues, as well as four oropharynx dysplastic tissues and 112 cervical intraepithelial neoplasia biopsies. Viral load was found higher in cervical SCC (<1 to 694 copies/cell) and CIN (<1 to 43 copies/cell) compared to oropharyngeal SCC (<1 to 4 copies/cell). HPV16 E2/E4 and E5 as well as L1 and L2 mRNA levels were low in cervical SCC and CIN and undetectable in oropharynx cases. The HPV16 E6 and E7 mRNAs were consistently high in cervical SCC and low in oropharyngeal SCC. The analysis of HPV16 E6 mRNA expression pattern showed statistically significant higher levels of E6*I versus E6*II isoform in cervical SCC (p = 0.002) and a slightly higher expression of E6*I versus E6*II in oropharyngeal cases. In conclusion, the HPV16 E5, E6, E6*I, E6*II and E7 mRNA levels were more abundant in cervical SCC compared to oropharyngeal SCC suggesting different carcinogenic mechanisms in the two types of HPV-related cancers. PMID:28423662

  16. Comparative analysis of HPV16 gene expression profiles in cervical and in oropharyngeal squamous cell carcinoma.

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    Cerasuolo, Andrea; Annunziata, Clorinda; Tortora, Marianna; Starita, Noemy; Stellato, Giovanni; Greggi, Stefano; Maglione, Maria Grazia; Ionna, Franco; Losito, Simona; Botti, Gerardo; Buonaguro, Luigi; Buonaguro, Franco M; Tornesello, Maria Lina

    2017-05-23

    Human papillomavirus type 16 (HPV16) is the major cause of cervical cancer and of a fraction of oropharyngeal carcinoma. Few studies compared the viral expression profiles in the two types of tumor. We analyzed HPV genotypes and viral load as well as early (E2/E4, E5, E6, E6*I, E6*II, E7) and late (L1 and L2) gene expression of HPV16 in cervical and oropharyngeal cancer biopsies. The study included 28 cervical squamous cell carcinoma (SCC) and ten oropharyngeal SCC, along with pair-matched non-tumor tissues, as well as four oropharynx dysplastic tissues and 112 cervical intraepithelial neoplasia biopsies. Viral load was found higher in cervical SCC (<1 to 694 copies/cell) and CIN (<1 to 43 copies/cell) compared to oropharyngeal SCC (<1 to 4 copies/cell). HPV16 E2/E4 and E5 as well as L1 and L2 mRNA levels were low in cervical SCC and CIN and undetectable in oropharynx cases. The HPV16 E6 and E7 mRNAs were consistently high in cervical SCC and low in oropharyngeal SCC. The analysis of HPV16 E6 mRNA expression pattern showed statistically significant higher levels of E6*I versus E6*II isoform in cervical SCC (p = 0.002) and a slightly higher expression of E6*I versus E6*II in oropharyngeal cases. In conclusion, the HPV16 E5, E6, E6*I, E6*II and E7 mRNA levels were more abundant in cervical SCC compared to oropharyngeal SCC suggesting different carcinogenic mechanisms in the two types of HPV-related cancers.

  17. Comparative Membranome expression analysis in primary tumors and derived cell lines.

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    Paolo Uva

    Full Text Available Despite the wide use of cell lines in cancer research, the extent to which their surface properties correspond to those of primary tumors is poorly characterized. The present study addresses this problem from a transcriptional standpoint, analyzing the expression of membrane protein genes--the Membranome--in primary tumors and immortalized in-vitro cultured tumor cells. 409 human samples, deriving from ten independent studies, were analyzed. These comprise normal tissues, primary tumors and tumor derived cell lines deriving from eight different tissues: brain, breast, colon, kidney, leukemia, lung, melanoma, and ovary. We demonstrated that the Membranome has greater power than the remainder of the transcriptome when used as input for the automatic classification of tumor samples. This feature is maintained in tumor derived cell lines. In most cases primary tumors show maximal similarity in Membranome expression with cell lines of same tissue origin. Differences in Membranome expression between tumors and cell lines were analyzed also at the pathway level and biological themes were identified that were differentially regulated in the two settings. Moreover, by including normal samples in the analysis, we quantified the degree to which cell lines retain the Membranome up- and down-regulations observed in primary tumors with respect to their normal counterparts. We showed that most of the Membranome up-regulations observed in primary tumors are lost in the in-vitro cultured cells. Conversely, the majority of Membranome genes down-regulated upon tumor transformation maintain lower expression levels also in the cell lines. This study points towards a central role of Membranome genes in the definition of the tumor phenotype. The comparative analysis of primary tumors and cell lines identifies the limits of cell lines as a model for the study of cancer-related processes mediated by the cell surface. Results presented allow for a more rational use of

  18. Comparative Analysis of Xenorhabdus koppenhoeferi Gene Expression during Symbiotic Persistence in the Host Nematode.

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    An, Ruisheng; Grewal, Parwinder S

    2016-01-01

    Species of Xenorhabdus and Photorhabdus bacteria form mutualistic associations with Steinernema and Heterorhabditis nematodes, respectively and serve as model systems for studying microbe-animal symbioses. Here, we profiled gene expression of Xenorhabdus koppenhoeferi during their symbiotic persistence in the newly formed infective juveniles of the host nematode Steinernema scarabaei through the selective capture of transcribed sequences (SCOTS). The obtained gene expression profile was then compared with other nematode-bacteria partnerships represented by Steinernema carpocapsae-Xenorhabdus nematophila and Heterorhabditis bacteriophora-Photorhabdus temperata. A total of 29 distinct genes were identified to be up-regulated and 53 were down-regulated in X. koppenhoeferi while in S. scarabaei infective juveniles. Of the identified genes, 8 of the up-regulated and 14 of the down-regulated genes were similarly expressed in X. nematophila during persistence in its host nematode S. carpocapsae. However, only one from each of these up- and down-regulated genes was common to the mutualistic partnership between the bacterium P. temperata and the nematode H. bacteriophora. Interactive network analysis of the shared genes between X. koppenhoeferi and X. nematophila demonstrated that the up-regulated genes were mainly involved in bacterial survival and the down-regulated genes were more related to bacterial virulence and active growth. Disruption of two selected genes pta (coding phosphotransacetylase) and acnB (coding aconitate hydratase) in X. nematophila with shared expression signature with X. koppenhoeferi confirmed that these genes are important for bacterial persistence in the nematode host. The results of our comparative analyses show that the two Xenorhabdus species share a little more than a quarter of the transcriptional mechanisms during persistence in their nematode hosts but these features are quite different from those used by P. temperata bacteria in their

  19. Comparative Analysis of Xenorhabdus koppenhoeferi Gene Expression during Symbiotic Persistence in the Host Nematode.

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    Ruisheng An

    Full Text Available Species of Xenorhabdus and Photorhabdus bacteria form mutualistic associations with Steinernema and Heterorhabditis nematodes, respectively and serve as model systems for studying microbe-animal symbioses. Here, we profiled gene expression of Xenorhabdus koppenhoeferi during their symbiotic persistence in the newly formed infective juveniles of the host nematode Steinernema scarabaei through the selective capture of transcribed sequences (SCOTS. The obtained gene expression profile was then compared with other nematode-bacteria partnerships represented by Steinernema carpocapsae-Xenorhabdus nematophila and Heterorhabditis bacteriophora-Photorhabdus temperata. A total of 29 distinct genes were identified to be up-regulated and 53 were down-regulated in X. koppenhoeferi while in S. scarabaei infective juveniles. Of the identified genes, 8 of the up-regulated and 14 of the down-regulated genes were similarly expressed in X. nematophila during persistence in its host nematode S. carpocapsae. However, only one from each of these up- and down-regulated genes was common to the mutualistic partnership between the bacterium P. temperata and the nematode H. bacteriophora. Interactive network analysis of the shared genes between X. koppenhoeferi and X. nematophila demonstrated that the up-regulated genes were mainly involved in bacterial survival and the down-regulated genes were more related to bacterial virulence and active growth. Disruption of two selected genes pta (coding phosphotransacetylase and acnB (coding aconitate hydratase in X. nematophila with shared expression signature with X. koppenhoeferi confirmed that these genes are important for bacterial persistence in the nematode host. The results of our comparative analyses show that the two Xenorhabdus species share a little more than a quarter of the transcriptional mechanisms during persistence in their nematode hosts but these features are quite different from those used by P. temperata

  20. Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton

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    Xueqiang Su

    2017-10-01

    Full Text Available Plant type III polyketide synthase (PKS can catalyse the formation of a series of secondary metabolites with different structures and different biological functions; the enzyme plays an important role in plant growth, development and resistance to stress. At present, the PKS gene has been identified and studied in a variety of plants. Here, we identified 11 PKS genes from upland cotton (Gossypium hirsutum and compared them with 41 PKS genes in Populus tremula, Vitis vinifera, Malus domestica and Arabidopsis thaliana. According to the phylogenetic tree, a total of 52 PKS genes can be divided into four subfamilies (I–IV. The analysis of gene structures and conserved motifs revealed that most of the PKS genes were composed of two exons and one intron and there are two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C of the PKS gene family. In our study of the five species, gene duplication was found in addition to Arabidopsis thaliana and we determined that purifying selection has been of great significance in maintaining the function of PKS gene family. From qRT-PCR analysis and a combination of the role of the accumulation of proanthocyanidins (PAs in brown cotton fibers, we concluded that five PKS genes are candidate genes involved in brown cotton fiber pigment synthesis. These results are important for the further study of brown cotton PKS genes. It not only reveals the relationship between PKS gene family and pigment in brown cotton, but also creates conditions for improving the quality of brown cotton fiber.

  1. Comparative analysis of gene expression data reveals novel targets of senescence-associated microRNAs.

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    Marco Napolitano

    Full Text Available In the last decades, cellular senescence is viewed as a complex mechanism involved in different processes, ranging from tumor suppression to induction of age-related degenerative alterations. Senescence-inducing stimuli are myriad and, recently, we and others have demonstrated the role exerted by microRNAs in the induction and maintenance of senescence, by the identification of a subset of Senescence-Associated microRNAs (SAmiRs up-regulated during replicative or stress-induced senescence and able to induce a premature senescent phenotype when over-expressed in human primary cells. With the intent to find novel direct targets of two specific SAmiRs, SAmiR-494 and -486-5p, and cellular pathways which they are involved in, we performed a comparative analysis of gene expression profiles available in literature to select genes down-regulated upon replicative senescence of human primary fibroblasts. Among them, we searched for SAmiR's candidate targets by analyzing with different target prediction algorithms their 3'UTR for the presence of SAmiR-binding sites. The expression profiles of selected candidates have been validated on replicative and stress-induced senescence and the targeting of the 3'UTRs was assessed by luciferase assay. Results allowed us to identify Cell Division Cycle Associated 2 (CDCA2 and Inhibitor of DNA binding/differentiation type 4 (ID4 as novel targets of SAmiR-494 and SAmiR-486-5p, respectively. Furthermore, we demonstrated that the over-expression of CDCA2 in human primary fibroblasts was able to partially counteract etoposide-induced senescence by mitigating the activation of DNA Damage Response.

  2. Comparative analysis of microRNA expression in mouse and human brown adipose tissue.

    Science.gov (United States)

    Güller, Isabelle; McNaughton, Sarah; Crowley, Tamsyn; Gilsanz, Vicente; Kajimura, Shingo; Watt, Matthew; Russell, Aaron P

    2015-10-19

    In small mammals brown adipose tissue (BAT) plays a predominant role in regulating energy expenditure (EE) via adaptive thermogenesis. New-born babies require BAT to control their body temperature, however its relevance in adults has been questioned. Active BAT has recently been observed in adult humans, albeit in much lower relative quantities than small mammals. Comparing and contrasting the molecular mechanisms controlling BAT growth and development in mice and humans will increase our understanding or how human BAT is developed and may identify potential therapeutic targets to increase EE. MicroRNAs are molecular mechanisms involved in mouse BAT development however, little is known about the miRNA profile in human BAT. The aims of this study were to establish a mouse BAT-enriched miRNA profile and compare this with miRNAs measured in human BAT. To achieve this we firstly established a mouse BAT enriched-miRNA profile by comparing miRNAs expressed in mouse BAT, white adipose tissue and skeletal muscle. Following this the BAT-enriched miRNAs predicted to target genes potentially involved in growth and development were identified. MiRNA levels were measured using PCR-based miRNA arrays. Results were analysed using ExpressionSuite software with the global mean expression value of all expressed miRNAs in a givensample used as the normalisation factor. Bio-informatic analyses was used to predict gene targets followed by Ingenuity Pathway Analysis. We identified 35 mouse BAT-enriched miRNAs that were predicted to target genes potentially involved in growth and development. We also identified 145 miRNAs expressed in both mouse and human BAT, of which 25 were enriched in mouse BAT. Of these 25 miRNAs, miR-20a was predicted to target MYF5 and PPARγ, two important genes involved in brown adipogenesis, as well as BMP2 and BMPR2, genes involved in white adipogenesis. For the first time, 69 miRNAs were identified in human BAT but absent in mouse BAT, and 181 miRNAs were

  3. Comparative analysis of differential gene expression tools for RNA sequencing time course data.

    Science.gov (United States)

    Spies, Daniel; Renz, Peter F; Beyer, Tobias A; Ciaudo, Constance

    2017-10-06

    RNA sequencing (RNA-seq) has become a standard procedure to investigate transcriptional changes between conditions and is routinely used in research and clinics. While standard differential expression (DE) analysis between two conditions has been extensively studied, and improved over the past decades, RNA-seq time course (TC) DE analysis algorithms are still in their early stages. In this study, we compare, for the first time, existing TC RNA-seq tools on an extensive simulation data set and validated the best performing tools on published data. Surprisingly, TC tools were outperformed by the classical pairwise comparison approach on short time series (tools improved this shortcoming, as the majority of false-positive, but not true-positive, candidates were unique for each method. On longer time series, pairwise approach was less efficient on the overall performance compared with splineTC and maSigPro, which did not identify any false-positive candidate. © The Author 2017. Published by Oxford University Press.

  4. Comparative analysis of peptidylarginine deiminase-2 expression in canine, feline and human mammary tumours.

    Science.gov (United States)

    Cherrington, B D; Mohanan, S; Diep, A N; Fleiss, R; Sudilovsky, D; Anguish, L J; Coonrod, S A; Wakshlag, J J

    2012-01-01

    The peptidylarginine deiminase (PAD) enzyme family converts arginine residues in proteins to citrulline. In the canine mammary gland, PAD2 expression is first detected in epithelial cells in oestrus and becomes more widely expressed during dioestrus. PAD2 appears to modify nuclear histones, suggesting a role for the enzyme in chromatin remodelling and gene regulation. Recent evidence suggests that PAD2 plays a role in gene regulation in primary human breast epithelial cells. PAD2 may therefore be involved in gene regulation as it relates to mammary development, the oestrus cycle and potentially to neoplasia. The aim of the present study was to determine whether PAD2 expression was increased or decreased in mammary carcinoma compared with normal mammary tissue. A human mammary tissue microarray and archival surgical biopsy tissues from canine and feline mammary tumours were used to demonstrate differential expression of PAD2 in mammary carcinoma that appeared to be consistent across species. Normal human and canine mammary epithelium showed strong cytoplasmic and nuclear expression of PAD2, but there was reduced PAD2 expression in mammary carcinomas from both species. Feline mammary carcinomas had complete loss of nuclear PAD2 expression. Loss of nuclear PAD2 expression may therefore represent a marker of progression towards more aggressive neoplasia. Copyright © 2012 Elsevier Ltd. All rights reserved.

  5. Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing

    DEFF Research Database (Denmark)

    Willenbrock, Hanni; Salomon, Jesper; Søkilde, Rolf

    2009-01-01

    Recently, next-generation sequencing has been introduced as a promising, new platform for assessing the copy number of transcripts, while the existing microarray technology is considered less reliable for absolute, quantitative expression measurements. Nonetheless, so far, results from the two...... technologies have only been compared based on biological data, leading to the conclusion that, although they are somewhat correlated, expression values differ significantly. Here, we use synthetic RNA samples, resembling human microRNA samples, to find that microarray expression measures actually correlate...... better with sample RNA content than expression measures obtained from sequencing data. In addition, microarrays appear highly sensitive and perform equivalently to next-generation sequencing in terms of reproducibility and relative ratio quantification....

  6. Comparative Analysis of Biologically Relevant Response Curves in Gene Expression Experiments: Heteromorphy, Heterochrony, and Heterometry

    OpenAIRE

    Baker, Stuart

    2014-01-01

    To gain biological insights, investigators sometimes compare sequences of gene expression measurements under two scenarios (such as two drugs or species). For this situation, we developed an algorithm to fit, identify, and compare biologically relevant response curves in terms of heteromorphy (different curves), heterochrony (different transition times), and heterometry (different magnitudes). The curves are flat, linear, sigmoid, hockey-stick (sigmoid missing a steady state), transient (sigm...

  7. Comparative gene expression analysis of Porphyromonas gingivalis ATCC 33277 in planktonic and biofilms states.

    Science.gov (United States)

    Romero-Lastra, P; Sánchez, M C; Ribeiro-Vidal, H; Llama-Palacios, A; Figuero, E; Herrera, D; Sanz, M

    2017-01-01

    Porphyromonas gingivalis is a keystone pathogen in the onset and progression of periodontitis. Its pathogenicity has been related to its presence and survival within the subgingival biofilm. The aim of the present study was to compare the genome-wide transcription activities of P. gingivalis in biofilm and in planktonic growth, using microarray technology. P. gingivalis ATCC 33277 was incubated in multi-well culture plates at 37°C for 96 hours under anaerobic conditions using an in vitro static model to develop both the planktonic and biofilm states (the latter over sterile ceramic calcium hydroxyapatite discs). The biofilm development was monitored by Confocal Laser Scanning Microscopy (CLSM) and Scanning Electron Microscopy (SEM). After incubation, the bacterial cells were harvested and total RNA was extracted and purified. Three biological replicates for each cell state were independently hybridized for transcriptomic comparisons. A linear model was used for determining differentially expressed genes and reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to confirm differential expression. The filtering criteria of ≥ ±2 change in gene expression and significance p-values of gingivalis growing in biofilm compared to planktonic. The 54 up-regulated genes in biofilm growth were mainly related to cell envelope, transport, and binding or outer membranes proteins. Thirty-eight showed decreased expression, mainly genes related to transposases or oxidative stress. The adaptive response of P. gingivalis in biofilm growth demonstrated a differential gene expression.

  8. Comparative Gene Expression Analysis of the Coronal Pulp and Apical Pulp Complex in Human Immature Teeth.

    Science.gov (United States)

    Kim, Soo-Hyun; Kim, Seunghye; Shin, Yooseok; Lee, Hyo-Seol; Jeon, Mijeong; Kim, Seong-Oh; Cho, Sung-Won; Ruparel, Nikita B; Song, Je Seon

    2016-05-01

    This study determined the gene expression profiles of the human coronal pulp (CP) and apical pulp complex (APC) with the aim of explaining differences in their functions. Total RNA was isolated from the CP and APC, and gene expression was analyzed using complementary DNA microarray technology. Gene ontology analysis was used to classify the biological function. Quantitative reverse-transcription polymerase chain reaction and immunohistochemical staining were performed to verify microarray data. In the microarray analyses, expression increases of at least 2-fold were present in 125 genes in the APC and 139 genes in the CP out of a total of 33,297 genes. Gene ontology class processes found more genes related to immune responses, cell growth and maintenance, and cell adhesion in the APC, whereas transport and neurogenesis genes predominated in the CP. Quantitative reverse-transcription polymerase chain reaction and immunohistochemical staining confirmed the microarray results, with DMP1, CALB1, and GABRB1 strongly expressed in the CP, whereas SMOC2, SHH, BARX1, CX3CR1, SPP1, COL XII, and LAMC2 were strongly expressed in the APC. The expression levels of genes related to dentin mineralization, neurogenesis, and neurotransmission are higher in the CP in human immature teeth, whereas those of immune-related and tooth development-related genes are higher in the APC. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  9. Comparative expression analysis of aquaporin-5 (AQP5) in keratoconic and healthy corneas.

    Science.gov (United States)

    Garfias, Yonathan; Navas, Alejandro; Pérez-Cano, Hector J; Quevedo, Jonathan; Villalvazo, Leonardo; Zenteno, Juan Carlos

    2008-04-25

    Keratoconus (KC) is a common progressive corneal disease characterized by excessive stromal thinning, central or paracentral conical protrusion, and disruptions in Bowman's layer. The etiology of KC is largely unknown, and a combination of genetic and environmental factors is believed to play a role in the origin of the disease. Recently, the absence of transcripts of the water channel, aquaporin-5 (AQP5), was demonstrated by reverse-transcription polymerase chain reaction (RT-PCR) in KC tissues and was proposed as a possible marker for KC. In this study, we sought to evaluate AQP5 mRNA and protein expression in KC and non-KC corneal tissues using a combination of techniques. A total of 69 samples of corneal tissue were analyzed including 39 corneal buttons from patients with advanced KC, 16 samples of non-KC corneal epithelium belonging to patients who underwent surface refractive surgery, 12 sclerocorneal rims obtained from healthy donor subjects, and two healthy corneal buttons. Determination of AQP5 transcript and protein expression patterns was performed by means of real time RT-PCR, immunohistochemistry, immunocytochemistry, and flow cytometry methods. Cell culture was performed to identify AQP5 protein expression in KC epithelial cells. AQP5 mRNA was expressed with no significant differences between KC and non-KC tissues. Moreover, AQP5 protein expression analysis did not reveal differences in protein levels and/or cell location among KC and non-KC tissues. Interestingly, AQP5 expression continues for up to 21 days in the isolated KC corneal epithelial cells. Our results do not support a role for AQP5 in KC etiopathogeny or as a disease marker. Genetic background differences or a distinct pathogenetic KC cascade specific to the analyzed population could account for the dissimilarities observed in KC-related AQP5 expression.

  10. Comparative transcriptional analysis reveals differential gene expression between asymmetric and symmetric zygotic divisions in tobacco.

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    Tian-Xiang Hu

    Full Text Available Asymmetric cell divisions occur widely during many developmental processes in plants. In most angiosperms, the first zygotic cell division is asymmetric resulting in two daughter cells of unequal size and with distinct fates. However, the critical molecular mechanisms regulating this division remain unknown. Previously we showed that treatment of tobacco zygotes with beta-glucosyl Yariv (βGlcY could dramatically alter the first zygotic asymmetric division to produce symmetric two-celled proembryos. In the present study, we isolated zygotes and two-celled asymmetric proembryos in vivo by micromanipulation, and obtained symmetric, two-celled proembryos by in vitro cell cultures. Using suppression-subtractive hybridization (SSH and macroarray analysis differential gene expression between the zygote and the asymmetric and symmetric two-celled proembryos was investigated. After sequencing of the differentially expressed clones, a total of 1610 EST clones representing 685 non-redundant transcripts were obtained. Gene ontology (GO term analysis revealed that these transcripts include those involved in physiological processes such as response to stimulus, regulation of gene expression, and localization and formation of anatomical structures. A homology search against known genes from Arabidopsis indicated that some of the above transcripts are involved in asymmetric cell division and embryogenesis. Quantitative real-time PCR confirmed the up- or down-regulation of the selected candidate transcripts during zygotic division. A few of these transcripts were expressed exclusively in the zygote, or in either type of the two-celled proembryos. Expression analyses of select genes in different tissues and organs also revealed potential roles of these transcripts in fertilization, seed maturation and organ development. The putative roles of few of the identified transcripts in the regulation of zygotic division are discussed. Further functional work on these

  11. Comparative gene expression study and pathway analysis of the human iris- and the retinal pigment epithelium.

    Science.gov (United States)

    Bennis, Anna; Ten Brink, Jacoline B; Moerland, Perry D; Heine, Vivi M; Bergen, Arthur A

    2017-01-01

    The retinal pigment epithelium (RPE) is a neural monolayer lining the back of the eye. Degeneration of the RPE leads to severe vision loss in, so far incurable, diseases such as age-related macular degeneration and some forms of retinitis pigmentosa. A promising future replacement therapy may be autologous iris epithelial cell transdifferentiation into RPE in vitro and, subsequently, transplantation. In this study we compared the gene expression profiles of the iris epithelium (IE) and the RPE. We collected both primary RPE- and IE cells from 5 freshly frozen human donor eyes, using respectively laser dissection microscopy and excision. We performed whole-genome expression profiling using 44k Agilent human microarrays. We investigated the gene expression profiles on both gene and functional network level, using R and the knowledge database Ingenuity. The major molecular pathways related to the RPE and IE were quite similar and yielded basic neuro-epithelial cell functions. Nonetheless, we also found major specific differences: For example, genes and molecular pathways, related to the visual cycle and retinol biosynthesis are significantly higher expressed in the RPE than in the IE. Interestingly, Wnt and aryl hydrocarbon receptor (AhR-) signaling pathways are much higher expressed in the IE than in the RPE, suggesting, respectively, a possible pluripotent and high detoxification state of the IE. This study provides a valuation of the similarities and differences between the expression profiles of the RPE and IE. Our data combined with that of the literature, represent a most comprehensive perspective on transcriptional variation, which may support future research in the development of therapeutic transplantation of IE.

  12. Comparative gene expression study and pathway analysis of the human iris- and the retinal pigment epithelium.

    Directory of Open Access Journals (Sweden)

    Anna Bennis

    Full Text Available The retinal pigment epithelium (RPE is a neural monolayer lining the back of the eye. Degeneration of the RPE leads to severe vision loss in, so far incurable, diseases such as age-related macular degeneration and some forms of retinitis pigmentosa. A promising future replacement therapy may be autologous iris epithelial cell transdifferentiation into RPE in vitro and, subsequently, transplantation. In this study we compared the gene expression profiles of the iris epithelium (IE and the RPE.We collected both primary RPE- and IE cells from 5 freshly frozen human donor eyes, using respectively laser dissection microscopy and excision. We performed whole-genome expression profiling using 44k Agilent human microarrays. We investigated the gene expression profiles on both gene and functional network level, using R and the knowledge database Ingenuity.The major molecular pathways related to the RPE and IE were quite similar and yielded basic neuro-epithelial cell functions. Nonetheless, we also found major specific differences: For example, genes and molecular pathways, related to the visual cycle and retinol biosynthesis are significantly higher expressed in the RPE than in the IE. Interestingly, Wnt and aryl hydrocarbon receptor (AhR- signaling pathways are much higher expressed in the IE than in the RPE, suggesting, respectively, a possible pluripotent and high detoxification state of the IE.This study provides a valuation of the similarities and differences between the expression profiles of the RPE and IE. Our data combined with that of the literature, represent a most comprehensive perspective on transcriptional variation, which may support future research in the development of therapeutic transplantation of IE.

  13. Comparative analysis of gene expression in normal and cancer human prostate cell lines

    Directory of Open Access Journals (Sweden)

    E. E. Rosenberg

    2014-04-01

    Full Text Available Prostate cancer is one of the main causes of mortality in men with malignant tumors. The urgent problem was a search for biomarkers of prostate cancer, which would allow distinguishing between aggressive metastatic and latent tumors. The aim of this work was to search for differentially expressed genes in normal epithelial cells PNT2 and prostate cancer cell lines LNCaP, DU145 and PC3, produced from tumors with different aggressiveness and metas­tatic ability. Such genes might be used to create a panel of prognostic markers for aggressiveness and metastasis. Relative gene expression of 65 cancer-related genes was determined by the quantitative polymerase chain reaction (Q-PCR. Expression of 29 genes was changed in LNCaP cells, 20 genes in DU145 and 16 genes in PC3 cell lines, compared with normal line PNT2. The obtained data make it possible to conclude that the epithelial-mesenchymal cell transition took place, which involved the loss of epithelial markers, reduced cell adhesion and increased migration. We have also found few differentially expressed genes among 3 prostate cancer cell lines. We have found that genes, involved in cell adhesion (CDH1, invasiveness and metastasis (IL8, CXCL2 and cell cycle control (P16, CCNE1 underwent most changes. These genes might be used for diagnosis and prognosis of invasive metastatic prostate tumors.

  14. Identification of differentially expressed genes associated with semigamy in Pima cotton (Gossypium barbadense L. through comparative microarray analysis

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    Stewart J McD

    2011-03-01

    Full Text Available Abstract Background Semigamy in cotton is a type of facultative apomixis controlled by an incompletely dominant autosomal gene (Se. During semigamy, the sperm and egg cells undergo cellular fusion, but the sperm and egg nucleus fail to fuse in the embryo sac, giving rise to diploid, haploid, or chimeric embryos composed of sectors of paternal and maternal origin. In this study we sought to identify differentially expressed genes related to the semigamy genotype by implementing a comparative microarray analysis of anthers and ovules between a non-semigametic Pima S-1 cotton and its doubled haploid natural isogenic mutant semigametic 57-4. Selected differentially expressed genes identified by the microarray results were then confirmed using quantitative reverse transcription PCR (qRT-PCR. Results The comparative analysis between isogenic 57-4 and Pima S-1 identified 284 genes in anthers and 1,864 genes in ovules as being differentially expressed in the semigametic genotype 57-4. Based on gene functions, 127 differentially expressed genes were common to both semigametic anthers and ovules, with 115 being consistently differentially expressed in both tissues. Nine of those genes were selected for qRT-PCR analysis, seven of which were confirmed. Furthermore, several well characterized metabolic pathways including glycolysis/gluconeogenesis, carbon fixation in photosynthetic organisms, sesquiterpenoid biosynthesis, and the biosynthesis of and response to plant hormones were shown to be affected by differentially expressed genes in the semigametic tissues. Conclusion As the first report using microarray analysis, several important metabolic pathways affected by differentially expressed genes in the semigametic cotton genotype have been identified and described in detail. While these genes are unlikely to be the semigamy gene itself, the effects associated with expression changes in those genes do mimic phenotypic traits observed in semigametic plants

  15. Genome-wide expression analysis comparing hypertrophic changes in normal and dysferlinopathy mice

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    Yun-Sil Lee

    2015-12-01

    Full Text Available Because myostatin normally limits skeletal muscle growth, there are extensive efforts to develop myostatin inhibitors for clinical use. One potential concern is that in muscle degenerative diseases, inducing hypertrophy may increase stress on dystrophic fibers. Our study shows that blocking this pathway in dysferlin deficient mice results in early improvement in histopathology but ultimately accelerates muscle degeneration. Hence, benefits of this approach should be weighed against these potential detrimental effects. Here, we present detailed experimental methods and analysis for the gene expression profiling described in our recently published study in Human Molecular Genetics (Lee et al., 2015. Our data sets have been deposited in the Gene Expression Omnibus (GEO database (GSE62945 and are available at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62945. Our data provide a resource for exploring molecular mechanisms that are related to hypertrophy-induced, accelerated muscular degeneration in dysferlinopathy.

  16. Comparative DNA methylation and gene expression analysis identifies novel genes for structural congenital heart diseases.

    Science.gov (United States)

    Grunert, Marcel; Dorn, Cornelia; Cui, Huanhuan; Dunkel, Ilona; Schulz, Kerstin; Schoenhals, Sophia; Sun, Wei; Berger, Felix; Chen, Wei; Sperling, Silke R

    2016-10-01

    For the majority of congenital heart diseases (CHDs), the full complexity of the causative molecular network, which is driven by genetic, epigenetic, and environmental factors, is yet to be elucidated. Epigenetic alterations are suggested to play a pivotal role in modulating the phenotypic expression of CHDs and their clinical course during life. Candidate approaches implied that DNA methylation might have a developmental role in CHD and contributes to the long-term progress of non-structural cardiac diseases. The aim of the present study is to define the postnatal epigenome of two common cardiac malformations, representing epigenetic memory, and adaption to hemodynamic alterations, which are jointly relevant for the disease course. We present the first analysis of genome-wide DNA methylation data obtained from myocardial biopsies of Tetralogy of Fallot (TOF) and ventricular septal defect patients. We defined stringent sets of differentially methylated regions between patients and controls, which are significantly enriched for genomic features like promoters, exons, and cardiac enhancers. For TOF, we linked DNA methylation with genome-wide expression data and found a significant overlap for hypermethylated promoters and down-regulated genes, and vice versa. We validated and replicated the methylation of selected CpGs and performed functional assays. We identified a hypermethylated novel developmental CpG island in the promoter of SCO2 and demonstrate its functional impact. Moreover, we discovered methylation changes co-localized with novel, differential splicing events among sarcomeric genes as well as transcription factor binding sites. Finally, we demonstrated the interaction of differentially methylated and expressed genes in TOF with mutated CHD genes in a molecular network. By interrogating DNA methylation and gene expression data, we identify two novel mechanism contributing to the phenotypic expression of CHDs: aberrant methylation of promoter CpG islands

  17. Comparative Analysis of Biologically Relevant Response Curves in Gene Expression Experiments: Heteromorphy, Heterochrony, and Heterometry.

    Science.gov (United States)

    Baker, Stuart G

    2014-02-14

    To gain biological insights, investigators sometimes compare sequences of gene expression measurements under two scenarios (such as two drugs or species). For this situation, we developed an algorithm to fit, identify, and compare biologically relevant response curves in terms of heteromorphy (different curves), heterochrony (different transition times), and heterometry (different magnitudes). The curves are flat, linear, sigmoid, hockey-stick (sigmoid missing a steady state), transient (sigmoid missing two steady states), impulse (with peak or trough), step (with intermediate-level plateau), impulse+ (impulse with an extra parameter), step+ (step with an extra parameter), further characterized by upward or downward trend. To reduce overfitting, we fit the curves to every other response, evaluated the fit in the remaining responses, and identified the most parsimonious curves that yielded a good fit. We measured goodness of fit using a statistic comparable over different genes, namely the square root of the mean squared prediction error as a percentage of the range of responses, which we call the relative prediction error (RPE). We illustrated the algorithm using data on gene expression at 14 times in the embryonic development in two species of frogs. Software written in Mathematica is freely available.

  18. Comparative Analysis of Biologically Relevant Response Curves in Gene Expression Experiments: Heteromorphy, Heterochrony, and Heterometry

    Directory of Open Access Journals (Sweden)

    Stuart G. Baker

    2014-02-01

    Full Text Available To gain biological insights, investigators sometimes compare sequences of gene expression measurements under two scenarios (such as two drugs or species. For this situation, we developed an algorithm to fit, identify, and compare biologically relevant response curves in terms of heteromorphy (different curves, heterochrony (different transition times, and heterometry (different magnitudes. The curves are flat, linear, sigmoid, hockey-stick (sigmoid missing a steady state, transient (sigmoid missing two steady states, impulse (with peak or trough, step (with intermediate-level plateau, impulse+ (impulse with an extra parameter, step+ (step with an extra parameter, further characterized by upward or downward trend. To reduce overfitting, we fit the curves to every other response, evaluated the fit in the remaining responses, and identified the most parsimonious curves that yielded a good fit. We measured goodness of fit using a statistic comparable over different genes, namely the square root of the mean squared prediction error as a percentage of the range of responses, which we call the relative prediction error (RPE. We illustrated the algorithm using data on gene expression at 14 times in the embryonic development in two species of frogs. Software written in Mathematica is freely available.

  19. Comparative analysis of differentially expressed sequence tags of sweet orange and mandarin infected with Xylella fastidiosa

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    Alessandra A. de Souza

    2007-01-01

    Full Text Available The Citrus ESTs Sequencing Project (CitEST conducted at Centro APTA Citros Sylvio Moreira/IAC has identified and catalogued ESTs representing a set of citrus genes expressed under relevant stress responses, including diseases such as citrus variegated chlorosis (CVC, caused by Xylella fastidiosa. All sweet orange (Citrus sinensis L. Osb. varieties are susceptible to X. fastidiosa. On the other hand, mandarins (C. reticulata Blanco are considered tolerant or resistant to the disease, although the bacterium can be sporadically detected within the trees, but no disease symptoms or economic losses are observed. To study their genetic responses to the presence of X. fastidiosa, we have compared EST libraries of leaf tissue of sweet orange Pêra IAC (highly susceptible cultivar to X. fastidiosa and mandarin ‘Ponkan’ (tolerant artificially infected with the bacterium. Using an in silico differential display, 172 genes were found to be significantly differentially expressed in such conditions. Sweet orange presented an increase in expression of photosynthesis related genes that could reveal a strategy to counterbalance a possible lower photosynthetic activity resulting from early effects of the bacterial colonization in affected plants. On the other hand, mandarin showed an active multi-component defense response against the bacterium similar to the non-host resistance pattern.

  20. Comparative analysis of gene expression in maternal peripheral blood and monocytes during spontaneous preterm labor.

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    Paquette, Alison G; Shynlova, Oksana; Kibschull, Mark; Price, Nathan D; Lye, Stephen J

    2018-03-01

    Preterm birth is the leading cause of newborn death worldwide, and is associated with significant cognitive and physiological challenges in later life. There is a pressing need to define the mechanisms that initiate spontaneous preterm labor, and for development of novel clinical biomarkers to identify high-risk pregnancies. Most preterm birth studies utilize fetal tissues, and there is limited understanding of the transcriptional changes that occur in mothers undergoing spontaneous preterm labor. Earlier work revealed that a specific population of maternal peripheral leukocytes (macrophages/monocytes) play an active role in the initiation of labor. Thus, we hypothesized that there are dynamic gene expression changes in maternal blood leukocytes during preterm labor. Using next-generation sequencing we aim to characterize the transcriptome in whole blood leukocytes and peripheral monocytes of women undergoing spontaneous preterm labor compared to healthy pregnant women who subsequently delivered at full term. RNA sequencing was performed in both whole blood and peripheral monocytes from women who underwent preterm labor (24-34 weeks of gestation, N = 20) matched for gestational age to healthy pregnant controls (N = 30). All participants were a part of the Ontario Birth Study cohort (Toronto, Ontario, Canada). We identified significant differences in expression of 262 genes in peripheral monocytes and 184 genes in whole blood of women who were in active spontaneous preterm labor compared to pregnant women of the same gestational age not undergoing labor, with 43 of these genes differentially expressed in both whole blood and peripheral monocytes. ADAMTS2 expression was significantly increased in women actively undergoing spontaneous preterm labor, which we validated through digital droplet reverse transcriptase polymerase chain reaction. Intriguingly, we have also identified a number of gene sets including signaling by stem cell factor-KIT, nucleotide metabolism

  1. Comparative gene expression analysis of avian embryonic facial structures reveals new candidates for human craniofacial disorders.

    Science.gov (United States)

    Brugmann, S A; Powder, K E; Young, N M; Goodnough, L H; Hahn, S M; James, A W; Helms, J A; Lovett, M

    2010-03-01

    Mammals and birds have common embryological facial structures, and appear to employ the same molecular genetic developmental toolkit. We utilized natural variation found in bird beaks to investigate what genes drive vertebrate facial morphogenesis. We employed cross-species microarrays to describe the molecular genetic signatures, developmental signaling pathways and the spectrum of transcription factor (TF) gene expression changes that differ between cranial neural crest cells in the developing beaks of ducks, quails and chickens. Surprisingly, we observed that the neural crest cells established a species-specific TF gene expression profile that predates morphological differences between the species. A total of 232 genes were differentially expressed between the three species. Twenty-two of these genes, including Fgfr2, Jagged2, Msx2, Satb2 and Tgfb3, have been previously implicated in a variety of mammalian craniofacial defects. Seventy-two of the differentially expressed genes overlap with un-cloned loci for human craniofacial disorders, suggesting that our data will provide a valuable candidate gene resource for human craniofacial genetics. The most dramatic changes between species were in the Wnt signaling pathway, including a 20-fold up-regulation of Dkk2, Fzd1 and Wnt1 in the duck compared with the other two species. We functionally validated these changes by demonstrating that spatial domains of Wnt activity differ in avian beaks, and that Wnt signals regulate Bmp pathway activity and promote regional growth in facial prominences. This study is the first of its kind, extending on previous work in Darwin's finches and provides the first large-scale insights into cross-species facial morphogenesis.

  2. Comparative Digital Gene Expression Analysis of the Arabidopsis Response to Volatiles Emitted by Bacillus amyloliquefaciens.

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    Hai-Ting Hao

    Full Text Available Some plant growth-promoting rhizobacteria (PGPR regulated plant growth and elicited plant basal immunity by volatiles. The response mechanism to the Bacillus amyloliquefaciens volatiles in plant has not been well studied. We conducted global gene expression profiling in Arabidopsis after treatment with Bacillus amyloliquefaciens FZB42 volatiles by Illumina Digital Gene Expression (DGE profiling of different growth stages (seedling and mature and tissues (leaves and roots. Compared with the control, 1,507 and 820 differentially expressed genes (DEGs were identified in leaves and roots at the seedling stage, respectively, while 1,512 and 367 DEGs were identified in leaves and roots at the mature stage. Seventeen genes with different regulatory patterns were validated using quantitative RT-PCR. Numerous DEGs were enriched for plant hormones, cell wall modifications, and protection against stress situations, which suggests that volatiles have effects on plant growth and immunity. Moreover, analyzes of transcriptome difference in tissues and growth stage using DGE profiling showed that the plant response might be tissue-specific and/or growth stage-specific. Thus, genes encoding flavonoid biosynthesis were downregulated in leaves and upregulated in roots, thereby indicating tissue-specific responses to volatiles. Genes related to photosynthesis were downregulated at the seedling stage and upregulated at the mature stage, respectively, thereby suggesting growth period-specific responses. In addition, the emission of bacterial volatiles significantly induced killing of cells of other organism pathway with up-regulated genes in leaves and the other three pathways (defense response to nematode, cell morphogenesis involved in differentiation and trichoblast differentiation with up-regulated genes were significantly enriched in roots. Interestingly, some important alterations in the expression of growth-related genes, metabolic pathways, defense response

  3. Comparative Transcriptome Analysis of Differentially Expressed Genes and Signaling Pathways between XY and YY Testis in Yellow Catfish.

    Science.gov (United States)

    Wu, Junjie; Xiong, Shuting; Jing, Jing; Chen, Xin; Wang, Weimin; Gui, Jian-Fang; Mei, Jie

    2015-01-01

    YY super-males have rarely been detected in nature and only been artificially created in some fish species including tilapia and yellow catfish (Pelteobagrusfulvidraco), which provides a promising model for testis development and spermatogenesis. In our previous study, significant differences in morphology and miRNA expression were detected between XY and YY testis of yellow catfish. Here, solexa sequencing technology was further performed to compare mRNA expression between XY and YY testis. Compared with unigenes expressed in XY testis, 1146 and 1235 unigenes have significantly higher and lower expression in YY testis, respectively. 605 differentially expressed unigenes were annotated to 1604 GO terms with 319 and 286 genes having relative higher expression in XY and YY testis. KEGG analysis suggested different levels of PI3K-AKT and G protein-coupled receptor (GPCR) signaling pathways between XY and YY testis. Down-regulation of miR-141/429 in YY testis was speculated to promote testis development and maturation, and several factors in PI3K-AKT and GPCR signaling pathways were found as predicted targets of miR-141/429, several of which were confirmed by dual-luciferase reporter assays. Our study provides a comparative transcriptome analysis between XY and YY testis, and reveals interactions between miRNAs and their target genes that are possibly involved in regulating testis development and spermatogenesis.

  4. Comparative Analysis of Cartilage Marker Gene Expression Patterns during Axolotl and Xenopus Limb Regeneration.

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    Kazumasa Mitogawa

    Full Text Available Axolotls (Ambystoma mexicanum can completely regenerate lost limbs, whereas Xenopus laevis frogs cannot. During limb regeneration, a blastema is first formed at the amputation plane. It is thought that this regeneration blastema forms a limb by mechanisms similar to those of a developing embryonic limb bud. Furthermore, Xenopus laevis frogs can form a blastema after amputation; however, the blastema results in a terminal cone-shaped cartilaginous structure called a "spike." The causes of this patterning defect in Xenopus frog limb regeneration were explored. We hypothesized that differences in chondrogenesis may underlie the patterning defect. Thus, we focused on chondrogenesis. Chondrogenesis marker genes, type I and type II collagen, were compared in regenerative and nonregenerative environments. There were marked differences between axolotls and Xenopus in the expression pattern of these chondrogenesis-associated genes. The relative deficit in the chondrogenic capacity of Xenopus blastema cells may account for the absence of total limb regenerative capacity.

  5. Classification, expression pattern and comparative analysis of sugarcane expressed sequences tags (ESTs) encoding glycine-rich proteins (GRPs)

    National Research Council Canada - National Science Library

    Adriana Fusaro; Amanda Mangeon; Ricardo Magrani Junqueira; Carla Andréa Benício Rocha; Tatiana Cardoso Coutinho; Rogério Margis; Gilberto Sachetto-Martins

    2001-01-01

    ... cell biology of plants. Complexly regulated promoters and distinct mechanisms for the regulation of gene expression have been demonstrated and new protein targeting pathways, as well as the exportation of GRPs from...

  6. A comparative analysis of gene expression patterns and cell phenotypes between cervical and peripheral blood mononuclear cells.

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    Rachel E Horton

    2009-12-01

    Full Text Available Studies of the immunological environment in the female genital tract (FGT are critical for the development of vaccines or microbicides to halt the spread of sexually transmitted infections. Challenges arise due to the difficulties of sampling from this site, and the majority of studies have been conducted utilising peripheral blood mononuclear cells. Identifying functional differences between immune cells of the FGT and peripheral blood would aid in our understanding of mucosal immunology. We compared the gene expression profile of mononuclear cells at these two sites. Messenger RNA expression analysis was performed using gene expression arrays on matched cervical mononuclear cells and peripheral blood mononuclear cells. Further cellular phenotyping was done by 10 colour flow cytometry. Of the 22,185 genes expressed by these samples, 5345 genes were significantly differentially expressed between the cell populations. Most differences can be explained by significantly lower levels of T and B cells and higher levels of macrophages and dendritic cells in the FGT compared with peripheral blood. Several immunologically relevant pathways such as apoptosis and innate immune signalling, and a variety of cytokines and cytokine receptors were differentially expressed. This study highlights the importance of the unique immunological environment of the FGT and identifies important differences between systemic and mucosal immune compartments.

  7. Comparative Analysis and Functional Annotation of a Large Expressed Sequence Tag Collection of Apple

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    Ksenija Gasic

    2009-03-01

    Full Text Available A total of 34 apple ( × Borkh. cDNA libraries were constructed from root, leaf, bud, shoot, flower, and fruit tissues, at various developmental stages and/or under biotic or abiotic stress conditions, and of several genotypes. From these libraries, 190,425 clones were partially sequenced from the 5′ end and 42,619 clones were sequenced from the 3′ end, and a total of 182,241 high-quality expressed sequence tags (ESTs were obtained. These coalesced into 23,442 tentative contigs and 9843 singletons, for a total of 33,825 apple unigenes. Functional annotation of this unigene set revealed an even distribution of apple sequences among the three main gene ontology categories. Of ∼33,000 apple unigenes, 8437 (25% had no detectable homologs ( >0.1 in the genome. When the entire apple unigene set was compared with the entire citrus [ (L. Osbeck] unigene set and the poplar ( Torr. & Gray predicted proteome, both members of the core eudicot and rosids clade, 13,521 of apple unigenes matched one or more sequences in citrus, while 25,817 had counterparts in the poplar protein database. Apple––citrus–poplar comparisons revealed closer evolutionary relationships between apple and poplar than with the other two species. Genes involved in basic metabolic pathways appear to be largely conserved among apple, citrus, poplar, and .

  8. Classification, expression pattern and comparative analysis of sugarcane expressed sequences tags (ESTs encoding glycine-rich proteins (GRPs

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    Fusaro Adriana

    2001-01-01

    Full Text Available Since the isolation of the first glycine-rich proteins (GRPs in plants a wealth of new GRPs have been identified. The highly specific but diverse expression pattern of grp genes, taken together with the distinct sub-cellular localization of some GRP groups, clearly indicate that these proteins are involved in several independent physiological processes. Notwithstanding the absence of a clear definition of the role of GRPs in plant cells, studies conducted with these proteins have provided new and interesting insights into the molecular biology and cell biology of plants. Complexly regulated promoters and distinct mechanisms for the regulation of gene expression have been demonstrated and new protein targeting pathways, as well as the exportation of GRPs from different cell types have been discovered. These data show that GRPs can be useful as markers and/or models to understand distinct aspects of plant biology. In this paper, the structural and functional features of these proteins in sugarcane (Saccharum officinarum L. are summarized. Since this is the first description of GRPs in sugarcane, special emphasis has been given to the expression pattern of these GRP genes by studying their abundance and prevalence in the different cDNA-libraries of the Sugarcane Expressed Sequence Tag (SUCEST project . The comparison of sugarcane GRPs with GRPs from other species is also discussed.

  9. Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris.

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    Marie Mooney

    Full Text Available Comparative oncology is a developing research discipline that is being used to assist our understanding of human neoplastic diseases. Companion canines are a preferred animal oncology model due to spontaneous tumor development and similarity to human disease at the pathophysiological level. We use a paired RNA sequencing (RNA-Seq/microarray analysis of a set of four normal canine lymph nodes and ten canine lymphoma fine needle aspirates to identify technical biases and variation between the technologies and convergence on biological disease pathways. Surrogate Variable Analysis (SVA provides a formal multivariate analysis of the combined RNA-Seq/microarray data set. Applying SVA to the data allows us to decompose variation into contributions associated with transcript abundance, differences between the technology, and latent variation within each technology. A substantial and highly statistically significant component of the variation reflects transcript abundance, and RNA-Seq appeared more sensitive for detection of transcripts expressed at low levels. Latent random variation among RNA-Seq samples is also distinct in character from that impacting microarray samples. In particular, we observed variation between RNA-Seq samples that reflects transcript GC content. Platform-independent variable decomposition without a priori knowledge of the sources of variation using SVA represents a generalizable method for accomplishing cross-platform data analysis. We identified genes differentially expressed between normal lymph nodes of disease free dogs and a subset of the diseased dogs diagnosed with B-cell lymphoma using each technology. There is statistically significant overlap between the RNA-Seq and microarray sets of differentially expressed genes. Analysis of overlapping genes in the context of biological systems suggests elevated expression and activity of PI3K signaling in B-cell lymphoma biopsies compared with normal biopsies, consistent with

  10. Comparative transcriptomic analysis identifies genes differentially expressed in human epicardial progenitors and hiPSC-derived cardiac progenitors.

    Science.gov (United States)

    Synnergren, Jane; Drowley, Lauren; Plowright, Alleyn T; Brolén, Gabriella; Goumans, Marie-José; Gittenberger-de Groot, Adriana C; Sartipy, Peter; Wang, Qing-Dong

    2016-11-01

    Regenerative therapies hold great potential to change the treatment paradigm for cardiac diseases. Human cardiac progenitor cells can be used for drug discovery in this area and also provide a renewable source of cardiomyocytes. However, a better understanding of their characteristics is critical for interpreting data obtained from drug screening using these cells. In the present study, we performed global transcriptional analysis of two important sources of cardiac progenitors, i.e., patient epicardium-derived cells (EPDCs) and cardiac progenitor cells (CPCs) derived from human induced pluripotent stem cells. In addition, we also compared the gene expression profiles of these cells when they were cultured under normoxic and hypoxic conditions. We identified 3,289 mRNAs that were differentially expressed between EPDCs and CPCs. Gene ontology annotation and pathway enrichment analyses further revealed possible unique functions of these two cell populations. Notably, the impact of hypoxia vs normoxia on gene expression was modest and only a few genes (e.g., AK4, ALDOC, BNIP3P1, PGK1, and SLC2A1) were upregulated in EPDCs and CPCs after the cells were exposed to low oxygen for 24 h. Finally, we also performed a focused analysis of the gene expression patterns of a predefined set of 92 paracrine factors. We identified 30 of these genes as differentially expressed, and 29 were expressed at higher levels in EPDCs compared with CPCs. Taken together, the results of the present study advance our understanding of the transcriptional programs in EPDCs and CPCs and highlights important differences and similarities between these cell populations. Copyright © 2016 the American Physiological Society.

  11. A comparative Analysis by SAGE of Gene Expression Profiles of Esophageal Adenocarcinoma and Esophageal Squamous Cell Carcinoma

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    Jantine W. P. M. van Baal

    2008-01-01

    Full Text Available Esophageal adenocarcinoma (EA and esophageal squamous cell carcinoma (ESCC are the two main types of esophageal cancer. Despite extensive research the exact molecular basis of these cancers is unclear. Therefore we evaluated the transcriptome of EA in comparison to non-dysplastic Barrett’s esophagus (BE, the metaplastic epithelium that predisposes for EA, and compared the transcriptome of ESCC to normal esophageal squamous epithelium. For obtaining the transcriptomes tissue biopsies were used and serial analysis of gene expression (SAGE was applied. Validation of results by RT-PCR and immunoblotting was performed using tissues of an additional 23 EA and ESCC patients. Over 58,000 tags were sequenced. Between EA and BE 1013, and between ESCC and normal squamous epithelium 1235 tags were significantly differentially expressed (p < 0.05. The most up-regulated genes in EA compared to BE were SRY-box 4 and Lipocalin2, whereas the most down-regulated genes in EA were Trefoil factors and Annexin A10. The most up-regulated genes in ESCC compared to normal squamous epithelium were BMP4, E-Cadherin and TFF3. The results could suggest that the BE expression profile is closer related to normal squamous esophagus then to EA. In addition, several uniquely expressed genes are identified.

  12. A Comparative Analysis of Recombinant Expression and Solubility Screening of Two Phytases in E. coli

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    Ashok Pandey

    2011-01-01

    Full Text Available Microbial phytases, especially from fungal and bacterial sources, have received much attention as food additives in human nutrition and as feed supplements for monogastric animals. An effective expression screening method for recombinant production of this enzyme on a small scale is industrially desirable. An effort has been made in this work to clone and express phytase genes from Aspergillus sp. and Escherichia coli with the selected host, vector and inducer combination. Albeit the formation of insoluble inclusion bodies by fungal phytase, recombinant E. coli appA was effectively expressed in a cost-effective manner in the periplasm of BL21plysS using an inducer concentration of 0.01 mM in 4 h of growth. Enzyme was purified in three consecutive steps and functional studies were carried out.

  13. Comparative Analysis of Peripheral Alkaline Phytase Protein Structures Expressed in E. coli

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    Mohammadreza Nassiri

    2015-10-01

    Full Text Available Background: Degradation of phytic acid to inorganic phosphate in domestic animals’ diets requires thermostable phytase. Although Basillus subtilis phytase shows a potential to be degraded phytate complex in high temperature, the enzyme activities and yields need to be increased to make them possible for industrial application. Methods: The phytase gene from Bacillus subtilis DR8886 was isolated from Dig Rostam hot mineral spring in Iran and cloned into pET21(+ and pET32(+. Expression was induced with 1.5 mM IPTG and the proteins were purified. Results: The recombinant protein affected by thioredoxin (Trx from pET32a-PhyC was estimated to constitute about 31% of the total soluble protein in the cells; its concentration was 3.5 μg/ml, and its maximal phytase activity was 15.9 U/ml, whereas the recombinant phytase from pET21a-PhyC was estimated to comprise about 19% of the total soluble protein; its concentration was 2.2 μg/ml, and its maximal phytase activity was 69 U/ml. The molecular masses of recombinant phytase with and without Trx were about 60 kDa and 42 kDa, respectively. Zymography confirmed that the recombinant enzymes were active. Although the concentration of the alkaline phytase expressed by pET32a was approximately 59% greater than that expressed by pET21, its phytase activity was approximately 77% less. Conclusion: This study showed that the peripheral gene (Trx encoded by the pET32a (+ vector are the principal reason for the decrease in recombinant phytase enzyme activity.

  14. Comparative Analysis of Renin-Angiotensin System (RAS)-Related Gene Expression Between Hypertensive and Normotensive Rats.

    Science.gov (United States)

    Williamson, Chad R; Khurana, Sandhya; Nguyen, Phong; Byrne, Collin J; Tai, T C

    2017-01-31

    BACKGROUND The renal renin-angiotensin system (RAS) is physiologically important for blood pressure regulation. Altered regulation of RAS-related genes has been observed in an animal model of hypertension (spontaneously hypertensive rats - SHRs). The current understanding of certain RAS-related gene expression differences between Wistar-Kyoto rats (WKYs) and SHRs is either limited or has not been compared. The purpose of this study was to compare the regulation of key RAS-related genes in the kidneys of adult WKYs and SHRs. MATERIAL AND METHODS Coronal sections were dissected through the hilus of kidneys from 16-week-old male WKYs and SHRs. RT-PCR analysis was performed for Ace, Ace2, Agt, Agtr1a, Agtr1b, Agtr2, Atp6ap2 (PRR), Mas1, Ren, Rnls, and Slc12a3 (NCC). RESULTS Increased mRNA expression was observed for Ace, Ace2, Agt, Agtr1a, Agtr1b, and Atp6ap2 in SHRs compared to WKYs. Mas1, Ren, Slc12a3, and Rnls showed no difference in expression between animal types. CONCLUSIONS This study shows that the upregulation of several key RAS-related genes in the kidney may account for the increased blood pressure of adult SHRs.

  15. Comparative Gene Expression Analysis of Lymphocytes Treated with Exosomes Derived from Ovarian Cancer and Ovarian Cysts

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    Yujuan Li

    2017-06-01

    Full Text Available Cancer cells employ many strategies to evade immune defense and to facilitate tumor growth and angiogenesis. As a novel mode of intercellular communication, cancer-derived exosomes contribute to the recruitment and mediation of lymphocytes within the tumor environment. However, the mechanisms and key molecules mediating the effect of exosomes on lymphocytes are unclear. We treated healthy peripheral blood lymphocytes with exosomes from ovarian cancer and ovarian cysts and screened for differentially expressed genes using the RT2 Profiler Cancer Inflammation and Immunity Crosstalk PCR Array. A total of 26 upregulated genes (mainly pro-inflammatory genes and immunostimulatory and immunosuppressive factor and two downregulated genes (antigen presentation HLA-A/B were identified. Western blotting using lymphocytes from malignant ascites and peritoneal washings of benign ovarian cysts suggested that the interferon and NF-κB signaling pathway were involved in the immune regulation of malignant exosomes. Out of 28 differentially expressed genes detected using the array, 11 were validated by real-time PCR using lymphocytes within ovarian cancer (n = 27 and ovarian cyst (n = 9 environments. In conclusion, our findings indicate that malignant cells secrete exosomes in the tumor microenvironment to recruit lymphocytes in order to suppress antitumor immunity (IL10, Foxp3, and HLA-A/B and enhance tumor invasion, angiogenesis, and dissemination of proinflammatory cytokines (such as IL6 and VEGFA via the interferon and NF-κB signaling pathways. These results clarify lymphocyte-cancer cell cross talk via exosomes and may facilitate the development of effective immunotherapeutic strategies for ovarian cancer.

  16. Comparative proteomic analysis of differentially expressed proteins induced by hydrogen sulfide in Spinacia oleracea leaves.

    Science.gov (United States)

    Chen, Juan; Liu, Ting-Wu; Hu, Wen-Jun; Simon, Martin; Wang, Wen-Hua; Chen, Juan; Liu, Xiang; Zheng, Hai-Lei

    2014-01-01

    Hydrogen sulfide (H2S), as a potential gaseous messenger molecule, has been suggested to play important roles in a wide range of physiological processes in plants. The aim of present study was to investigate which set of proteins is involved in H2S-regulated metabolism or signaling pathways. Spinacia oleracea seedlings were treated with 100 µM NaHS, a donor of H2S. Changes in protein expression profiles were analyzed by 2-D gel electrophoresis coupled with MALDI-TOF MS. Over 1000 protein spots were reproducibly resolved, of which the abundance of 92 spots was changed by at least 2-fold (sixty-five were up-regulated, whereas 27 were down-regulated). These proteins were functionally divided into 9 groups, including energy production and photosynthesis, cell rescue, development and cell defense, substance metabolism, protein synthesis and folding, cellular signal transduction. Further, we found that these proteins were mainly localized in cell wall, plasma membrane, chloroplast, mitochondria, nucleus, peroxisome and cytosol. Our results demonstrate that H2S is involved in various cellular and physiological activities and has a distinct influence on photosynthesis, cell defense and cellular signal transduction in S. oleracea leaves. These findings provide new insights into proteomic responses in plants under physiological levels of H2S.

  17. Comparative proteomic analysis of differentially expressed proteins induced by hydrogen sulfide in Spinacia oleracea leaves.

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    Juan Chen

    Full Text Available Hydrogen sulfide (H2S, as a potential gaseous messenger molecule, has been suggested to play important roles in a wide range of physiological processes in plants. The aim of present study was to investigate which set of proteins is involved in H2S-regulated metabolism or signaling pathways. Spinacia oleracea seedlings were treated with 100 µM NaHS, a donor of H2S. Changes in protein expression profiles were analyzed by 2-D gel electrophoresis coupled with MALDI-TOF MS. Over 1000 protein spots were reproducibly resolved, of which the abundance of 92 spots was changed by at least 2-fold (sixty-five were up-regulated, whereas 27 were down-regulated. These proteins were functionally divided into 9 groups, including energy production and photosynthesis, cell rescue, development and cell defense, substance metabolism, protein synthesis and folding, cellular signal transduction. Further, we found that these proteins were mainly localized in cell wall, plasma membrane, chloroplast, mitochondria, nucleus, peroxisome and cytosol. Our results demonstrate that H2S is involved in various cellular and physiological activities and has a distinct influence on photosynthesis, cell defense and cellular signal transduction in S. oleracea leaves. These findings provide new insights into proteomic responses in plants under physiological levels of H2S.

  18. Towards a ZP-based contraceptive for marsupials: comparative analysis and developmental expression of marsupial ZP genes.

    Science.gov (United States)

    McCartney, Carmen A; Harris, Merrilee S; Rodger, John C; Mate, Karen E

    2007-12-01

    Fertility control in the form of a zona pellucida (ZP)-based immunocontraceptive has shown potential as a humane form of control for overabundant marsupials including the brushtail possum and macropods. Further refinement and development of a ZP-based vaccine requires detailed knowledge of the protein structure and expression in order to ensure maximum efficacy and specificity. Sequencing and comparative analysis of the ZP3 protein from three marsupial orders in this study found a high overall level of conservation; within order Diprotodontia, the ZP3 protein is 86.9-98.9% identical. ZP3 identity falls to 56.6-57.2%, when the grey, short-tailed opossum (a Didelphimorphian) is compared to dasyurid and diprotodontan marsupials. This is similar to its amino acid identity with ZP3 from eutherian species (50.7-52.8%). Comparison of a 21 amino acid epitope in marsupial ZP3 that has shown contraceptive effects, reveals 95-100% identity between the four macropodid species, 81-86% amino acid identity between brushtail possum and the macropods and 67-71% identity between the diprotodontans and the fat-tailed dunnart (a dasyurid). This is comparable to the level of identity between related eutherian mammals. The expression pattern of three ZP genes during brushtail possum and tammar wallaby pouch young development was examined by RT-PCR. This analysis of ZP gene expression has confirmed that ZP mRNA transcription begins in the ovary during pouch young development by about 51 days of age. The presence of ZP transcripts at this stage in pouch young development suggests that marsupial ZP gene transcription begins before the onset of follicular development. (c) 2007 Wiley-Liss, Inc.

  19. Meta-analysis of randomized controlled trials comparing EX-PRESS implantation with trabeculectomy for open-angle glaucoma.

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    Wei Wang

    Full Text Available PURPOSE: To evaluate the efficacy and safety of EX-PRESS implantation compared with trabeculectomy for uncontrolled open-angle glaucoma. METHODS: Pertinent randomized controlled trials were identified through systematic searches of the PubMed, EMBASE, and Cochrane Library. The efficacy measures utilized were the weighted mean differences (WMDs for the intraocular pressure reduction (IOPR, the reduction in glaucoma medications, the change of visual acuity, and the relative risks (RRs for operative success rates. The safety measures utilized were RRs for postoperative complications. The pooled effects were calculated using the random-effects model. RESULTS: Four randomized controlled trials of 292 eyes were included in this meta-analysis. The WMDs of the IOPR comparing the EX-PRESS with trabeculectomy were -0.25 (95% Cl: -3.61 to 3.11 at 6 month, 0.053 (-4.31 to 4.42 at 12 months, 0.81 (-4.06 to 5.67 at 24 months, and 0.20 (-2.11 to 2.51 at final follow-up. There was no statistically significance for IOPR at any point after surgery. There were also no significant differences in the reduction in glaucoma medications or visual acuity between the groups. The pooled relative risks comparing EX-PRESS with Trabeculectomy were 1.36 (1.11 to 1.66 for the complete operative success rate and 1.05 (0.94 to 1.17 for the qualified operative success rate. EX-PRESS and Trabeculectomy were associated with similar incidences in most complications with the exception of hyphema, with pooled RR being 0.18 (0.046 to 0.66. CONCLUSIONS: EX-PRESS implantation and trabeculectomy have similar efficacy in IOP-lowering, medication reduction, vision recovery, and qualified operative success rates. EX-PRESS associated with higher rates of complete operative success and fewer hyphema than with Trabeculectomy. However, these should be interpreted with caution because of the inherent limitations of the included studies.

  20. Meta-analysis of microRNA-183 family expression in human cancer studies comparing cancer tissues with noncancerous tissues.

    Science.gov (United States)

    Zhang, Qing-He; Sun, Hong-Min; Zheng, Rui-Zhi; Li, Ying-Chun; Zhang, Qian; Cheng, Pan; Tang, Zhen-Hai; Huang, Fen

    2013-09-15

    MicroRNA-183 (miR-183) family is proposed as promising biomarkers for early cancer detection and accurate prognosis as well as targets for more efficient treatment. The results of their expression feature in cancer tissues are inconsistent and controversy still exists in identifying them as new biomarkers of cancers. Therefore, to systemically evaluate the most frequently reported cancers in which miR-183 family members were up- or down-regulated is critical for further investigation on physiological impact of its aberrant regulation in specific cancers. The published studies that compared the level of miR-183 family expression in cancer tissues with those in noncancerous tissues were reviewed by the meta-analysis with a vote-counting strategy. Among the 49 included studies, a total of 18 cancers were reported, with 11 cancers reported in at least two studies. In the panel of miR-183 family members' expression analysis, colorectal cancer and prostate cancer ranked at the top among consistently reported cancer types with up-regulated feature. Bladder cancer, lung cancer and hepatocellular carcinoma were the third most frequently reported cancer types with significant over-expression of miR-96, miR-182 and miR-183 respectively. Breast cancer and gastric cancer were presented with inconsistent regulations and the members of this family had their own distinct regulated features in other different cancers. MiR-183 family, either individually or as a cluster, may be useful prognostic markers and/or therapeutic targets in several cancers. Further studies and repeat efforts are still required to determine the role of miR-183 family in various cancer progressions. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Comparative Analysis of Expression Profiles of Panicle Development among Tolerant and Sensitive Rice in Response to Drought Stress.

    Science.gov (United States)

    Wei, Haibin; Chen, Chen; Ma, Xiaosong; Zhang, Yu; Han, Jing; Mei, Hanwei; Yu, Shunwu

    2017-01-01

    Water deficit caused a serious threat to crops, especially panicle development at reproductive growth phase. We investigated grain yield components and gene expression profiles of panicle among tolerant and sensitive rice in response to drought stress. Panicle morphologies exhibited that secondary branches per panicle were more severely affected as compared to primary branches per panicle. Moreover, grain weight per panicle showed significant decrease for both tolerant and sensitive varieties except for MILT1444. Expression profile analysis revealed that 783 differentially expressed genes (DEGs) were identified to be drought-induced from young panicles in 2 cm length. Hierarchical clustering indicated that 76.8% of DEGs were up-regulated for all six rice varieties, and the percentage of down-regulated genes was higher in sensitive group than tolerant group. Biological process category revealed that the shared Gene Ontology (GO) terms were involved in response to abiotic stimulus and stress, whereas the specific GO terms in tolerant group were identified as regulation of biological quality, homeostatic process, cell growth, anatomical structure morphogenesis and development, and the unique terms in sensitive varieties were identified as lipid metabolic process and secondary metabolic process. Furthermore, the gene-based association analysis narrowed down list of DEGs, and four genes common to all six varieties were selected as candidate for breeders. Together, we found several shared and distinct biological processes between tolerant and sensitive varieties, and candidate stress-responsive genes. These findings provided insight into functional mechanisms regulating drought stress response in panicle development and may also help to crop tolerant improvement.

  2. Comparative Analysis of Fruit Metabolites and Pungency Candidate Genes Expression between Bhut Jolokia and Other Capsicum Species

    Science.gov (United States)

    M, Sarpras; Gaur, Rashmi; Sharma, Vineet; Chhapekar, Sushil Satish; Das, Jharna; Kumar, Ajay; Yadava, Satish Kumar; Nitin, Mukesh; Brahma, Vijaya; Abraham, Suresh K.; Ramchiary, Nirala

    2016-01-01

    Bhut jolokia, commonly known as Ghost chili, a native Capsicum species found in North East India was recorded as the naturally occurring hottest chili in the world by the Guinness Book of World Records in 2006. Although few studies have reported variation in pungency content of this particular species, no study till date has reported detailed expression analysis of candidate genes involved in capsaicinoids (pungency) biosynthesis pathway and other fruit metabolites. Therefore, the present study was designed to evaluate the diversity of fruit morphology, fruiting habit, capsaicinoids and other metabolite contents in 136 different genotypes mainly collected from North East India. Significant intra and inter-specific variations for fruit morphological traits, fruiting habits and 65 fruit metabolites were observed in the collected Capsicum germplasm belonging to three Capsicum species i.e., Capsicum chinense (Bhut jolokia, 63 accessions), C. frutescens (17 accessions) and C. annuum (56 accessions). The pungency level, measured in Scoville Heat Unit (SHU) and antioxidant activity measured by 2, 2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging assay showed maximum levels in C. chinense accessions followed by C. frutescens accessions, while C. annuum accessions showed the lowest value for both the traits. The number of different fruit metabolites detected did not vary significantly among the different species but the metabolite such as benzoic acid hydroxyl esters identified in large percentage in majority of C. annuum genotypes was totally absent in the C. chinense genotypes and sparingly present in few genotypes of C. frutescens. Significant correlations were observed between fruit metabolites capsaicin, dihydrocapsaicin, hexadecanoic acid, cyclopentane, α-tocopherol and antioxidant activity. Furthermore, comparative expression analysis (through qRT-PCR) of candidate genes involved in capsaicinoid biosynthesis pathway revealed many fold higher expression of

  3. Comparative Analysis of Fruit Metabolites and Pungency Candidate Genes Expression between Bhut Jolokia and Other Capsicum Species.

    Directory of Open Access Journals (Sweden)

    Sarpras M

    Full Text Available Bhut jolokia, commonly known as Ghost chili, a native Capsicum species found in North East India was recorded as the naturally occurring hottest chili in the world by the Guinness Book of World Records in 2006. Although few studies have reported variation in pungency content of this particular species, no study till date has reported detailed expression analysis of candidate genes involved in capsaicinoids (pungency biosynthesis pathway and other fruit metabolites. Therefore, the present study was designed to evaluate the diversity of fruit morphology, fruiting habit, capsaicinoids and other metabolite contents in 136 different genotypes mainly collected from North East India. Significant intra and inter-specific variations for fruit morphological traits, fruiting habits and 65 fruit metabolites were observed in the collected Capsicum germplasm belonging to three Capsicum species i.e., Capsicum chinense (Bhut jolokia, 63 accessions, C. frutescens (17 accessions and C. annuum (56 accessions. The pungency level, measured in Scoville Heat Unit (SHU and antioxidant activity measured by 2, 2-diphenyl-1-picrylhydrazyl (DPPH free radical scavenging assay showed maximum levels in C. chinense accessions followed by C. frutescens accessions, while C. annuum accessions showed the lowest value for both the traits. The number of different fruit metabolites detected did not vary significantly among the different species but the metabolite such as benzoic acid hydroxyl esters identified in large percentage in majority of C. annuum genotypes was totally absent in the C. chinense genotypes and sparingly present in few genotypes of C. frutescens. Significant correlations were observed between fruit metabolites capsaicin, dihydrocapsaicin, hexadecanoic acid, cyclopentane, α-tocopherol and antioxidant activity. Furthermore, comparative expression analysis (through qRT-PCR of candidate genes involved in capsaicinoid biosynthesis pathway revealed many fold higher

  4. Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq

    Science.gov (United States)

    Anderson, Letícia; Amaral, Murilo S.; Beckedorff, Felipe; Silva, Lucas F.; Dazzani, Bianca; Oliveira, Katia C.; Almeida, Giulliana T.; Gomes, Monete R.; Pires, David S.; Setubal, João C.; DeMarco, Ricardo; Verjovski-Almeida, Sergio

    2015-01-01

    Background Schistosomiasis is one of the most prevalent parasitic diseases worldwide and is a public health problem. Schistosoma mansoni is the most widespread species responsible for schistosomiasis in the Americas, Middle East and Africa. Adult female worms (mated to males) release eggs in the hepatic portal vasculature and are the principal cause of morbidity. Comparative separate transcriptomes of female and male adult worms were previously assessed with using microarrays and Serial Analysis of Gene Expression (SAGE), thus limiting the possibility of finding novel genes. Moreover, the egg transcriptome was analyzed only once with limited bacterially cloned cDNA libraries. Methodology/Principal findings To compare the gene expression of S. mansoni eggs, females, and males, we performed RNA-Seq on these three parasite forms using 454/Roche technology and reconstructed the transcriptome using Trinity de novo assembly. The resulting contigs were mapped to the genome and were cross-referenced with predicted Smp genes and H3K4me3 ChIP-Seq public data. For the first time, we obtained separate, unbiased gene expression profiles for S. mansoni eggs and female and male adult worms, identifying enriched biological processes and specific enriched functions for each of the three parasite forms. Transcripts with no match to predicted genes were analyzed for their protein-coding potential and the presence of an encoded conserved protein domain. A set of 232 novel protein-coding genes with putative functions related to reproduction, metabolism, and cell biogenesis was detected, which contributes to the understanding of parasite biology. Conclusions/Significance Large-scale RNA-Seq analysis using de novo assembly associated with genome-wide information for histone marks in the vicinity of gene models constitutes a new approach to transcriptome analysis that has not yet been explored in schistosomes. Importantly, all data have been consolidated into a UCSC Genome Browser search

  5. Comparative Analysis of Fruit Metabolites and Pungency Candidate Genes Expression between Bhut Jolokia and Other Capsicum Species

    National Research Council Canada - National Science Library

    M, Sarpras; Gaur, Rashmi; Sharma, Vineet; Chhapekar, Sushil Satish; Das, Jharna; Kumar, Ajay; Yadava, Satish Kumar; Nitin, Mukesh; Brahma, Vijaya; Abraham, Suresh K; Ramchiary, Nirala

    2016-01-01

    .... Although few studies have reported variation in pungency content of this particular species, no study till date has reported detailed expression analysis of candidate genes involved in capsaicinoids (pungency...

  6. Comparative Analysis of mRNA Isoform Expression in Cardiac Hypertrophy and Development Reveals Multiple Post-Transcriptional Regulatory Modules

    Science.gov (United States)

    Park, Ji Yeon; Li, Wencheng; Zheng, Dinghai; Zhai, Peiyong; Zhao, Yun; Matsuda, Takahisa; Vatner, Stephen F.; Sadoshima, Junichi; Tian, Bin

    2011-01-01

    Cardiac hypertrophy is enlargement of the heart in response to physiological or pathological stimuli, chiefly involving growth of myocytes in size rather than in number. Previous studies have shown that the expression pattern of a group of genes in hypertrophied heart induced by pressure overload resembles that at the embryonic stage of heart development, a phenomenon known as activation of the “fetal gene program”. Here, using a genome-wide approach we systematically defined genes and pathways regulated in short- and long-term cardiac hypertrophy conditions using mice with transverse aortic constriction (TAC), and compared them with those regulated at different stages of embryonic and postnatal development. In addition, exon-level analysis revealed widespread mRNA isoform changes during cardiac hypertrophy resulting from alternative usage of terminal or internal exons, some of which are also developmentally regulated and may be attributable to decreased expression of Fox-1 protein in cardiac hypertrophy. Genes with functions in certain pathways, such as cell adhesion and cell morphology, are more likely to be regulated by alternative splicing. Moreover, we found 3′UTRs of mRNAs were generally shortened through alternative cleavage and polyadenylation in hypertrophy, and microRNA target genes were generally de-repressed, suggesting coordinated mechanisms to increase mRNA stability and protein production during hypertrophy. Taken together, our results comprehensively delineated gene and mRNA isoform regulation events in cardiac hypertrophy and revealed their relations to those in development, and suggested that modulation of mRNA isoform expression plays an importance role in heart remodeling under pressure overload. PMID:21799842

  7. Comparative transcriptomics analysis reveals difference of key gene expression between banana and plantain in response to cold stress.

    Science.gov (United States)

    Yang, Qiao-Song; Gao, Jie; He, Wei-Di; Dou, Tong-Xin; Ding, Li-Jie; Wu, Jun-Hua; Li, Chun-Yu; Peng, Xin-Xiang; Zhang, Sheng; Yi, Gan-Jun

    2015-06-10

    Banana and plantain (Musa spp.) comprise an important part of diets for millions of people around the globe. Low temperature is one of the key environmental stresses which greatly affects the global banana production. To understand the molecular mechanism of the cold-tolerance in plantain we used RNA-Seq based comparative transcriptomics analyses for both cold-sensitive banana and cold-tolerant plantain subjected to the cold stress for 0, 3 and 6 h. The cold-response genes at early stage are identified and grouped in both species by GO analysis. The results show that 10 and 68 differentially expressed genes (DEGs) are identified for 3 and 6 h of cold stress respectively in plantain, while 40 and 238 DEGs are identified respectively in banana. GO classification analyses show that the majority of DEGs identified in both banana and plantain belong to 11 categories including regulation of transcription, response to stress signal transduction, etc. A similar profile for 28 DEGs was found in both banana and plantain for 6 h of cold stress, suggesting both share some common adaptation processes in response to cold stress. There are 17 DEGs found uniquely in cold-tolerance plantain, which were involved in signal transduction, abiotic stress, copper ion equilibrium, photosynthesis and photorespiration, sugar stimulation, protein modifications etc. Twelve early responsive genes including ICE1 and MYBS3 were selected and further assessed and confirmed by qPCR in the extended time course experiments (0, 3, 6, 24 and 48 h), which revealed significant expression difference of key genes in response to cold stress, especially ICE1 and MYBS3 between cold-sensitive banana and cold-tolerant plantain. We found that the cold-tolerance pathway appears selectively activated by regulation of ICE1 and MYBS3 expression in plantain under different stages of cold stress. We conclude that the rapid activation and selective induction of ICE1 and MYBS3 cold tolerance pathways in plantain, along

  8. Comparative analysis of viral gene expression programs during poxvirus infection: a transcriptional map of the vaccinia and monkeypox genomes.

    Directory of Open Access Journals (Sweden)

    Kathleen H Rubins

    2008-07-01

    Full Text Available Poxviruses engage in a complex and intricate dialogue with host cells as part of their strategy for replication. However, relatively little molecular detail is available with which to understand the mechanisms behind this dialogue.We designed a specialized microarray that contains probes specific to all predicted ORFs in the Monkeypox Zaire (MPXV and Vaccinia Western Reserve (VACV genomes, as well as >18,000 human genes, and used this tool to characterize MPXV and VACV gene expression responses in vitro during the course of primary infection of human monocytes, primary human fibroblasts and HeLa cells. The two viral transcriptomes show distinct features of temporal regulation and species-specific gene expression, and provide an early foundation for understanding global gene expression responses during poxvirus infection.The results provide a temporal map of the transcriptome of each virus during infection, enabling us to compare viral gene expression across species, and classify expression patterns of previously uncharacterized ORFs.

  9. 'You're my heart and liver'. A comparative analysis of the metaphorical expression of love in Catalan and Chinese in terms of cognitive semantics

    Directory of Open Access Journals (Sweden)

    Mònica-Marta Moyano

    2005-06-01

    Full Text Available The main aim of this article is to respond to a twofold question: how do the Chinese express their love? And the Catalans? Are there many differences in their views on this same feeling? To find out the author carries out comparative analysis of metaphoric expression in terms of cognitive theory of language.

  10. Comparative gene expression between two yeast species

    Directory of Open Access Journals (Sweden)

    Guan Yuanfang

    2013-01-01

    Full Text Available Abstract Background Comparative genomics brings insight into sequence evolution, but even more may be learned by coupling sequence analyses with experimental tests of gene function and regulation. However, the reliability of such comparisons is often limited by biased sampling of expression conditions and incomplete knowledge of gene functions across species. To address these challenges, we previously systematically generated expression profiles in Saccharomyces bayanus to maximize functional coverage as compared to an existing Saccharomyces cerevisiae data repository. Results In this paper, we take advantage of these two data repositories to compare patterns of ortholog expression in a wide variety of conditions. First, we developed a scalable metric for expression divergence that enabled us to detect a significant correlation between sequence and expression conservation on the global level, which previous smaller-scale expression studies failed to detect. Despite this global conservation trend, between-species gene expression neighborhoods were less well-conserved than within-species comparisons across different environmental perturbations, and approximately 4% of orthologs exhibited a significant change in co-expression partners. Furthermore, our analysis of matched perturbations collected in both species (such as diauxic shift and cell cycle synchrony demonstrated that approximately a quarter of orthologs exhibit condition-specific expression pattern differences. Conclusions Taken together, these analyses provide a global view of gene expression patterns between two species, both in terms of the conditions and timing of a gene's expression as well as co-expression partners. Our results provide testable hypotheses that will direct future experiments to determine how these changes may be specified in the genome.

  11. Molecular Cloning of phd1 and Comparative Analysis of phd1, 2, and 3 Expression in Xenopus laevis

    Directory of Open Access Journals (Sweden)

    Dandan Han

    2012-01-01

    Full Text Available Intensive gene targeting studies in mice have revealed that prolyl hydroxylase domain proteins (PHDs play important roles in murine embryonic development; however, the expression patterns and function of these genes during embryogenesis of other vertebrates remain largely unknown. Here we report the molecular cloning of phd1 and systematic analysis of phd1, phd2, and phd3 expression in embryos as well as adult tissues of Xenopus laevis. All three phds are maternally provided during Xenopus early development. The spatial expression patterns of phds genes in Xenopus embryos appear to define a distinct synexpression group. Frog phd2 and phd3 showed complementary expression in adult tissues with phd2 transcription levels being high in the eye, brain, and intestine, but low in the liver, pancreas, and kidney. On the contrary, expression levels of phd3 are high in the liver, pancreas, and kidney, but low in the eye, brain, and intestine. All three phds are highly expressed in testes, ovary, gall bladder, and spleen. Among three phds, phd3 showed strongest expression in heart.

  12. Comparative proteomics analysis of chronic atrophic gastritis: changes of protein expression in chronic atrophic gastritis with out Helicobacter pylori infection

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Lin; Hou, Yanhong; Wu, Kai; Li, Dan [Department of Gastroenterology and Hepatology, The 309 Hospital of People' s Liberation Army, Beijing (China)

    2012-03-02

    Chronic atrophic gastritis (CAG) is a very common gastritis and one of the major precursor lesions of gastric cancer, one of the most common cancers worldwide. The molecular mechanism underlying CAG is unclear, but its elucidation is essential for the prevention and early detection of gastric cancer and appropriate intervention. A combination of two-dimensional gel electrophoresis and mass spectrometry was used in the present study to analyze the differentially expressed proteins. Samples from 21 patients (9 females and 12 males; mean age: 61.8 years) were used. We identified 18 differentially expressed proteins in CAG compared with matched normal mucosa. Eight proteins were up-regulated and 10 down-regulated in CAG when compared with the same amounts of proteins in individually matched normal gastric mucosa. Two novel proteins, proteasome activator subunit 1 (PSME1), which was down-regulated in CAG, and ribosomal protein S12 (RPS12), which was up-regulated in CAG, were further investigated. Their expression was validated by Western blot and RT-PCR in 15 CAG samples matched with normal mucosa. The expression level of RPS12 was significantly higher in CAG than in matched normal gastric mucosa (P < 0.05). In contrast, the expression level of PSME1 in CAG was significantly lower than in matched normal gastric mucosa (P < 0.05). This study clearly demonstrated that there are some changes in protein expression between CAG and normal mucosa. In these changes, down-regulation of PSME1 and up-regulation of RPS12 could be involved in the development of CAG. Thus, the differentially expressed proteins might play important roles in CAG as functional molecules.

  13. Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2.

    Science.gov (United States)

    Liu, Chang; Lu, Lili; Kong, Quan; Li, Yan; Wu, Haihua; Yang, William; Xu, Shandan; Yang, Xinyu; Song, Xiaolei; Yang, Jack Y; Yang, Mary; Deng, Youping

    2014-01-01

    Diabetes mellitus of type 2 (T2D), also known as noninsulin-dependent diabetes mellitus (NIDDM) or adult-onset diabetes, is a common disease. It is estimated that more than 300 million people worldwide suffer from T2D. In this study, we investigated the T2D, pre-diabetic and healthy human (no diabetes) bloodstream samples using genomic, genealogical, and phonemic information. We identified differentially expressed genes and pathways. The study has provided deeper insights into the development of T2D, and provided useful information for further effective prevention and treatment of the disease. A total of 142 bloodstream samples were collected, including 47 healthy humans, 22 pre-diabetic and 73 T2D patients. Whole genome scale gene expression profiles were obtained using the Agilent Oligo chips that contain over 20,000 human genes. We identified 79 significantly differentially expressed genes that have fold change ≥ 2. We mapped those genes and pinpointed locations of those genes on human chromosomes. Amongst them, 3 genes were not mapped well on the human genome, but the rest of 76 differentially expressed genes were well mapped on the human genome. We found that most abundant differentially expressed genes are on chromosome one, which contains 9 of those genes, followed by chromosome two that contains 7 of the 76 differentially expressed genes. We performed gene ontology (GO) functional analysis of those 79 differentially expressed genes and found that genes involve in the regulation of cell proliferation were among most common pathways related to T2D. The expression of the 79 genes was combined with clinical information that includes age, sex, and race to construct an optimal discriminant model. The overall performance of the model reached 95.1% accuracy, with 91.5% accuracy on identifying healthy humans, 100% accuracy on pre-diabetic patients and 95.9% accuract on T2D patients. The higher performance on identifying pre-diabetic patients was resulted from more

  14. Genetic profiles of gastroesophageal cancer: combined analysis using expression array and tiling array--comparative genomic hybridization

    DEFF Research Database (Denmark)

    Isinger-Ekstrand, Anna; Johansson, Jan; Ohlsson, Mattias

    2010-01-01

    We aimed to characterize the genomic profiles of adenocarcinomas in the gastroesophageal junction in relation to cancers in the esophagus and the stomach. Profiles of gains/losses as well as gene expression profiles were obtained from 27 gastroesophageal adenocarcinomas by means of 32k high-resolution...... array-based comparative genomic hybridization and 27k oligo gene expression arrays, and putative target genes were validated in an extended series. Adenocarcinomas in the distal esophagus and the gastroesophageal junction showed strong similarities with the most common gains at 20q13, 8q24, 1q21-23, 5p...

  15. Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in five Salmonella genomes

    Directory of Open Access Journals (Sweden)

    Mondal U

    2008-01-01

    Full Text Available Purpose: To anlyse codon usage patterns of five complete genomes of Salmonella , predict highly expressed genes, examine horizontally transferred pathogenicity-related genes to detect their presence in the strains, and scrutinize the nature of highly expressed genes to infer upon their lifestyle. Methods: Protein coding genes, ribosomal protein genes, and pathogenicity-related genes were analysed with Codon W and CAI (codon adaptation index Calculator. Results: Translational efficiency plays a role in codon usage variation in Salmonella genes. Low bias was noticed in most of the genes. GC3 (guanine cytosine at third position composition does not influence codon usage variation in the genes of these Salmonella strains. Among the cluster of orthologous groups (COGs, translation, ribosomal structure biogenesis [J], and energy production and conversion [C] contained the highest number of potentially highly expressed (PHX genes. Correspondence analysis reveals the conserved nature of the genes. Highly expressed genes were detected. Conclusions: Selection for translational efficiency is the major source of variation of codon usage in the genes of Salmonella . Evolution of pathogenicity-related genes as a unit suggests their ability to infect and exist as a pathogen. Presence of a lot of PHX genes in the information and storage-processing category of COGs indicated their lifestyle and revealed that they were not subjected to genome reduction.

  16. Comparative gene expression analysis of Dtg, a novel target gene of Dpp signaling pathway in the early Drosophila melanogaster embryo.

    Science.gov (United States)

    Hodar, Christian; Zuñiga, Alejandro; Pulgar, Rodrigo; Travisany, Dante; Chacon, Carlos; Pino, Michael; Maass, Alejandro; Cambiazo, Verónica

    2014-02-10

    In the early Drosophila melanogaster embryo, Dpp, a secreted molecule that belongs to the TGF-β superfamily of growth factors, activates a set of downstream genes to subdivide the dorsal region into amnioserosa and dorsal epidermis. Here, we examined the expression pattern and transcriptional regulation of Dtg, a new target gene of Dpp signaling pathway that is required for proper amnioserosa differentiation. We showed that the expression of Dtg was controlled by Dpp and characterized a 524-bp enhancer that mediated expression in the dorsal midline, as well as, in the differentiated amnioserosa in transgenic reporter embryos. This enhancer contained a highly conserved region of 48-bp in which bioinformatic predictions and in vitro assays identified three Mad binding motifs. Mutational analysis revealed that these three motifs were necessary for proper expression of a reporter gene in transgenic embryos, suggesting that short and highly conserved genomic sequences may be indicative of functional regulatory regions in D. melanogaster genes. Dtg orthologs were not detected in basal lineages of Dipterans, which unlike D. melanogaster develop two extra-embryonic membranes, amnion and serosa, nevertheless Dtg orthologs were identified in the transcriptome of Musca domestica, in which dorsal ectoderm patterning leads to the formation of a single extra-embryonic membrane. These results suggest that Dtg was recruited as a new component of the network that controls dorsal ectoderm patterning in the lineage leading to higher Cyclorrhaphan flies, such as D. melanogaster and M. domestica. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. A comparative gene expression database for invertebrates

    Directory of Open Access Journals (Sweden)

    Ormestad Mattias

    2011-08-01

    Full Text Available Abstract Background As whole genome and transcriptome sequencing gets cheaper and faster, a great number of 'exotic' animal models are emerging, rapidly adding valuable data to the ever-expanding Evo-Devo field. All these new organisms serve as a fantastic resource for the research community, but the sheer amount of data, some published, some not, makes detailed comparison of gene expression patterns very difficult to summarize - a problem sometimes even noticeable within a single lab. The need to merge existing data with new information in an organized manner that is publicly available to the research community is now more necessary than ever. Description In order to offer a homogenous way of storing and handling gene expression patterns from a variety of organisms, we have developed the first web-based comparative gene expression database for invertebrates that allows species-specific as well as cross-species gene expression comparisons. The database can be queried by gene name, developmental stage and/or expression domains. Conclusions This database provides a unique tool for the Evo-Devo research community that allows the retrieval, analysis and comparison of gene expression patterns within or among species. In addition, this database enables a quick identification of putative syn-expression groups that can be used to initiate, among other things, gene regulatory network (GRN projects.

  18. Comparative proteomic analysis of differentially expressed proteins in the Bombyx mori fat body during the microsporidia Nosema bombycis infection.

    Science.gov (United States)

    Li, ZhiHong; Pan, GuoQing; Ma, ZhenGang; Han, Bing; Sun, Bin; Ni, Qi; Chen, Jie; Li, Tian; Liu, TongBao; Long, MengXian; Li, ChunFeng; Zhou, ZeYang

    2017-10-01

    Nosema bombycis is an obligate intracellular parasite, which can cause pébrine disease. To investigate the effects of N. bombycis infection, 5th-instar silkworms were challenged with N. bombycis isolate CQ1, and two-dimensional gel electrophoresis analysis was performed to analyze the differentially expressed proteins in infected and uninfected silkworm fat bodies 1, 2, 4, 6 and 8days post-infection (dpi). 46 differentially expressed proteins were identified at the 5 time points using MALDI-TOF/TOF MS. The changed proteins mainly involved in immune response, energy metabolism, and molecular synthesis. Overall, the identified proteins may provide important insights into the mechanisms of the silkworm response to N. bombycis infection. Copyright © 2017. Published by Elsevier Inc.

  19. Comparative expression analysis of genes induced during development of bacterial rot and induction of hypersensitive cell death in lettuce.

    Science.gov (United States)

    Kiba, Akinori; Lee, Kyon-Ye; Ohnishi, Kouhei; Hikichi, Yasufumi

    2008-11-28

    The development of bacterial rot disease caused by Pseudomonas cichorii is closely associated with programmed cell death. To investigate the molecular events occurring during the development of bacterial rot, we isolated 20 P. cichorii-responsive genes (PcRGs) in lettuce by differential display. Among these PcRGs, signal transduction-, transcription/translation- and defense/stress responses-related PcRGs were subjected to a comparative expression study. We used RNA samples isolated from lettuce leaves inoculated with P. cichorii and hypersensitive response-inducing Pseudomonas syringae pv. syringae. Expression of PcRG1-5-5 (spliceosomal protein), 2-9-2 (protein kinase) and 1-6-2 (ACC oxidase), 7-5 (alternative oxidase) and BI-I (bax inhibitor I) significantly increased in lettuce leaves inoculated with both P. cichorii and P. syringae pv. syringae. Intriguingly, PcRG 1-2-6 (protein phosphatase 2C) and 4-D-5 (protein kinase) were only up-regulated in P. cichorii-inoculated lettuce, whereas expression of PcRG1-3-2 (ribonucleoprotein) was only enhanced in P. syringae pv. syringae-inoculated lettuce. Expressions of PcRG1-3-2, 1-5-5, 1-6-2, 2-9-2, 7-5 and BI-I were induced by treatments with salicylic acid and/or methyl jasmonate. However, expression of PcRG1-2-6 and 4-D-5, which were specifically up-regulated by P. cichorii, were scarcely affected by these chemicals. Pharmacological studies suggested that ethylene and alternative oxidase were commonly related to disease development and hypersensitive responses. By contrast, there may be a different role for protein synthesis and protein kinase during disease development and in hypersensitive responses. These results suggested the overall similarity of genes expressed during disease development and in hypersensitive responses. However, there were differences not only in induction kinetics and the level of gene expression but also in the signal transduction pathway between hypersensitive responses and disease development.

  20. Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data.

    Science.gov (United States)

    Ning, Kang; Fermin, Damian; Nesvizhskii, Alexey I

    2012-04-06

    An increasing number of studies involve integrative analysis of gene and protein expression data taking advantage of new technologies such as next-generation transcriptome sequencing (RNA-Seq) and highly sensitive mass spectrometry (MS) instrumentation. Thus, it becomes interesting to revisit the correlative analysis of gene and protein expression data using more recently generated data sets. Furthermore, within the proteomics community there is a substantial interest in comparing the performance of different label-free quantitative proteomic strategies. Gene expression data can be used as an indirect benchmark for such protein-level comparisons. In this work we use publicly available mouse data to perform a joint analysis of genomic and proteomic data obtained on the same organism. First, we perform a comparative analysis of different label-free protein quantification methods (intensity based and spectral count based and using various associated data normalization steps) using several software tools on the proteomic side. Similarly, we perform correlative analysis of gene expression data derived using microarray and RNA-Seq methods on the genomic side. We also investigate the correlation between gene and protein expression data, and various factors affecting the accuracy of quantitation at both levels. It is observed that spectral count based protein abundance metrics, which are easy to extract from any published data, are comparable to intensity based measures with respect to correlation with gene expression data. The results of this work should be useful for designing robust computational pipelines for extraction and joint analysis of gene and protein expression data in the context of integrative studies.

  1. Comparative proteomics and expression analysis of five genes in Epicauta chinensis larvae from the first to fifth instar.

    Directory of Open Access Journals (Sweden)

    Qiurong Li

    Full Text Available Blister beetle is an important insect model for both medicinal and pure research. Previous research has mainly focused on its biology and biochemistry, but very little data is yet available in the molecular biology. This study uses differential proteomics technology to analyze the soluble proteins extracted from each of the 5 instars larvae of Epicauta chinensis. 42 of the differentially-expressed proteins were identified successfully by MALDI-TOF/TOF-MS. Some of these proteins' function and their expression profiles are analyzed. Our analysis revealed dynamics regulation of the following proteins: Axin-like protein pry-1 (APR-1, dihydrolipoyl dehydrogenase (DLD, vitellogenin (Vg and lysozyme C (Lmz-S. APR-1 negatively regulates the Wnt signaling pathway. Its overexpression could result in embryo, leg, eye and ovary ectopica or malformation. DLD catalyzes the pyruvate into acetyl-CoA, the latter is the starting material of juvenile hormone (JH and ipsdienol biosynthesis through the MVA pathway in insects. While Vg synthesis can be regulated by JH and stimulated by food factors. So DLD may affect the synthesis of JH, ipsdienol and Vg indirectly. The activity of lysozyme is an indicator of the immunity. Nutrition/food should be taken into account for its potential role during the development of larva in the future. Among the five genes and their corresponding proteins' expression, only hsc70 gene showed a good correspondence with the protein level. This reflects the fluctuating relationship between mRNA and protein levels.

  2. De novo transcriptome sequencing of Isaria cateniannulata and comparative analysis of gene expression in response to heat and cold stresses.

    Directory of Open Access Journals (Sweden)

    Dingfeng Wang

    Full Text Available Isaria cateniannulata is a very important and virulent entomopathogenic fungus that infects many insect pest species. Although I. cateniannulata is commonly exposed to extreme environmental temperature conditions, little is known about its molecular response mechanism to temperature stress. Here, we sequenced and de novo assembled the transcriptome of I. cateniannulata in response to high and low temperature stresses using Illumina RNA-Seq technology. Our assembly encompassed 17,514 unigenes (mean length = 1,197 bp, in which 11,445 unigenes (65.34% showed significant similarities to known sequences in NCBI non-redundant protein sequences (Nr database. Using digital gene expression analysis, 4,483 differentially expressed genes (DEGs were identified after heat treatment, including 2,905 up-regulated genes and 1,578 down-regulated genes. Under cold stress, 1,927 DEGs were identified, including 1,245 up-regulated genes and 682 down-regulated genes. The expression patterns of 18 randomly selected candidate DEGs resulting from quantitative real-time PCR (qRT-PCR were consistent with their transcriptome analysis results. Although DEGs were involved in many pathways, we focused on the genes that were involved in endocytosis: In heat stress, the pathway of clathrin-dependent endocytosis (CDE was active; however at low temperature stresses, the pathway of clathrin-independent endocytosis (CIE was active. Besides, four categories of DEGs acting as temperature sensors were observed, including cell-wall-major-components-metabolism-related (CWMCMR genes, heat shock protein (Hsp genes, intracellular-compatible-solutes-metabolism-related (ICSMR genes and glutathione S-transferase (GST. These results enhance our understanding of the molecular mechanisms of I. cateniannulata in response to temperature stresses and provide a valuable resource for the future investigations.

  3. A comparative antibody analysis of Pannexin1 expression in four rat brain regions reveals varying subcellular localizations

    Directory of Open Access Journals (Sweden)

    Angela C Cone

    2013-02-01

    Full Text Available Pannexin1 (Panx1 channels release cytosolic ATP in response to signaling pathways. Panx1 is highly expressed in the central nervous system. We used four antibodies with different Panx1 anti-peptide epitopes to analyze four regions of rat brain. These antibodies labeled the same bands in Western blots and had highly similar patterns of immunofluorescence in tissue culture cells expressing Panx1, but Western blots of brain lysates from Panx1 knockout and control mice showed different banding patterns. Localizations of Panx1 in brain slices were generated using automated wide-field mosaic confocal microscopy for imaging large regions of interest while retaining maximum resolution for examining cell populations and compartments. We compared Panx1 expression over the cerebellum, hippocampus with adjacent cortex, thalamus and olfactory bulb. While Panx1 localizes to the same neuronal cell types, subcellular localizations differ. Two antibodies with epitopes against the intracellular loop and one against the carboxy terminus preferentially labeled cell bodies, while an antibody raised against an N-terminal peptide highlighted neuronal processes more than cell bodies. These labeling patterns may be a reflection of different cellular and subcellular localizations of full-length and/or modified Panx1 channels where each antibody is highlighting unique or differentially accessible Panx1 populations. However, we cannot rule out that one or more of these antibodies have specificity issues. All data associated with experiments from these four antibodies are presented in a manner that allows them to be compared and our claims thoroughly evaluated, rather than eliminating results that were questionable. Each antibody is given a unique identifier through the NIF Antibody Registry that can be used to track usage of individual antibodies across papers and all image and metadata are made available in the public repository, the Cell Centered Database, for on

  4. Comparative microarray analysis of Rhipicephalus (Boophilus microplus expression profiles of larvae pre-attachment and feeding adult female stages on Bos indicus and Bos taurus cattle

    Directory of Open Access Journals (Sweden)

    Gondro Cedric

    2010-07-01

    Full Text Available Abstract Background Rhipicephalus (Boophilus microplus is an obligate blood feeder which is host specific to cattle. Existing knowledge pertaining to the host or host breed effects on tick transcript expression profiles during the tick - host interaction is poor. Results Global analysis of gene expression changes in whole R. microplus ticks during larval, pre-attachment and early adult stages feeding on Bos indicus and Bos taurus cattle were compared using gene expression microarray analysis. Among the 13,601 R. microplus transcripts from BmiGI Version 2 we identified 297 high and 17 low expressed transcripts that were significantly differentially expressed between R. microplus feeding on tick resistant cattle [Bos indicus (Brahman] compared to R. microplus feeding on tick susceptible cattle [Bos taurus (Holstein-Friesian] (p ≤ 0.001. These include genes encoding enzymes involved in primary metabolism, and genes related to stress, defence, cell wall modification, cellular signaling, receptor, and cuticle formation. Microarrays were validated by qRT-PCR analysis of selected transcripts using three housekeeping genes as normalization controls. Conclusion The analysis of all tick stages under survey suggested a coordinated regulation of defence proteins, proteases and protease inhibitors to achieve successful attachment and survival of R. microplus on different host breeds, particularly Bos indicus cattle. R. microplus ticks demonstrate different transcript expression patterns when they encounter tick resistant and susceptible breeds of cattle. In this study we provide the first transcriptome evidence demonstrating the influence of tick resistant and susceptible cattle breeds on transcript expression patterns and the molecular physiology of ticks during host attachment and feeding. The microarray data used in this analysis have been submitted to NCBI GEO database under accession number GSE20605 http://www.ncbi

  5. Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress.

    Science.gov (United States)

    Deokar, Amit A; Kondawar, Vishwajith; Jain, Pradeep K; Karuppayil, S Mohan; Raju, N L; Vadez, Vincent; Varshney, Rajeev K; Srinivasan, R

    2011-04-22

    Chickpea (Cicer arietinum L.) is an important grain-legume crop that is mainly grown in rainfed areas, where terminal drought is a major constraint to its productivity. We generated expressed sequence tags (ESTs) by suppression subtraction hybridization (SSH) to identify differentially expressed genes in drought-tolerant and -susceptible genotypes in chickpea. EST libraries were generated by SSH from root and shoot tissues of IC4958 (drought tolerant) and ICC 1882 (drought resistant) exposed to terminal drought conditions by the dry down method. SSH libraries were also constructed by using 2 sets of bulks prepared from the RNA of root tissues from selected recombinant inbred lines (RILs) (10 each) for the extreme high and low root biomass phenotype. A total of 3062 unigenes (638 contigs and 2424 singletons), 51.4% of which were novel in chickpea, were derived by cluster assembly and sequence alignment of 5949 ESTs. Only 2185 (71%) unigenes showed significant BLASTX similarity (drought stress was evaluated using macro-array (dot blots). The expression of few selected genes was validated by northern blotting and quantitative real-time PCR assay. Our study compares not only genes that are up- and down-regulated in a drought-tolerant genotype under terminal drought stress and a drought susceptible genotype but also between the bulks of the selected RILs exhibiting extreme phenotypes. More than 50% of the genes identified have been shown to be associated with drought stress in chickpea for the first time. This study not only serves as resource for marker discovery, but can provide a better insight into the selection of candidate genes (both up- and downregulated) associated with drought tolerance. These results can be used to identify suitable targets for manipulating the drought-tolerance trait in chickpea.

  6. Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress

    Science.gov (United States)

    2011-01-01

    Background Chickpea (Cicer arietinum L.) is an important grain-legume crop that is mainly grown in rainfed areas, where terminal drought is a major constraint to its productivity. We generated expressed sequence tags (ESTs) by suppression subtraction hybridization (SSH) to identify differentially expressed genes in drought-tolerant and -susceptible genotypes in chickpea. Results EST libraries were generated by SSH from root and shoot tissues of IC4958 (drought tolerant) and ICC 1882 (drought resistant) exposed to terminal drought conditions by the dry down method. SSH libraries were also constructed by using 2 sets of bulks prepared from the RNA of root tissues from selected recombinant inbred lines (RILs) (10 each) for the extreme high and low root biomass phenotype. A total of 3062 unigenes (638 contigs and 2424 singletons), 51.4% of which were novel in chickpea, were derived by cluster assembly and sequence alignment of 5949 ESTs. Only 2185 (71%) unigenes showed significant BLASTX similarity (<1E-06) in the NCBI non-redundant (nr) database. Gene ontology functional classification terms (BLASTX results and GO term), were retrieved for 2006 (92.0%) sequences, and 656 sequences were further annotated with 812 Enzyme Commission (EC) codes and were mapped to 108 different KEGG pathways. In addition, expression status of 830 unigenes in response to terminal drought stress was evaluated using macro-array (dot blots). The expression of few selected genes was validated by northern blotting and quantitative real-time PCR assay. Conclusion Our study compares not only genes that are up- and down-regulated in a drought-tolerant genotype under terminal drought stress and a drought susceptible genotype but also between the bulks of the selected RILs exhibiting extreme phenotypes. More than 50% of the genes identified have been shown to be associated with drought stress in chickpea for the first time. This study not only serves as resource for marker discovery, but can provide

  7. The extracellular Leucine-Rich Repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns

    Directory of Open Access Journals (Sweden)

    Miller Suzanne FC

    2007-09-01

    Full Text Available Abstract Background Leucine-rich repeats (LRRs are highly versatile and evolvable protein-ligand interaction motifs found in a large number of proteins with diverse functions, including innate immunity and nervous system development. Here we catalogue all of the extracellular LRR (eLRR proteins in worms, flies, mice and humans. We use convergent evidence from several transmembrane-prediction and motif-detection programs, including a customised algorithm, LRRscan, to identify eLRR proteins, and a hierarchical clustering method based on TribeMCL to establish their evolutionary relationships. Results This yields a total of 369 proteins (29 in worm, 66 in fly, 135 in mouse and 139 in human, many of them of unknown function. We group eLRR proteins into several classes: those with only LRRs, those that cluster with Toll-like receptors (Tlrs, those with immunoglobulin or fibronectin-type 3 (FN3 domains and those with some other domain. These groups show differential patterns of expansion and diversification across species. Our analyses reveal several clusters of novel genes, including two Elfn genes, encoding transmembrane proteins with eLRRs and an FN3 domain, and six genes encoding transmembrane proteins with eLRRs only (the Elron cluster. Many of these are expressed in discrete patterns in the developing mouse brain, notably in the thalamus and cortex. We have also identified a number of novel fly eLRR proteins with discrete expression in the embryonic nervous system. Conclusion This study provides the necessary foundation for a systematic analysis of the functions of this class of genes, which are likely to include prominently innate immunity, inflammation and neural development, especially the specification of neuronal connectivity.

  8. Comparative analysis of expressed sequence tags (ESTs between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress

    Directory of Open Access Journals (Sweden)

    Raju N L

    2011-04-01

    Full Text Available Abstract Background Chickpea (Cicer arietinum L. is an important grain-legume crop that is mainly grown in rainfed areas, where terminal drought is a major constraint to its productivity. We generated expressed sequence tags (ESTs by suppression subtraction hybridization (SSH to identify differentially expressed genes in drought-tolerant and -susceptible genotypes in chickpea. Results EST libraries were generated by SSH from root and shoot tissues of IC4958 (drought tolerant and ICC 1882 (drought resistant exposed to terminal drought conditions by the dry down method. SSH libraries were also constructed by using 2 sets of bulks prepared from the RNA of root tissues from selected recombinant inbred lines (RILs (10 each for the extreme high and low root biomass phenotype. A total of 3062 unigenes (638 contigs and 2424 singletons, 51.4% of which were novel in chickpea, were derived by cluster assembly and sequence alignment of 5949 ESTs. Only 2185 (71% unigenes showed significant BLASTX similarity ( Conclusion Our study compares not only genes that are up- and down-regulated in a drought-tolerant genotype under terminal drought stress and a drought susceptible genotype but also between the bulks of the selected RILs exhibiting extreme phenotypes. More than 50% of the genes identified have been shown to be associated with drought stress in chickpea for the first time. This study not only serves as resource for marker discovery, but can provide a better insight into the selection of candidate genes (both up- and downregulated associated with drought tolerance. These results can be used to identify suitable targets for manipulating the drought-tolerance trait in chickpea.

  9. Comparative gene expression analysis of two mouse models of autism:transcriptome profiling of the BTBR and En2-/- hippocampus

    Directory of Open Access Journals (Sweden)

    Giovanni Provenzano

    2016-08-01

    Full Text Available Autism spectrum disorders (ASD are characterized by a high degree of genetic heterogeneity. Genomic studies identified common pathological processes underlying the heterogeneous clinical manifestations of ASD, and transcriptome analyses revealed that gene networks involved in synapse development, neuronal activity and immune function are deregulated in ASD. Mouse models provide unique tools to investigate the neurobiological basis of ASD; however, a comprehensive approach to identify transcriptional abnormalities in different ASD models has never been performed. Here we used two well-recognized ASD mouse models, BTBR T+ Itpr3tf/J (BTBR and Engrailed-2 knockout (En2-/-, to identify conserved ASD-related molecular signatures. En2-/- mice bear a mutation within the EN2 transcription factor homeobox, while BTBR is an inbred strain with unknown genetic defects. Hippocampal RNA samples from BTBR, En2-/- and respective control (C57Bl/6J and En2+/+ adult mice were assessed for differential gene expression using microarrays. A total of 153 genes were similarly deregulated in the BTBR and En2-/- hippocampus. Mouse phenotype and gene ontology enrichment analyses were performed on BTBR and En2-/- hippocampal differentially expressed genes (DEGs. Pathways represented in both BTBR and En2-/- hippocampal DEGs included abnormal behavioral response and chemokine/MAP kinase signaling. Genes involved in abnormal function of the immune system and abnormal synaptic transmission/seizures were significantly represented among BTBR and En2-/- DEGs, respectively. Interestingly, both BTBR and En2-/- hippocampal DEGs showed a significant enrichment of ASD and schizophrenia (SCZ-associated genes. Specific gene sets were enriched in the two models: microglial genes were significantly enriched among BTBR DEGs, whereas GABAergic/glutamatergic postsynaptic genes, FMRP-interacting genes and epilepsy-related genes were significantly enriched among En2-/- DEGs. Weighted

  10. Comparative analysis of the EGF-receptor family in pancreatic cancer: expression of HER-4 correlates with a favourable tumor stage.

    Science.gov (United States)

    Thybusch-Bernhardt, A; Beckmann, S; Juhl, H

    2001-01-01

    Of major interest for a better molecular understanding of pancreatic cancer is the EGF receptor family. While HER-1 (EGF-receptor) and HER-2 have been extensively studied, little is known about the clinical significance of HER-3 and especially HER-4 expression. We investigated the expression of HER-1, HER-2, HER-3 and HER-4 in 11 pancreatic cancer cell lines using FACS-analysis and determined expression and overexpression of these receptors in 24 pancreatic cancer specimens. Therefore, we used two different immunostaining techniques: a highly sensitive streptavidin-biotin method showed receptor expression while an approximatly 10-fold less sensitive indirect immunperoxidase technique determined receptor-overexpression. HER-1 and HER-2 were expressed by all 11 pancreatic cancer cell lines, HER-3 was found in 82% and HER-4 in 54% of the cell lines. Low levels of HER-1, HER-2 and HER-3 were detected in all tumor samples but overexpression was only found in 33%, 25% and 50% of the cases, respectively. HER-4 was expressed by 37% of the tumor specimens but overexpression was seen in one patient only. HER-1 and HER-2 overexpression increased in parallel with the tumor stage and R0-resected tumors showed significantly less often overexpression compared to R1/R2 resected tumors (p HER-1 and HER-2 overexpression contributes to a more aggressive phenotype. In contrast, the lack of HER-4 expression might increase the metastatic capacity of pancreatic cancer cells.

  11. Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures.

    Science.gov (United States)

    Iandolino, Alberto; Nobuta, Kan; da Silva, Francisco Goes; Cook, Douglas R; Meyers, Blake C

    2008-05-12

    Vitis vinifera (V. vinifera) is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS) and combined it with available Expressed Sequence Tag (EST) data. These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry. The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS). A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was approximately 49 TPM (Transcripts Per Million). Comparisons of the MPSS signatures with available Vitis species' ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera. The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed evidence of antisense expression not

  12. Comparative expression profiling in grape (Vitis vinifera berries derived from frequency analysis of ESTs and MPSS signatures

    Directory of Open Access Journals (Sweden)

    Cook Douglas R

    2008-05-01

    evidence of antisense expression not previously reported in grapes but comparable to that reported in other plant species. Finally, we developed a novel web-based, public resource for utilization of the grape MPSS data 1.

  13. A comparative immunohistochemical analysis of COX-2, p53, and Ki-67 expression in keratocystic odontogenic tumors

    NARCIS (Netherlands)

    Mendes, R.A.; Carvalho, J.F.C.; van der Waal, I.

    2011-01-01

    Objective. The aim of the present study was to investigate the association between the expression of cyclooxygenase-2 (COX-2) in keratocystic odontogenic tumors (KCOT) and more commonly used markers, such as p53 and Ki-67. Study design. Expression of cyclooxygenase-2 (COX-2) in 20 biopsy specimens

  14. Comparative gene expression analysis between coronary arteries and internal mammary arteries identifies a role for the TES gene in endothelial cell functions relevant to coronary artery disease.

    Science.gov (United States)

    Archacki, Stephen R; Angheloiu, George; Moravec, Christine S; Liu, Hui; Topol, Eric J; Wang, Qing Kenneth

    2012-03-15

    Coronary artery disease (CAD) is the leading cause of death worldwide. It has been established that internal mammary arteries (IMA) are resistant to the development of atherosclerosis, whereas left anterior descending (LAD) coronary arteries are athero-prone. The contrasting properties of these two arteries provide an innovative strategy to identify the genes that play important roles in the development of atherosclerosis. We carried out microarray analysis to identify genes differentially expressed between IMA and LAD. Twenty-nine genes showed significant differences in their expression levels between IMA and LAD, which included the TES gene encoding Testin. The role of TES in the cardiovascular system is unknown. Here we show that TES is involved in endothelial cell (EC) functions relevant to atherosclerosis. Western blot analysis showed higher TES expression in IMA than in LAD. Reverse transcription polymerase chain reaction and western blot analyses showed that TES was consistently and markedly down-regulated by more than 6-fold at both mRNA and protein levels in patients with CAD compared with controls without CAD (P= 0.000049). The data suggest that reduced TES expression is associated with the development of CAD. Knockdown of TES expression by small-interfering RNA promoted oxidized-LDL-mediated monocyte adhesion to ECs, EC migration and the transendothelial migration of monocytes, while the over-expression of TES in ECs blunted these processes. These results demonstrate association between reduced TES expression and CAD, establish a novel role for TES in EC functions and raise the possibility that reduced TES expression increases susceptibility to the development of CAD.

  15. Comparative proteomic analysis of malignant pleural mesothelioma evidences an altered expression of nuclear lamin and filament-related proteins.

    Science.gov (United States)

    Giusti, Laura; Da Valle, Ylenia; Bonotti, Alessandra; Donadio, Elena; Ciregia, Federica; Ventroni, Tiziana; Foddis, Rudy; Giannaccini, Gino; Guglielmi, Giovanni; Cristaudo, Alfonso; Lucacchini, Antonio

    2014-04-01

    Malignant mesothelioma is a neoplastic disease linked to asbestos exposure whose diagnosis is limited, so detection methods for an early diagnosis and treatment result essential. Here, we compared proteomic profiles of malignant pleural mesothelioma (MPM) and benign biopsies to search potential biomarkers useful in differential diagnosis. Tissue biopsies were obtained from 53 patients who were subjected to a diagnostic thoracoscopy. 2DE/MS based approach was used for proteomic analysis and protein validation was carried out by Western blot analysis versus benign and lung carcinoma samples. Among the proteins identified we confirmed known MPM biomarkers such as calretinin and suggested the new ones as prelamin A/C, desmin, vimentin, calretinin, fructose-bisphosphate aldolase A, myosin regulatory light chain 2, ventricular/cardiac muscle isoform, myosin light chain 3 and myosin light chain 6B. Ingenuity software was used to identify the biological processes to which these proteins belong and to construct a potential network. Overall, our results suggest potential biomarkers that can be useful in occupational medicine for the early identification of the onset of disease in health surveillance of past asbestos-exposed workers, for monitoring the progress of disease and for assessing the response to treatment. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (Melampsora spp.

    Directory of Open Access Journals (Sweden)

    Tanguay Philippe

    2010-07-01

    Full Text Available Abstract Background Obligate biotrophs such as rust fungi are believed to establish long-term relationships by modulating plant defenses through a plethora of effector proteins, whose most recognizable feature is the presence of a signal peptide for secretion. Since the phenotypes of these effectors extend to host cells, their genes are expected to be under accelerated evolution stimulated by host-pathogen coevolutionary arms races. Recently, whole genome sequence data has allowed the prediction of secretomes, facilitating the identification of putative effectors. Results We generated cDNA libraries from four poplar leaf rust pathogens (Melampsora spp. and used computational approaches to identify and annotate putative secreted proteins with the aim of uncovering new knowledge about the nature and evolution of the rust secretome. While more than half of the predicted secretome members encoded lineage-specific proteins, similarities with experimentally characterized fungal effectors were also identified. A SAGE analysis indicated a strong stage-specific regulation of transcripts encoding secreted proteins. The average sequence identity of putative secreted proteins to their closest orthologs in the wheat stem rust Puccinia graminis f. sp. tritici was dramatically reduced compared with non-secreted ones. A comparative genomics approach based on homologous gene groups unravelled positive selection in putative members of the secretome. Conclusion We uncovered robust evidence that different evolutionary constraints are acting on the rust secretome when compared to the rest of the genome. These results are consistent with the view that these genes are more likely to exhibit an effector activity and be involved in coevolutionary arms races with host factors.

  17. Prediction of drug efficacy for cancer treatment based on comparative analysis of chemosensitivity and gene expression data

    DEFF Research Database (Denmark)

    Wan, Peng; Li, Qiyuan; Larsen, Jens Erik Pontoppidan

    2012-01-01

    The NCI60 database is the largest available collection of compounds with measured anti-cancer activity. The strengths and limitations for using the NCI60 database as a source of new anti-cancer agents are explored and discussed in relation to previous studies. We selected a sub-set of 2333...... and in a data set of expression profiles of 1901 genes for the corresponding tumor cell lines. Five clusters were identified based on the gene expression data using self-organizing maps (SOM), comprising leukemia, melanoma, ovarian and prostate, basal breast, and luminal breast cancer cells, respectively....... The strong difference in gene expression between basal and luminal breast cancer cells was reflected clearly in the chemosensitivity data. Although most compounds in the data set were of low potency, high efficacy compounds that showed specificity with respect to tissue of origin could be found. Furthermore...

  18. Nutritional and reproductive signaling revealed by comparative gene expression analysis in Chrysopa pallens (Rambur) at different nutritional statuses.

    Science.gov (United States)

    Han, Benfeng; Zhang, Shen; Zeng, Fanrong; Mao, Jianjun

    2017-01-01

    The green lacewing, Chrysopa pallens Rambur, is one of the most important natural predators because of its extensive spectrum of prey and wide distribution. However, what we know about the nutritional and reproductive physiology of this species is very scarce. By cDNA amplification and Illumina short-read sequencing, we analyzed transcriptomes of C. pallens female adult under starved and fed conditions. In total, 71236 unigenes were obtained with an average length of 833 bp. Four vitellogenins, three insulin-like peptides and two insulin receptors were annotated. Comparison of gene expression profiles suggested that totally 1501 genes were differentially expressed between the two nutritional statuses. KEGG orthology classification showed that these differentially expression genes (DEGs) were mapped to 241 pathways. In turn, the top 4 are ribosome, protein processing in endoplasmic reticulum, biosynthesis of amino acids and carbon metabolism, indicating a distinct difference in nutritional and reproductive signaling between the two feeding conditions. Our study yielded large-scale molecular information relevant to C. pallens nutritional and reproductive signaling, which will contribute to mass rearing and commercial use of this predaceous insect species.

  19. Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare)WRKY transcription factor family reveals putatively retained functions betweenmonocots and dicots

    Energy Technology Data Exchange (ETDEWEB)

    Mangelsen, Elke; Kilian, Joachim; Berendzen, Kenneth W.; Kolukisaoglu, Uner; Harter, Klaus; Jansson, Christer; Wanke, Dierk

    2008-02-01

    WRKY proteins belong to the WRKY-GCM1 superfamily of zinc finger transcription factors that have been subject to a large plant-specific diversification. For the cereal crop barley (Hordeum vulgare), three different WRKY proteins have been characterized so far, as regulators in sucrose signaling, in pathogen defense, and in response to cold and drought, respectively. However, their phylogenetic relationship remained unresolved. In this study, we used the available sequence information to identify a minimum number of 45 barley WRKY transcription factor (HvWRKY) genes. According to their structural features the HvWRKY factors were classified into the previously defined polyphyletic WRKY subgroups 1 to 3. Furthermore, we could assign putative orthologs of the HvWRKY proteins in Arabidopsis and rice. While in most cases clades of orthologous proteins were formed within each group or subgroup, other clades were composed of paralogous proteins for the grasses and Arabidopsis only, which is indicative of specific gene radiation events. To gain insight into their putative functions, we examined expression profiles of WRKY genes from publicly available microarray data resources and found group specific expression patterns. While putative orthologs of the HvWRKY transcription factors have been inferred from phylogenetic sequence analysis, we performed a comparative expression analysis of WRKY genes in Arabidopsis and barley. Indeed, highly correlative expression profiles were found between some of the putative orthologs. HvWRKY genes have not only undergone radiation in monocot or dicot species, but exhibit evolutionary traits specific to grasses. HvWRKY proteins exhibited not only sequence similarities between orthologs with Arabidopsis, but also relatedness in their expression patterns. This correlative expression is indicative for a putative conserved function of related WRKY proteins in mono- and dicot species.

  20. Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots.

    Science.gov (United States)

    Mangelsen, Elke; Kilian, Joachim; Berendzen, Kenneth W; Kolukisaoglu, Uner H; Harter, Klaus; Jansson, Christer; Wanke, Dierk

    2008-04-28

    WRKY proteins belong to the WRKY-GCM1 superfamily of zinc finger transcription factors that have been subject to a large plant-specific diversification. For the cereal crop barley (Hordeum vulgare), three different WRKY proteins have been characterized so far as regulators in sucrose signaling, pathogen defense, and in response to cold and drought. However, their phylogenetic relationship remained unresolved. In this study, we used available sequence information to identify a minimum number of 45 barley WRKY transcription factor (HvWRKY) genes. According to their structural features, the HvWRKY factors were classified into the previously defined polyphyletic WRKY subgroups 1 to 3. Furthermore, we could assign putative orthologs of the HvWRKY proteins in Arabidopsis and rice. While in most cases clades of orthologous proteins were formed within each group or subgroup, other clades were composed of paralogous proteins for the grasses and Arabidopsis only, which is indicative of specific gene radiation events. To gain insight into their putative functions, we examined expression profiles of WRKY genes from publicly available microarray data resources and found group specific expression patterns. While putative orthologs of the HvWRKY transcription factors have been inferred from phylogenetic sequence analysis, we performed a comparative expression analysis of WRKY genes in Arabidopsis and barley. Indeed, highly correlative expression profiles were found between some of the putative orthologs. HvWRKY genes have not only undergone radiation in monocot or dicot species, but exhibit evolutionary traits specific to grasses. HvWRKY proteins exhibited not only sequence similarities between orthologs with Arabidopsis, but also relatedness in their expression patterns. This correlative expression is indicative for a putative conserved function of related WRKY proteins in monocot and dicot species.

  1. Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare WRKY transcription factor family reveals putatively retained functions between monocots and dicots

    Directory of Open Access Journals (Sweden)

    Jansson Christer

    2008-04-01

    Full Text Available Abstract Background WRKY proteins belong to the WRKY-GCM1 superfamily of zinc finger transcription factors that have been subject to a large plant-specific diversification. For the cereal crop barley (Hordeum vulgare, three different WRKY proteins have been characterized so far as regulators in sucrose signaling, pathogen defense, and in response to cold and drought. However, their phylogenetic relationship remained unresolved. Results In this study, we used available sequence information to identify a minimum number of 45 barley WRKY transcription factor (HvWRKY genes. According to their structural features, the HvWRKY factors were classified into the previously defined polyphyletic WRKY subgroups 1 to 3. Furthermore, we could assign putative orthologs of the HvWRKY proteins in Arabidopsis and rice. While in most cases clades of orthologous proteins were formed within each group or subgroup, other clades were composed of paralogous proteins for the grasses and Arabidopsis only, which is indicative of specific gene radiation events. To gain insight into their putative functions, we examined expression profiles of WRKY genes from publicly available microarray data resources and found group specific expression patterns. While putative orthologs of the HvWRKY transcription factors have been inferred from phylogenetic sequence analysis, we performed a comparative expression analysis of WRKY genes in Arabidopsis and barley. Indeed, highly correlative expression profiles were found between some of the putative orthologs. Conclusion HvWRKY genes have not only undergone radiation in monocot or dicot species, but exhibit evolutionary traits specific to grasses. HvWRKY proteins exhibited not only sequence similarities between orthologs with Arabidopsis, but also relatedness in their expression patterns. This correlative expression is indicative for a putative conserved function of related WRKY proteins in monocot and dicot species.

  2. Comparative RNA-Seq Analysis Reveals That Regulatory Network of Maize Root Development Controls the Expression of Genes in Response to N Stress.

    Directory of Open Access Journals (Sweden)

    Xiujing He

    Full Text Available Nitrogen (N is an essential nutrient for plants, and it directly affects grain yield and protein content in cereal crops. Plant root systems are not only critical for anchorage in the soil, but also for N acquisition. Therefore, genes controlling root development might also affect N uptake by plants. In this study, the responses of nitrogen on root architecture of mutant rtcs and wild-type of maize were investigated by morphological and physiological analysis. Subsequently, we performed a comparative RNA-Seq analysis to compare gene expression profiles between mutant rtcs roots and wild-type roots under different N conditions. We identified 786 co-modulated differentially expressed genes (DEGs related to root development. These genes participated in various metabolic processes. A co-expression cluster analysis and a cis-regulatory motifs analysis revealed the importance of the AP2-EREBP transcription factor family in the rtcs-dependent regulatory network. Some genotype-specific DEGs contained at least one LBD motif in their promoter region. Further analyses of the differences in gene transcript levels between rtcs and wild-type under different N conditions revealed 403 co-modulated DEGs with distinct functions. A comparative analysis revealed that the regulatory network controlling root development also controlled gene expression in response to N-deficiency. Several AP2-EREBP family members involved in multiple hormone signaling pathways were among the DEGs. These transcription factors might play important roles in the rtcs-dependent regulatory network related to root development and the N-deficiency response. Genes encoding the nitrate transporters NRT2-1, NAR2.1, NAR2.2, and NAR2.3 showed much higher transcript levels in rtcs than in wild-type under normal-N conditions. This result indicated that the LBD gene family mainly functions as transcriptional repressors, as noted in other studies. In summary, using a comparative RNA-Seq-based approach

  3. Analysis of Facial Expression by Taste Stimulation

    Science.gov (United States)

    Tobitani, Kensuke; Kato, Kunihito; Yamamoto, Kazuhiko

    In this study, we focused on the basic taste stimulation for the analysis of real facial expressions. We considered that the expressions caused by taste stimulation were unaffected by individuality or emotion, that is, such expressions were involuntary. We analyzed the movement of facial muscles by taste stimulation and compared real expressions with artificial expressions. From the result, we identified an obvious difference between real and artificial expressions. Thus, our method would be a new approach for facial expression recognition.

  4. Comparative Expression Analysis of Gametogenesis-Associated Genes in Foetal and Adult Bubaline (Bubalus bubalis) Ovaries and Testes.

    Science.gov (United States)

    Shah, S M; Saini, N; Ashraf, S; Zandi, M; Singh, M K; Manik, R S; Singla, S K; Palta, P; Chauhan, M S

    2015-06-01

    This study was conducted to identify and analyse the expression of gametogenesis-associated genes and proteins in foetal and adult buffalo gonads of both the sexes. Relative quantification of the genes was determined by qPCR and Western blotting. Immunohistochemistry was also performed for various gametogenesis-associated proteins in foetal and adult gonads of both the sexes. We observed significantly (p gametogenesis-associated proteins in ovarian follicles and seminiferous tubules of testes, while the surrounding somatic tissues were devoid of these proteins. The study gives an understanding of the sequential and temporal events of gene expression as well as mRNA translation during male and female gametogenesis. It could also be concluded that follicles and seminiferous tubules are the functional units of the female and male gonads, respectively, and their function could be enhanced by appropriate chemical and genetic intervention of the somatic tissue immediately surrounding them. This assumes importance in the context that buffalo attains sexual maturity at an older age of 2-3 years and have smaller ovaries with lesser number of primordial follicles in comparison with cattle, which is suggested to be the main reason of their poor breeding performance. © 2015 Blackwell Verlag GmbH.

  5. Comparative Analysis of Stress Induced Gene Expression in Caenorhabditis elegans following Exposure to Environmental and Lab Reconstituted Complex Metal Mixture.

    Directory of Open Access Journals (Sweden)

    Ranjeet Kumar

    Full Text Available Metals are essential for many physiological processes and are ubiquitously present in the environment. However, high metal concentrations can be harmful to organisms and lead to physiological stress and diseases. The accumulation of transition metals in the environment due to either natural processes or anthropogenic activities such as mining results in the contamination of water and soil environments. The present study used Caenorhabditis elegans to evaluate gene expression as an indicator of physiological response, following exposure to water collected from three different locations downstream of a Swedish mining site and a lab reconstituted metal mixture. Our results indicated that the reconstituted metal mixture exerted a direct stress response in C. elegans whereas the environmental waters elicited either a diminished or abrogated response. This suggests that it is not sufficient to use the biological effects observed from laboratory mixtures to extrapolate the effects observed in complex aquatic environments and apply this to risk assessment and intervention.

  6. Comparative mapping, genomic structure, and expression analysis of eight pseudo-response regulator genes in Brassica rapa.

    Science.gov (United States)

    Kim, Jin A; Kim, Jung Sun; Hong, Joon Ki; Lee, Yeon-Hee; Choi, Beom-Soon; Seol, Young-Joo; Jeon, Chang Hoo

    2012-05-01

    Circadian clocks regulate plant growth and development in response to environmental factors. In this function, clocks influence the adaptation of species to changes in location or climate. Circadian-clock genes have been subject of intense study in models such as Arabidopsis thaliana but the results may not necessarily reflect clock functions in species with polyploid genomes, such as Brassica species, that include multiple copies of clock-related genes. The triplicate genome of Brassica rapa retains high sequence-level co-linearity with Arabidopsis genomes. In B. rapa we had previously identified five orthologs of the five known Arabidopsis pseudo-response regulator (PRR) genes that are key regulators of the circadian clock in this species. Three of these B. rapa genes, BrPRR1, BrPPR5, and BrPPR7, are present in two copies each in the B. rapa genome, for a total of eight B. rapa PRR (BrPRR) orthologs. We have now determined sequences and expression characteristics of the eight BrPRR genes and mapped their positions in the B. rapa genome. Although both members of each paralogous pair exhibited the same expression pattern, some variation in their gene structures was apparent. The BrPRR genes are tightly linked to several flowering genes. The knowledge about genome location, copy number variation and structural diversity of these B. rapa clock genes will improve our understanding of clock-related functions in this important crop. This will facilitate the development of Brassica crops for optimal growth in new environments and under changing conditions.

  7. Development of visual-motor perception in pupils with expressive writing disorder and pupils without expressive writing disorder: a comparative statistical analysis

    Science.gov (United States)

    Sedighi, Mohammadreza

    2013-01-01

    Background Learning disability is one of the most noticed subjects for behavioral specialists. Most of thelearning difficulties are caused by senso-motor development and neurological organization. The main purposeof the present research is to examine the role of delayed perceptual-motor development and brain damage inorigination of expressive writing disorder (EWD). Methods The studied sample is 89 pupils divided into two groups, one of which is pupils with expressivewriting disorder (n=43) and the other is pupils without expressive writing disorder (n=46), consisted of secondand third grade elementary school students. First of all, students with EWD are selected through dictation testand intelligence test, and then the two groups, students with and without EWD, would take the Bender Gestalttest. The average score of perceptual visual-motor development and brain damage of two groups is comparedusing T test for independent groups and χ2 test. Results Results show that there is a significant difference in perceptual visual-motor development betweenstudents with EWD and students without EWD (p 0.05). Conclusion Based on our findings it could be concluded that those who are relatively more developed thantheir peers, in terms of visual-motor perception, are more successful in education, especially in expressive writing. PMID:24791121

  8. A comparative analysis by SAGE of gene expression profiles of Barrett's esophagus, normal squamous esophagus, and gastric cardia

    NARCIS (Netherlands)

    Van Baal, JWPM; Milano, F; Rygiel, AM; Bergman, JJGHM; Rosmolen, WD; Van Deventer, SJH; Wang, KK; Peppelenbosch, MP; Krishnadath, KK

    2005-01-01

    Background & Aims: The metaplastic process In which the normal squamous epithelium of the distal esophagus is replaced by columnar-lined epithelium, known as Barrett's esophagus (BE), is poorly understood. The aim of this study was to define, analyze, and compare transcription profiles of BE, normal

  9. Comparative analysis of preservation method and intermittent perfusion volume on the expression of endothelial and inflammatory markers by coronal artery and myocardium in porcine donor hearts.

    Science.gov (United States)

    Hu, Zhibin; Yan, Zhikun; Wang, Haitao; Meng, Qun; Pan, Xiaohua

    2014-01-01

    Although continuous perfusion of donor hearts for preservation during transportation has been widely applied, intermittent perfusion has been suggested as an alternative. The aim of this study was to identify the optimal intermittent perfusion protocol by investigating the effects of perfusion volume on endothelial and inflammatory marker expression by the coronary artery. Donor porcine hearts were perfused with various volumes of Celsior solution supplemented with diazoxide (50, 100, 150, 200, and 250 ml) every 2 h for 30 min each for a 10 h period. The effects on cardiomyocytes and vascular endothelial cell morphology and marker expression were compared to the immersion control group. Whereas an incomplete endothelial cell layer with disorganized connective tissue was observed in the control and 50, 100, and 150 ml intermittent perfusion groups, transmission electron microscopic analysis revealed a complete endothelial cell layer in the intima with an organized subendothelium. A perfusion volume-dependent increase in eNOS expression that coincided with a decrease in ET-1, ICAM-1, vWF, and P-selectin expression was detected (all p porcine donor heart over a clinically relevant preservation period.

  10. Immunohistochemical analysis of cytokeratin expression in reactive eccrine syringofibroadenoma-like lesion: a comparative study with eccrine syringofibroadenoma.

    Science.gov (United States)

    Ohnishi, T; Watanabe, S; Nomura, K

    2000-04-01

    In addition to solitary eccrine syringofibroadenoma (ESFA), there is another type of ESFA which is associated with underlying dermatoses (reactive ESFA-like lesion). Five lesions in 4 patients of reactive ESFA-like lesion were analyzed by an immunohistochemical method using 13 kinds of anti-cytokeratin (CK) antibodies. Two cases of solitary ESFA were also studied by the same procedure for comparison. Suprabasal staining pattern of AE1 and MNF116, which stain CKs 6, 16 and 17, markers of hyperproliferative state, was observed diffusely in 5 lesions of reactive ESFA-like lesions except for focal negative staining in one case, and was observed focally in one case of solitary ESFA. Furthermore, differentiation-specific cytokeratin expression was reduced in 3 of 5 lesions of reactive ESFA-like lesions. Both ESFA and reactive ESFA showed basically similar immunoreactivity suggesting differentiation toward the dermal duct. The above slight difference in immunoreactivity between both lesions may be explained due to inflammatory infiltrates associated with underlying dermatoses.

  11. Comparative Analysis of RNAi-Based Methods to Down-Regulate Expression of Two Genes Expressed at Different Levels in Myzus persicae.

    Science.gov (United States)

    Mulot, Michaël; Boissinot, Sylvaine; Monsion, Baptiste; Rastegar, Maryam; Clavijo, Gabriel; Halter, David; Bochet, Nicole; Erdinger, Monique; Brault, Véronique

    2016-11-19

    With the increasing availability of aphid genomic data, it is necessary to develop robust functional validation methods to evaluate the role of specific aphid genes. This work represents the first study in which five different techniques, all based on RNA interference and on oral acquisition of double-stranded RNA (dsRNA), were developed to silence two genes, ALY and Eph , potentially involved in polerovirus transmission by aphids. Efficient silencing of only Eph transcripts, which are less abundant than those of ALY , could be achieved by feeding aphids on transgenic Arabidopsis thaliana expressing an RNA hairpin targeting Eph , on Nicotiana benthamiana infected with a Tobacco rattle virus (TRV)-Eph recombinant virus, or on in vitro-synthesized Eph -targeting dsRNA. These experiments showed that the silencing efficiency may differ greatly between genes and that aphid gut cells seem to be preferentially affected by the silencing mechanism after oral acquisition of dsRNA. In addition, the use of plants infected with recombinant TRV proved to be a promising technique to silence aphid genes as it does not require plant transformation. This work highlights the need to pursue development of innovative strategies to reproducibly achieve reduction of expression of aphid genes.

  12. Comparative proteomic analysis of differentially expressed proteins in β-aminobutyric acid enhanced Arabidopsis thaliana tolerance to simulated acid rain.

    Science.gov (United States)

    Liu, Tingwu; Jiang, Xinwu; Shi, Wuliang; Chen, Juan; Pei, Zhenming; Zheng, Hailei

    2011-05-01

    Acid rain is a worldwide environmental issue that has seriously destroyed forest ecosystems. As a highly effective and broad-spectrum plant resistance-inducing agent, β-aminobutyric acid could elevate the tolerance of Arabidopsis when subjected to simulated acid rain. Using comparative proteomic strategies, we analyzed 203 significantly varied proteins of which 175 proteins were identified responding to β-aminobutyric acid in the absence and presence of simulated acid rain. They could be divided into ten groups according to their biological functions. Among them, the majority was cell rescue, development and defense-related proteins, followed by transcription, protein synthesis, folding, modification and destination-associated proteins. Our conclusion is β-aminobutyric acid can lead to a large-scale primary metabolism change and simultaneously activate antioxidant system and salicylic acid, jasmonic acid, abscisic acid signaling pathways. In addition, β-aminobutyric acid can reinforce physical barriers to defend simulated acid rain stress. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Exploring the midgut transcriptome of Phlebotomus papatasi: comparative analysis of expression profiles of sugar-fed, blood-fed and Leishmania major-infected sandflies

    Directory of Open Access Journals (Sweden)

    Pham Van-My

    2007-08-01

    Full Text Available Abstract Background In sandflies, the blood meal is responsible for the induction of several physiologic processes that culminate in egg development and maturation. During blood feeding, infected sandflies are also able to transmit the parasite Leishmania to a suitable host. Many blood-induced molecules play significant roles during Leishmania development in the sandfly midgut, including parasite killing within the endoperitrophic space. In this work, we randomly sequenced transcripts from three distinct high quality full-length female Phlebotomus papatasi midgut-specific cDNA libraries from sugar-fed, blood-fed and Leishmania major-infected sandflies. Furthermore, we compared the transcript expression profiles from the three different cDNA libraries by customized bioinformatics analysis and validated these findings by semi-quantitative PCR and real-time PCR. Results Transcriptome analysis of 4010 cDNA clones resulted in the identification of the most abundant P. papatasi midgut-specific transcripts. The identified molecules included those with putative roles in digestion and peritrophic matrix formation, among others. Moreover, we identified sandfly midgut transcripts that are expressed only after a blood meal, such as microvilli associated-like protein (PpMVP1, PpMVP2 and PpMVP3, a peritrophin (PpPer1, trypsin 4 (PpTryp4, chymotrypsin PpChym2, and two unknown proteins. Of interest, many of these overabundant transcripts such as PpChym2, PpMVP1, PpMVP2, PpPer1 and PpPer2 were of lower abundance when the sandfly was given a blood meal in the presence of L. major. Conclusion This tissue-specific transcriptome analysis provides a comprehensive look at the repertoire of transcripts present in the midgut of the sandfly P. papatasi. Furthermore, the customized bioinformatic analysis allowed us to compare and identify the overall transcript abundance from sugar-fed, blood-fed and Leishmania-infected sandflies. The suggested upregulation of specific

  14. A Microarray Platform-Independent Classification Tool for Cell of Origin Class Allows Comparative Analysis of Gene Expression in Diffuse Large B-cell Lymphoma

    Science.gov (United States)

    Care, Matthew A.; Barrans, Sharon; Worrillow, Lisa; Jack, Andrew; Westhead, David R.; Tooze, Reuben M.

    2013-01-01

    Cell of origin classification of diffuse large B-cell lymphoma (DLBCL) identifies subsets with biological and clinical significance. Despite the established nature of the classification existing studies display variability in classifier implementation, and a comparative analysis across multiple data sets is lacking. Here we describe the validation of a cell of origin classifier for DLBCL, based on balanced voting between 4 machine-learning tools: the DLBCL automatic classifier (DAC). This shows superior survival separation for assigned Activated B-cell (ABC) and Germinal Center B-cell (GCB) DLBCL classes relative to a range of other classifiers. DAC is effective on data derived from multiple microarray platforms and formalin fixed paraffin embedded samples and is parsimonious, using 20 classifier genes. We use DAC to perform a comparative analysis of gene expression in 10 data sets (2030 cases). We generate ranked meta-profiles of genes showing consistent class-association using ≥6 data sets as a cut-off: ABC (414 genes) and GCB (415 genes). The transcription factor ZBTB32 emerges as the most consistent and differentially expressed gene in ABC-DLBCL while other transcription factors such as ARID3A, BATF, and TCF4 are also amongst the 24 genes associated with this class in all datasets. Analysis of enrichment of 12323 gene signatures against meta-profiles and all data sets individually confirms consistent associations with signatures of molecular pathways, chromosomal cytobands, and transcription factor binding sites. We provide DAC as an open access Windows application, and the accompanying meta-analyses as a resource. PMID:23424639

  15. A microarray platform-independent classification tool for cell of origin class allows comparative analysis of gene expression in diffuse large B-cell lymphoma.

    Directory of Open Access Journals (Sweden)

    Matthew A Care

    Full Text Available Cell of origin classification of diffuse large B-cell lymphoma (DLBCL identifies subsets with biological and clinical significance. Despite the established nature of the classification existing studies display variability in classifier implementation, and a comparative analysis across multiple data sets is lacking. Here we describe the validation of a cell of origin classifier for DLBCL, based on balanced voting between 4 machine-learning tools: the DLBCL automatic classifier (DAC. This shows superior survival separation for assigned Activated B-cell (ABC and Germinal Center B-cell (GCB DLBCL classes relative to a range of other classifiers. DAC is effective on data derived from multiple microarray platforms and formalin fixed paraffin embedded samples and is parsimonious, using 20 classifier genes. We use DAC to perform a comparative analysis of gene expression in 10 data sets (2030 cases. We generate ranked meta-profiles of genes showing consistent class-association using ≥6 data sets as a cut-off: ABC (414 genes and GCB (415 genes. The transcription factor ZBTB32 emerges as the most consistent and differentially expressed gene in ABC-DLBCL while other transcription factors such as ARID3A, BATF, and TCF4 are also amongst the 24 genes associated with this class in all datasets. Analysis of enrichment of 12323 gene signatures against meta-profiles and all data sets individually confirms consistent associations with signatures of molecular pathways, chromosomal cytobands, and transcription factor binding sites. We provide DAC as an open access Windows application, and the accompanying meta-analyses as a resource.

  16. Phylogenetic analysis of gene expression.

    Science.gov (United States)

    Dunn, Casey W; Luo, Xi; Wu, Zhijin

    2013-11-01

    Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary changes in morphological, physiological, and developmental characters of interest. This will provide entirely new opportunities to identify genes related to particular phenotypes. There are, however, 3 key challenges that must be addressed for such studies to realize their potential. First, data on gene expression must be measured from multiple species, some of which may be field-collected, and parameterized in such a way that they can be compared across species. Second, it will be necessary to develop comparative phylogenetic methods suitable for large multidimensional datasets. In most phylogenetic comparative studies to date, the number n of independent observations (independent contrasts) has been greater than the number p of variables (characters). The behavior of comparative methods for these classic problems is now well understood under a wide variety of conditions. In studies of gene expression, and in studies based on other high-throughput tools, the number n of samples is dwarfed by the number p of variables. The estimated covariance matrices will be singular, complicating their analysis and interpretation, and prone to spurious results. Third, new approaches are needed to investigate the expression of the many genes whose phylogenies are not congruent with species phylogenies due to gene loss, gene duplication, and incomplete lineage sorting. Here we outline general considerations of project design for phylogenetic analyses of gene expression and suggest solutions to these three categories of challenges. These topics are relevant to high-throughput phenotypic data well beyond gene expression.

  17. Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes

    Directory of Open Access Journals (Sweden)

    Tamby Jean-Philippe

    2010-11-01

    Full Text Available Abstract Background Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induced responses were analysed in leaves and root apices and were compared with available transcriptome data from other Populus species. Results Using a multi-species designed microarray, a genomic DNA-based selection of probesets provided an unambiguous between-genotype comparison. Analyses of functional group enrichment enabled the extraction of processes physiologically relevant to drought response. The drought-driven changes in gene expression occurring in root apices were consistent across treatments and genotypes. For mature leaves, the transcriptome response varied weakly but in accordance with the duration of water deficit. A differential clustering algorithm revealed similar and divergent gene co-expression patterns among the two genotypes. Since moderate stress levels induced similar physiological responses in both genotypes, the genotype-dependent transcriptional responses could be considered as intrinsic divergences in genome functioning. Our meta-analysis detected several candidate genes and processes that are differentially regulated in root and leaf, potentially under developmental control, and preferentially involved in early and long-term responses to drought. Conclusions In poplar, the well-known drought-induced activation of sensing and signalling cascades was specific to the early response in leaves but was found to be general in root apices. Comparing our results to what is known in arabidopsis, we found that transcriptional remodelling included signalling and a response to energy deficit in roots in parallel with transcriptional indices of hampered assimilation in leaves, particularly in the drought

  18. A Comparative Analysis of Cytokeratin 18 and 19 Expressions in Odontogenic Keratocyst, Dentigerous Cyst and Radicular Cyst with a Review of Literature.

    Science.gov (United States)

    Bhakhar, Vikas Parshottam; Shah, Vandana Sandip; Ghanchi, Mohsin Jiva; Gosavi, Sandesh Sachchidanand; Srivastava, Himanshu Mahesh; Pachore, Nivedita Javahir

    2016-07-01

    Odontogenic cysts viz Odontogenic Keratocyst (OKC), Dentigerous Cyst (DC) and Radicular Cyst (RC) occur commonly in the oral and maxillofacial region. Cytokeratin (CK) expression studies have been done to evaluate diagnostic accuracy, role in pathogenesis, elucidate behaviour and role in treatment protocols. However, variations have been reported in the expression of CK patterns in these odontogenic cysts, which could be due to the lack of standardization of laboratory techniques. The present study has tried to shed light on CK 18 and 19 expression in odontogenic cysts and offer the brief review of previous studies on these CK. The aim of the present study was to evaluate the intensity and expression patterns of CK 18 and 19 in OKCs, DCs and RCs. A total of 60 cases, 20 each of OKC, DC and RC were confirmed histologically and evaluated for immunohistochemical expression pattern and intensity of CK 18 and 19. A focal and variable expression of CK 18 was observed in 25% of OKCs, 15% of DCs and 10% of RCs. CK 19 was expressed in 75% of OKCs and 100% in DCs as well as RCs. The intensity and expression of Cytokeratin 19 was more in all three cysts compared to Cytokeratin 18.

  19. Comparative analysis of the immunohistochemical expression of vascular endothelial growth factor and matrix metalloproteinase-9 in keratocystic odontogenic tumor, dentigerous cyst and radicular cyst

    Directory of Open Access Journals (Sweden)

    Komal Khot

    2015-01-01

    Full Text Available Background: Vascular endothelial growth factor (VEGF and matrix metalloproteinase-9 (MMP-9 have been implicated in the pathogenesis of cysts. Both these factors seem to be interrelated to each other. The importance of the MMPs in the induction of the angiogenic process has recently been described. MMPs, which are produced by microvascular endothelial cells, break down the extracellular matrix. This is one of the earliest and sustained events in the process of new capillary formation. Thus, we studied the expression of VEGF and MMP-9 in Keratocystic odontogenic tumors (KCOTs, dentigerous cysts (DCs and radicular cysts (RCs. Materials and Methods: Ten cases each of KCOTs, DCs and RCs and were included in the study and immunohistochemistry was performed using anti-VEGF and anti-MMP-9 antibody using standard protocol. Result: When the data of positive cells in the epithelium of KCOTs was compared with DCs and RCs, it showed highly significant results (P < 0.05. Furthermore, the expression of VEGF and MMP-9 in the stroma of KCOTs showed a significant result when compared to DCs and RCs. The expression of VEGF in inflammatory cells was more in RCs when compared to DCs. Also, the expression of MMP-9 was more in RCs and DCs as compared to KCOTs. Conclusion: Higher expression of VEGF and MMP-9 in KCOTs could be responsible for the aggressive behavior of this cyst that is currently considered a cystic tumor rather than a developmental cyst.

  20. Chondrocyte density, proteoglycan content and gene expressions from native cartilage are species specific and not dependent on cartilage thickness: a comparative analysis between rat, rabbit and goat.

    Science.gov (United States)

    Kamisan, Norazian; Naveen, Sangeetha Vasudevaraj; Ahmad, Raja Elina; Kamarul, Tunku; Tunku, Kamarul

    2013-04-01

    In many pre-clinical studies of cartilage tissue, it has been generally assumed that the major difference of the tissue between the species is the tissue thickness, which is related to the size of the animal itself. At present, there appear to be lack of studies demonstrating the relationship between chondrocyte densities, protein content, gene expressions and cartilage thickness in the various animal models that are commonly used. The present study was conducted to determine whether or not chondrocyte density, proteoglycan/protein content and selective chondrocyte gene expression are merely related to the cartilage thickness (thus animal size), and not the intrinsic nature of the species being investigated. Mature animals (rabbit, rats and goats) were sacrificed for their hind knee cartilages. Image analyses were performed on five consecutive histological sections, sampled from three pre-defined locations at the lateral and medial femoral condyles. Cartilage thickness, chondrocyte density, Glycosaminoglycan (GAGs)/protein content and gene expression levels for collagen II and SOX-9 were compared across the groups. Correlation analysis was done between cartilage thickness and the other variables. The mean cartilage thickness of rats, rabbits and goats were 166.5 ± 10.9, 356.2 ± 25.0 907.5 ± 114.6 μm, respectively. The mean cartilage cell densities were 3.3 ± 0.4×10(-3) for rats, 2.6 ± 0.3×10(-3) for rabbits and 1.3 ± 0.2×10(-3) cells/μm2 for goats. The mean μg GAG/mg protein content were 23.8 ± 8.6 in rats, 20.5 ± 5.3 in rabbits and 328.7 ± 64.5 in goats; collagen II gene expressions were increased by 0.5 ± 0.1 folds in rats; 0.6 ± 0.1 folds in rabbits, and 0.1 ± 0.1 folds in goats, whilst the fold increase of SOX-9 gene expression was 0.5 ± 0.1 in rats, 0.7 ± 0.1 in rabbits and 0.1 ± 0.0 in goats. Cartilage thickness correlated positively with animals' weight (R2 =0.9856, p = 0

  1. Comparative analysis of chemical compositions between non-transgenic soybean seeds and those from plants over-expressing AtJMT, the gene for jasmonic acid carboxyl methyltransferase.

    Science.gov (United States)

    Nam, Kyong-Hee; Kim, Do Young; Pack, In-Soon; Park, Jung-Ho; Seo, Jun Sung; Choi, Yang Do; Cheong, Jong-Joo; Kim, Chung Ho; Kim, Chang-Gi

    2016-04-01

    Transgenic overexpression of the Arabidopsis gene for jasmonic acid carboxyl methyltransferase (AtJMT) is involved in regulating jasmonate-related plant responses. To examine its role in the compositional profile of soybean (Glycine max), we compared the seeds from field-grown plants that over-express AtJMT with those of the non-transgenic, wild-type (WT) counterpart. Our analysis of chemical compositions included proximates, amino acids, fatty acids, isoflavones, and antinutrients. Overexpression of AtJMT in the seeds resulted in decreased amounts of tryptophan, palmitic acid, linolenic acid, and stachyose, but increased levels of gadoleic acid and genistein. In particular, seeds from the transgenic soybeans contained 120.0-130.5% more genistein and 60.5-82.1% less stachyose than the WT. A separate evaluation of ingredient values showed that all were within the reference ranges reported for commercially available soybeans, thereby demonstrating the substantial equivalence of these transgenic and non-transgenic seeds. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Identification and comparative analysis of differentially expressed proteins in rat striatum following 6-hydroxydopamine lesions of the nigrostriatal pathway: up-regulation of amyloid precursor-like protein 2 expression.

    Science.gov (United States)

    Shen, Yan; Yu, Yi; Guo, Hong; Tang, Zhongshu; Yu, Fu-Shin X; Zhou, Jiawei

    2002-09-01

    During neurodegenerative processes, cascades of degeneration and subsequent regeneration are triggered. However, the molecular nature of the factors involved in the neurodegeneration of the CNS remains largely unknown. In this study, the variations of protein expression in the striatum of adult Sprague-Dawley rats following 6-hydroxydopamine lesions were investigated, in order to better understand the molecular events occurring in the denervated target tissue. The rat striatum, ipsilateral to the lesion was analysed by two-dimensional gel electrophoresis followed by matrix assisted laser desorption/ionization-time of flight mass spectrometry. Seven proteins were up-regulated (188.1-750% compared to control) in response to the lesion: amyloid precursor-like protein 2 (APLP2), kininogen, glucokinase, tropomyosin alpha chain, type brain-1 and calpactin I light chain; whilst four proteins, neural epidermal growth factor-like 2, minichromosome maintenance 6, and thyroid hormone receptor beta-2, were down-regulated (to between 36% and 59% of levels in sham-operated controls). Three proteins that did not match with available data in the SWISS-PROT protein database were also determined. Immunohistochemical analysis demonstrated colocalization of APLP2 and tyrosine hydroxylase in the nigral neurons. Moreover, reduction of APLP2-positive neurons in the substantia nigra pars compacta as well as the increases in the substantia nigra pars reticulata and in the striatum were observed. Furthermore, the conditioned medium of the Chinese hamster ovary cells over-expressing APLP2-751 (chondroitin sulphate-modified), but not APLP2-763 (nonchondroitin sulphate-modified), was able to increase the number of the tyrosine hydroxylase-positive neurons in fetal mesencephalic cultures. These results suggest that the expression of APLP2, a protein that has been thought to be associated with Alzheimer's disease, is up-regulated in the striatum following dopaminergic denervation. They also

  3. Comparative Expression Analysis of HSP70, HSP90, IL-4, TNF, KITLG and KIT-receptor Gene between Varicocele-Induced and Non-Varicocele Testes of Dog

    Directory of Open Access Journals (Sweden)

    Hossein Hassanpour

    2017-09-01

    Full Text Available Background This study was designed to create an experimental varicocele model by a simple surgical procedure in dog with minimum invasion and to investigate the effect of varicocele-induced infertility on the expression of six related genes (HSP90, HSP70, IL-4, TNF, KITLG and KIT receptor. Materials and Methods In this experimental study, the proximal part of the pampini-form plexus of dog testes was partially occluded without abdominal incision which was confirmed by venographic examination. To evaluate varicocele in its acute form, dogs were castrated after 15 days and testes were dissected. Histopathologic evaluation was undertaken and the relative expression of the six genes was assessed by quantitative realtime polymerase chain reaction (PCR. Results Microscopic changes showed tubule degeneration. The Johnson score was significantly decreased in the varicocele testes when compared with non-varicocele testes. Expressions of HSP90, TNF, KITLG and the KIT-receptor gene were significantly downregulated (P=0.029, 0.047, 0.004 and 0.035 respectively in varicocele-induced testes while HSP70 was upregulated (P=0.018. IL-4 did not show differential expression (P=0.377. Conclusion We conclude that partial occlusion of the proximal part of the pampiniform plexus induces varicocele in the testis of dog. Differential expression of the mentioned genes may be responsible for the pathophysiology of varicocele and related subfertility.

  4. Tracking down the "head blob": comparative analysis of wingless expression in the developing insect procephalon reveals progressive reduction of embryonic visual system patterning in higher insects.

    Science.gov (United States)

    Liu, Zhenyi; Yang, Xiaoyun; Dong, Ying; Friedrich, Markus

    2006-12-01

    The evolution of larval head morphology in holometabolous insects is characterized by reduction of antennal appendages and the visual system components. Little insight has been gained into molecular developmental changes underlying this morphological diversification. Here we compare the expression of the segment polarity gene wingless (wg) in the pregnathal head of fruit fly, flour beetle and grasshopper embryos. We provide evidence that wg activity contributes to segment border formation, and, subsequently, the separation of the visual system and protocerebrum anlagen in the anterior procephalon. In directly developing insects like grasshopper, seven expression domains are formed during this process. The activation of four of these, which correspond to polar expression pairs in the optic lobe anlagen and the protocerebral ectoderm, has shifted to postembryonic stages in flour beetle and Drosophila. The remaining three domains map to the protocerebral neuroectoderm, and form by disintegration of a large precursor domain in flour beetle and grasshopper. In Drosophila, the precursor domain remains intact, constituting the previously described "head blob". These data document major changes in the expression of an early patterning gene correlated with the dramatic evolution of embryonic visual system development in the Holometabola.

  5. Comparative genomics: Difference of expression

    DEFF Research Database (Denmark)

    Nielsen, Rasmus

    2006-01-01

    Evolutionary studies tend to focus on alterations in proteins. But evolutionary change can often occur through modified gene expression, a process that is now under investigation with species-specific microarrays.......Evolutionary studies tend to focus on alterations in proteins. But evolutionary change can often occur through modified gene expression, a process that is now under investigation with species-specific microarrays....

  6. Comparative microarray analysis of microRNA expression profiles in primary cutaneous malignant melanoma, cutaneous malignant melanoma metastases, and benign melanocytic nevi.

    Science.gov (United States)

    Sand, Michael; Skrygan, Marina; Sand, Daniel; Georgas, Dimitrios; Gambichler, Thilo; Hahn, Stephan A; Altmeyer, Peter; Bechara, Falk G

    2013-01-01

    Perturbations in microRNA (miRNA) expression profiles have been reported for cutaneous malignant melanoma (CMM) predominantly when examined in cell lines. Despite the rapidly growing number of newly discovered human miRNA sequences, the availability of up-to-date miRNA expression profiles for clinical samples of primary cutaneous malignant melanoma (PCMM), cutaneous malignant melanoma metastases (CMMM), and benign melanocytic nevi (BMN) is limited. Specimens excised from the center of tumors (lesional) from patients with PCMM (n=9), CMMM (n=4), or BMN (n=8) were obtained during surgery. An exploratory microarray analysis was performed by miRNA expression profiling based on Agilent platform screening for 1205 human miRNAs. The results from the microarray analysis were validated by TaqMan quantitative real-time polymerase chain reaction. In addition to several miRNAs previously known to be associated with CMM, 19 unidentified miRNA candidates were found to be dysregulated in CMM patient samples. Among the 19 novel miRNA candidates, the genes hsa-miR-22, hsa-miR-130b, hsa-miR-146b-5p, hsa-miR-223, hsa-miR-301a, hsa-miR-484, hsa-miR-663, hsa-miR-720, hsa-miR-1260, hsa-miR-1274a, hsa-miR-1274b, hsa-miR-3663-3p, hsa-miR-4281, and hsa-miR-4286 were upregulated, and the genes hsa-miR-24-1*, hsa-miR-26a, hsa-miR-4291, hsa-miR-4317, and hsa-miR-4324 were downregulated. The results of this study partially confirm previous CMM miRNA profiling studies identifying miRNAs that are dysregulated in CMM. However, we report several novel miRNA candidates in CMM tumors; these miRNA sequences require further validation and functional analysis to evaluate whether they play a role in the pathogenesis of CMM.

  7. Precise Analysis of String Expressions

    DEFF Research Database (Denmark)

    Christensen, Aske Simon; Møller, Anders; Schwartzbach, Michael Ignatieff

    2003-01-01

    We perform static analysis of Java programs to answer a simple question: which values may occur as results of string expressions? The answers are summarized for each expression by a regular language that is guaranteed to contain all possible values. We present several applications of this analysis......, including statically checking the syntax of dynamically generated expressions, such as SQL queries. Our analysis constructs flow graphs from class files and generates a context-free grammar with a nonterminal for each string expression. The language of this grammar is then widened into a regular language...... through a variant of an algorithm previously used for speech recognition. The collection of resulting regular languages is compactly represented as a special kind of multi-level automaton from which individual answers may be extracted. If a program error is detected, examples of invalid strings...

  8. Comparative analysis of the immunohistochemical expression of vascular endothelial growth factor and matrix metalloproteinase-9 in keratocystic odontogenic tumor, dentigerous cyst and radicular cyst.

    Science.gov (United States)

    Khot, Komal; Deshmukh, Siddharth B; Alex, Sheeba

    2015-01-01

    Vascular endothelial growth factor (VEGF) and matrix metalloproteinase-9 (MMP-9) have been implicated in the pathogenesis of cysts. Both these factors seem to be interrelated to each other. The importance of the MMPs in the induction of the angiogenic process has recently been described. MMPs, which are produced by microvascular endothelial cells, break down the extracellular matrix. This is one of the earliest and sustained events in the process of new capillary formation. Thus, we studied the expression of VEGF and MMP-9 in Keratocystic odontogenic tumors (KCOTs), dentigerous cysts (DCs) and radicular cysts (RCs). Ten cases each of KCOTs, DCs and RCs and were included in the study and immunohistochemistry was performed using anti-VEGF and anti-MMP-9 antibody using standard protocol. When the data of positive cells in the epithelium of KCOTs was compared with DCs and RCs, it showed highly significant results (Pcyst that is currently considered a cystic tumor rather than a developmental cyst.

  9. p53 gene mutations and expression of p53 and mdm2 proteins in invasive breast carcinoma. A comparative analysis with clinico-pathological factors.

    Science.gov (United States)

    Günther, T; Schneider-Stock, R; Rys, J; Niezabitowski, A; Roessner, A

    1997-01-01

    The aim of the study was to analyze p53 gene mutations and the expression of p53 and mdm2 proteins in 31 randomly selected invasive breast carcinomas. The results were then correlated with tumor grade, stage, estrogen receptor status, nodal status, and DNA ploidy. The expression of the proteins p53 and mdm2 was determined immunohistochemically using formalin-fixed, paraffin-embedded material. Screening for p53 mutation involved analysis of the highly conserved regions of the p53 gene (exons 5-9) by the polymerase chain reaction/ single-strand conformation polymorphism (PCR-SSCP) technique. PCR products with band shifts were directly sequenced. Immunohistochemical staining of p53 was positive in 9 cases (29.0%), only 2 of which showed a p53 gene mutation. These were identified as a C-->G transversion at the second position of codon 278 in exon 8 and an A-->G transition at the second position of codon 205 in exon 6. A third case with a mutation was observed (C-->T transition, position 1 of codon 250 in exon 7) that did not show p53 immunohistochemically. Of the 9 p53-positive tumors, 2 were moderately differentiated (grade II). The remaining tumors were poorly differentiated (7/9). By contrast, p53-negative carcinomas were well differentiated (grade I) in most cases (P = 0.02). DNA cytometry in 8 of the 9 p53-positive carcinomas revealed an aneuploid stem line. The majority of the p53-negative tumors were diploid (P = 0.01). Mdm2 oncoprotein was detected in 10 tumors (32.2%), 4 of which were p53-positive, including the 3 with mutations. The grading of the mdm2-positive tumors was moderate or poor, G1 carcinomas were always noted to be mdm2-negative (P = 0.04). Overexpression of p53 protein is a complex mechanism and does not merely indicate the detection of mutations in the p53 gene. This study has shown that p53 expression correlates with tumor grade and DNA ploidy. Mdm2 expression was also associated with the tumor grade. Immunohistological demonstration of the p53

  10. A comparative expression analysis of gene transcripts in brain tissue of non-transgenic and GH-transgenic zebrafish (Danio rerio using a DDRT-PCR approach

    Directory of Open Access Journals (Sweden)

    Fernanda A. Alves-Costa

    2012-06-01

    Full Text Available The presence of higher level of exogenous growth hormone (GH in transgenic animals could lead to several physiological alterations. A GH transgenic zebrafish (Danio rerio line was compared to nontransgenic (NT samples of the species through a DDRT-PCR approach, with the goal of identifying candidate differentially expressed transcripts in brain tissues that could be involved in GH overexpression. Densitometric analyses of two selected amplification products, p300 and ADCY2, pointed to a significant lower gene expression in the transgenic zebrafish (104.02 ± 57.71; 224.10 ± 91.73 when compared to NT samples (249.75 ± 30.08; 342.95 ± 65.19. The present data indicate that p300 and ADCY2 are involved in a regulation system for GH when high circulating levels of this hormone are found in zebrafishes.A presença de níveis mais elevados do hormônio de crescimento (GH em animais transgênicos poderia levar a várias alterações fisiológicas. Uma linhagem transgênica de paulistinha (Danio rerio para o GH foi comparada com amostras não transgênicas (NT desta espécie, através de uma abordagem de DDRT-PCR, com o objetivo de identificar transcritos candidatos diferencialmente expressos em tecido cerebral que poderiam estar envolvidos na superexpressão de GH. Análises densitométricas de dois produtos de amplificação selecionados, p300 e ADCY2, apontaram uma expressão gênica significativamente menor nas amostras transgênicas de paulistinha (104.02 ± 57.71; 224.10 ± 91.73, quando comparadas com as amostras NT (249.75 ± 30.08; 342.95±65.19. Os presentes dados indicam que p300 e ADCY2 estão envolvidos em um sistema de regulação do GH, quando altos níveis circulantes desse hormônio são encontrados em paulistinha.

  11. Meta-Analysis of Aedes aegypti Expression Datasets: Comparing Virus Infection and Blood-Fed Transcriptomes to Identify Markers of Virus Presence

    Directory of Open Access Journals (Sweden)

    Kiyoshi Ferreira Fukutani

    2018-01-01

    Full Text Available The mosquito Aedes aegypti (L. is vector of several arboviruses including dengue, yellow fever, chikungunya, and more recently zika. Previous transcriptomic studies have been performed to elucidate altered pathways in response to viral infection. However, the intrinsic coupling between alimentation and infection were unappreciated in these studies. Feeding is required for the initial mosquito contact with the virus and these events are highly dependent. Addressing this relationship, we reinterrogated datasets of virus-infected mosquitoes with two different diet schemes (fed and unfed mosquitoes, evaluating the metabolic cross-talk during both processes. We constructed coexpression networks with the differentially expressed genes of these comparison: virus-infected versus blood-fed mosquitoes and virus-infected versus unfed mosquitoes. Our analysis identified one module with 110 genes that correlated with infection status (representing ~0.7% of the A. aegypti genome. Furthermore, we performed a machine-learning approach and summarized the infection status using only four genes (AAEL012128, AAEL014210, AAEL002477, and AAEL005350. While three of the four genes were annotated as hypothetical proteins, AAEL012128 gene is a membrane amino acid transporter correlated with viral envelope binding. This gene alone is able to discriminate all infected samples and thus should have a key role to discriminate viral infection in the A. aegypti mosquito. Moreover, validation using external datasets found this gene as differentially expressed in four transcriptomic experiments. Therefore, these genes may serve as a proxy of viral infection in the mosquito and the others 106 identified genes provides a framework to future studies.

  12. Meta-Analysis ofAedes aegyptiExpression Datasets: Comparing Virus Infection and Blood-Fed Transcriptomes to Identify Markers of Virus Presence.

    Science.gov (United States)

    Fukutani, Kiyoshi Ferreira; Kasprzykowski, José Irahe; Paschoal, Alexandre Rossi; Gomes, Matheus de Souza; Barral, Aldina; de Oliveira, Camila I; Ramos, Pablo Ivan Pereira; de Queiroz, Artur Trancoso Lopo

    2017-01-01

    The mosquito Aedes aegypti (L.) is vector of several arboviruses including dengue, yellow fever, chikungunya, and more recently zika. Previous transcriptomic studies have been performed to elucidate altered pathways in response to viral infection. However, the intrinsic coupling between alimentation and infection were unappreciated in these studies. Feeding is required for the initial mosquito contact with the virus and these events are highly dependent. Addressing this relationship, we reinterrogated datasets of virus-infected mosquitoes with two different diet schemes (fed and unfed mosquitoes), evaluating the metabolic cross-talk during both processes. We constructed coexpression networks with the differentially expressed genes of these comparison: virus-infected versus blood-fed mosquitoes and virus-infected versus unfed mosquitoes. Our analysis identified one module with 110 genes that correlated with infection status (representing ~0.7% of the A. aegypti genome). Furthermore, we performed a machine-learning approach and summarized the infection status using only four genes (AAEL012128, AAEL014210, AAEL002477, and AAEL005350). While three of the four genes were annotated as hypothetical proteins, AAEL012128 gene is a membrane amino acid transporter correlated with viral envelope binding. This gene alone is able to discriminate all infected samples and thus should have a key role to discriminate viral infection in the A. aegypti mosquito. Moreover, validation using external datasets found this gene as differentially expressed in four transcriptomic experiments. Therefore, these genes may serve as a proxy of viral infection in the mosquito and the others 106 identified genes provides a framework to future studies.

  13. Comparative analysis reveals dynamic changes in miRNAs and their targets and expression during somatic embryogenesis in longan (Dimocarpus longan Lour..

    Directory of Open Access Journals (Sweden)

    Yuling Lin

    Full Text Available Somatic embryogenesis (SE, which resembles zygotic embryogenesis, is an essential component of the process of plant cell differentiation and embryo development. Although microRNAs (miRNAs are important regulators of many plant develop- mental processes, their roles in SE have not been thoroughly investigated. In this study, we used deep-sequencing, computational, and qPCR methods to identify, profile, and describe conserved and novel miRNAs involved in longan (Dimocarpus longan SE. A total of 643 conserved and 29 novel miRNAs (including star strands from more than 169 miRNA families were identified in longan embryogenic tissue using Solexa sequencing. By combining computational and degradome sequencing approaches, we were able to predict 2063 targets of 272 miRNAs and verify 862 targets of 181 miRNAs. Target annotation revealed that the putative targets were involved in a broad variety of biological processes, including plant metabolism, signal transduction, and stimulus response. Analysis of stage- and tissue-specific expressions of 20 conserved and 4 novel miRNAs indicated their possible roles in longan SE. These miRNAs were dlo-miR156 family members and dlo-miR166c* associated with early embryonic culture developmental stages; dlo-miR26, dlo-miR160a, and families dlo-miR159, dlo-miR390, and dlo-miR398b related to heart-shaped and torpedo- shaped embryo formation; dlo-miR4a, dlo-miR24, dlo-miR167a, dlo-miR168a*, dlo-miR397a, dlo-miR398b.1, dlo-miR398b.2, dlo-miR808 and dlo-miR5077 involved in cotyledonary embryonic development; and dlo-miR17 and dlo-miR2089*-1 that have regulatory roles during longan SE. In addition, dlo-miR167a, dlo-miR808, and dlo-miR5077 may be required for mature embryo formation. This study is the first reported investigation of longan SE involving large-scale cloning, characterization, and expression profiling of miRNAs and their targets. The reported results contribute to our knowledge of somatic embryo miRNAs and

  14. Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant (Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato.

    Science.gov (United States)

    Fukuoka, Hiroyuki; Yamaguchi, Hirotaka; Nunome, Tsukasa; Negoro, Satomi; Miyatake, Koji; Ohyama, Akio

    2010-01-15

    Eggplant (Solanum melongena L.) is a widely grown vegetable crop that belongs to the genus Solanum, which is comprised of more than 1000 species of wide genetic and phenotypic variation. Unlike tomato and potato, Solanum crops that belong to subgenus Potatoe and have been targets for comprehensive genomic studies, eggplant is endemic to the Old World and belongs to a different subgenus, Leptostemonum, and therefore, would be a unique member for comparative molecular biology in Solanum. In this study, more than 60,000 eggplant cDNA clones from various tissues and treatments were sequenced from both the 5'- and 3'-ends, and a unigene set consisting of 16,245 unique sequences was constructed. Functional annotations based on sequence similarity to known plant reference datasets revealed a distribution of functional categories almost similar to that of tomato, while 1316 unigenes were suggested to be eggplant-specific. Sequence-based comparative analysis using putative orthologous gene groups setup by reciprocal sequence comparison among six solanaceous species suggested that eggplant and its wild ally Solanum torvum were clustered separately from subgenus Potatoe species, and then, all Solanum species were clustered separately from the genus Capsicum. Microsatellite motif distribution was different among species and likely to be coincident with the phylogenetic relationships. Furthermore, the eggplant unigene dataset exhibited its utility in transcriptome analysis by the SAGE strategy where a considerable number of short tag sequences of interest were successfully assigned to unigenes and their functional annotations. The eggplant ESTs and 16k unigene set developed in this study would be a useful resource not only for molecular genetics and breeding in eggplant itself, but for expanding the scope of comparative biology in Solanum species.

  15. BANK RATING. A COMPARATIVE ANALYSIS

    Directory of Open Access Journals (Sweden)

    Batrancea Ioan

    2015-07-01

    Full Text Available Banks in Romania offers its customers a wide range of products but which involves both risk taking. Therefore researchers seek to build rating models to help managers of banks to risk of non-recovery of loans and interest. In the following we highlight rating Raiffeisen Bank, BCR-ERSTE Bank and Transilvania Bank, based on the models CAAMPL and Stickney making a comparative analysis of the two rating models.

  16. Comparative expression pattern analysis of WUSCHEL-related homeobox 2 (WOX2) and WOX8/9 in developing seeds and somatic embryos of the gymnosperm Picea abies.

    Science.gov (United States)

    Palovaara, Joakim; Hallberg, Henrik; Stasolla, Claudio; Hakman, Inger

    2010-10-01

    • In seed plants, current knowledge concerning embryonic pattern formation by polar auxin transport (PAT) and WUSCHEL-related homeobox (WOX) gene activity is primarily derived from studies on angiosperms, while less is known about these processes in gymnosperms. In view of the differences in their embryogeny, and the fact that somatic embryogenesis is used for mass propagation of conifers, a better understanding of embryo development is vital. • The expression patterns of PaWOX2 and PaWOX8/9 were followed with quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and in situ hybridization (ISH) during seed and somatic embryo development in Norway spruce (Picea abies), and in somatic embryos treated with the PAT inhibitor N-1-naphthylphthalamic acid (NPA). • Both PaWOX2 and PaWOX8/9 were highly expressed at the early growth stages of zygotic and somatic embryos, and shared a similar expression pattern over the entire embryo. At later embryo stages, high expression of PaWOX8/9 became restricted to cotyledon primordia, epidermis, procambium and root apical meristem (RAM), which became most evident in NPA-treated somatic embryos, while expression of PaWOX2 was much lower. • Our results suggest an ancestral role of WOX in seed plant embryo development, and strengthen the proposed connection between PAT, PIN-FORMED (PIN) and WOX in the regulation of embryo patterning in seed plants.

  17. Comparative analysis of recombinant Human Papillomavirus 8 L1 production in plants by a variety of expression systems and purification methods.

    Science.gov (United States)

    Matić, Slavica; Masenga, Vera; Poli, Alice; Rinaldi, Riccardo; Milne, Robert G; Vecchiati, Manuela; Noris, Emanuela

    2012-05-01

    Human papillomavirus 8 (HPV-8), one of the high-risk cutaneous papillomaviruses (cHPVs), is associated with epidermodysplasia verruciformis and nonmelanoma skin cancer in immuno-compromised individuals. Currently, no vaccines against cHPVs have been reported; however, recent studies on cross-neutralizing properties of their capsid proteins (CP) have fostered an interest in vaccine production against these viruses. We examined the potential of producing HPV-8 major CP L1 in Nicotiana benthamiana by agroinfiltration of different transient expression vectors: (i) the binary vector pBIN19 with or without silencing suppressor constructs, (ii) the nonreplicating Cowpea mosaic virus-derived expression vector pEAQ-HT and (iii) a replicating Tobacco mosaic virus (TMV)-based vector alone or with signal peptides. Although HPV-8 L1 was successfully expressed using pEAQ-HT and TMV, a 15-fold increase was obtained with pEAQ-HT. In contrast, no L1 protein could be immune detected using pBIN19 irrespective of whether silencing suppressors were coexpressed, although such constructs were required for identifying L1-specific transcripts. A fourfold yield increase in L1 expression was obtained when 22 C-terminal amino acids were deleted (L1ΔC22), possibly eliminating a nuclear localization signal. Electron microscopy showed that plant-made HPV-8 L1 proteins assembled in appropriate virus-like particles (VLPs) of T = 1 or T = 7 symmetry. Ultrathin sections of L1ΔC22-expressing cells revealed their accumulation in the cytoplasm in the form of VLPs or paracrystalline arrays. These results show for the first time the production and localization of HPV-8 L1 protein in planta and its assembly into VLPs representing promising candidate for potential vaccine production. © 2012 The Authors. Plant Biotechnology Journal © 2012 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

  18. Whole transcriptome analysis of Acinetobacter baumannii assessed by RNA-sequencing reveals different mRNA expression profiles in biofilm compared to planktonic cells.

    Directory of Open Access Journals (Sweden)

    Soraya Rumbo-Feal

    Full Text Available Acinetobacterbaumannii has emerged as a dangerous opportunistic pathogen, with many strains able to form biofilms and thus cause persistent infections. The aim of the present study was to use high-throughput sequencing techniques to establish complete transcriptome profiles of planktonic (free-living and sessile (biofilm forms of A. baumannii ATCC 17978 and thereby identify differences in their gene expression patterns. Collections of mRNA from planktonic (both exponential and stationary phase cultures and sessile (biofilm cells were sequenced. Six mRNA libraries were prepared following the mRNA-Seq protocols from Illumina. Reads were obtained in a HiScanSQ platform and mapped against the complete genome to describe the complete mRNA transcriptomes of planktonic and sessile cells. The results showed that the gene expression pattern of A. baumannii biofilm cells was distinct from that of planktonic cells, including 1621 genes over-expressed in biofilms relative to stationary phase cells and 55 genes expressed only in biofilms. These differences suggested important changes in amino acid and fatty acid metabolism, motility, active transport, DNA-methylation, iron acquisition, transcriptional regulation, and quorum sensing, among other processes. Disruption or deletion of five of these genes caused a significant decrease in biofilm formation ability in the corresponding mutant strains. Among the genes over-expressed in biofilm cells were those in an operon involved in quorum sensing. One of them, encoding an acyl carrier protein, was shown to be involved in biofilm formation as demonstrated by the significant decrease in biofilm formation by the corresponding knockout strain. The present work serves as a basis for future studies examining the complex network systems that regulate bacterial biofilm formation and maintenance.

  19. Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq

    Directory of Open Access Journals (Sweden)

    Wei Chen

    2016-07-01

    Full Text Available Drought and flooding are two major causes of severe yield loss in soybean worldwide. A lack of knowledge of the molecular mechanisms involved in drought and flood stress has been a limiting factor for the effective management of soybeans; therefore, it is imperative to assess the expression of genes involved in response to flood and drought stress. In this study, differentially expressed genes under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. A total of 2,724 and 3,498 differentially expressed genes (DEGs were identified under drought and flooding treatments, respectively. These genes comprise 289 Transcription Factors (TFs representing Basic Helix-loop Helix (bHLH, Ethylene Response Factors (ERFs, myeloblastosis (MYB, No apical meristem (NAC, and WRKY amino acid motif (WRKY type major families known to be involved in the mechanism of stress tolerance. The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. However, cell wall synthesis related genes were up-regulated under drought stress and down-regulated under flooding stress. Transcript profiles involved in the starch and sugar metabolism pathways were also affected under both stress conditions. The changes in expression of genes involved in regulating the flux of cell wall precursors and starch/sugar content can serve as an adaptive mechanism for soybean survival under stress conditions. This study has revealed the involvement of TFs, transporters, and photosynthetic genes, and has also given a glimpse of hormonal cross talk under the extreme water regimes, which will aid as an important resource for soybean crop improvement.

  20. Genome-wide identification and comparative expression analysis reveal a rapid expansion and functional divergence of duplicated genes in the WRKY gene family of cabbage, Brassica oleracea var. capitata.

    Science.gov (United States)

    Yao, Qiu-Yang; Xia, En-Hua; Liu, Fei-Hu; Gao, Li-Zhi

    2015-02-15

    WRKY transcription factors (TFs), one of the ten largest TF families in higher plants, play important roles in regulating plant development and resistance. To date, little is known about the WRKY TF family in Brassica oleracea. Recently, the completed genome sequence of cabbage (B. oleracea var. capitata) allows us to systematically analyze WRKY genes in this species. A total of 148 WRKY genes were characterized and classified into seven subgroups that belong to three major groups. Phylogenetic and synteny analyses revealed that the repertoire of cabbage WRKY genes was derived from a common ancestor shared with Arabidopsis thaliana. The B. oleracea WRKY genes were found to be preferentially retained after the whole-genome triplication (WGT) event in its recent ancestor, suggesting that the WGT event had largely contributed to a rapid expansion of the WRKY gene family in B. oleracea. The analysis of RNA-Seq data from various tissues (i.e., roots, stems, leaves, buds, flowers and siliques) revealed that most of the identified WRKY genes were positively expressed in cabbage, and a large portion of them exhibited patterns of differential and tissue-specific expression, demonstrating that these gene members might play essential roles in plant developmental processes. Comparative analysis of the expression level among duplicated genes showed that gene expression divergence was evidently presented among cabbage WRKY paralogs, indicating functional divergence of these duplicated WRKY genes. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Airline Safety: A Comparative Analysis.

    Science.gov (United States)

    1987-01-01

    S.TP OFR O T PEIDCV E Airline Safety: A Comparative Analysis TRlES IS1j0’~fJ 6. PERFORMING 01G. REPORT NUMBER AU TNOR( ) Sign . CONTRACT OR GRANT NUMBER...accidents. Perhaps because of an airline’s understandable sensitivity to public knowledge of its accidents, one has little assurance that each airline...62,169 0 Royal Air Maroc 81,451 0 80,861 0 (Morocco) Royal Nepal 11,885 0 19,785 0 SAA (South Africa) 57,226 0 61,618 0 SAHSA (Honduras) 32,658 0 34,894 0

  2. Comparative genomic analysis of N2-fixing and non-N2-fixing Paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes.

    Directory of Open Access Journals (Sweden)

    Jian-Bo Xie

    2014-03-01

    Full Text Available We provide here a comparative genome analysis of 31 strains within the genus Paenibacillus including 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ(70-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe-S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus and Frankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf genes. This study not only reveals the organization and distribution of nitrogen fixation genes in Paenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation.

  3. Comparative Immunohistochemical Analysis of Ochratoxin A Tumourigenesis in Rats and Urinary Tract Carcinoma in Humans; Mechanistic Significance of p-S6 Ribosomal Protein Expression

    Directory of Open Access Journals (Sweden)

    Sarah Pinder

    2012-09-01

    Full Text Available Ochratoxin A (OTA is considered to be a possible human urinary tract carcinogen, based largely on a rat model, but no molecular genetic changes in the rat carcinomas have yet been defined. The phosphorylated-S6 ribosomal protein is a marker indicating activity of the mammalian target of rapamycin, which is a serine/threonine kinase with a key role in protein biosynthesis, cell proliferation, transcription, cellular metabolism and apoptosis, while being functionally deregulated in cancer. To assess p-S6 expression we performed immunohistochemistry on formalin-fixed and paraffin-embedded tumours and normal tissues. Marked intensity of p-S6 expression was observed in highly proliferative regions of rat renal carcinomas and a rare angiosarcoma, all of which were attributed to prolonged exposure to dietary OTA. Only very small OTA-generated renal adenomas were negative for p-S6. Examples of rat subcutaneous fibrosarcoma and testicular seminoma, as well as of normal renal tissue, showed no or very weak positive staining. In contrast to the animal model, human renal cell carcinoma, upper urinary tract transitional cell carcinoma from cases of Balkan endemic nephropathy, and a human angiosarcoma were negative for p-S6. The combined findings are reminiscent of constitutive changes in the rat tuberous sclerosis gene complex in the Eker strain correlated with renal neoplasms, Therefore rat renal carcinogenesis caused by OTA does not obviously mimic human urinary tract tumourigenesis.

  4. Comparative analysis of single and combined APP/APLP knockouts reveals reduced spine density in APP-KO mice that is prevented by APPsα expression.

    Science.gov (United States)

    Weyer, Sascha W; Zagrebelsky, Marta; Herrmann, Ulrike; Hick, Meike; Ganss, Lennard; Gobbert, Julia; Gruber, Morna; Altmann, Christine; Korte, Martin; Deller, Thomas; Müller, Ulrike C

    2014-03-31

    Synaptic dysfunction and synapse loss are key features of Alzheimer's pathogenesis. Previously, we showed an essential function of APP and APLP2 for synaptic plasticity, learning and memory. Here, we used organotypic hippocampal cultures to investigate the specific role(s) of APP family members and their fragments for dendritic complexity and spine formation of principal neurons within the hippocampus. Whereas CA1 neurons from APLP1-KO or APLP2-KO mice showed normal neuronal morphology and spine density, APP-KO mice revealed a highly reduced dendritic complexity in mid-apical dendrites. Despite unaltered morphology of APLP2-KO neurons, combined APP/APLP2-DKO mutants showed an additional branching defect in proximal apical dendrites, indicating redundancy and a combined function of APP and APLP2 for dendritic architecture. Remarkably, APP-KO neurons showed a pronounced decrease in spine density and reductions in the number of mushroom spines. No further decrease in spine density, however, was detectable in APP/APLP2-DKO mice. Mechanistically, using APPsα-KI mice lacking transmembrane APP and expressing solely the secreted APPsα fragment we demonstrate that APPsα expression alone is sufficient to prevent the defects in spine density observed in APP-KO mice. Collectively, these studies reveal a combined role of APP and APLP2 for dendritic architecture and a unique function of secreted APPs for spine density.

  5. Microarray based comparative genome-wide expression profiling of ...

    African Journals Online (AJOL)

    Microarray based comparative genome-wide expression profiling of major subtypes of leukemia. ... similar patterns of result in terms of gene expression but it demonstrates statistically significant relationship only among CML and ALL which are of myeloid and lymphoid origin, respectively, in contrast to other combinations.

  6. Comparative Digital Gene Expression Analysis of Tissue-Cultured Plantlets of Highly Resistant and Susceptible Banana Cultivarsin Response to Fusarium oxysporum

    Directory of Open Access Journals (Sweden)

    Yuqing Niu

    2018-01-01

    Full Text Available Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc is one of the most destructive soil-borne diseases. In this study, young tissue-cultured plantlets of banana (Musa spp. AAA cultivars differing in Foc susceptibility were used to reveal their differential responses to this pathogen using digital gene expression (DGE. Data were evaluated by various bioinformatic tools (Venn diagrams, gene ontology (GO annotation and Kyoto encyclopedia of genes and genomes (KEGG pathway analyses and immunofluorescence labelling method to support the identification of gene candidates determining the resistance of banana against Foc. Interestingly, we have identified MaWRKY50 as an important gene involved in both constitutive and induced resistance. We also identified new genes involved in the resistance of banana to Foc, including several other transcription factors (TFs, pathogenesis-related (PR genes and some genes related to the plant cell wall biosynthesis or degradation (e.g., pectinesterases, β-glucosidases, xyloglucan endotransglucosylase/hydrolase and endoglucanase. The resistant banana cultivar shows activation of PR-3 and PR-4 genes as well as formation of different constitutive cell barriers to restrict spreading of the pathogen. These data suggest new mechanisms of banana resistance to Foc.

  7. COMPARATIVE ANALYSIS AND CLINICAL VALUE OF THE EXPRESSION OF METALLOPROTEASES AND THEIR INHIBITORS BY INTRATUMOR STROMAL MONONUCLEAR INFLAMMATORY CELLS AND THOSE AT THE INVASIVE FRONT OF BREAST CARCINOMAS

    OpenAIRE

    2010-01-01

    Abstract Aims: Matrix metalloproteases (MMPs) and their inhibitors (TIMPs) play an essential role in the degradation of stromal connective tissue and basement membrane components. The dynamic analysis of these components might help predict tumor agressiveness. Methods and Results: An immunohistochemical study was performed using tissue arrays and specific antibodies against MMPs -1, 2, 7, 9, 11, 13, 14, and TIMPs -1, 2 and 3. More than 5,000 determinations on cancer specimens ...

  8. [Comparative analysis in artificial nutrition].

    Science.gov (United States)

    Csomós, Akos; Okrös, Ilona

    2003-03-23

    It is well known to Hungarian experts in the field of nutrition that hospital inpatients in this country do not have the required nutrition. To compare data of intensive care national costing analysis from England and intensive care unit in County Hospital, Eger, Hungary in order to advise a cost effective nutrition protocol. English data were extracted from the report of Intensive Care National Cost Block Programme, year 1999. The Hungarian data were obtained by top down method from annual costing report of the same year. The authors used Purchasing Power Parity to make international cost comparison between these countries. In proportion to Purchasing Power Parity, the hospital budget per patient for nutrition is more than double in England than in the studied intensive care unit in Hungary. Intensive care units in England spend 1% on nutrition, 13% on drugs and 10% on disposables. There is only 0.2% spent on nutrition, 29.8% on drugs and 8% on disposables in the studied intensive care unit in Hungary. Cost of nutrition per patient day is HUF 117 in Hungary, which is even lower than the hospital budget per patient day for nutrition. On the basis of the above findings and literature review as well, the authors set up a cost effective nutrition guideline: 1. Identify malnourished patient. 2. Nutrition can be delayed for 4-5 days in not malnourished patient. 3. Enteral nutrition should always be the first choice. 4. Total parenteral nutrition is beneficial only if given over at least 7 days. 5) It is cost effective to prevent nosocomial infections even at higher cost.

  9. Gene Expression Analysis of Breast Cancer Progression

    National Research Council Canada - National Science Library

    Gerald, Wiliam L

    2004-01-01

    ... to identify genes, gene expression profiles and molecular pathways associated with metastatic BC we have performed genome-wide gene expression analysis of a large number of breast cancer samples...

  10. Comparative De Novo Transcriptome Analysis of Fertilized Ovules in Xanthoceras sorbifolium Uncovered a Pool of Genes Expressed Specifically or Preferentially in the Selfed Ovule That Are Potentially Involved in Late-Acting Self-Incompatibility.

    Directory of Open Access Journals (Sweden)

    Qingyuan Zhou

    Full Text Available Xanthoceras sorbifolium, a tree species endemic to northern China, has high oil content in its seeds and is recognized as an important biodiesel crop. The plant is characterized by late-acting self-incompatibility (LSI. LSI was found to occur in many angiosperm species and plays an important role in reducing inbreeding and its harmful effects, as do gametophytic self-incompatibility (GSI and sporophytic self-incompatibility (SSI. Molecular mechanisms of conventional GSI and SSI have been well characterized in several families, but no effort has been made to identify the genes involved in the LSI process. The present studies indicated that there were no significant differences in structural and histological features between the self- and cross-pollinated ovules during the early stages of ovule development until 5 days after pollination (DAP. This suggests that 5 DAP is likely to be a turning point for the development of the selfed ovules. Comparative de novo transcriptome analysis of the selfed and crossed ovules at 5 DAP identified 274 genes expressed specifically or preferentially in the selfed ovules. These genes contained a significant proportion of genes predicted to function in the biosynthesis of secondary metabolites, consistent with our histological observations in the fertilized ovules. The genes encoding signal transduction-related components, such as protein kinases and protein phosphatases, are overrepresented in the selfed ovules. X. sorbifolium selfed ovules also specifically or preferentially express many unique transcription factor (TF genes that could potentially be involved in the novel mechanisms of LSI. We also identified 42 genes significantly up-regulated in the crossed ovules compared to the selfed ovules. The expression of all 16 genes selected from the RNA-seq data was validated using PCR in the selfed and crossed ovules. This study represents the first genome-wide identification of genes expressed in the fertilized

  11. Gene expression analysis of flax seed development

    Directory of Open Access Journals (Sweden)

    Sharpe Andrew

    2011-04-01

    Full Text Available Abstract Background Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. Results We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages seed coats (globular and torpedo stages and endosperm (pooled globular to torpedo stages and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST (GenBank accessions LIBEST_026995 to LIBEST_027011 were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152 had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. Conclusions We have developed a foundational database of expressed sequences and collection of plasmid

  12. Gene expression analysis of flax seed development.

    Science.gov (United States)

    Venglat, Prakash; Xiang, Daoquan; Qiu, Shuqing; Stone, Sandra L; Tibiche, Chabane; Cram, Dustin; Alting-Mees, Michelle; Nowak, Jacek; Cloutier, Sylvie; Deyholos, Michael; Bekkaoui, Faouzi; Sharpe, Andrew; Wang, Edwin; Rowland, Gordon; Selvaraj, Gopalan; Datla, Raju

    2011-04-29

    Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages) seed coats (globular and torpedo stages) and endosperm (pooled globular to torpedo stages) and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST) (GenBank accessions LIBEST_026995 to LIBEST_027011) were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152) had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise even low-expressed genes such as

  13. Comparative Chromatographic Analysis and Pharmacodynamic ...

    African Journals Online (AJOL)

    The laboratory analysis of the Garcinia Kolanuts extracts showed receptors inhibition of Beta adrenergic sites, adenosine, melatonin, opiate, purine, calcium channel L-type and 5HT5A. Conclusion: Garcinia kolanut extract exhibits a combined effects of all the known antiglaucoma drugs used in comparison. NQJHM Vol.

  14. Expression profiling and comparative sequence derived insights into lipid metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Callow, Matthew J.; Rubin, Edward M.

    2001-12-19

    Expression profiling and genomic DNA sequence comparisons are increasingly being applied to the identification and analysis of the genes involved in lipid metabolism. Not only has genome-wide expression profiling aided in the identification of novel genes involved in important processes in lipid metabolism such as sterol efflux, but the utilization of information from these studies has added to our understanding of the regulation of pathways participating in the process. Coupled with these gene expression studies, cross species comparison, searching for sequences conserved through evolution, has proven to be a powerful tool to identify important non-coding regulatory sequences as well as the discovery of novel genes relevant to lipid biology. An example of the value of this approach was the recent chance discovery of a new apolipoprotein gene (apo AV) that has dramatic effects upon triglyceride metabolism in mice and humans.

  15. Application of multidisciplinary analysis to gene expression.

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xuefel (University of New Mexico, Albuquerque, NM); Kang, Huining (University of New Mexico, Albuquerque, NM); Fields, Chris (New Mexico State University, Las Cruces, NM); Cowie, Jim R. (New Mexico State University, Las Cruces, NM); Davidson, George S.; Haaland, David Michael; Sibirtsev, Valeriy (New Mexico State University, Las Cruces, NM); Mosquera-Caro, Monica P. (University of New Mexico, Albuquerque, NM); Xu, Yuexian (University of New Mexico, Albuquerque, NM); Martin, Shawn Bryan; Helman, Paul (University of New Mexico, Albuquerque, NM); Andries, Erik (University of New Mexico, Albuquerque, NM); Ar, Kerem (University of New Mexico, Albuquerque, NM); Potter, Jeffrey (University of New Mexico, Albuquerque, NM); Willman, Cheryl L. (University of New Mexico, Albuquerque, NM); Murphy, Maurice H. (University of New Mexico, Albuquerque, NM)

    2004-01-01

    Molecular analysis of cancer, at the genomic level, could lead to individualized patient diagnostics and treatments. The developments to follow will signal a significant paradigm shift in the clinical management of human cancer. Despite our initial hopes, however, it seems that simple analysis of microarray data cannot elucidate clinically significant gene functions and mechanisms. Extracting biological information from microarray data requires a complicated path involving multidisciplinary teams of biomedical researchers, computer scientists, mathematicians, statisticians, and computational linguists. The integration of the diverse outputs of each team is the limiting factor in the progress to discover candidate genes and pathways associated with the molecular biology of cancer. Specifically, one must deal with sets of significant genes identified by each method and extract whatever useful information may be found by comparing these different gene lists. Here we present our experience with such comparisons, and share methods developed in the analysis of an infant leukemia cohort studied on Affymetrix HG-U95A arrays. In particular, spatial gene clustering, hyper-dimensional projections, and computational linguistics were used to compare different gene lists. In spatial gene clustering, different gene lists are grouped together and visualized on a three-dimensional expression map, where genes with similar expressions are co-located. In another approach, projections from gene expression space onto a sphere clarify how groups of genes can jointly have more predictive power than groups of individually selected genes. Finally, online literature is automatically rearranged to present information about genes common to multiple groups, or to contrast the differences between the lists. The combination of these methods has improved our understanding of infant leukemia. While the complicated reality of the biology dashed our initial, optimistic hopes for simple answers from

  16. How to assess and compare inter-rater reliability, agreement and correlation of ratings: an exemplary analysis of mother-father and parent-teacher expressive vocabulary rating pairs

    Directory of Open Access Journals (Sweden)

    Margarita eStolarova

    2014-06-01

    Full Text Available This report has two main purposes. First, we combine well-known analytical approaches to conduct a comprehensive assessment of agreement and correlation of rating-pairs and to dis-entangle these often confused concepts, providing a best-practice example on concrete data and a tutorial for future reference. Second, we explore whether a screening questionnaire deve-loped for use with parents can be reliably employed with daycare teachers when assessing early expressive vocabulary. A total of 53 vocabulary rating pairs (34 parent-teacher and 19 mother-father pairs collected for two-year-old children (12 bilingual are evaluated. First, inter-rater reliability both within and across subgroups is assessed using the intra-class correlation coefficient (ICC. Next, based on this analysis of reliability and on the test-retest reliability of the employed tool, inter-rater agreement is analyzed, magnitude and direction of rating differences are considered. Finally, Pearson correlation coefficients of standardized vocabulary scores are calculated and compared across subgroups. The results underline the necessity to distinguish between reliability measures, agreement and correlation. They also demonstrate the impact of the employed reliability on agreement evaluations. This study provides evidence that parent-teacher ratings of children’s early vocabulary can achieve agreement and correlation comparable to those of mother-father ratings on the assessed vocabulary scale. Bilingualism of the evaluated child decreased the likelihood of raters’ agreement. We conclude that future reports of agree-ment, correlation and reliability of ratings will benefit from better definition of terms and stricter methodological approaches. The methodological tutorial provided here holds the potential to increase comparability across empirical reports and can help improve research practices and knowledge transfer to educational and therapeutic settings.

  17. How to assess and compare inter-rater reliability, agreement and correlation of ratings: an exemplary analysis of mother-father and parent-teacher expressive vocabulary rating pairs.

    Science.gov (United States)

    Stolarova, Margarita; Wolf, Corinna; Rinker, Tanja; Brielmann, Aenne

    2014-01-01

    This report has two main purposes. First, we combine well-known analytical approaches to conduct a comprehensive assessment of agreement and correlation of rating-pairs and to dis-entangle these often confused concepts, providing a best-practice example on concrete data and a tutorial for future reference. Second, we explore whether a screening questionnaire developed for use with parents can be reliably employed with daycare teachers when assessing early expressive vocabulary. A total of 53 vocabulary rating pairs (34 parent-teacher and 19 mother-father pairs) collected for two-year-old children (12 bilingual) are evaluated. First, inter-rater reliability both within and across subgroups is assessed using the intra-class correlation coefficient (ICC). Next, based on this analysis of reliability and on the test-retest reliability of the employed tool, inter-rater agreement is analyzed, magnitude and direction of rating differences are considered. Finally, Pearson correlation coefficients of standardized vocabulary scores are calculated and compared across subgroups. The results underline the necessity to distinguish between reliability measures, agreement and correlation. They also demonstrate the impact of the employed reliability on agreement evaluations. This study provides evidence that parent-teacher ratings of children's early vocabulary can achieve agreement and correlation comparable to those of mother-father ratings on the assessed vocabulary scale. Bilingualism of the evaluated child decreased the likelihood of raters' agreement. We conclude that future reports of agreement, correlation and reliability of ratings will benefit from better definition of terms and stricter methodological approaches. The methodological tutorial provided here holds the potential to increase comparability across empirical reports and can help improve research practices and knowledge transfer to educational and therapeutic settings.

  18. Automatic emotional expression analysis from eye area

    Science.gov (United States)

    Akkoç, Betül; Arslan, Ahmet

    2015-02-01

    Eyes play an important role in expressing emotions in nonverbal communication. In the present study, emotional expression classification was performed based on the features that were automatically extracted from the eye area. Fırst, the face area and the eye area were automatically extracted from the captured image. Afterwards, the parameters to be used for the analysis through discrete wavelet transformation were obtained from the eye area. Using these parameters, emotional expression analysis was performed through artificial intelligence techniques. As the result of the experimental studies, 6 universal emotions consisting of expressions of happiness, sadness, surprise, disgust, anger and fear were classified at a success rate of 84% using artificial neural networks.

  19. Comparative gene expression profiles between heterotic and non-heterotic hybrids of tetraploid Medicago sativa

    Directory of Open Access Journals (Sweden)

    Nettleton Dan

    2009-08-01

    Full Text Available Abstract Background Heterosis, the superior performance of hybrids relative to parents, has clear agricultural value, but its genetic control is unknown. Our objective was to test the hypotheses that hybrids expressing heterosis for biomass yield would show more gene expression levels that were different from midparental values and outside the range of parental values than hybrids that do not exhibit heterosis. Results We tested these hypotheses in three Medicago sativa (alfalfa genotypes and their three hybrids, two of which expressed heterosis for biomass yield and a third that did not, using Affymetrix M. truncatula GeneChip arrays. Alfalfa hybridized to approximately 47% of the M. truncatula probe sets. Probe set signal intensities were analyzed using MicroArray Suite v.5.0 (MAS and robust multi-array average (RMA algorithms. Based on MAS analysis, the two heterotic hybrids performed similarly, with about 27% of genes showing differential expression among the parents and their hybrid compared to 12.5% for the non-heterotic hybrid. At a false discovery rate of 0.15, 4.7% of differentially expressed genes in hybrids (~300 genes showed nonadditive expression compared to only 0.5% (16 genes in the non-heterotic hybrid. Of the nonadditively expressed genes, approximately 50% showed expression levels that fell outside the parental range in heterotic hybrids, but only one of 16 showed a similar profile in the non-heterotic hybrid. Genes whose expression differed in the parents were three times more likely to show nonadditive expression than genes whose parental transcript levels were equal. Conclusion The higher proportions of probe sets with expression level that differed from the parental midparent value and that were more extreme than either parental value in the heterotic hybrids compared to a non-heterotic hybrid were also found using RMA. We conclude that nonadditive expression of transcript levels may contribute to heterosis for biomass

  20. An expression analysis package for REDUCE

    NARCIS (Netherlands)

    van Hulzen, J.A.; Hulshof, B.J.A.

    1982-01-01

    An expression analysis package for REDUCE 2 is presented. This package, completely written in Standard LISP, can be considered as an extension of the algebraic mode. It allows to interactively dismantled and/or modify the last output expression as it is desplayed or printed. An interface with the

  1. Serial analysis of gene expression (SAGE)

    NARCIS (Netherlands)

    van Ruissen, Fred; Baas, Frank

    2007-01-01

    In 1995, serial analysis of gene expression (SAGE) was developed as a versatile tool for gene expression studies. SAGE technology does not require pre-existing knowledge of the genome that is being examined and therefore SAGE can be applied to many different model systems. In this chapter, the SAGE

  2. Comparing the Recognition of Emotional Facial Expressions in Patients with

    Directory of Open Access Journals (Sweden)

    Abdollah Ghasempour

    2014-05-01

    Full Text Available Background: Recognition of emotional facial expressions is one of the psychological factors which involve in obsessive-compulsive disorder (OCD and major depressive disorder (MDD. The aim of present study was to compare the ability of recognizing emotional facial expressions in patients with Obsessive-Compulsive Disorder and major depressive disorder. Materials and Methods: The present study is a cross-sectional and ex-post facto investigation (causal-comparative method. Forty participants (20 patients with OCD, 20 patients with MDD were selected through available sampling method from the clients referred to Tabriz Bozorgmehr clinic. Data were collected through Structured Clinical Interview and Recognition of Emotional Facial States test. The data were analyzed utilizing MANOVA. Results: The obtained results showed that there is no significant difference between groups in the mean score of recognition emotional states of surprise, sadness, happiness and fear; but groups had a significant difference in the mean score of diagnosing disgust and anger states (p<0.05. Conclusion: Patients suffering from both OCD and MDD show equal ability to recognize surprise, sadness, happiness and fear. However, the former are less competent in recognizing disgust and anger than the latter.

  3. Comparing Techniques for Certified Static Analysis

    Science.gov (United States)

    Cachera, David; Pichardie, David

    2009-01-01

    A certified static analysis is an analysis whose semantic validity has been formally proved correct with a proof assistant. The recent increasing interest in using proof assistants for mechanizing programming language metatheory has given rise to several approaches for certification of static analysis. We propose a panorama of these techniques and compare their respective strengths and weaknesses.

  4. Comparative Evaluation of Two Serial Gene Expression Experiments | Division of Cancer Prevention

    Science.gov (United States)

    Stuart G. Baker, 2014 Introduction This program fits biologically relevant response curves in comparative analysis of the two gene expression experiments involving same genes but under different scenarios and at least 12 responses. The program outputs gene pairs with biologically relevant response curve shapes including flat, linear, sigmoid, hockey stick, impulse and step curves. |

  5. Microarray Analysis of the Gene Expression Profile in Triethylene ...

    African Journals Online (AJOL)

    2018-01-24

    Jan 24, 2018 ... Data were analyzed using the Expression Console and. Transcriptome Analysis Console/Partek Genomic Suite. Raw data were normalized by the robust multiarray average algorithm. Array data were filtered by detection. P < 0.05. A comparative analysis between each sample was carried out using ...

  6. Comparative analysis of codon usage bias in Crenarchaea and ...

    Indian Academy of Sciences (India)

    The present study was undertaken to investigate the pattern of optimal codon usage in Archaea. Comparative analysis was executed to understand the pattern of codon usage bias between the high expression genes (HEG) and the whole genomes in two Archaeal phyla, Crenarchaea and Euryarchaea. The G+C% of the ...

  7. A Comparative Analysis of Task Modeling Notations

    Directory of Open Access Journals (Sweden)

    Jean Vanderdonckt

    2012-03-01

    paper a comparative analysis of selected models involving multiple users in an interaction is provided in order to identify concepts which are underexplored in today's multi-user interaction task modeling. This comparative analysis is based on three families of criteria: information criteria, conceptual coverage, and expressiveness. Merging the meta-models of the selected models enables to come up with a broader meta-model that could be instantiated in most situations involving multi-user interaction, like workflow information systems, CSCW.

  8. Comparative study of leptin and leptin receptor gene expression in different swine breeds.

    Science.gov (United States)

    Georgescu, S E; Manea, M A; Dinescu, S; Costache, M

    2014-02-14

    Leptin is an important regulator of appetite, energy metabolism, and reproduction and is mainly synthesized in the adipocytes and then secreted into the bloodstream. The leptin receptor was classified as type I cytokine receptor due to its structural homology with IL-6 receptors and the signaling pathways in which they are both involved. The aim of our study is to comparatively assess the gene expression levels of leptin (lep) and leptin receptor (lepr) in different swine breeds specialized either in meat production (Duroc, Belgian Landrace, Large White, Synthetic Lines LS-345, and LSP-2000) or fat production (Mangalitsa) in order to correlate them with morphological and productivity characteristics. Additionally, lepr pattern of expression was evaluated comparatively between different tissue types in the Mangalitsa breed. Our results revealed high expression of the lep gene in Mangalitsa compared to those of all the other breeds, while for the lepr gene, average/medium levels were registered in Mangalitsa and increased pattern of expression was found in the synthetic lines LS-345 and LSP-2000. Regarding the comparative analysis of lepr gene expression in various tissues in the Mangalitsa breed, elevated levels were found in the liver and kidney, while the lowest expression was identified in the brain and muscles. Our results suggest that the Mangalitsa population exhibits leptin resistance, which might be correlated with atypical morpho-productive characteristics for this breed, such as below-average prolificacy and a strong tendency to accumulate fat.

  9. A comparative analysis of existing oligonucleotides selection ...

    African Journals Online (AJOL)

    A computational comparative analysis of the methods used to select oligos is important since the design and quality of the microarray probes are of critical importance for the hybridization experiments as well as subsequent analysis of the ... most are non-intuitive to use and lack important oligo design and software features.

  10. COMPARATIVE ANALYSIS OF THE COMPRESSIVE STRENGTH ...

    African Journals Online (AJOL)

    Previous analysis showed that cavity size and number on one hand and combinations thickness affect the compressive strength of hollow sandcrete blocks. Series arrangement of the cavities is common but parallel arrangement has been recommended. This research performed a comparative analysis of the compressive ...

  11. A Comparative Study on Error Analysis

    DEFF Research Database (Denmark)

    Wu, Xiaoli; Zhang, Chun

    2015-01-01

    students (N= 54 students from LU; and N= 33 students from AU) participating in the studies, among them 44 are 2nd-year students (n=28 from LU and n=16 from AU) and 43 3rd-year students (n=26 from LU and n=17 from AU). Students’ writing samples were first collected and the errors on the use of comparative...... of the grammatical errors with using comparative sentences is developed, which include comparative item-related errors, comparative result-related errors and blend errors. The results further indicate that these errors could attribute to negative L1 transfer and overgeneralization of grammatical rule and structures......Title: A Comparative Study on Error Analysis Subtitle: - Belgian (L1) and Danish (L1) learners’ use of Chinese (L2) comparative sentences in written production Xiaoli Wu, Chun Zhang Abstract: Making errors is an inevitable and necessary part of learning. The collection, classification and analysis...

  12. Kaiso is highly expressed in TNBC tissues of women of African ancestry compared to Caucasian women.

    Science.gov (United States)

    Bassey-Archibong, Blessing I; Hercules, Shawn M; Rayner, Lyndsay G A; Skeete, Desiree H A; Smith Connell, Suzanne P; Brain, Ian; Daramola, Adetola; Banjo, Adekunbiola A F; Byun, Jung S; Gardner, Kevin; Dushoff, Jonathan; Daniel, Juliet M

    2017-11-01

    Triple-negative breast cancer (TNBC) is most prevalent in young women of African ancestry (WAA) compared to women of other ethnicities. Recent studies found a correlation between high expression of the transcription factor Kaiso, TNBC aggressiveness, and ethnicity. However, little is known about Kaiso expression and localization patterns in TNBC tissues of WAA. Herein, we analyze Kaiso expression patterns in TNBC tissues of African (Nigerian), Caribbean (Barbados), African American (AA), and Caucasian American (CA) women. Formalin-fixed and paraffin embedded (FFPE) TNBC tissue blocks from Nigeria and Barbados were utilized to construct a Nigerian/Barbadian tissue microarray (NB-TMA). This NB-TMA and a commercially available TMA comprising AA and CA TNBC tissues (AA-CA-YTMA) were subjected to immunohistochemistry to assess Kaiso expression and subcellular localization patterns, and correlate Kaiso expression with TNBC clinical features. Nigerian and Barbadian women in our study were diagnosed with TNBC at a younger age than AA and CA women. Nuclear and cytoplasmic Kaiso expression was observed in all tissues analyzed. Analysis of Kaiso expression in the NB-TMA and AA-CA-YTMA revealed that nuclear Kaiso H scores were significantly higher in Nigerian, Barbadian, and AA women compared with CA women. However, there was no statistically significant difference in nuclear Kaiso expression between Nigerian versus Barbadian women, or Barbadian versus AA women. High levels of nuclear Kaiso expression were detected in patients with a higher degree of African heritage compared to their Caucasian counterparts, suggesting a role for Kaiso in TNBC racial disparity.

  13. Athletic humans and horses: Comparative analysis of interleukin-6 (IL-6 and IL-6 receptor (IL-6R expression in peripheral blood mononuclear cells in trained and untrained subjects at rest

    Directory of Open Access Journals (Sweden)

    Supplizi Andrea

    2011-01-01

    Full Text Available Abstract Background Horses and humans share a natural proclivity for athletic performance. In this respect, horses can be considered a reference species in studies designed to optimize physical training and disease prevention. In both species, interleukin-6 (IL-6 plays a major role in regulating the inflammatory process induced during exercise as part of an integrated metabolic regulatory network. The aim of this study was to compare IL-6 and IL-6 receptor (IL-6R mRNA expression in peripheral blood mononuclear cells (PBMCs in trained and untrained humans and horses. Results Nine highly trained male swimmers (training volume: 21.6 ± 1.7 h/wk in 10-12 sessions were compared with two age-matched control groups represented by eight lightly trained runners (training volume: 6.4 ± 2.6 h/wk in 3-5 sessions and nine untrained subjects. In addition, eight trained horses (training volume: 8.0 ± 2.1 h/wk in 3-4 sessions were compared with eight age-matched sedentary mares. In humans, IL-6 mRNA levels in PBMCs determined by quantitative reverse transcription-polymerase chain reaction were significantly higher in highly trained subjects, whereas IL-6R expression did not differ among groups. In horses, transcripts of both IL-6 and IL-6R were significantly up-regulated in the trained group. Conclusions Up-regulation of IL-6R expression in PBMCs in horses could reflect a mechanism that maintains an adequate anti-inflammatory environment at rest through ubiquitous production of anti-inflammatory cytokines throughout the body. These findings suggest that the system that controls the inflammatory response in horses is better adapted to respond to exercise than that in humans.

  14. Athletic humans and horses: comparative analysis of interleukin-6 (IL-6) and IL-6 receptor (IL-6R) expression in peripheral blood mononuclear cells in trained and untrained subjects at rest.

    Science.gov (United States)

    Capomaccio, Stefano; Cappelli, Katia; Spinsanti, Giacomo; Mencarelli, Marzia; Muscettola, Michela; Felicetti, Michela; Verini Supplizi, Andrea; Bonifazi, Marco

    2011-01-21

    Horses and humans share a natural proclivity for athletic performance. In this respect, horses can be considered a reference species in studies designed to optimize physical training and disease prevention. In both species, interleukin-6 (IL-6) plays a major role in regulating the inflammatory process induced during exercise as part of an integrated metabolic regulatory network. The aim of this study was to compare IL-6 and IL-6 receptor (IL-6R) mRNA expression in peripheral blood mononuclear cells (PBMCs) in trained and untrained humans and horses. Nine highly trained male swimmers (training volume: 21.6 ± 1.7 h/wk in 10-12 sessions) were compared with two age-matched control groups represented by eight lightly trained runners (training volume: 6.4 ± 2.6 h/wk in 3-5 sessions) and nine untrained subjects. In addition, eight trained horses (training volume: 8.0 ± 2.1 h/wk in 3-4 sessions) were compared with eight age-matched sedentary mares. In humans, IL-6 mRNA levels in PBMCs determined by quantitative reverse transcription-polymerase chain reaction were significantly higher in highly trained subjects, whereas IL-6R expression did not differ among groups. In horses, transcripts of both IL-6 and IL-6R were significantly up-regulated in the trained group. Up-regulation of IL-6R expression in PBMCs in horses could reflect a mechanism that maintains an adequate anti-inflammatory environment at rest through ubiquitous production of anti-inflammatory cytokines throughout the body. These findings suggest that the system that controls the inflammatory response in horses is better adapted to respond to exercise than that in humans.

  15. Comparative genomics of the relationship between gene structure and expression

    NARCIS (Netherlands)

    Ren, X.

    2006-01-01

    The relationship between the structure of genes and their expression is a relatively new aspect of genome organization and regulation. With more genome sequences and expression data becoming available, bioinformatics approaches can help the further elucidation of the relationships between gene

  16. Comparative Analysis of Protein Domain Organization

    OpenAIRE

    Ye, Yuzhen; Godzik, Adam

    2004-01-01

    We have developed a set of graph theory-based tools, which we call Comparative Analysis of Protein Domain Organization (CADO), to survey and compare protein domain organizations of different organisms. In the language of CADO, the organization of protein domains in a given organism is shown as a domain graph in which protein domains are represented as vertices, and domain combinations, defined as instances of two domains found in one protein, are represented as edges. CADO provides a new way ...

  17. Expression and functional analysis of polygalacturonase gene ...

    African Journals Online (AJOL)

    DR TONUKARI

    2012-02-02

    Feb 2, 2012 ... RNA excluded any DNA contamination. Western blot analysis of Pcipg5 expression in diseased pepper leaves. We used antibody developed against recombinant protein. PCIPG5 to detect the crude proteins extracted from diseased leaves at one day intervals from 1 to 7dpi. A special protein band (40 KDa) ...

  18. Comparative sequence analysis of the complete set of 40S ribosomal proteins in the Senegalese sole (Solea senegalensis Kaup and Atlantic halibut (Hippoglossus hippoglossus L. (Teleostei: Pleuronectiformes: phylogeny and tissue- and development-specific expression

    Directory of Open Access Journals (Sweden)

    Cañavate Jose

    2007-07-01

    Full Text Available Abstract Background Ribosomal proteins (RPs are key components of ribosomes, the cellular organelle responsible for protein biosynthesis in cells. Their levels can vary as a function of organism growth and development; however, some RPs have been associated with other cellular processes or extraribosomal functions. Their high representation in cDNA libraries has resulted in the increase of RP sequences available from different organisms and their proposal as appropriate molecular markers for phylogenetic analysis. Results The development of large-scale genomics of Senegalese sole (Solea senegalensis and Atlantic halibut (Hippoglossus hippoglossus, two commercially important flatfish species, has made possible the identification and systematic analysis of the complete set of RP sequences for the small (40S ribosome subunit. Amino acid sequence comparisons showed a high similarity both between these two flatfish species and with respect to other fish and human. EST analysis revealed the existence of two and four RPS27 genes in Senegalese sole and Atlantic halibut, respectively. Phylogenetic analysis clustered RPS27 in two separate clades with their fish and mammalian counterparts. Steady-state transcript levels for eight RPs (RPS2, RPS3a, RPS15, RPS27-1, RPS27-2, RPS27a, RPS28, and RPS29 in sole were quantitated during larval development and in tissues, using a real-time PCR approach. All eight RPs exhibited different expression patterns in tissues with the lowest levels in brain. On the contrary, RP transcripts increased co-ordinately after first larval feeding reducing progressively during the metamorphic process. Conclusion The genomic resources and knowledge developed in this survey will provide new insights into the evolution of Pleuronectiformes. Expression data will contribute to a better understanding of RP functions in fish, especially the mechanisms that govern growth and development in larvae, with implications in aquaculture.

  19. Different Cytokine and Chemokine Expression Patterns in Malignant Compared to Those in Nonmalignant Renal Cells

    Directory of Open Access Journals (Sweden)

    Nadine Gelbrich

    2017-01-01

    Full Text Available Objective. Cytokines and chemokines are widely involved in cancer cell progression and thus represent promising candidate factors for new biomarkers. Methods. Four renal cell cancer (RCC cell lines (Caki-1, 786-O, RCC4, and A498 and a nonmalignant renal cell line (RC-124 were examined with respect to their proliferation. The cytokine and chemokine expression pattern was examined by a DNA array (Human Cytokines & Chemokines RT2 Profiler PCR Array; Qiagen, Hilden, Germany, and expression profiles were compared. Results. Caki-1 and 786-O cells exhibited significantly increased proliferation rates, whereas RCC4 and A498 cells demonstrated attenuated proliferation, compared to nonmalignant RC-124 cells. Expression analysis revealed 52 cytokines and chemokines primarily involved in proliferation and inflammation and differentially expressed not only in malignant and nonmalignant renal cells but also in the four RCC cell lines. Conclusion. This is the first study examining the expression of 84 cytokines and chemokines in four RCC cell lines compared to that in a nonmalignant renal cell line. VEGFA, NODAL, and BMP6 correlated with RCC cell line proliferation and, thus, may represent putative clinical biomarkers for RCC progression as well as for RCC diagnosis and prognosis.

  20. The first facial expression recognition and analysis challenge

    NARCIS (Netherlands)

    Valstar, Michel F.; Jiang, Bihan; Mehu, Marc; Pantic, Maja; Scherer, Klaus

    Automatic Facial Expression Recognition and Analysis, in particular FACS Action Unit (AU) detection and discrete emotion detection, has been an active topic in computer science for over two decades. Standardisation and comparability has come some way; for instance, there exist a number of commonly

  1. Comparative Analysis of Households' Socioeconomic and ...

    African Journals Online (AJOL)

    Comparative Analysis of Households' Socioeconomic and Demographic Characteristics and Food Security Status in Urban and Rural Areas of Kwara and Kogi States ... Journal Home > Vol 12, No 3 (2012) > ... Food security is a critical issue in Nigeria today as the country struggles with high rates of food prices and poverty.

  2. Teacher Policy: A Framework for Comparative Analysis

    Science.gov (United States)

    Tatto, Maria Teresa

    2008-01-01

    This article outlines a framework for analysis of teacher focused policy studies within an international and comparative perspective. Using the notion of the professional life cycle of teachers, the article examines examples of key empirical studies that illustrate the impact of policy on addressing such issues as teacher recruitment, education,…

  3. MycoCAP - Mycobacterium Comparative Analysis Platform.

    Science.gov (United States)

    Choo, Siew Woh; Ang, Mia Yang; Dutta, Avirup; Tan, Shi Yang; Siow, Cheuk Chuen; Heydari, Hamed; Mutha, Naresh V R; Wee, Wei Yee; Wong, Guat Jah

    2015-12-15

    Mycobacterium spp. are renowned for being the causative agent of diseases like leprosy, Buruli ulcer and tuberculosis in human beings. With more and more mycobacterial genomes being sequenced, any knowledge generated from comparative genomic analysis would provide better insights into the biology, evolution, phylogeny and pathogenicity of this genus, thus helping in better management of diseases caused by Mycobacterium spp.With this motivation, we constructed MycoCAP, a new comparative analysis platform dedicated to the important genus Mycobacterium. This platform currently provides information of 2108 genome sequences of at least 55 Mycobacterium spp. A number of intuitive web-based tools have been integrated in MycoCAP particularly for comparative analysis including the PGC tool for comparison between two genomes, PathoProT for comparing the virulence genes among the Mycobacterium strains and the SuperClassification tool for the phylogenic classification of the Mycobacterium strains and a specialized classification system for strains of Mycobacterium abscessus. We hope the broad range of functions and easy-to-use tools provided in MycoCAP makes it an invaluable analysis platform to speed up the research discovery on mycobacteria for researchers. Database URL: http://mycobacterium.um.edu.my.

  4. Comparative analysis of technical efficiencies between compound ...

    African Journals Online (AJOL)

    This study was designed to compare the level of technical efficiency in the compound and non compound farms in Imo state. A multi-stage random sampling technique was used to select 120 food crop farmers from two out of the three agricultural zones in Imo state. Using the Chow (1960) analysis of covariance technique ...

  5. National Launch System comparative economic analysis

    Science.gov (United States)

    Prince, A.

    1992-01-01

    Results are presented from an analysis of economic benefits (or losses), in the form of the life cycle cost savings, resulting from the development of the National Launch System (NLS) family of launch vehicles. The analysis was carried out by comparing various NLS-based architectures with the current Shuttle/Titan IV fleet. The basic methodology behind this NLS analysis was to develop a set of annual payload requirements for the Space Station Freedom and LEO, to design launch vehicle architectures around these requirements, and to perform life-cycle cost analyses on all of the architectures. A SEI requirement was included. Launch failure costs were estimated and combined with the relative reliability assumptions to measure the effects of losses. Based on the analysis, a Shuttle/NLS architecture evolving into a pressurized-logistics-carrier/NLS architecture appears to offer the best long-term cost benefit.

  6. Comparative analysis of genomic signal processing for microarray data clustering.

    Science.gov (United States)

    Istepanian, Robert S H; Sungoor, Ala; Nebel, Jean-Christophe

    2011-12-01

    Genomic signal processing is a new area of research that combines advanced digital signal processing methodologies for enhanced genetic data analysis. It has many promising applications in bioinformatics and next generation of healthcare systems, in particular, in the field of microarray data clustering. In this paper we present a comparative performance analysis of enhanced digital spectral analysis methods for robust clustering of gene expression across multiple microarray data samples. Three digital signal processing methods: linear predictive coding, wavelet decomposition, and fractal dimension are studied to provide a comparative evaluation of the clustering performance of these methods on several microarray datasets. The results of this study show that the fractal approach provides the best clustering accuracy compared to other digital signal processing and well known statistical methods.

  7. Analysis of a Hybrid DC Comparator

    Directory of Open Access Journals (Sweden)

    Li Web

    2006-06-01

    Full Text Available The traditional controllable saturation reactor (CSR consists of single toroidal core, DC (direct current controlled loop (including DC controlled winding and DC biasing source and AC (alternating current excitation loop (including excitation winding and AC source. A detection winding and secondary winding are added up to the CSR configuration and form a hybrid DC comparator. The excitation current is asymmetric waveform when the CSR core is commonly stimulated by both AC and DC biasing sources, which just is the fundamental characteristic for the proposed comparator. Research shows the terminal voltage of the detection winding is asymmetric waveform when the secondary winding of the comparator is open and the CSR core is stimulated both by AC and DC biasing sources. Both theory analysis and experiment verify the feasibility of the differential RMS (root-mean-square between positive and negative half waves of the terminal voltage from the detection winding fitting for the feedback variance to balance DC biasing magnetic potential and form a self-balancing comparator. The zero-flux technique that the primary ampere-turn is equal to the secondary is the function base for the comparator. The operation details of the comparator including the control characteristics both of open-loop and close loop, the satiability judgment criterion, static error property and test range are introduced. The experimental results testify to the truth of the principle of the proposed DC comparator.

  8. Heightened sensitivity to emotional expressions in generalised anxiety disorder, compared to social anxiety disorder, and controls.

    Science.gov (United States)

    Bui, Eric; Anderson, Eric; Goetter, Elizabeth M; Campbell, Allison A; Fischer, Laura E; Barrett, Lisa Feldman; Simon, Naomi M

    2017-01-01

    Few studies have examined potential differences between social anxiety disorder (SAD) and generalised anxiety disorder (GAD) in the sensitivity to detect emotional expressions. The present study aims to compare the detection of emotional expressions in SAD and GAD. Participants with a primary diagnosis of GAD (n = 46), SAD (n = 70), and controls (n = 118) completed a morph movies task. The task presented faces expressing increasing degrees of emotional intensity, slowly changing from a neutral to a full-intensity happy, sad, or angry expressions. Participants used a slide bar to view the movie frames from left to right, and to stop at the first frame where they perceived an emotion. The frame selected thus indicated the intensity of emotion required to identify the facial expression. Participants with GAD detected the onset of facial emotions at lower intensity of emotion than participants with SAD (p = 0.002) and controls (p = 0.039). In a multiple regression analysis controlling for age, race, and depressive symptom severity, lower frame at which the emotion was detected was independently associated and GAD diagnosis (B = -5.73, SE = 1.74, p < 0.01). Our findings suggest that individuals with GAD exhibit enhanced detection of facial emotions compared to those with SAD or controls.

  9. A comparative analysis of angiopoietin 2 immunohistochemical ...

    African Journals Online (AJOL)

    There was a significant correlation between Ang 2 expression rate of expression and the histologic type of lung cancer (P = 0.033). Ang 2 expression rate in tumor cells of cancer tissues diagnosed with adenocarcinoma was low. There was a significant correlation between Ang 2 expression rate in stromal cells of cancer ...

  10. Comparative Study on Facial Expression Recognition using Gabor and Dual-Tree Complex Wavelet Transforms

    Directory of Open Access Journals (Sweden)

    Alaa Eleyan

    2017-04-01

    Full Text Available Moving from manually interaction with machines to automated systems, stressed on the importance of facial expression recognition for human computer interaction (HCI. In this article, an investigation and comparative study about the use of complex wavelet transforms for Facial Expression Recognition (FER problem was conducted. Two complex wavelets were used as feature extractors; Gabor wavelets transform (GWT and dual-tree complex wavelets transform (DT-CWT. Extracted feature vectors were fed to principal component analysis (PCA or local binary patterns (LBP. Extensive experiments were carried out using three different databases, namely; JAFFE, CK and MUFE databases. For evaluation of the performance of the system, k-nearest neighbor (kNN, neural networks (NN and support vector machines (SVM classifiers were implemented. The obtained results show that the complex wavelet transform together with sophisticated classifiers can serve as a powerful tool for facial expression recognition problem.

  11. Comparative analysis of twelve Dothideomycete plant pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Ohm, Robin; Aerts, Andrea; Salamov, Asaf; Goodwin, Stephen B.; Grigoriev, Igor

    2011-03-11

    The Dothideomycetes are one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops grown for biofuel, food or feed. Most Dothideomycetes have only a single host and related Dothideomycete species can have very diverse host plants. Twelve Dothideomycete genomes have currently been sequenced by the Joint Genome Institute and other sequencing centers. They can be accessed via Mycocosm which has tools for comparative analysis

  12. Computerised analysis of facial emotion expression in eating disorders.

    Science.gov (United States)

    Leppanen, Jenni; Dapelo, Marcela Marin; Davies, Helen; Lang, Katie; Treasure, Janet; Tchanturia, Kate

    2017-01-01

    Problems with social-emotional processing are known to be an important contributor to the development and maintenance of eating disorders (EDs). Diminished facial communication of emotion has been frequently reported in individuals with anorexia nervosa (AN). Less is known about facial expressivity in bulimia nervosa (BN) and in people who have recovered from AN (RecAN). This study aimed to pilot the use of computerised facial expression analysis software to investigate emotion expression across the ED spectrum and recovery in a large sample of participants. 297 participants with AN, BN, RecAN, and healthy controls were recruited. Participants watched film clips designed to elicit happy or sad emotions, and facial expressions were then analysed using FaceReader. The finding mirrored those from previous work showing that healthy control and RecAN participants expressed significantly more positive emotions during the positive clip compared to the AN group. There were no differences in emotion expression during the sad film clip. These findings support the use of computerised methods to analyse emotion expression in EDs. The findings also demonstrate that reduced positive emotion expression is likely to be associated with the acute stage of AN illness, with individuals with BN showing an intermediate profile.

  13. Analysis of musical expression in audio signals

    Science.gov (United States)

    Dixon, Simon

    2003-01-01

    In western art music, composers communicate their work to performers via a standard notation which specificies the musical pitches and relative timings of notes. This notation may also include some higher level information such as variations in the dynamics, tempo and timing. Famous performers are characterised by their expressive interpretation, the ability to convey structural and emotive information within the given framework. The majority of work on audio content analysis focusses on retrieving score-level information; this paper reports on the extraction of parameters describing the performance, a task which requires a much higher degree of accuracy. Two systems are presented: BeatRoot, an off-line beat tracking system which finds the times of musical beats and tracks changes in tempo throughout a performance, and the Performance Worm, a system which provides a real-time visualisation of the two most important expressive dimensions, tempo and dynamics. Both of these systems are being used to process data for a large-scale study of musical expression in classical and romantic piano performance, which uses artificial intelligence (machine learning) techniques to discover fundamental patterns or principles governing expressive performance.

  14. Comparative genome analysis of Enterobacter cloacae.

    Directory of Open Access Journals (Sweden)

    Wing-Yee Liu

    Full Text Available The Enterobacter cloacae species includes an extremely diverse group of bacteria that are associated with plants, soil and humans. Publication of the complete genome sequence of the plant growth-promoting endophytic E. cloacae subsp. cloacae ENHKU01 provided an opportunity to perform the first comparative genome analysis between strains of this dynamic species. Examination of the pan-genome of E. cloacae showed that the conserved core genome retains the general physiological and survival genes of the species, while genomic factors in plasmids and variable regions determine the virulence of the human pathogenic E. cloacae strain; additionally, the diversity of fimbriae contributes to variation in colonization and host determination of different E. cloacae strains. Comparative genome analysis further illustrated that E. cloacae strains possess multiple mechanisms for antagonistic action against other microorganisms, which involve the production of siderophores and various antimicrobial compounds, such as bacteriocins, chitinases and antibiotic resistance proteins. The presence of Type VI secretion systems is expected to provide further fitness advantages for E. cloacae in microbial competition, thus allowing it to survive in different environments. Competition assays were performed to support our observations in genomic analysis, where E. cloacae subsp. cloacae ENHKU01 demonstrated antagonistic activities against a wide range of plant pathogenic fungal and bacterial species.

  15. Inpatient care in Kazakhstan: A comparative analysis.

    Science.gov (United States)

    Kumar, Ainur B; Izekenova, Aigulsum; Abikulova, Akmaral

    2013-07-01

    Reforms in inpatient care are critical for the enhancement of the efficiency of health systems. It still remains the main costly sector of the health system, accounting for more than 60% of all expenditures. Inappropriate and ineffective use of the hospital infrastructure is also a big issue. We aimed to analyze statistical data on health indices and dynamics of the hospital stock in Kazakhstan in comparison with those of developed countries. Study design is comparative quantitative analysis of inpatient care indicators. We used information and analytical methods, content analysis, mathematical treatment, and comparative analysis of statistical data on health system and dynamics of hospital stock in Kazakhstan and some other countries of the world [Organization for Economic Cooperation and Development (OECD), USA, Canada, Russia, China, Japan, and Korea] over the period 2001-2011. Despite substantial and continuous reductions over the past 10 years, hospitalization rates in Kazakhstan still remain high compared to some developed countries, including those of the OECD. In fact, the hospital stay length for all patients in Kazakhstan in 2011 is around 9.9 days, hospitalization ratio per 100 people is 16.3, and hospital beds capacity is 100 per 10,000 inhabitants. The decreased level of beds may adversely affect both medical organization and health system operations. Alternatives to the existing inpatient care are now being explored. The introduction of the unified national healthcare system allows shifting the primary focus on primary care organizations, which can decrease the demand on inpatient care as a result of improving the health status of people at the primary care level.

  16. Inpatient care in Kazakhstan: A comparative analysis

    Directory of Open Access Journals (Sweden)

    Ainur B Kumar

    2013-01-01

    Full Text Available Background: Reforms in inpatient care are critical for the enhancement of the efficiency of health systems. It still remains the main costly sector of the health system, accounting for more than 60% of all expenditures. Inappropriate and ineffective use of the hospital infrastructure is also a big issue. We aimed to analyze statistical data on health indices and dynamics of the hospital stock in Kazakhstan in comparison with those of developed countries. Materials and Methods: Study design is comparative quantitative analysis of inpatient care indicators. We used information and analytical methods, content analysis, mathematical treatment, and comparative analysis of statistical data on health system and dynamics of hospital stock in Kazakhstan and some other countries of the world [Organization for Economic Cooperation and Development (OECD, USA, Canada, Russia, China, Japan, and Korea] over the period 2001-2011. Results : Despite substantial and continuous reductions over the past 10 years, hospitalization rates in Kazakhstan still remain high compared to some developed countries, including those of the OECD. In fact, the hospital stay length for all patients in Kazakhstan in 2011 is around 9.9 days, hospitalization ratio per 100 people is 16.3, and hospital beds capacity is 100 per 10,000 inhabitants. Conclusion: The decreased level of beds may adversely affect both medical organization and health system operations. Alternatives to the existing inpatient care are now being explored. The introduction of the unified national healthcare system allows shifting the primary focus on primary care organizations, which can decrease the demand on inpatient care as a result of improving the health status of people at the primary care level.

  17. Comparative analysis of black carbon in soils

    Science.gov (United States)

    Schmidt, Michael W. I.; Skjemstad, Jan O.; Czimczik, Claudia I.; Glaser, Bruno; Prentice, Ken M.; Gelinas, Yves; Kuhlbusch, Thomas A. J.

    2001-03-01

    Black carbon (BC), produced by incomplete combustion of fossil fuels and vegetation, occurs ubiquitously in soils and sediments. BC exists as a continuum from partly charred material to highly graphitized soot particles, with no general agreement on clear-cut boundaries of definition or analysis. In a comparative analysis, we measured BC forms in eight soil samples by six established methods. All methods involved removal of the non-BC components from the sample by thermal or chemical means or a combination of both. The remaining carbon, operationally defined as BC, was quantified via mass balance, elemental composition or by exploiting benzenecarboxylic acids as molecular markers or applying 13C MAS NMR (magic angle spinning nuclear magnetic resonance) spectroscopy. BC concentrations measured for individual samples vary over 2 orders of magnitude (up to a factor of 571). One possible explanation for this wide range of results is that the individual BC methods rely on operational definitions with clear-cut but different boundaries and developed for specific scientific questions, whereas BC represents a continuum of materials with widely contrasting physicochemical properties. Thus the methods are inherently designed to analytically determine different parts of the continuum, and it is crucial to know how measurements made by different techniques relate to each other. It is clear from this preliminary comparative analysis that a collection of BC reference materials should be established as soon as possible 1 ) to ensure long-term intralaboratory and interlaboratory data quality and 2) to facilitate comparative analyses between different analytical techniques and scientific approaches

  18. Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles

    Directory of Open Access Journals (Sweden)

    Boussaha Mekki

    2006-05-01

    Full Text Available Abstract Background The Fragile Histidine Triad gene (FHIT is an oncosuppressor implicated in many human cancers, including vesical tumors. FHIT is frequently hit by deletions caused by fragility at FRA3B, the most active of human common fragile sites, where FHIT lays. Vesical tumors affect also cattle, including animals grazing in the wild on bracken fern; compounds released by the fern are known to induce chromosome fragility and may trigger cancer with the interplay of latent Papilloma virus. Results The bovine FHIT was characterized by assembling a contig of 78 BACs. Sequence tags were designed on human exons and introns and used directly to select bovine BACs, or compared with sequence data in the bovine genome database or in the trace archive of the bovine genome sequencing project, and adapted before use. FHIT is split in ten exons like in man, with exons 5 to 9 coding for a 149 amino acids protein. VISTA global alignments between bovine genomic contigs retrieved from the bovine genome database and the human FHIT region were performed. Conservation was extremely high over a 2 Mb region spanning the whole FHIT locus, including the size of introns. Thus, the bovine FHIT covers about 1.6 Mb compared to 1.5 Mb in man. Expression was analyzed by RT-PCR and Northern blot, and was found to be ubiquitous. Four cDNA isoforms were isolated and sequenced, that originate from an alternative usage of three variants of exon 4, revealing a size very close to the major human FHIT cDNAs. Conclusion A comparative genomic approach allowed to assemble a contig of 78 BACs and to completely annotate a 1.6 Mb region spanning the bovine FHIT gene. The findings confirmed the very high level of conservation between human and bovine genomes and the importance of comparative mapping to speed the annotation process of the recently sequenced bovine genome. The detailed knowledge of the genomic FHIT region will allow to study the role of FHIT in bovine cancerogenesis

  19. Gene expression model (invalidation by Fourier analysis

    Directory of Open Access Journals (Sweden)

    Konopka Tomasz

    2010-09-01

    Full Text Available Abstract Background The determination of the right model structure describing a gene regulation network and the identification of its parameters are major goals in systems biology. The task is often hampered by the lack of relevant experimental data with sufficiently low noise level, but the subset of genes whose concentration levels exhibit an oscillatory behavior in time can readily be analyzed on the basis of their Fourier spectrum, known to turn complex signals into few relatively noise-free parameters. Such genes therefore offer opportunities of understanding gene regulation quantitatively. Results Fourier analysis is applied to data on gene expression levels in mouse liver cells that oscillate according to the circadian rhythm. Several model structures in the form of linear and nonlinear differential equations are matched to the data and it is shown that although the considered models can reproduce many features of the oscillatory patterns, some can be excluded on the basis of Fourier analysis without appeal to prior knowledge of regulatory pathways. A systematic method for testing models is also proposed based on measuring the effects of variations in gene copy-number on the expression levels of coupled genes. Conclusions Fourier analysis is a technique that is well-adapted to the study of biological oscillators and can be used instead or in addition to conventional modeling techniques. Its usefulness will increase as more high-resolution data become available.

  20. BLAT-Based Comparative Analysis for Transposable Elements: BLATCAT

    Directory of Open Access Journals (Sweden)

    Sangbum Lee

    2014-01-01

    Full Text Available The availability of several whole genome sequences makes comparative analyses possible. In primate genomes, the priority of transposable elements (TEs is significantly increased because they account for ~45% of the primate genomes, they can regulate the gene expression level, and they are associated with genomic fluidity in their host genomes. Here, we developed the BLAST-like alignment tool (BLAT based comparative analysis for transposable elements (BLATCAT program. The BLATCAT program can compare specific regions of six representative primate genome sequences (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque on the basis of BLAT and simultaneously carry out RepeatMasker and/or Censor functions, which are widely used Windows-based web-server functions to detect TEs. All results can be stored as a HTML file for manual inspection of a specific locus. BLATCAT will be very convenient and efficient for comparative analyses of TEs in various primate genomes.

  1. Comparative Analysis of 37 Acinetobacter Bacteriophages

    Directory of Open Access Journals (Sweden)

    Dann Turner

    2017-12-01

    Full Text Available Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A comparative bioinformatics analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The comparative analysis and clustering presented enables an updated taxonomic framing of these clades.

  2. Comparative analysis of solar photovoltaic monitoring systems

    Science.gov (United States)

    Madeti, Siva Ramakrishna; Singh, S. N.

    2017-07-01

    This paper is focused on comparative analysis of photovoltaic (PV) monitoring system for observing the performance and stability of the system. The cost and complexity of existing PV monitoring systems restricted their use to large scale PV plants. Over the past decade, different aspects of the PV monitoring systems were reported in the wide range of literature. In this paper, a comparative analysis of various PV monitoring systems is presented for the first time. It is based on analyzing six main characteristics of PV monitoring system, such as data transfer mechanism, controller, monitoring parameters, sampling interval, program development software and monitoring methods. The comparison of methodologies and the description of implementation process are discussed in this context. The key findings of this study will contribute to the development of a new PV monitoring system. The acquaintance of all these aspects is crucial for the development of effective, low cost, and viable PV monitoring systems for the small and medium scale PV plants without compromising on the desired performance.

  3. Sports dance artistic expression culture analysis

    OpenAIRE

    Chen Zegang

    2017-01-01

    At present, the sports dance has entered every stage of the people’s life, has become the public’s favorite sport. Sports dance has been well developed. This article mainly uses the literature material law to carry on the detailed analysis to the sports dance constitution, elaborated in detail the sports dance artistic expression. The composition of sports dance elements; sports dance is a form of dance art show; sports dance through the dance art can be divided into three aspects, namely, fo...

  4. Comparative genome analysis of Basidiomycete fungi

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert; Salamov, Asaf; Henrissat, Bernard; Nagy, Laszlo; Brown, Daren; Held, Benjamin; Baker, Scott; Blanchette, Robert; Boussau, Bastien; Doty, Sharon L.; Fagnan, Kirsten; Floudas, Dimitris; Levasseur, Anthony; Manning, Gerard; Martin, Francis; Morin, Emmanuelle; Otillar, Robert; Pisabarro, Antonio; Walton, Jonathan; Wolfe, Ken; Hibbett, David; Grigoriev, Igor

    2013-08-07

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprotrophs including the majority of wood decaying and ectomycorrhizal species. To better understand the genetic diversity of this phylum we compared the genomes of 35 basidiomycetes including 6 newly sequenced genomes. These genomes span extremes of genome size, gene number, and repeat content. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) found in only one organism. Correlations between lifestyle and certain gene families are evident. Phylogenetic patterns of plant biomass-degrading genes in Agaricomycotina suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. Based on phylogenetically-informed PCA analysis of wood decay genes, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has typical ligninolytic class II fungal peroxidases (PODs). This prediction is supported by growth assays in which both fungi exhibit wood decay with white rot-like characteristics. Based on this, we suggest that the white/brown rot dichotomy may be inadequate to describe the full range of wood decaying fungi. Analysis of the rate of discovery of proteins with no or few homologs suggests the value of continued sequencing of basidiomycete fungi.

  5. Comparative expression profiling reveals gene functions in female meiosis and gametophyte development in Arabidopsis.

    Science.gov (United States)

    Zhao, Lihua; He, Jiangman; Cai, Hanyang; Lin, Haiyan; Li, Yanqiang; Liu, Renyi; Yang, Zhenbiao; Qin, Yuan

    2014-11-01

    Megasporogenesis is essential for female fertility, and requires the accomplishment of meiosis and the formation of functional megaspores. The inaccessibility and low abundance of female meiocytes make it particularly difficult to elucidate the molecular basis underlying megasporogenesis. We used high-throughput tag-sequencing analysis to identify genes expressed in female meiocytes (FMs) by comparing gene expression profiles from wild-type ovules undergoing megasporogenesis with those from the spl mutant ovules, which lack megasporogenesis. A total of 862 genes were identified as FMs, with levels that are consistently reduced in spl ovules in two biological replicates. Fluorescence-assisted cell sorting followed by RNA-seq analysis of DMC1:GFP-labeled female meiocytes confirmed that 90% of the FMs are indeed detected in the female meiocyte protoplast profiling. We performed reverse genetic analysis of 120 candidate genes and identified four FM genes with a function in female meiosis progression in Arabidopsis. We further revealed that KLU, a putative cytochrome P450 monooxygenase, is involved in chromosome pairing during female meiosis, most likely by affecting the normal expression pattern of DMC1 in ovules during female meiosis. Our studies provide valuable information for functional genomic analyses of plant germline development as well as insights into meiosis. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

  6. Comparative transcriptome analysis of four prymnesiophyte algae.

    Directory of Open Access Journals (Sweden)

    Amy E Koid

    Full Text Available Genomic studies of bacteria, archaea and viruses have provided insights into the microbial world by unveiling potential functional capabilities and molecular pathways. However, the rate of discovery has been slower among microbial eukaryotes, whose genomes are larger and more complex. Transcriptomic approaches provide a cost-effective alternative for examining genetic potential and physiological responses of microbial eukaryotes to environmental stimuli. In this study, we generated and compared the transcriptomes of four globally-distributed, bloom-forming prymnesiophyte algae: Prymnesium parvum, Chrysochromulina brevifilum, Chrysochromulina ericina and Phaeocystis antarctica. Our results revealed that the four transcriptomes possess a set of core genes that are similar in number and shared across all four organisms. The functional classifications of these core genes using the euKaryotic Orthologous Genes (KOG database were also similar among the four study organisms. More broadly, when the frequencies of different cellular and physiological functions were compared with other protists, the species clustered by both phylogeny and nutritional modes. Thus, these clustering patterns provide insight into genomic factors relating to both evolutionary relationships as well as trophic ecology. This paper provides a novel comparative analysis of the transcriptomes of ecologically important and closely related prymnesiophyte protists and advances an emerging field of study that uses transcriptomics to reveal ecology and function in protists.

  7. Comparative transcriptome analysis of four prymnesiophyte algae.

    Science.gov (United States)

    Koid, Amy E; Liu, Zhenfeng; Terrado, Ramon; Jones, Adriane C; Caron, David A; Heidelberg, Karla B

    2014-01-01

    Genomic studies of bacteria, archaea and viruses have provided insights into the microbial world by unveiling potential functional capabilities and molecular pathways. However, the rate of discovery has been slower among microbial eukaryotes, whose genomes are larger and more complex. Transcriptomic approaches provide a cost-effective alternative for examining genetic potential and physiological responses of microbial eukaryotes to environmental stimuli. In this study, we generated and compared the transcriptomes of four globally-distributed, bloom-forming prymnesiophyte algae: Prymnesium parvum, Chrysochromulina brevifilum, Chrysochromulina ericina and Phaeocystis antarctica. Our results revealed that the four transcriptomes possess a set of core genes that are similar in number and shared across all four organisms. The functional classifications of these core genes using the euKaryotic Orthologous Genes (KOG) database were also similar among the four study organisms. More broadly, when the frequencies of different cellular and physiological functions were compared with other protists, the species clustered by both phylogeny and nutritional modes. Thus, these clustering patterns provide insight into genomic factors relating to both evolutionary relationships as well as trophic ecology. This paper provides a novel comparative analysis of the transcriptomes of ecologically important and closely related prymnesiophyte protists and advances an emerging field of study that uses transcriptomics to reveal ecology and function in protists.

  8. In silico comparative genomic analysis of GABAA receptor transcriptional regulation

    Directory of Open Access Journals (Sweden)

    Joyce Christopher J

    2007-06-01

    Full Text Available Abstract Background Subtypes of the GABAA receptor subunit exhibit diverse temporal and spatial expression patterns. In silico comparative analysis was used to predict transcriptional regulatory features in individual mammalian GABAA receptor subunit genes, and to identify potential transcriptional regulatory components involved in the coordinate regulation of the GABAA receptor gene clusters. Results Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π subunit genes. Putative core elements and proximal transcriptional factors were identified within these predicted promoters, and within the experimentally determined promoters of other subunit genes. Conserved intergenic regions of sequence in the mammalian GABAA receptor gene cluster comprising the α1, β2, γ2 and α6 subunits were identified as potential long range transcriptional regulatory components involved in the coordinate regulation of these genes. A region of predicted DNase I hypersensitive sites within the cluster may contain transcriptional regulatory features coordinating gene expression. A novel model is proposed for the coordinate control of the gene cluster and parallel expression of the α1 and β2 subunits, based upon the selective action of putative Scaffold/Matrix Attachment Regions (S/MARs. Conclusion The putative regulatory features identified by genomic analysis of GABAA receptor genes were substantiated by cross-species comparative analysis and now require experimental verification. The proposed model for the coordinate regulation of genes in the cluster accounts for the head-to-head orientation and parallel expression of the α1 and β2 subunit genes, and for the disruption of transcription caused by insertion of a neomycin gene in the close vicinity of the α6 gene, which is proximal to a putative critical S/MAR.

  9. Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids.

    Science.gov (United States)

    Jiang, Jinjin; Wang, Yue; Zhu, Bao; Fang, Tingting; Fang, Yujie; Wang, Youping

    2015-01-27

    Brassica includes many successfully cultivated crop species of polyploid origin, either by ancestral genome triplication or by hybridization between two diploid progenitors, displaying complex repetitive sequences and transposons. The U's triangle, which consists of three diploids and three amphidiploids, is optimal for the analysis of complicated genomes after polyploidization. Next-generation sequencing enables the transcriptome profiling of polyploids on a global scale. We examined the gene expression patterns of three diploids (Brassica rapa, B. nigra, and B. oleracea) and three amphidiploids (B. napus, B. juncea, and B. carinata) via digital gene expression analysis. In total, the libraries generated between 5.7 and 6.1 million raw reads, and the clean tags of each library were mapped to 18547-21995 genes of B. rapa genome. The unambiguous tag-mapped genes in the libraries were compared. Moreover, the majority of differentially expressed genes (DEGs) were explored among diploids as well as between diploids and amphidiploids. Gene ontological analysis was performed to functionally categorize these DEGs into different classes. The Kyoto Encyclopedia of Genes and Genomes analysis was performed to assign these DEGs into approximately 120 pathways, among which the metabolic pathway, biosynthesis of secondary metabolites, and peroxisomal pathway were enriched. The non-additive genes in Brassica amphidiploids were analyzed, and the results indicated that orthologous genes in polyploids are frequently expressed in a non-additive pattern. Methyltransferase genes showed differential expression pattern in Brassica species. Our results provided an understanding of the transcriptome complexity of natural Brassica species. The gene expression changes in diploids and allopolyploids may help elucidate the morphological and physiological differences among Brassica species.

  10. A comparative neurological approach to emotional expressions in primate vocalizations.

    Science.gov (United States)

    Gruber, Thibaud; Grandjean, Didier

    2017-02-01

    Different approaches from different research domains have crystallized debate over primate emotional processing and vocalizations in recent decades. On one side, researchers disagree about whether emotional states or processes in animals truly compare to those in humans. On the other, a long-held assumption is that primate vocalizations are innate communicative signals over which nonhuman primates have limited control and a mirror of the emotional state of the individuals producing them, despite growing evidence of intentional production for some vocalizations. Our goal is to connect both sides of the discussion in deciphering how the emotional content of primate calls compares with emotional vocal signals in humans. We focus particularly on neural bases of primate emotions and vocalizations to identify cerebral structures underlying emotion, vocal production, and comprehension in primates, and discuss whether particular structures or neuronal networks solely evolved for specific functions in the human brain. Finally, we propose a model to classify emotional vocalizations in primates according to four dimensions (learning, control, emotional, meaning) to allow comparing calls across species. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Mammalian comparative sequence analysis of the Agrp locus.

    Directory of Open Access Journals (Sweden)

    Christopher B Kaelin

    2007-08-01

    Full Text Available Agouti-related protein encodes a neuropeptide that stimulates food intake. Agrp expression in the brain is restricted to neurons in the arcuate nucleus of the hypothalamus and is elevated by states of negative energy balance. The molecular mechanisms underlying Agrp regulation, however, remain poorly defined. Using a combination of transgenic and comparative sequence analysis, we have previously identified a 760 bp conserved region upstream of Agrp which contains STAT binding elements that participate in Agrp transcriptional regulation. In this study, we attempt to improve the specificity for detecting conserved elements in this region by comparing genomic sequences from 10 mammalian species. Our analysis reveals a symmetrical organization of conserved sequences upstream of Agrp, which cluster into two inverted repeat elements. Conserved sequences within these elements suggest a role for homeodomain proteins in the regulation of Agrp and provide additional targets for functional evaluation.

  12. Comparative Analysis of VNSA Complex Engineering Efforts

    Directory of Open Access Journals (Sweden)

    Gary Ackerman

    2016-03-01

    Full Text Available The case studies undertaken in this special issue demonstrate unequivocally that, despite being forced to operate clandestinely and facing the pressures of security forces seeking to hunt them down and neutralize them, at least a subset of violent non-state actors (VNSAs are capable of some genuinely impressive feats of engineering. At the same time, success in such endeavours is not guaranteed and VNSAs will undoubtedly face a number of obstacles along the way. A comparative analysis of the cases also reveals new insights about the factors influencing the decision to pursue complex engineering efforts, the implementation of such decisions and the determinants of the ultimate outcome. These result in a set of hypotheses and indicators that, if confirmed by future research, can contribute to both operational and strategic intelligence assessments. Overall, the current study enriches our understanding of how and why VNSAs might engage in complex engineering efforts.

  13. Comparative Genome Analysis of Basidiomycete Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert; Salamov, Asaf; Morin, Emmanuelle; Nagy, Laszlo; Manning, Gerard; Baker, Scott; Brown, Daren; Henrissat, Bernard; Levasseur, Anthony; Hibbett, David; Martin, Francis; Grigoriev, Igor

    2012-03-19

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, symbionts, and plant and animal pathogens. To better understand the diversity of phenotypes in basidiomycetes, we performed a comparative analysis of 35 basidiomycete fungi spanning the diversity of the phylum. Phylogenetic patterns of lignocellulose degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay. Patterns of secondary metabolic enzymes give additional insight into the broad array of phenotypes found in the basidiomycetes. We suggest that the profile of an organism in lignocellulose-targeting genes can be used to predict its nutritional mode, and predict Dacryopinax sp. as a brown rot; Botryobasidium botryosum and Jaapia argillacea as white rots.

  14. Comparative Analysis of Students’ Media Competences Levels

    Directory of Open Access Journals (Sweden)

    Alexander Fedorov

    2015-08-01

    Full Text Available This article analyzed the results of survey of university students’ media literacy competence (on the base of a classification of indicators of media literacy competence of the audience as an effective tool for comparative analysis of the levels of development of media competence of students of the control and experimental groups: the level of media competence of students who have a one-year training course in the framework of media literacy education courses four times higher than in similar indicators in the control group. Analysis of the results of this survey confirmed the general trend of media contacts of student audience – its orientation to entertainment genres of audiovisual media, visually appealing; positive, active, unmarried, childless, educated, highly qualified characters (primarily – male characters aged 19 to 35 years. These heroes are characteristic optimism, independence, intelligence, emotion. They have an excellent command of the life situation and have a positive impact on the development progress of the plot of a media text.

  15. Comparative metagenome analysis of an Alaskan glacier.

    Science.gov (United States)

    Choudhari, Sulbha; Lohia, Ruchi; Grigoriev, Andrey

    2014-04-01

    The temperature in the Arctic region has been increasing in the recent past accompanied by melting of its glaciers. We took a snapshot of the current microbial inhabitation of an Alaskan glacier (which can be considered as one of the simplest possible ecosystems) by using metagenomic sequencing of 16S rRNA recovered from ice/snow samples. Somewhat contrary to our expectations and earlier estimates, a rich and diverse microbial population of more than 2,500 species was revealed including several species of Archaea that has been identified for the first time in the glaciers of the Northern hemisphere. The most prominent bacterial groups found were Proteobacteria, Bacteroidetes, and Firmicutes. Firmicutes were not reported in large numbers in a previously studied Alpine glacier but were dominant in an Antarctic subglacial lake. Representatives of Cyanobacteria, Actinobacteria and Planctomycetes were among the most numerous, likely reflecting the dependence of the ecosystem on the energy obtained through photosynthesis and close links with the microbial community of the soil. Principal component analysis (PCA) of nucleotide word frequency revealed distinct sequence clusters for different taxonomic groups in the Alaskan glacier community and separate clusters for the glacial communities from other regions of the world. Comparative analysis of the community composition and bacterial diversity present in the Byron glacier in Alaska with other environments showed larger overlap with an Arctic soil than with a high Arctic lake, indicating patterns of community exchange and suggesting that these bacteria may play an important role in soil development during glacial retreat.

  16. P63 marker Expression in Usual Skin Cancers Compared With Non Tumoral Skin Lesions

    Directory of Open Access Journals (Sweden)

    Abdolhamid Esmaili

    2017-07-01

    Full Text Available Background: Non-melanoma skin cancers including basal cell carcinoma and squamous cell carcinoma are the most common cancers in human. The aim of this study was to determine the expression of P63 marker in usual skin cancers compared with non-tomoral skin lesions. Materials and Methods: In this cross-sectional study, sampling was performed from archival blocks of Shahid Mohammadi hospital patients during 2010-2011. 60 samples (including 30 samples of non tumoral skin lesions and 30 samples of basal cell carcinoma and squamous cell carcinoma were studied and evaluation of p63 gene expression was done with Immunohistochemistry method. T-test and Chi-square were used for analysis of data. Results: P63 gene were expressed in 4 cases (13.33 % of non tumoral lesions and all tumoral lesions (100 %. In tumoral lesions, 5 cases (16.66 % showed 1+ severity experssion, 11 cases (36.66% 2 + severity experssion and 14 cases (46.66 % 3+severity experssion. All 4 non tumoral lesions shoed 1+ severity experssion of P63gene. Conclusion: The results of this study indicated that the incidence and severity of gene expression of P63 can be use for differentiation between basal cell carcinoma and squamous cell carcinoma as well as non-tumoral skin lesions. 

  17. Inflammatory gene expression in whole blood cells after EPA vs. DHA supplementation: Results from the ComparED study.

    Science.gov (United States)

    Vors, Cécile; Allaire, Janie; Marin, Johanne; Lépine, Marie-Claude; Charest, Amélie; Tchernof, André; Couture, Patrick; Lamarche, Benoît

    2017-02-01

    Whether EPA and DHA exert similar anti-inflammatory effects through modulation of gene expression in immune cells remains unclear. The aim of the study was to compare the impact of EPA and DHA supplementation on inflammatory gene expression in subjects at risk for cardiometabolic diseases. In this randomized double-blind crossover trial, 154 men and women with abdominal obesity and low-grade inflammation were subjected to three 10-wk supplementation phases: 1) EPA (2.7 g/d); 2) DHA (2.7 g/d); 3) corn oil (3 g/d), separated by a 9-wk washout. Pro- and anti-inflammatory gene expression was assessed in whole blood cells by RT-qPCR after each treatment in a representative sample of 44 participants. No significant difference was observed between EPA and DHA in the expression of any of the genes investigated. Compared with control, EPA enhanced TRAF3 and PPARA expression and lowered CD14 expression (p DHA increased expression of PPARA and TNFA and decreased CD14 expression (p DHA were strongly correlated for PPARA (r = 0.73, p DHA has similar effects on the expression of many inflammation-related genes in immune cells of men and women at risk for cardiometabolic diseases. The effects of EPA and of DHA on anti-inflammatory gene expression may be more consistent than their effects on expression of pro-inflammatory genes in whole blood cells. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Comparative Genomics and Transcriptomic Analysis of Mycobacterium Kansasii

    KAUST Repository

    Alzahid, Yara

    2014-04-01

    The group of Mycobacteria is one of the most intensively studied bacterial taxa, as they cause the two historical and worldwide known diseases: leprosy and tuberculosis. Mycobacteria not identified as tuberculosis or leprosy complex, have been referred to by ‘environmental mycobacteria’ or ‘Nontuberculous mycobacteria (NTM). Mycobacterium kansasii (M. kansasii) is one of the most frequent NTM pathogens, as it causes pulmonary disease in immuno-competent patients and pulmonary, and disseminated disease in patients with various immuno-deficiencies. There have been five documented subtypes of this bacterium, by different molecular typing methods, showing that type I causes tuberculosis-like disease in healthy individuals, and type II in immune-compromised individuals. The remaining types are said to be environmental, thereby, not causing any diseases. The aim of this project was to conduct a comparative genomic study of M. kansasii types I-V and investigating the gene expression level of those types. From various comparative genomics analysis, provided genomics evidence on why M. kansasii type I is considered pathogenic, by focusing on three key elements that are involved in virulence of Mycobacteria: ESX secretion system, Phospholipase c (plcb) and Mammalian cell entry (Mce) operons. The results showed the lack of the espA operon in types II-V, which renders the ESX- 1 operon dysfunctional, as espA is one of the key factors that control this secretion system. However, gene expression analysis showed this operon to be deleted in types II, III and IV. Furthermore, plcB was found to be truncated in types III and IV. Analysis of Mce operons (1-4) show that mce-1 operon is duplicated, mce-2 is absent and mce-3 and mce-4 is present in one copy in M. kansasii types I-V. Gene expression profiles of type I-IV, showed that the secreted proteins of ESX-1 were slightly upregulated in types II-IV when compared to type I and the secreted forms of ESX-5 were highly down

  19. A comparative analysis of angiopoietin 2 immunohistochemical ...

    African Journals Online (AJOL)

    2016-07-12

    , extension, and metastasis is not fully elucidated. The presented study aimed to investigate the relationship between Ang 2 staining intensity, expression rate in tumor tissue, and the stage of lung cancer. Materials and ...

  20. Sports dance artistic expression culture analysis

    Directory of Open Access Journals (Sweden)

    Chen Zegang

    2017-01-01

    Full Text Available At present, the sports dance has entered every stage of the people’s life, has become the public’s favorite sport. Sports dance has been well developed. This article mainly uses the literature material law to carry on the detailed analysis to the sports dance constitution, elaborated in detail the sports dance artistic expression. The composition of sports dance elements; sports dance is a form of dance art show; sports dance through the dance art can be divided into three aspects, namely, form, music, shape of the expressive force. In this paper, the study will be more in-depth excavation of the cultural connotation of sports dance, and promote the development of sports dance can be more comprehensive. In 20s of last century, Chinese Sports Dance Association officially joined the International Sports Dance Association, which also makes our country’s sports dance and international exchange more frequent. However, due to China’s sports dance sports dance learning time is not long, while learning is influenced by Chinese traditional culture, the sports dance movements are too conservative, there is a very large gap and international enthusiasm, bold and unrestrained, the pursuit of individual sports dance in the dance style, music and performance hand. Sports dance originated from abroad, it is produced in the daily life of people in foreign countries. China’s domestic sports dance players in learning dance at the same time, the production and the connotation of dance is not very understanding, therefore, it is difficult to better reflect the emotional expression of sports dance. Although the sports dance is a kind of similar to the competitive projects, but it is also a kind of dance culture, and to constitute a force from the dance art show a detailed study, detailed mining playing officer of sports dance performance further, reducing China’s sports dance and international sports dance gap.

  1. Comparative proteomic analysis of fibrosarcoma and skin fibroblast cell lines.

    Science.gov (United States)

    Meral, Ogunc; Uysal, Hamdi

    2015-02-01

    Comparative proteomic analysis of normal and cancer cell lines provides for a better understanding of the molecular mechanism of cancer development and is essential for developing more effective strategies for new biomarker or drug target discovery. The purpose of this study is to compare protein expression levels between fibrosarcoma and fibroblast cell lines. In our study, two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) techniques were carried out to compare the protein profile between fibrosarcoma and fibroblast cell lines. We prepared cell lysate samples to analyze intracellular proteins and secretome samples to analyze extracellular proteins in both cell lines. Our results revealed 13 upregulated proteins and 1 downregulated protein of which all of them identified in fibrosarcoma cell line after the comparison with fibroblast cell line cell lysates. When comparing secretome profiles of both cell lines, we found and identified 13 proteins only expressed in fibrosarcoma cell line. These identified proteins have common functions such as cell proliferation, cell differentiation, invasion, metastasis, and apoptosis in cancer. The data obtained from this study indicates that these proteins have importance on understanding the molecular mechanism of fibrosarcoma. These proteins may serve as candidate biomarkers and drug targets for future clinical studies.

  2. Transcriptomics and comparative analysis of three antarctic notothenioid fishes.

    Directory of Open Access Journals (Sweden)

    Seung Chul Shin

    Full Text Available For the past 10 to 13 million years, Antarctic notothenioid fish have undergone extraordinary periods of evolution and have adapted to a cold and highly oxygenated Antarctic marine environment. While these species are considered an attractive model with which to study physiology and evolutionary adaptation, they are poorly characterized at the molecular level, and sequence information is lacking. The transcriptomes of the Antarctic fishes Notothenia coriiceps, Chaenocephalus aceratus, and Pleuragramma antarcticum were obtained by 454 FLX Titanium sequencing of a normalized cDNA library. More than 1,900,000 reads were assembled in a total of 71,539 contigs. Overall, 40% of the contigs were annotated based on similarity to known protein or nucleotide sequences, and more than 50% of the predicted transcripts were validated as full-length or putative full-length cDNAs. These three Antarctic fishes shared 663 genes expressed in the brain and 1,557 genes expressed in the liver. In addition, these cold-adapted fish expressed more Ub-conjugated proteins compared to temperate fish; Ub-conjugated proteins are involved in maintaining proteins in their native state in the cold and thermally stable Antarctic environments. Our transcriptome analysis of Antarctic notothenioid fish provides an archive for future studies in molecular mechanisms of fundamental genetic questions, and can be used in evolution studies comparing other fish.

  3. Analysis of gene expression in rabbit muscle

    Directory of Open Access Journals (Sweden)

    Alena Gálová

    2014-02-01

    Full Text Available Increasing consumer knowledge of the link between diet and health has raised the demand for high quality food. Meat and meat products may be considered as irreplaceable in human nutrition. Breeding livestock to higher content of lean meat and the use of modern hybrids entails problems with the quality of meat. Analysing of livestock genomes could get us a great deal of important information, which may significantly affect the improvement process. Domestic animals are invaluable resources for study of the molecular architecture of complex traits. Although the mapping of quantitative trait loci (QTL responsible for economically important traits in domestic animals has achieved remarkable results in recent decades, not all of the genetic variation in the complex traits has been captured because of the low density of markers used in QTL mapping studies. The genome wide association study (GWAS, which utilizes high-density single-nucleotide polymorphism (SNP, provides a new way to tackle this issue. New technologies now allow producing microarrays containing thousands of hybridization probes on a single membrane or other solid support. We used microarray analysis to study gene expression in rabbit muscle during different developmental age stages. The outputs from GeneSpring GX sotware are presented in this work. After the evaluation of gene expression in rabbits, will be selected genes of interest in relation to meat quality parameters and will be further analyzed by the available methods of molecular biology and genetics.

  4. Glimma: interactive graphics for gene expression analysis.

    Science.gov (United States)

    Su, Shian; Law, Charity W; Ah-Cann, Casey; Asselin-Labat, Marie-Liesse; Blewitt, Marnie E; Ritchie, Matthew E

    2017-07-01

    graphics for RNA-sequencing and microarray gene expression analyses may contain upwards of tens of thousands of points. Details about certain genes or samples of interest are easily obscured in such dense summary displays. Incorporating interactivity into summary plots would enable additional information to be displayed on demand and facilitate intuitive data exploration. The open-source Glimma package creates interactive graphics for exploring gene expression analysis with a few simple R commands. It extends popular plots found in the limma package, such as multi-dimensional scaling plots and mean-difference plots, to allow individual data points to be queried and additional annotation information to be displayed upon hovering or selecting particular points. It also offers links between plots so that more information can be revealed on demand. Glimma is widely applicable, supporting data analyses from a number of well-established Bioconductor workflows ( limma , edgeR and DESeq2 ) and uses D3/JavaScript to produce HTML pages with interactive displays that enable more effective data exploration by end-users. Results from Glimma can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility. The Glimma R package is available from http://bioconductor.org/packages/Glimma/ . su.s@wehi.edu.au , law@wehi.edu.au or mritchie@wehi.edu.au.

  5. Predictive and comparative analysis of Ebolavirus proteins.

    Science.gov (United States)

    Cong, Qian; Pei, Jimin; Grishin, Nick V

    2015-01-01

    Ebolavirus is the pathogen for Ebola Hemorrhagic Fever (EHF). This disease exhibits a high fatality rate and has recently reached a historically epidemic proportion in West Africa. Out of the 5 known Ebolavirus species, only Reston ebolavirus has lost human pathogenicity, while retaining the ability to cause EHF in long-tailed macaque. Significant efforts have been spent to determine the three-dimensional (3D) structures of Ebolavirus proteins, to study their interaction with host proteins, and to identify the functional motifs in these viral proteins. Here, in light of these experimental results, we apply computational analysis to predict the 3D structures and functional sites for Ebolavirus protein domains with unknown structure, including a zinc-finger domain of VP30, the RNA-dependent RNA polymerase catalytic domain and a methyltransferase domain of protein L. In addition, we compare sequences of proteins that interact with Ebolavirus proteins from RESTV-resistant primates with those from RESTV-susceptible monkeys. The host proteins that interact with GP and VP35 show an elevated level of sequence divergence between the RESTV-resistant and RESTV-susceptible species, suggesting that they may be responsible for host specificity. Meanwhile, we detect variable positions in protein sequences that are likely associated with the loss of human pathogenicity in RESTV, map them onto the 3D structures and compare their positions to known functional sites. VP35 and VP30 are significantly enriched in these potential pathogenicity determinants and the clustering of such positions on the surfaces of VP35 and GP suggests possible uncharacterized interaction sites with host proteins that contribute to the virulence of Ebolavirus.

  6. Comparative expression analysis of senescence gene CsNAP and B-class floral development gene CsAP3 during different stages of flower development in Saffron (Crocus sativus L.).

    Science.gov (United States)

    Wafai, Asrar H; Bukhari, Shoiab; Mokhdomi, Taseem A; Amin, Asif; Wani, Zubair; Hussaini, Amjad; Mir, Javid I; Qadri, Raies A

    2015-07-01

    Crocus sativus, a monocot triploid species belonging to the Iridaceae family, is cultivated for its red stigmatic lobes of the carpel that constitute saffron. Flower development has been extensively studied in different plants. Different floral developmental pathways have been deciphered in many plants. In Crocus sativus, flower is the most important part and understanding the pathway underlying the flower development can pave the way for new avenues to improve its productivity and quality. The combination of class A genes (including APETALA1; CsAP1 and APETALA2; CsAP2), class B genes (including APETALA3; CsAP3 and PISTILLATA; CsPI) and class C genes (including AGAMOUS; CsAG) that are active in each whorl, determines the identity of the organs that will later develop in that whorl. CsAP3 is a class B homeotic gene which promotes petal and stamen formation and has a very important role in flower development. It also activates other genes playing pivotal role in flower development. It has been earlier reported that CsAP3 gene has direct role in activation of CsNAP gene which promotes senescence in plants. Present work was focused on study of relative gene expression changes of CsAP3 and CsNAP gene during different stages of flower development. CsAP3 gene expression was found maximum during late-preanthesis stages of stigma development. Expression increases from stage 5 to stage 6 of flower development and then reduces again from stage 6 to stage 7. CsNAP gene had moderate expression during stage 3 to stage 4 transition and its expression increased abruptly from stage 6 to stage 7 of flower development. There is no direct concordance in the expression of CsAP3 and CsNAP gene expression in saffron. We may conclude that some other factor(s) may be responsible for initiation of CsNAP expression and CsAP3 gene may directly/indirectly be involved in regulating the factors responsible for CsNAP activation.

  7. Comparative analysis of haplotype association mapping algorithms

    Directory of Open Access Journals (Sweden)

    Pletcher Mathew T

    2006-02-01

    Full Text Available Abstract Background Finding the genetic causes of quantitative traits is a complex and difficult task. Classical methods for mapping quantitative trail loci (QTL in miceuse an F2 cross between two strains with substantially different phenotype and an interval mapping method to compute confidence intervals at each position in the genome. This process requires significant resources for breeding and genotyping, and the data generated are usually only applicable to one phenotype of interest. Recently, we reported the application of a haplotype association mapping method which utilizes dense genotyping data across a diverse panel of inbred mouse strains and a marker association algorithm that is independent of any specific phenotype. As the availability of genotyping data grows in size and density, analysis of these haplotype association mapping methods should be of increasing value to the statistical genetics community. Results We describe a detailed comparative analysis of variations on our marker association method. In particular, we describe the use of inferred haplotypes from adjacent SNPs, parametric and nonparametric statistics, and control of multiple testing error. These results show that nonparametric methods are slightly better in the test cases we study, although the choice of test statistic may often be dependent on the specific phenotype and haplotype structure being studied. The use of multi-SNP windows to infer local haplotype structure is critical to the use of a diverse panel of inbred strains for QTL mapping. Finally, because the marginal effect of any single gene in a complex disease is often relatively small, these methods require the use of sensitive methods for controlling family-wise error. We also report our initial application of this method to phenotypes cataloged in the Mouse Phenome Database. Conclusion The use of inbred strains of mice for QTL mapping has many advantages over traditional methods. However, there are also

  8. Comparative analysis of safety related site characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, Johan (ed.)

    2010-12-15

    This document presents a comparative analysis of site characteristics related to long-term safety for the two candidate sites for a final repository for spent nuclear fuel in Forsmark (municipality of Oesthammar) and in Laxemar (municipality of Oskarshamn) from the point of view of site selection. The analyses are based on the updated site descriptions of Forsmark /SKB 2008a/ and Laxemar /SKB 2009a/, together with associated updated repository layouts and designs /SKB 2008b and SKB 2009b/. The basis for the comparison is thus two equally and thoroughly assessed sites. However, the analyses presented here are focussed on differences between the sites rather than evaluating them in absolute terms. The document serves as a basis for the site selection, from the perspective of long-term safety, in SKB's application for a final repository. A full evaluation of safety is made for a repository at the selected site in the safety assessment SR-Site /SKB 2011/, referred to as SR-Site main report in the following

  9. Comparative Analysis of Virtual Education Applications

    Directory of Open Access Journals (Sweden)

    Mehmet KURT

    2006-10-01

    Full Text Available The research was conducted in order to make comparative analysis of virtual education applications. The research is conducted in survey model. The study group consists of total 300 institutes providing virtual education in the fall, spring and summer semesters of 2004; 246 in USA, 10 in Australia, 3 in South Africa, 10 in India, 21 in UK, 6 in Japan, 4 in Turkey. The information has been collected by online questionnaire sent to the target mass by e-mail. The questionnaire has been developed in two information categories as personal information and institutes and their virtual education applications. The English web design of the online questionnaire and the database has been prepared by Microsoft ASP codes which is the script language of Microsoft Front Page editor and has been tested on personal web site. The questionnaire has been pre applied in institutions providing virtual education in Australia. The English text of the questionnaire and web site design have been sent to educational technology and virtual education specialists in the countries of the study group. With the feedback received, the spelling mistakes have been corrected and concept and language validity have been completed. The application of the questionnaire has taken 40 weeks during March-November 2004. Only 135 institutes have replied. Two of the questionnaires have been discharged because they included mistaken coding, names of the institutions and countries. Valid 133 questionnaires cover approximately 44% of the study group. Questionnaires saved in the online database have been transferred to Microsoft Excel and then to SPSS by external database connection. In regards of the research objectives, the data collected has been analyzed on computer and by using SPSS statistics package program. In data analysis frequency (f, percentage (% and arithmetic mean ( have been used. In comparisons of country, institute, year, and other variables, che-square test, independent t

  10. Semantic Signature: Comparative Interpretation of Gene Expression on a Semantic Space

    Directory of Open Access Journals (Sweden)

    Jihun Kim

    2016-01-01

    Full Text Available Background. Interpretation of microarray data remains challenging because biological meaning should be extracted from enormous numeric matrices and be presented explicitly. Moreover, huge public repositories of microarray dataset are ready to be exploited for comparative analysis. This study aimed to provide a platform where essential implication of a microarray experiment could be visually expressed and various microarray datasets could be intuitively compared. Results. On the semantic space, gene sets from Molecular Signature Database (MSigDB were plotted as landmarks and their relative distances were calculated by Lin’s semantic similarity measure. By formal concept analysis, a microarray dataset was transformed into a concept lattice with gene clusters as objects and Gene Ontology terms as attributes. Concepts of a lattice were located on the semantic space reflecting semantic distance from landmarks and edges between concepts were drawn; consequently, a specific geographic pattern could be observed from a microarray dataset. We termed a distinctive geography shared by microarray datasets of the same category as “semantic signature.” Conclusions. “Semantic space,” a map of biological entities, could serve as a universal platform for comparative microarray analysis. When microarray data were displayed on the semantic space as concept lattices, “semantic signature,” characteristic geography for a microarray experiment, could be discovered.

  11. A comparative study of effect of autograft compared with allograft anterior cruciate ligament reconstruction on expressions ofLOXsandMMPs.

    Science.gov (United States)

    Wang, Wei-Ming; Ma, Xiao-Jun; Huang, Shi-Bo; Ren, Liu-Bao; Liu, Yu-Peng

    2017-04-30

    The present study aimed to compare the effect of autograft or allograft anterior cruciate ligament (ACL) reconstruction on the expressions of lipoxygenases ( LOXs ) and matrix metalloproteinases ( MMPs ) in a New Zealand white rabbit model. New Zealand white rabbits were divided randomly into control, sham, autograft and allograft groups. At the 4th and 8th week after operation, biomechanical testing was performed to measure the primary length, cross-sectional area, maximum tensile load and stiffness of ACL, and HE staining was used to observe cell morphology and fibre alignment of ACL. At the 2nd, 4th and 8th week after operation, quantitative real-time PCR (qRT-PCR), Western blotting and immunohistochemistry were applied to detect LOXs and MMPs expressions, and expressions of adenomatous polyposis coli (APC)/Wnt signalling pathway-related proteins. At the 4th and 8th week after operation, the maximum tensile load and stiffness were higher in the autograft group than in the allograft group, and the values at the 8th week were higher than those at the 4th week after operation. The fibroblast proliferation in the allograft group was more significant than that in the autograft group. Compared with the control group, LOXs and MMPs expressions and the positive expression rates of LOXs and MMPs proteins were elevated, and the values in the allograft group were higher than those in the autograft group at all time points. At 8th week after operation, compared with the autograft group, Wnt expression was higher and APC expression was lower in the allograft group. Autograft and allograft ACL reconstruction can promote LOXs and MMPs expressions by activating the APC/Wnt signalling pathway. © 2017 The Author(s).

  12. Comparative analysis of planetary laser ranging concepts

    Science.gov (United States)

    Dirkx, D.; Bauer, S.; Noomen, R.; Vermeersen, B. L. A.; Visser, P. N.

    2014-12-01

    missions for various combinations of clock and state arc length. Thereby, we quantify the relative capabilities of the one- and two-way laser range systems. In addition, we study the optimal data analysis strategies for these missions, which we apply for LRO orbit determination. Finally, we compare the performance of the laser ranging systems with typical DSN tracking.

  13. A comparative analysis of influenza vaccination programs.

    Directory of Open Access Journals (Sweden)

    Shweta Bansal

    2006-10-01

    Full Text Available BACKGROUND: The threat of avian influenza and the 2004-2005 influenza vaccine supply shortage in the United States have sparked a debate about optimal vaccination strategies to reduce the burden of morbidity and mortality caused by the influenza virus. METHODS AND FINDINGS: We present a comparative analysis of two classes of suggested vaccination strategies: mortality-based strategies that target high-risk populations and morbidity-based strategies that target high-prevalence populations. Applying the methods of contact network epidemiology to a model of disease transmission in a large urban population, we assume that vaccine supplies are limited and then evaluate the efficacy of these strategies across a wide range of viral transmission rates and for two different age-specific mortality distributions. We find that the optimal strategy depends critically on the viral transmission level (reproductive rate of the virus: morbidity-based strategies outperform mortality-based strategies for moderately transmissible strains, while the reverse is true for highly transmissible strains. These results hold for a range of mortality rates reported for prior influenza epidemics and pandemics. Furthermore, we show that vaccination delays and multiple introductions of disease into the community have a more detrimental impact on morbidity-based strategies than mortality-based strategies. CONCLUSIONS: If public health officials have reasonable estimates of the viral transmission rate and the frequency of new introductions into the community prior to an outbreak, then these methods can guide the design of optimal vaccination priorities. When such information is unreliable or not available, as is often the case, this study recommends mortality-based vaccination priorities.

  14. AUDITOR ROTATION - A CRITICAL AND COMPARATIVE ANALYSIS

    Directory of Open Access Journals (Sweden)

    Mocanu Mihaela

    2011-12-01

    Full Text Available The present paper starts out from the challenge regarding auditor tenure launched in 2010 by the Green Paper of the European Commission Audit Policy: Lessons from the Crisis. According to this document, the European Commission speaks both in favor of the mandatory rotation of the audit firm, and in favor of the mandatory rotation of audit partners. Rotation is considered a solution to mitigate threats to independence generated by familiarity, intimidation and self-interest in the context of a long-term audit-client relationship. At international level, there are several studies on auditor rotation, both empirical (e.g. Lu and Sivaramakrishnan, 2009, Li, 2010, Kaplan and Mauldin, 2008, Jackson et al., 2008 and normative in nature (e.g. Marten et al., 2007, Muller, 2006 and Gelter, 2004. The objective of the present paper is to perform a critical and comparative analysis of the regulations on internal and external rotation in force at international level, in the European Union and in the United States of America. Moreover, arguments both in favor and against mandatory rotation are brought into discussion. With regard to the research design, the paper has a normative approach. The main findings are first of all that by comparison, all regulatory authorities require internal rotation at least in the case of public interest entities, while the external rotation is not in the focus of the regulators. In general, the most strict and detailed requirements are those issued by the Securities and Exchange Commission from the United States of America. Second of all, in favor of mandatory rotation speaks the fact that the auditor becomes less resilient in case of divergence of opinions between him and company management, less stimulated to follow his own interest, and more scrupulous in conducting the audit. However, mandatory rotation may also have negative consequences, thus the debate on the opportunity of this regulatory measure remains open-ended.

  15. RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species.

    Science.gov (United States)

    Lei, Xintao; Xiao, Yong; Xia, Wei; Mason, Annaliese S; Yang, Yaodong; Ma, Zilong; Peng, Ming

    2014-01-01

    Elaeis guineensis as a tropical oil-crop is particularly sensitive to low temperature. Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide. We sequenced cold-treated and control (untreated) samples of Elaeis guineensis. De novo assembly generated 51,452 unigenes with an average length of 703 bp. Subsequently, these expressed sequences were functionally annotated. In the K category (transcription factors) of COG (Cluster of Orthologous Group) annotation, the largest proportion of genes induced and repressed at least two-fold under cold stress were from the AP2/ERE family, indicating that C-repeat binding factor, (CBFs, members of the AP2/ERE family) may play a central role in cold tolerance in Elaeis guineensis. Subsequently, the CBF-mediated signal transduction pathway was reconstructed based on transcriptome data and the gene expression profile involving the pathway was examined using real-time quantitative RT-PCR (qRT-PCR). CBFs reached maximum transcript level both at medium (4 h) and long period time points (7 days), contrary to the expression pattern of CBFs in Arabidopsis and rice. Moreover, the promoters of downstream Cold Responsive gene (CORs) regulated by CBFs were analyzed. Conservation, mutation and absence of the DRE core motif were detected in the promoters of six CORs. These mutations in DRE motifs suggest that CORs may not be induced via cold stress in Elaeis guineensis.

  16. RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF mediated gene expression pattern in Elaeis guineensis compared to other species.

    Directory of Open Access Journals (Sweden)

    Xintao Lei

    Full Text Available Elaeis guineensis as a tropical oil-crop is particularly sensitive to low temperature. Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide. We sequenced cold-treated and control (untreated samples of Elaeis guineensis. De novo assembly generated 51,452 unigenes with an average length of 703 bp. Subsequently, these expressed sequences were functionally annotated. In the K category (transcription factors of COG (Cluster of Orthologous Group annotation, the largest proportion of genes induced and repressed at least two-fold under cold stress were from the AP2/ERE family, indicating that C-repeat binding factor, (CBFs, members of the AP2/ERE family may play a central role in cold tolerance in Elaeis guineensis. Subsequently, the CBF-mediated signal transduction pathway was reconstructed based on transcriptome data and the gene expression profile involving the pathway was examined using real-time quantitative RT-PCR (qRT-PCR. CBFs reached maximum transcript level both at medium (4 h and long period time points (7 days, contrary to the expression pattern of CBFs in Arabidopsis and rice. Moreover, the promoters of downstream Cold Responsive gene (CORs regulated by CBFs were analyzed. Conservation, mutation and absence of the DRE core motif were detected in the promoters of six CORs. These mutations in DRE motifs suggest that CORs may not be induced via cold stress in Elaeis guineensis.

  17. Comparative analysis of the virulence characteristics of epidemic methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from Chinese children: ST59 MRSA highly expresses core gene-encoded toxin.

    Science.gov (United States)

    Li, Shipeng; Sun, Jing; Zhang, Jianzhong; Li, Xiangmei; Tao, Xiaoxia; Wang, Lijuan; Sun, Mingjiao; Liu, Yingchao; Li, Juan; Qiao, Yanhong; Yu, Sangjie; Yao, Kaihu; Yang, Yonghong; Shen, Xuzhuang

    2014-02-01

    This study aims to investigate the prevalence of a novel cell wall-anchored protein gene, sasX, and to obtain information on the genetic basis for the pathogenic potential of the MRSA strains isolated from Chinese children. The molecular and virulence characteristics of the clinical strains were analyzed. Twenty-two sequence types (STs) were obtained, with six epidemic clones ST59, ST239, ST1, ST910, ST88, and ST338 accounting for 35.8, 22, 6.6, 6.6, 5.3, and 4.1% respectively. The expression levels of hla, psmα, and RNAIII were higher in ST59 than in other STs (p MRSA isolates. ST239-MRSA-SCCmecIII-t037 (61.5%) was the predominant sasX-positive MRSA clone. The expressions of PSMα and RNAIII were higher in sasX-positive ST239 isolates than in sasX-negative ST239 ones (p MRSA was higher than that by sasX-negative ST239 MRSA (p = 0.008). This study indicated that ST59 was the predominant clone in the MRSA isolates obtained from Chinese children and might have stronger pathogenic potential. The prevalence of the sasX gene in the MRSA isolates from children was relatively low. Furthermore, the sasX gene might be related to the expressions of PSMα and RNAIII and infection invasiveness. © 2013 APMIS Published by John Wiley & Sons Ltd.

  18. A comparative study of syndecan-1 expression in different odontogenic tumors.

    Science.gov (United States)

    Etemad-Moghadam, Shahroo; Alaeddini, Mojgan

    2017-01-01

    Expression of various cellular/molecular factors change during the course of tumor formation from odontogenic tissues of the tooth germ. Evaluation of these factors can help provide a better perception of the tumorigenesis and biologic behavior of odontogenic tumors (OTs). Syndecan-1 is a heparan sulfate proteoglycan which has not been extensively investigated in these lesions. The objective of the present study was to assess the immunohistochemical expression of CD138 in adenomatoid odontogenic tumor (AOT), ameloblastic fibroma (AF) and odontogenic myxoma (OM) and to compare it with ameloblastoma and keratocystic odontogenic tumor (KCOT). A total of 58 OTs consisting of 7 AOTs, 5 OMs, 7 AFs, 29 KCOTs and 10 ameloblastomas were immunohistochemically stained with monoclonal antibody against syndecan-1 and the percentage and intensity of the immunostained cells was assessed. Kruskal-Wallis test followed by Bonferroni analysis was used for comparisons (P tumors. Syndecan-1 may be involved in the pathogenesis of AOT, AF, KCOT and ameloblastoma. However, considering the different behaviors of these tumors along with their similar expression of syndecan-1, it seems that its effect on clinical aggressiveness is limited. The significance of negative immunoexpression of this protein in OM requires further investigation.

  19. Gene set analysis for longitudinal gene expression data

    Directory of Open Access Journals (Sweden)

    Piepho Hans-Peter

    2011-07-01

    Full Text Available Abstract Background Gene set analysis (GSA has become a successful tool to interpret gene expression profiles in terms of biological functions, molecular pathways, or genomic locations. GSA performs statistical tests for independent microarray samples at the level of gene sets rather than individual genes. Nowadays, an increasing number of microarray studies are conducted to explore the dynamic changes of gene expression in a variety of species and biological scenarios. In these longitudinal studies, gene expression is repeatedly measured over time such that a GSA needs to take into account the within-gene correlations in addition to possible between-gene correlations. Results We provide a robust nonparametric approach to compare the expressions of longitudinally measured sets of genes under multiple treatments or experimental conditions. The limiting distributions of our statistics are derived when the number of genes goes to infinity while the number of replications can be small. When the number of genes in a gene set is small, we recommend permutation tests based on our nonparametric test statistics to achieve reliable type I error and better power while incorporating unknown correlations between and within-genes. Simulation results demonstrate that the proposed method has a greater power than other methods for various data distributions and heteroscedastic correlation structures. This method was used for an IL-2 stimulation study and significantly altered gene sets were identified. Conclusions The simulation study and the real data application showed that the proposed gene set analysis provides a promising tool for longitudinal microarray analysis. R scripts for simulating longitudinal data and calculating the nonparametric statistics are posted on the North Dakota INBRE website http://ndinbre.org/programs/bioinformatics.php. Raw microarray data is available in Gene Expression Omnibus (National Center for Biotechnology Information with

  20. Comparative pharmacoeconomic analysis of benzathine penicillin ...

    African Journals Online (AJOL)

    Subjecting the cost and effectiveness to sensitivity analysis did not change this conclusion. Statistical analysis shows that there is a statistically significant difference in the effectiveness (outcome) of benzathine penicillin and procaine penicillin injection, (56.2%) (χ2 = 48.58, P<0.5), Therefore there is association between ...

  1. Human Capital Development: Comparative Analysis of BRICs

    Science.gov (United States)

    Ardichvili, Alexandre; Zavyalova, Elena; Minina, Vera

    2012-01-01

    Purpose: The goal of this article is to conduct macro-level analysis of human capital (HC) development strategies, pursued by four countries commonly referred to as BRICs (Brazil, Russia, India, and China). Design/methodology/approach: This analysis is based on comparisons of macro indices of human capital and innovativeness of the economy and a…

  2. Question analysis for Indonesian comparative question

    Science.gov (United States)

    Saelan, A.; Purwarianti, A.; Widyantoro, D. H.

    2017-01-01

    Information seeking is one of human needs today. Comparing things using search engine surely take more times than search only one thing. In this paper, we analyzed comparative questions for comparative question answering system. Comparative question is a question that comparing two or more entities. We grouped comparative questions into 5 types: selection between mentioned entities, selection between unmentioned entities, selection between any entity, comparison, and yes or no question. Then we extracted 4 types of information from comparative questions: entity, aspect, comparison, and constraint. We built classifiers for classification task and information extraction task. Features used for classification task are bag of words, whether for information extraction, we used lexical, 2 previous and following words lexical, and previous label as features. We tried 2 scenarios: classification first and extraction first. For classification first, we used classification result as a feature for extraction. Otherwise, for extraction first, we used extraction result as features for classification. We found that the result would be better if we do extraction first before classification. For the extraction task, classification using SMO gave the best result (88.78%), while for classification, it is better to use naïve bayes (82.35%).

  3. Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes.

    Directory of Open Access Journals (Sweden)

    Greg Boyle

    Full Text Available From photosynthetic bacteria to mammals, the circadian clock evolved to track diurnal rhythms and enable organisms to anticipate daily recurring changes such as temperature and light. It orchestrates a broad spectrum of physiology such as the sleep/wake and eating/fasting cycles. While we have made tremendous advances in our understanding of the molecular details of the circadian clock mechanism and how it is synchronized with the environment, we still have rudimentary knowledge regarding its connection to help regulate diurnal physiology. One potential reason is the sheer size of the output network. Diurnal/circadian transcriptomic studies are reporting that around 10% of the expressed genome is rhythmically controlled. Zebrafish is an important model system for the study of the core circadian mechanism in vertebrate. As Zebrafish share more than 70% of its genes with human, it could also be an additional model in addition to rodent for exploring the diurnal/circadian output with potential for translational relevance. Here we performed comparative diurnal/circadian transcriptome analysis with established mouse liver and other tissue datasets. First, by combining liver tissue sampling in a 48h time series, transcription profiling using oligonucleotide arrays and bioinformatics analysis, we profiled rhythmic transcripts and identified 2609 rhythmic genes. The comparative analysis revealed interesting features of the output network regarding number of rhythmic genes, proportion of tissue specific genes and the extent of transcription factor family expression. Undoubtedly, the Zebrafish model system will help identify new vertebrate outputs and their regulators and provides leads for further characterization of the diurnal cis-regulatory network.

  4. Comparative transcriptomic analysis of streptococcus pseudopneumoniae with viridans group streptococci

    Directory of Open Access Journals (Sweden)

    Park Hee

    2012-07-01

    Full Text Available Abstract Background Streptococcus pseudopneumoniae, is a novel member of the genus Streptococcus, falling close to related members like S. pneumoniae, S. mitis, and S. oralis. Its recent appearance has shed light on streptococcal infections, which has been unclear till recently. In this study, the transcriptome of S. pseudopneumoniae CCUG 49455T was analyzed using the S. pneumoniae R6 microarray platform and compared with those of S. pneumoniae KCTC 5080T, S. mitis KCTC 3556T, and S. oralis KCTC 13048T strains. Results Comparative transcriptome analysis revealed the extent of genetic relatedness among the species, and implies that S. pseudopneumoniae is the most closely related to S. pneumoniae. A total of 489, 444 and 470 genes were upregulated while 347, 484 and 443 were downregulated relative to S. pneumoniae in S. pseudopneumoniae, S. oralis and S. mitis respectively. Important findings were the up-regulation of TCS (two component systems and transposase which were found to be specific to S. pseudopneumoniae. Conclusions This study provides insight to the current understanding of the genomic content of S. pseudopneumoniae. The comparative transcriptome analysis showed hierarchical clustering of expression data of S. pseudopneumoniae with S. pneumoniae and S. mitis with S. oralis. This proves that transcriptional profiling can facilitate in elucidating the genetic distance between closely related strains.

  5. MANAGEMENT AND COMPARATIVE ANALYSIS OF DATASET ENSEMBLES

    Energy Technology Data Exchange (ETDEWEB)

    Geveci, Berk [Senior Director, Scientific Computing

    2010-05-17

    The primary Phase I technical objective was to develop a prototype that demonstrates the functionality of all components required for an end-to-end meta-data management and comparative visualization system.

  6. Comparative analysis of seismic risk assessment methodology

    Energy Technology Data Exchange (ETDEWEB)

    Park, Chang Kyoo; Kim, Tae Woon; Hwang, Mi Jung [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1994-07-01

    SRA methodologies are separated into SPSA and SMM. SPSA methodology that has been widely used for seismic risk analysis has two kinds of methodologies such as Zion method and SSMRP method. SPSA methodology is suitable to interfacing with the analysis of internal event. However, the results of SPSA have uncertainties because of uncertainties in seismic hazard analysis and subjective judgement. Zion method specially developed for commercial use is less expensive and less time consuming but more uncertain than SSMRP method, since the former performs the fragility analysis less in detail than the latter. SMM is impossible to interface with the analysis of internal event but the uncertainties that are occurred during seismic hazard analysis is reduced because of the screening using RLE (review level earthquake). Therefore, if SPSA-based SMM methodology is chosen to be developed, the results of SRA will be more reliable and it requires low costs and time. In addition, the new methodology will require the development of a new evaluating code for SRA. (Author) 26 refs., 25 figs., 16 tabs.

  7. Comparing Results from Constant Comparative and Computer Software Methods: A Reflection about Qualitative Data Analysis

    Science.gov (United States)

    Putten, Jim Vander; Nolen, Amanda L.

    2010-01-01

    This study compared qualitative research results obtained by manual constant comparative analysis with results obtained by computer software analysis of the same data. An investigated about issues of trustworthiness and accuracy ensued. Results indicated that the inductive constant comparative data analysis generated 51 codes and two coding levels…

  8. Comparative gene expression profiling in two congenic mouse strains following Bordetella pertussis infection

    Directory of Open Access Journals (Sweden)

    Demant Peter

    2007-10-01

    Full Text Available Abstract Background Susceptibility to Bordetella pertussis infection varies widely. These differences can partly be explained by genetic host factors. HcB-28 mice are more resistant to B. pertussis infection than C3H mice, which could partially be ascribed to the B. pertussis susceptibility locus-1 (Bps1 on chromosome 12. The presence of C57BL/10 genome on this locus instead of C3H genome resulted in a decreased number of bacteria in the lung. To further elucidate the role of host genetic factors, in particular in the Bps1 locus, in B. pertussis infection, and to identify candidate genes within in this region, we compared expression profiles in the lungs of the C3H and HcB-28 mouse strains following B. pertussis inoculation. Twelve and a half percent of the genomes of these mice are from a different genetic background. Results Upon B. pertussis inoculation 2,353 genes were differentially expressed in the lungs of both mouse strains. Two hundred and six genes were differentially expressed between the two mouse strains, but, remarkably, none of these were up- or down-regulated upon B. pertussis infection. Of these 206 genes, 17 were located in the Bps1 region. Eight of these genes, which showed a strong difference in gene expression between the two mouse strains, map to the immunoglobulin heavy chain complex (Igh. Conclusion Gene expression changes upon B. pertussis infection are highly identical between the two mouse strains despite the differences in the course of B. pertussis infection. Because the genes that were differentially regulated between the mouse strains only showed differences in expression before infection, it appears likely that such intrinsic differences in gene regulation are involved in determining differences in susceptibility to B. pertussis infection. Alternatively, such genetic differences in susceptibility may be explained by genes that are not differentially regulated between these two mouse strains. Genes in the Igh

  9. Expression of core clock genes in colorectal tumour cells compared with normal mucosa

    DEFF Research Database (Denmark)

    Fonnes, S; Donatsky, A M; Gögenur, I

    2015-01-01

    AIM: Experimental studies have shown that some circadian core clock genes may act as tumour suppressors and have an important role in the response to oncological treatment. This study investigated the evidence regarding modified expression of core clock genes in colorectal cancer and its...... expression of colorectal cancer cells compared with healthy mucosa cells from specimens analysed by real-time or quantitative real-time polymer chain reaction. The expression of the core clock genes Period, Cryptochrome, Bmal1 and Clock in colorectal tumours were compared with healthy mucosa and correlated...... with clinicopathological features and survival. RESULTS: Seventy-four articles were identified and 11 studies were included. Overall, gene expression of Period was significantly decreased in colorectal cancer cells compared with healthy mucosa cells. This tendency was also seen in the gene expression of Clock. Other core...

  10. Analysis of the promoters involved in enterocin AS-48 expression.

    Directory of Open Access Journals (Sweden)

    Rubén Cebrián

    Full Text Available The enterocin AS-48 is the best characterized antibacterial circular protein in prokaryotes. It is a hydrophobic and cationic bacteriocin, which is ribosomally synthesized by enterococcal cells and post-translationally cyclized by a head-to-tail peptide bond. The production of and immunity towards AS-48 depend upon the coordinated expression of ten genes organized in two operons, as-48ABC (where genes encoding enzymes with processing, secretion, and immunity functions are adjacent to the structural as-48A gene and as-48C1DD1EFGH. The current study describes the identification of the promoters involved in AS-48 expression. Seven putative promoters have been here amplified, and separately inserted into the promoter-probe vector pTLR1, to create transcriptional fusions with the mCherry gene used as a reporter. The activity of these promoter regions was assessed measuring the expression of the fluorescent mCherry protein using the constitutive pneumococcal promoter PX as a reference. Our results revealed that only three promoters PA, P2(2 and PD1 were recognized in Enterococcus faecalis, Lactococcus lactis and Escherichia coli, in the conditions tested. The maximal fluorescence was obtained with PX in all the strains, followed by the P2(2 promoter, which level of fluorescence was 2-fold compared to PA and 4-fold compared to PD1. Analysis of putative factors influencing the promoter activity in single and double transformants in E. faecalis JH2-2 demonstrated that, in general, a better expression was achieved in presence of pAM401-81. In addition, the P2(2 promoter could be regulated in a negative fashion by genes existing in the native pMB-2 plasmid other than those of the as-48 cluster, while the pH seems to affect differently the as-48 promoter expression.

  11. Gene expression profiling and bioinformatics analysis of gastric carcinoma.

    Science.gov (United States)

    Liu, Ningning; Liu, Xuan; Zhou, Ning; Wu, Qiong; Zhou, Lihong; Li, Qi

    2014-06-01

    Gastric cancer remains one of the major health problems worldwide, and it is one of the most common cancers and the leading cause of cancer-related deaths in China. This study was to analyze the expression profiles of genes in gastric carcinoma, and predict potential regulating factors. The gene expression profile data GSE13911 was downloaded from Gene Expression Omnibus and the differentially expressed genes (DEGs) were identified by t-test. Gene modules were constructed using hierarchical clustering in R based on average linkage and Pearson's correlation coefficient and functional analysis for these genes were performed with DAVID. Genes in each module with Pearson's correlation coefficient >0.3 were obtained to construct co-expression network. Protein-protein interactions (PPIs) were identified by comparing protein-protein interaction (PPI) network with co-expression networks. In addition, the potential regulatory microRNAs and the transcription factors for each module were screened out. In this study, six modules associated with protein degradation, cell cycle, protein trafficking and immunoreaction were identified. COPS5 (COP9 Subunit 5) was the core protein in the largest PPI network of module 1. The transcription factors MYC and MAZ (Myc-associated zinc-finger protein) were enriched in module 1. A total of 9 microRNA-target bi-clusters were identified and module 1 enriched 20 genes targeting to miR-17-92 gene cluster(miR-17/20ab)and miR-106b-25 gene cluster (miR-106b/93). In conclusion, we constructed 6 gene modules and screened out some genes, transcriptional factors and microRNAs that may be used as potential molecular biomarkers for gastric carcinoma. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Recombinant protein expression and solubility screening in Escherichia coli: a comparative study

    NARCIS (Netherlands)

    Berrow, N.S.; Folkers, G.E.

    2006-01-01

    Producing soluble proteins in Escherichia coli is still a major bottleneck for structural proteomics. Therefore, screening for soluble expression on a small scale is an attractive way of identifying constructs that are likely to be amenable to structural analysis. Avariety of expression-screening

  13. Gene Expression Signature in Endemic Osteoarthritis by Microarray Analysis

    Directory of Open Access Journals (Sweden)

    Xi Wang

    2015-05-01

    Full Text Available Kashin-Beck Disease (KBD is an endemic osteochondropathy with an unknown pathogenesis. Diagnosis of KBD is effective only in advanced cases, which eliminates the possibility of early treatment and leads to an inevitable exacerbation of symptoms. Therefore, we aim to identify an accurate blood-based gene signature for the detection of KBD. Previously published gene expression profile data on cartilage and peripheral blood mononuclear cells (PBMCs from adults with KBD were compared to select potential target genes. Microarray analysis was conducted to evaluate the expression of the target genes in a cohort of 100 KBD patients and 100 healthy controls. A gene expression signature was identified using a training set, which was subsequently validated using an independent test set with a minimum redundancy maximum relevance (mRMR algorithm and support vector machine (SVM algorithm. Fifty unique genes were differentially expressed between KBD patients and healthy controls. A 20-gene signature was identified that distinguished between KBD patients and controls with 90% accuracy, 85% sensitivity, and 95% specificity. This study identified a 20-gene signature that accurately distinguishes between patients with KBD and controls using peripheral blood samples. These results promote the further development of blood-based genetic biomarkers for detection of KBD.

  14. Comparative Distributions of Hazard Modeling Analysis

    Directory of Open Access Journals (Sweden)

    Rana Abdul Wajid

    2006-07-01

    Full Text Available In this paper we present the comparison among the distributions used in hazard analysis. Simulation technique has been used to study the behavior of hazard distribution modules. The fundamentals of Hazard issues are discussed using failure criteria. We present the flexibility of the hazard modeling distribution that approaches to different distributions.

  15. COMPARATIVE ANALYSIS OF MECHANICAL AND MANUAL ...

    African Journals Online (AJOL)

    This study aims to analyze the current road traffic data collection methods - comparing both mechanical and manual mode of Traffic Survey simulation - in terms of capabilities and limitations on Nigeria roads using Ogoja (Mbok) Junction and Mfum road in Cross River State as a case study. The tendency of the mechanical ...

  16. Comparative pharmacokinetic analysis with two omeprazole ...

    African Journals Online (AJOL)

    The pharmacokinetics of omeprazole pharmaceutical products Proceptin® 20mg capsule and Losec® 20mg MUPS tablet were compared in healthy subjects. The study was an open-‐label, randomized, two-‐treatment, two-sequence, two-way crossover, single-dose bioavailability study conducted under fasting conditions ...

  17. Comparative analysis of aggregate agricultural productivity between ...

    African Journals Online (AJOL)

    GREGORY

    2010-08-23

    Aug 23, 2010 ... used animal manure had a higher aggregate agricultural productivity than the HEIT farmers who used inorganic fertilizer. ... utilization of animal manure be put in place by the government. Key words: Aggregate agricultural .... (Kelly et al., 1995). To compare input productivities across goods or to aggregate.

  18. Comparative analysis of aggregate agricultural productivity between ...

    African Journals Online (AJOL)

    The study compared the aggregate agricultural productivity between the Low External Input Technology (LEIT) and High External Input Technology (HEIT) Farms in Imo State of Nigeria. The state is divided into three agricultural zones, out of which two were randomly selected for the study. Using a multistage sampling ...

  19. Explaining the judicial independence of international courts: a comparative analysis

    DEFF Research Database (Denmark)

    Beach, Derek

    What factors allow some international courts (ICs) to rule against the express preferences of powerful member states, whereas others routinely defer to governments? While judicial independence is not the only factor explaining the strength of a given international institution, it is a necessary...... condition. The paper first develops three sets of competing explanatory variables that potentially can explain variations in the judicial independence of ICs. The causal effects of these explanatory variables upon variance in judicial independence are investigated in a comparative analysis of the ACJ, ECJ......, ECtHR and IACHR. It is found that the threat of governmental noncompliance and the strength of the constituency possessed by an IC have the most explanatory power, although there is still a significant residual that can only be explained by looking at factors relating to judicial choices and agency....

  20. Clusters of adjacent and similarly expressed genes across normal human tissues complicate comparative transcriptomic discovery.

    Science.gov (United States)

    Liu, Chang; Ghosh, Sujoy; Searls, David B; Saunders, Ann M; Cossman, Jeffrey; Roses, Allen D

    2005-01-01

    Transcriptomic techniques are valuable tools with which to validate genetic and biological hypotheses and are now widely available for research. However, with the exception of tumor biology, comparative genomics analyses have been difficult to use as discovery engines to describe biologically relevant expression changes. We propose that physical proximity of human genes correlates with similar mRNA expression, so that increased expression might include a disease-relevant gene and many other genes in the adjacent region. To increase the efficiency of combining susceptibility gene mapping and interpretation of transcriptomics, we developed a method to identify clusters of adjacent and similarly expressed genes. Gene expression profiles for 28,945 genes across 101 normal human tissues were obtained from the Gene Logic BioExpress system. The expression similarity for genes in sliding-windows was measured using average pair-wise Pearson correlation coefficients. We identified 187 clusters (p < 10e-4) of co-regulated genes, including 2648 genes, or 9.1% of all genes considered and termed these "clusters of adjacent and similarly expressed genes" (CASEGs). Genes in 15 (8.2%) of these clusters demonstrate a significant co-expression enrichment (p < 10e-10). This study demonstrates the coordinate expression of neighboring genes and provides a comprehensive view of expression-based compartmentalization of the human genome, which can be overlaid on genetic susceptibility gene maps.

  1. Cloning and expression analysis of a partial LEAFY homologue from ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-14

    Nov 14, 2011 ... 2South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang, Guangdong ... RT-PCR analysis showed that the AcLFY could be expressed constitutionally. Moreover, it was expressed in the flesh of young fruit and bract at low levels, and was highly expressed ...

  2. Comparative gene expression profiles induced by PPARγ and PPARα/γ agonists in human hepatocytes.

    Directory of Open Access Journals (Sweden)

    Alexandra Rogue

    Full Text Available BACKGROUND: Several glitazones (PPARγ agonists and glitazars (dual PPARα/γ agonists have been developed to treat hyperglycemia and, simultaneously, hyperglycemia and dyslipidemia, respectively. However, most have caused idiosyncratic hepatic or extrahepatic toxicities through mechanisms that remain largely unknown. Since the liver plays a key role in lipid metabolism, we analyzed changes in gene expression profiles induced by these two types of PPAR agonists in human hepatocytes. METHODOLOGY/PRINCIPAL FINDINGS: Primary human hepatocytes and the well-differentiated human hepatoma HepaRG cells were exposed to different concentrations of two PPARγ (troglitazone and rosiglitazone and two PPARα/γ (muraglitazar and tesaglitazar agonists for 24 h and their transcriptomes were analyzed using human pangenomic Agilent microarrays. Principal Component Analysis, hierarchical clustering and Ingenuity Pathway Analysis® revealed large inter-individual variability in the response of the human hepatocyte populations to the different compounds. Many genes involved in lipid, carbohydrate, xenobiotic and cholesterol metabolism, as well as inflammation and immunity, were regulated by both PPARγ and PPARα/γ agonists in at least a number of human hepatocyte populations and/or HepaRG cells. Only a few genes were selectively deregulated by glitazars when compared to glitazones, indicating that PPARγ and PPARα/γ agonists share most of their target genes. Moreover, some target genes thought to be regulated only in mouse or to be expressed in Kupffer cells were also found to be responsive in human hepatocytes and HepaRG cells. CONCLUSIONS/SIGNIFICANCE: This first comprehensive analysis of gene regulation by PPARγ and PPARα/γ agonists favor the conclusion that glitazones and glitazars share most of their target genes and induce large differential changes in gene profiles in human hepatocytes depending on hepatocyte donor, the compound class and/or individual

  3. Comparing methods for single paragraph similarity analysis.

    Science.gov (United States)

    Stone, Benjamin; Dennis, Simon; Kwantes, Peter J

    2011-01-01

    The focus of this paper is two-fold. First, similarities generated from six semantic models were compared to human ratings of paragraph similarity on two datasets-23 World Entertainment News Network paragraphs and 50 ABC newswire paragraphs. Contrary to findings on smaller textual units such as word associations (Griffiths, Tenenbaum, & Steyvers, 2007), our results suggest that when single paragraphs are compared, simple nonreductive models (word overlap and vector space) can provide better similarity estimates than more complex models (LSA, Topic Model, SpNMF, and CSM). Second, various methods of corpus creation were explored to facilitate the semantic models' similarity estimates. Removing numeric and single characters, and also truncating document length improved performance. Automated construction of smaller Wikipedia-based corpora proved to be very effective, even improving upon the performance of corpora that had been chosen for the domain. Model performance was further improved by augmenting corpora with dataset paragraphs. Copyright © 2010 Cognitive Science Society, Inc.

  4. Comparative expression profiling of Leishmania: modulation in gene expression between species and in different host genetic backgrounds.

    Directory of Open Access Journals (Sweden)

    Daniel P Depledge

    2009-07-01

    Full Text Available Genome sequencing of Leishmania species that give rise to a range of disease phenotypes in the host has revealed highly conserved gene content and synteny across the genus. Only a small number of genes are differentially distributed between the three species sequenced to date, L. major, L. infantum and L. braziliensis. It is not yet known how many of these genes are expressed in the disease-promoting intracellular amastigotes of these species or whether genes conserved between the species are differentially expressed in the host.We have used customised oligonucleotide microarrays to confirm that all of the differentially distributed genes identified by genome comparisons are expressed in intracellular amastigotes, with only a few of these subject to regulation at the RNA level. In the first large-scale study of gene expression in L. braziliensis, we show that only approximately 9% of the genes analysed are regulated in their RNA expression during the L. braziliensis life cycle, a figure consistent with that observed in other Leishmania species. Comparing amastigote gene expression profiles between species confirms the proposal that Leishmania transcriptomes undergo little regulation but also identifies conserved genes that are regulated differently between species in the host. We have also investigated whether host immune competence influences parasite gene expression, by comparing RNA expression profiles in L. major amastigotes derived from either wild-type (BALB/c or immunologically compromised (Rag2(-/- gamma(c (-/- mice. While parasite dissemination from the site of infection is enhanced in the Rag2(-/- gamma(c (-/- genetic background, parasite RNA expression profiles are unperturbed.These findings support the hypothesis that Leishmania amastigotes are pre-adapted for intracellular survival and undergo little dynamic modulation of gene expression at the RNA level. Species-specific parasite factors contributing to virulence and pathogenicity

  5. Comparative proteomic analysis of ductal and lobular invasive breast carcinoma.

    Science.gov (United States)

    Oliveira, N C S; Gomig, T H B; Milioli, H H; Cordeiro, F; Costa, G G; Urban, C A; Lima, R S; Cavalli, I J; Ribeiro, E M S F

    2016-04-04

    Breast cancer is the second most common cancer worldwide and the first among women. Invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) are the two major histological subtypes, and the clinical and molecular differences between them justify the search for new markers to distinguish them. As proteomic analysis allows for a powerful and analytical approach to identify potential biomarkers, we performed a comparative analysis of IDC and ILC samples by using two-dimensional electrophoresis and mass spectrometry. Twenty-three spots were identified corresponding to 10 proteins differentially expressed between the two subtypes. ACTB, ACTG, TPM3, TBA1A, TBA1B, VIME, TPIS, PDIA3, PDIA6, and VTDB were upregulated in ductal carcinoma compared to in lobular carcinoma samples. Overall, these 10 proteins have a key role in oncogenesis. Their specific functions and relevance in cancer initiation and progression are further discussed in this study. The identified peptides represent promising biomarkers for the differentiation of ductal and lobular breast cancer subtypes, and for future interventions based on tailored therapy.

  6. Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution.

    Science.gov (United States)

    Davidson, Rebecca M; Gowda, Malali; Moghe, Gaurav; Lin, Haining; Vaillancourt, Brieanne; Shiu, Shin-Han; Jiang, Ning; Robin Buell, C

    2012-08-01

    The Poaceae family, also known as the grasses, includes agronomically important cereal crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown that much of the gene content is shared among the grasses; however, functional conservation of orthologous genes has yet to be explored. To gain an understanding of the genome-wide patterns of evolution of gene expression across reproductive tissues, we employed a sequence-based approach to compare analogous transcriptomes in species representing three Poaceae subgroups including the Pooideae (Brachypodium distachyon), the Panicoideae (sorghum), and the Ehrhartoideae (rice). Our transcriptome analyses reveal that only a fraction of orthologous genes exhibit conserved expression patterns. A high proportion of conserved orthologs include genes that are upregulated in physiologically similar tissues such as leaves, anther, pistil, and embryo, while orthologs that are highly expressed in seeds show the most diverged expression patterns. More generally, we show that evolution of gene expression profiles and coding sequences in the grasses may be linked. Genes that are highly and broadly expressed tend to be conserved at the coding sequence level while genes with narrow expression patterns show accelerated rates of sequence evolution. We further show that orthologs in syntenic genomic blocks are more likely to share correlated expression patterns compared with non-syntenic orthologs. These findings are important for agricultural improvement because sequence information is transferred from model species, such as Brachypodium, rice, and sorghum to crop plants without sequenced genomes. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  7. [Amaranth flour: characteristics, comparative analysis, application possibilities].

    Science.gov (United States)

    Zharkov, I M; Miroshnichenko, L A; Zviagin, A A; Bavykina, I A

    2014-01-01

    Amaranth flour--a product of amaranth seeds processing--is a valuable industrial raw material that has an unique chemical composition and may be used for nutrition of people suffering from intolerance to traditional cereals protein, including celiac disease patients. The research aim was to study the composition of amaranth flour of two types compared with semolina which is traditionally used for nutrition by Russian population, as well as to compare the composition of milk amaranth flour porridge with milk semolina porridge. The composition of amaranth whole-ground flour and amaranth flour of premium grade processed from amaranth seeds grown in Voronezh region has been researched. It is to be noted that protein content in amaranth flour was 10.8-24.3% higher than in semolina, and its biological value and NPU-coefficient were higher by 22.65 and 46.51% respectively; lysine score in amaranth flour protein of premium grade came up to 107.54%, and in semolina protein only 40.95%. The level of digestible carbohydrates, including starch, was lower in amaranth flour than in semolina by 2.79-12.85 and 4.76-15.85% respectively, while fiber content was 15.5-30 fold higher. Fat content in amaranth flour of premium grade was 2,4 fold lower than in whole-ground amaranth flour but it was 45% higher than in semolina. The main advantage of amaranth flour protein compared to wheat protein is the predominance of albumins and globulins and a minimal content of prolamines and alpha-gliadin complete absence. The specifics of chemical composition allow the amaranth flour to be recommended for being included into nutrition of both healthy children and adults and also celiac disease patients.

  8. Comparative Analysis of GOCI Ocean Color Products

    Directory of Open Access Journals (Sweden)

    Ruhul Amin

    2015-10-01

    Full Text Available The Geostationary Ocean Color Imager (GOCI is the first geostationary ocean color sensor in orbit that provides bio-optical properties from coastal and open waters around the Korean Peninsula at unprecedented temporal resolution. In this study, we compare the normalized water-leaving radiance (nLw products generated by the Naval Research Laboratory Automated Processing System (APS with those produced by the stand-alone software package, the GOCI Data Processing System (GDPS, developed by the Korean Ocean Research & Development Institute (KORDI. Both results are then compared to the nLw measured by the above water radiometer at the Ieodo site. This above-water radiometer is part of the Aerosol Robotic NETwork (AeroNET. The results indicate that the APS and GDPS processed  correlates well within the same image slot where the coefficient of determination (r2 is higher than 0.84 for all the bands from 412 nm to 745 nm. The agreement between APS and the AeroNET data is higher when compared to the GDPS results. The Root-Mean-Squared-Error (RMSE between AeroNET and APS data ranges from 0.24 [mW/(cm2srμm] at 555 nm to 0.52 [mW/(cm2srμm]  at 412 nm while RMSE between AeroNET and GDPS data ranges from 0.47 [mW/(cm2srμm] at 443 nm to 0.69 [mW/(cm2srμm]  at 490 nm.

  9. Suicide by aircraft: a comparative analysis.

    Science.gov (United States)

    Bills, Corey B; Grabowski, Jurek George; Li, Guohua

    2005-08-01

    Suicide is the 11 th leading cause of death in the United States. The objective of this study is to document the characteristics of aviation-related suicides and suicide attempts. Aviation accidents reported by the National Transportation Safety Board between 1983 and 2003 were screened for cases in which suicide was listed as a probable cause. For each suicide case, two accidents were randomly selected as controls, matched on sex of pilot, type of flight, state, and year of occurrence. Mantel-Haenszel summary Chi-square tests were used to compare cases to controls. Conditional logistic regression modeling was performed to assess the association of pilot and flight characteristics with suicide-related crashes. During the 21-yr study period, 37 pilots committed or attempted suicide by aircraft, with 36 resulting in at least one fatality. All the cases were men and involved general aviation flights. Toxicological test results revealed that 24% of the cases had used alcohol and 14% had used other illicit drugs. Underlying factors included domestic and social problems (46%), legal trouble (40%), and pre-existing psychiatric conditions (38%). Compared with controls, suicide cases involved younger pilots (p aircraft (p crashes caused by suicide differ from unintentional aviation accidents in pilot characteristics, crash circumstances, and outcomes.

  10. Comparative expression profiling of distinct T cell subsets undergoing oxidative stress.

    Directory of Open Access Journals (Sweden)

    Rudolf Lichtenfels

    Full Text Available The clinical outcome of adoptive T cell transfer-based immunotherapies is often limited due to different escape mechanisms established by tumors in order to evade the hosts' immune system. The establishment of an immunosuppressive micromilieu by tumor cells along with distinct subsets of tumor-infiltrating lymphocytes is often associated with oxidative stress that can affect antigen-specific memory/effector cytotoxic T cells thereby substantially reducing their frequency and functional activation. Therefore, protection of tumor-reactive cytotoxic T lymphocytes from oxidative stress may enhance the anti-tumor-directed immune response. In order to better define the key pathways/proteins involved in the response to oxidative stress a comparative 2-DE-based proteome analysis of naïve CD45RA(+ and their memory/effector CD45RO(+ T cell counterparts in the presence and absence of low dose hydrogen peroxide (H(2O(2 was performed in this pilot study. Based on the profiling data of these T cell subpopulations under the various conditions, a series of differentially expressed spots were defined, members thereof identified by mass spectrometry and subsequently classified according to their cellular function and localization. Representative targets responding to oxidative stress including proteins involved in signaling pathways, in regulating the cellular redox status as well as in shaping/maintaining the structural cell integrity were independently verified at the transcript and protein level under the same conditions in both T cell subsets. In conclusion the resulting profiling data describe complex, oxidative stress-induced, but not strictly concordant changes within the respective expression profiles of CD45RA(+ and CD45RO(+ T cells. Some of the differentially expressed genes/proteins might be further exploited as potential targets toward modulating the redox capacity of the distinct lymphocyte subsets thereby providing the basis for further studies

  11. Comparative Modal Analysis of Sieve Hardware Designs

    Science.gov (United States)

    Thompson, Nathaniel

    2012-01-01

    The CMTB Thwacker hardware operates as a testbed analogue for the Flight Thwacker and Sieve components of CHIMRA, a device on the Curiosity Rover. The sieve separates particles with a diameter smaller than 150 microns for delivery to onboard science instruments. The sieving behavior of the testbed hardware should be similar to the Flight hardware for the results to be meaningful. The elastodynamic behavior of both sieves was studied analytically using the Rayleigh Ritz method in conjunction with classical plate theory. Finite element models were used to determine the mode shapes of both designs, and comparisons between the natural frequencies and mode shapes were made. The analysis predicts that the performance of the CMTB Thwacker will closely resemble the performance of the Flight Thwacker within the expected steady state operating regime. Excitations of the testbed hardware that will mimic the flight hardware were recommended, as were those that will improve the efficiency of the sieving process.

  12. A Comparative Analysis of Crime Guns

    Directory of Open Access Journals (Sweden)

    Megan E. Collins

    2017-10-01

    Full Text Available Information is limited on how firearms move from legal possession to illegal possession and use in criminal activities, largely because of data collection capacity and a lack of recent, exhaustive recovery data across jurisdictions. This article includes both an analysis of firearms trace data and prisoner interviews across multiple jurisdictions: New Orleans, Louisiana, Prince George’s County, Maryland, and Chicago, Illinois. Findings indicate that recoveries and trace successes vary across jurisdictions and by type of crime. Jurisdiction regulations were associated with the proportion of guns purchased in state and time to recovery but not with purchaser characteristics. Interviews from imprisoned offenders in two jurisdictions revealed the most common method of obtaining a crime gun was to steal it or buy it off the street.

  13. Gallus expression in situ hybridization analysis: a chicken embryo gene expression database.

    Science.gov (United States)

    Antin, P B; Kaur, S; Stanislaw, S; Davey, S; Konieczka, J H; Yatskievych, T A; Darnell, D K

    2007-07-01

    With sequencing of the chicken genome largely completed, significant effort is focusing on gene annotation, including acquiring information about the patterns of gene expression. The chicken embryo is ideally suited to provide detailed temporal and spatial expression information through in situ hybridization gene expression analysis in vivo. We have developed the Gallus expression in situ hybridization analysis (GEISHA) database and user interface (http://geisha.arizona.edu) to serve as a centralized repository of in situ hybridization photos and metadata from chicken embryos. This report describes the design and implementation the GEISHA database and Web site and illustrates its usefulness for researchers in the biomedical and poultry science communities. Results from a recent comprehensive expression analysis of microRNA expression in chicken embryos are also presented.

  14. Comparative analysis of some search engines

    Directory of Open Access Journals (Sweden)

    Taiwo O. Edosomwan

    2010-10-01

    Full Text Available We compared the information retrieval performances of some popular search engines (namely, Google, Yahoo, AlltheWeb, Gigablast, Zworks and AltaVista and Bing/MSN in response to a list of ten queries, varying in complexity. These queries were run on each search engine and the precision and response time of the retrieved results were recorded. The first ten documents on each retrieval output were evaluated as being ‘relevant’ or ‘non-relevant’ for evaluation of the search engine’s precision. To evaluate response time, normalised recall ratios were calculated at various cut-off points for each query and search engine. This study shows that Google appears to be the best search engine in terms of both average precision (70% and average response time (2 s. Gigablast and AlltheWeb performed the worst overall in this study.

  15. Comparative analysis of cystatin superfamily in platyhelminths.

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    Aijiang Guo

    Full Text Available The cystatin superfamily is comprised of cysteine proteinase inhibitors and encompasses at least 3 subfamilies: stefins, cystatins and kininogens. In this study, the platyhelminth cystatin superfamily was identified and grouped into stefin and cystatin subfamilies. The conserved domain of stefins (G, QxVxG was observed in all members of platyhelminth stefins. The three characteristics of cystatins, the cystatin-like domain (G, QxVxG, PW, a signal peptide, and one or two conserved disulfide bonds, were observed in platyhelminths, with the exception of cestodes, which lacked the conserved disulfide bond. However, it is noteworthy that cestode cystatins had two tandem repeated domains, although the second tandem repeated domain did not contain a cystatin-like domain, which has not been previously reported. Tertiary structure analysis of Taenia solium cystatin, one of the cestode cystatins, demonstrated that the N-terminus of T. solium cystatin formed a five turn α-helix, a five stranded β-pleated sheet and a hydrophobic edge, similar to the structure of chicken cystatin. Although no conserved disulfide bond was found in T. solium cystatin, the models of T. solium cystatin and chicken cystatin corresponded at the site of the first disulfide bridge of the chicken cystatin. However, the two models were not similar regarding the location of the second disulfide bridge of chicken cystatin. These results showed that T. solium cystatin and chicken cystatin had similarities and differences, suggesting that the biochemistry of T. solium cystatin could be similar to chicken cystatin in its inhibitory function and that it may have further functional roles. The same results were obtained for other cestode cystatins. Phylogenetic analysis showed that cestode cystatins constituted an independent clade and implied that cestode cystatins should be considered to have formed a new clade during evolution.

  16. Global Gene Expression Analysis Using Machine Learning Methods

    OpenAIRE

    Xu, Min

    2015-01-01

    Microarray is a technology to quantitatively monitor the expression of large number of genes in parallel. It has become one of the main tools for global gene expression analysis in molecular biology research in recent years. The large amount of expression data generated by this technology makes the study of certain complex biological problems possible and machine learning methods are playing a crucial role in the analysis process. At present, many machine learning methods have been or have th...

  17. RESEARCH ARTICLE Cloning and expression analysis of chalcone ...

    Indian Academy of Sciences (India)

    Praveen Awasthi

    Expression analysis of CfCHS in different tissues and elicitor treatments showed that methyl jasmonate (MeJA) .... The PCR was followed by a dissociation curve analysis (heating to 95°C for. 10 s at normal ... were expressed as mg quercitin equivalent (mg QAE) per gram dry weight of plant material. The experiment was ...

  18. Biclustering methods: biological relevance and application in gene expression analysis.

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    Ali Oghabian

    Full Text Available DNA microarray technologies are used extensively to profile the expression levels of thousands of genes under various conditions, yielding extremely large data-matrices. Thus, analyzing this information and extracting biologically relevant knowledge becomes a considerable challenge. A classical approach for tackling this challenge is to use clustering (also known as one-way clustering methods where genes (or respectively samples are grouped together based on the similarity of their expression profiles across the set of all samples (or respectively genes. An alternative approach is to develop biclustering methods to identify local patterns in the data. These methods extract subgroups of genes that are co-expressed across only a subset of samples and may feature important biological or medical implications. In this study we evaluate 13 biclustering and 2 clustering (k-means and hierarchical methods. We use several approaches to compare their performance on two real gene expression data sets. For this purpose we apply four evaluation measures in our analysis: (1 we examine how well the considered (biclustering methods differentiate various sample types; (2 we evaluate how well the groups of genes discovered by the (biclustering methods are annotated with similar Gene Ontology categories; (3 we evaluate the capability of the methods to differentiate genes that are known to be specific to the particular sample types we study and (4 we compare the running time of the algorithms. In the end, we conclude that as long as the samples are well defined and annotated, the contamination of the samples is limited, and the samples are well replicated, biclustering methods such as Plaid and SAMBA are useful for discovering relevant subsets of genes and samples.

  19. Recognizing chemicals in patents: a comparative analysis.

    Science.gov (United States)

    Habibi, Maryam; Wiegandt, David Luis; Schmedding, Florian; Leser, Ulf

    2016-01-01

    Recently, methods for Chemical Named Entity Recognition (NER) have gained substantial interest, driven by the need for automatically analyzing todays ever growing collections of biomedical text. Chemical NER for patents is particularly essential due to the high economic importance of pharmaceutical findings. However, NER on patents has essentially been neglected by the research community for long, mostly because of the lack of enough annotated corpora. A recent international competition specifically targeted this task, but evaluated tools only on gold standard patent abstracts instead of full patents; furthermore, results from such competitions are often difficult to extrapolate to real-life settings due to the relatively high homogeneity of training and test data. Here, we evaluate the two state-of-the-art chemical NER tools, tmChem and ChemSpot, on four different annotated patent corpora, two of which consist of full texts. We study the overall performance of the tools, compare their results at the instance level, report on high-recall and high-precision ensembles, and perform cross-corpus and intra-corpus evaluations. Our findings indicate that full patents are considerably harder to analyze than patent abstracts and clearly confirm the common wisdom that using the same text genre (patent vs. scientific) and text type (abstract vs. full text) for training and testing is a pre-requisite for achieving high quality text mining results.

  20. LINGUISTIC AND POLITICAL ANALYSIS: COMPARATIVE ASPECTS

    Directory of Open Access Journals (Sweden)

    V. M. Alpatov

    2012-01-01

    Full Text Available Abstract: The article analyses the book on political systems and processes in the East prepared by MGIMO-University authors and edited by Alexei D. Voskressenski in order to show the differences in approach and methods used in linguistics and political science. The author shows two significant differences in present-day stressing that linguistics of the XIX century was closer to the present-day political science? As he believes. The first difference includes monism of political science approach, since the book reveals monistic scale from totalitarianism to democracy, while linguistic has abandoned the monistic view on typology. The second difference is the value-addedness of the political science approach. The value-free norm in linguistics presupposes setting up of a single standard for all speakers in order to reach full mutual understanding. In political science subjective criteria are decisive for evaluation. The article gives examples from the book to prove that political science, compared to linguistics, is not aimed at overcoming contradictions, distinguishing between the terms, avoiding unproved statements and subjective evaluations.

  1. SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis.

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    Raul Aguirre-Gamboa

    Full Text Available Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included. The website was implemented in JSP, JavaScript, MySQL, and R.

  2. Identification of Gene Networks Associated with Acute Myeloid Leukemia by Comparative Molecular Methylation and Expression Profiling

    Directory of Open Access Journals (Sweden)

    Margaret Dellett

    2010-01-01

    Full Text Available Around 80% of acute myeloid leukemia (AML patients achieve a complete remission, however many will relapse and ultimately die of their disease. The association between karyotype and prognosis has been studied extensively and identified patient cohorts as having favourable [e.g. t(8; 21, inv (16/t(16; 16, t(15; 17], intermediate [e.g. cytogenetically normal (NK-AML] or adverse risk [e.g. complex karyotypes]. Previous studies have shown that gene expression profiling signatures can classify the sub-types of AML, although few reports have shown a similar feature by using methylation markers. The global methylation patterns in 19 diagnostic AML samples were investigated using the Methylated CpG Island Amplification Microarray (MCAM method and CpG island microarrays containing 12,000 CpG sites. The first analysis, comparing favourable and intermediate cytogenetic risk groups, revealed significantly differentially methylated CpG sites (594 CpG islands between the two subgroups. Mutations in the NPM1 gene occur at a high frequency (40% within the NK-AML subgroup and are associated with a more favourable prognosis in these patients. A second analysis comparing the NPM1 mutant and wild-type research study subjects again identified distinct methylation profiles between these two subgroups. Network and pathway analysis revealed possible molecular mechanisms associated with the different risk and/or mutation sub-groups. This may result in a better classification of the risk groups, improved monitoring targets, or the identification of novel molecular therapies.

  3. Comparative and demographic analysis of orangutan genomes

    Science.gov (United States)

    Locke, Devin P.; Hillier, LaDeana W.; Warren, Wesley C.; Worley, Kim C.; Nazareth, Lynne V.; Muzny, Donna M.; Yang, Shiaw-Pyng; Wang, Zhengyuan; Chinwalla, Asif T.; Minx, Pat; Mitreva, Makedonka; Cook, Lisa; Delehaunty, Kim D.; Fronick, Catrina; Schmidt, Heather; Fulton, Lucinda A.; Fulton, Robert S.; Nelson, Joanne O.; Magrini, Vincent; Pohl, Craig; Graves, Tina A.; Markovic, Chris; Cree, Andy; Dinh, Huyen H.; Hume, Jennifer; Kovar, Christie L.; Fowler, Gerald R.; Lunter, Gerton; Meader, Stephen; Heger, Andreas; Ponting, Chris P.; Marques-Bonet, Tomas; Alkan, Can; Chen, Lin; Cheng, Ze; Kidd, Jeffrey M.; Eichler, Evan E.; White, Simon; Searle, Stephen; Vilella, Albert J.; Chen, Yuan; Flicek, Paul; Ma, Jian; Raney, Brian; Suh, Bernard; Burhans, Richard; Herrero, Javier; Haussler, David; Faria, Rui; Fernando, Olga; Darré, Fleur; Farré, Domènec; Gazave, Elodie; Oliva, Meritxell; Navarro, Arcadi; Roberto, Roberta; Capozzi, Oronzo; Archidiacono, Nicoletta; Valle, Giuliano Della; Purgato, Stefania; Rocchi, Mariano; Konkel, Miriam K.; Walker, Jerilyn A.; Ullmer, Brygg; Batzer, Mark A.; Smit, Arian F. A.; Hubley, Robert; Casola, Claudio; Schrider, Daniel R.; Hahn, Matthew W.; Quesada, Victor; Puente, Xose S.; Ordoñez, Gonzalo R.; López-Otín, Carlos; Vinar, Tomas; Brejova, Brona; Ratan, Aakrosh; Harris, Robert S.; Miller, Webb; Kosiol, Carolin; Lawson, Heather A.; Taliwal, Vikas; Martins, André L.; Siepel, Adam; RoyChoudhury, Arindam; Ma, Xin; Degenhardt, Jeremiah; Bustamante, Carlos D.; Gutenkunst, Ryan N.; Mailund, Thomas; Dutheil, Julien Y.; Hobolth, Asger; Schierup, Mikkel H.; Chemnick, Leona; Ryder, Oliver A.; Yoshinaga, Yuko; de Jong, Pieter J.; Weinstock, George M.; Rogers, Jeffrey; Mardis, Elaine R.; Gibbs, Richard A.; Wilson, Richard K.

    2011-01-01

    “Orangutan” is derived from the Malay term “man of the forest” and aptly describes the Southeast Asian great apes native to Sumatra and Borneo. The orangutan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orangutan draft genome assembly and short read sequence data from five Sumatran and five Bornean orangutan genomes. Our analyses reveal that, compared to other primates, the orangutan genome has many unique features. Structural evolution of the orangutan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe the first primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orangutan genome structure. Orangutans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400k years ago (ya), is more recent than most previous studies and underscores the complexity of the orangutan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities

  4. Gene expression analysis of zebrafish heart regeneration.

    Directory of Open Access Journals (Sweden)

    Ching-Ling Lien

    2006-08-01

    Full Text Available Mammalian hearts cannot regenerate. In contrast, zebrafish hearts regenerate even when up to 20% of the ventricle is amputated. The mechanism of zebrafish heart regeneration is not understood. To systematically characterize this process at the molecular level, we generated transcriptional profiles of zebrafish cardiac regeneration by microarray analyses. Distinct gene clusters were identified based on temporal expression patterns. Genes coding for wound response/inflammatory factors, secreted molecules, and matrix metalloproteinases are expressed in regenerating heart in sequential patterns. Comparisons of gene expression profiles between heart and fin regeneration revealed a set of regeneration core molecules as well as tissue-specific factors. The expression patterns of several secreted molecules around the wound suggest that they play important roles in heart regeneration. We found that both platelet-derived growth factor-a and -b (pdgf-a and pdgf-b are upregulated in regenerating zebrafish hearts. PDGF-B homodimers induce DNA synthesis in adult zebrafish cardiomyocytes. In addition, we demonstrate that a chemical inhibitor of PDGF receptor decreases DNA synthesis of cardiomyocytes both in vitro and in vivo during regeneration. Our data indicate that zebrafish heart regeneration is associated with sequentially upregulated wound healing genes and growth factors and suggest that PDGF signaling is required.

  5. Proteomic Analysis of Bacterial Expression Profiles Following ...

    African Journals Online (AJOL)

    Results: Five differentially expressed bacterial proteins (four from Escherichia coli and one from Staphylococcus aureus), were identified via proteomic approach. Among the bacterial proteins identified, glutamate decarboxylase, elongation factor-Tu and α-hemolysin are especially noteworthy, as they are implicated in ...

  6. Comparative analysis of gene expression profiles of OPN signalling ...

    Indian Academy of Sciences (India)

    migration, cell proliferation were remarkably increased, while that of apoptosis, stress and inflammatory reaction were reduced in four kinds of liver diseases. ... OPN was involved in multiple liver diseases by promoting inflammatory reaction, ...... obesity-induced inflammation and insulin resistance. Diabetes. 59, 935–946.

  7. Pathway level analysis of gene expression using singular value decomposition.

    Science.gov (United States)

    Tomfohr, John; Lu, Jun; Kepler, Thomas B

    2005-09-12

    A promising direction in the analysis of gene expression focuses on the changes in expression of specific predefined sets of genes that are known in advance to be related (e.g., genes coding for proteins involved in cellular pathways or complexes). Such an analysis can reveal features that are not easily visible from the variations in the individual genes and can lead to a picture of expression that is more biologically transparent and accessible to interpretation. In this article, we present a new method of this kind that operates by quantifying the level of 'activity' of each pathway in different samples. The activity levels, which are derived from singular value decompositions, form the basis for statistical comparisons and other applications. We demonstrate our approach using expression data from a study of type 2 diabetes and another of the influence of cigarette smoke on gene expression in airway epithelia. A number of interesting pathways are identified in comparisons between smokers and non-smokers including ones related to nicotine metabolism, mucus production, and glutathione metabolism. A comparison with results from the related approach, 'gene-set enrichment analysis', is also provided. Our method offers a flexible basis for identifying differentially expressed pathways from gene expression data. The results of a pathway-based analysis can be complementary to those obtained from one more focused on individual genes. A web program PLAGE (Pathway Level Analysis of Gene Expression) for performing the kinds of analyses described here is accessible at http://dulci.biostat.edu/pathways.

  8. Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq.

    Science.gov (United States)

    Williams, Claire R; Baccarella, Alyssa; Parrish, Jay Z; Kim, Charles C

    2017-01-17

    RNA-Seq has supplanted microarrays as the preferred method of transcriptome-wide identification of differentially expressed genes. However, RNA-Seq analysis is still rapidly evolving, with a large number of tools available for each of the three major processing steps: read alignment, expression modeling, and identification of differentially expressed genes. Although some studies have benchmarked these tools against gold standard gene expression sets, few have evaluated their performance in concert with one another. Additionally, there is a general lack of testing of such tools on real-world, physiologically relevant datasets, which often possess qualities not reflected in tightly controlled reference RNA samples or synthetic datasets. Here, we evaluate 219 combinatorial implementations of the most commonly used analysis tools for their impact on differential gene expression analysis by RNA-Seq. A test dataset was generated using highly purified human classical and nonclassical monocyte subsets from a clinical cohort, allowing us to evaluate the performance of 495 unique workflows, when accounting for differences in expression units and gene- versus transcript-level estimation. We find that the choice of methodologies leads to wide variation in the number of genes called significant, as well as in performance as gauged by precision and recall, calculated by comparing our RNA-Seq results to those from four previously published microarray and BeadChip analyses of the same cell populations. The method of differential gene expression identification exhibited the strongest impact on performance, with smaller impacts from the choice of read aligner and expression modeler. Many workflows were found to exhibit similar overall performance, but with differences in their calibration, with some biased toward higher precision and others toward higher recall. There is significant heterogeneity in the performance of RNA-Seq workflows to identify differentially expressed genes

  9. Molecular analysis and expression of phenylalanine ammonia-lyase ...

    African Journals Online (AJOL)

    ... contains a 2166-bp open reading frame (ORF) encoding 721 amino acids. The sequence of genomic DNA was 3315 bp, and the transcript was divided into two exons by an 886-bp long intron which located at 416 bp downstream initiation codon. Expression analysis of EpPAL in poinsettia revealed that expression levels ...

  10. Genome-wide gene expression analysis of anguillid herpesvirus 1

    NARCIS (Netherlands)

    Beurden, van S.J.; Peeters, B.P.H.; Rottier, P.J.M.; Davison, A.A.; Engelsma, M.Y.

    2013-01-01

    Background Whereas temporal gene expression in mammalian herpesviruses has been studied extensively, little is known about gene expression in fish herpesviruses. Here we report a genome-wide transcription analysis of a fish herpesvirus, anguillid herpesvirus 1, in cell culture, studied during the

  11. Cloning, structural analysis and expression of cardiac troponin C ...

    African Journals Online (AJOL)

    Yomi

    2012-02-23

    Feb 23, 2012 ... This study may provide more insight into the molecular structure, expression patterns and evolution of TNNC1 gene in animal. Key words: TroponinC1 gene, molecular cloning, structural analysis, expression, goat. INTRODUCTION ..... relationships of troponin C. Physiological Genomics, 32: 16. Johnson J ...

  12. Molecular cloning, structural analysis and expression of a zinc ...

    African Journals Online (AJOL)

    Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis confirmed the correct expression of the protein. pCAMBIA2300-35S-OCS was used as a eukaryotic expression vector. The recombinant plasmid pCAMBIA2300-ZnBP was used to transform competent Agrobacterium GV3101 ...

  13. Meta-Analysis of the First Facial Expression Recognition Challenge

    NARCIS (Netherlands)

    Valstar, M.F.; Mehu, M.; Jiang, Bihan; Pantic, Maja; Scherer, K.

    Automatic facial expression recognition has been an active topic in computer science for over two decades, in particular facial action coding system action unit (AU) detection and classification of a number of discrete emotion states from facial expressive imagery. Standardization and comparability

  14. A Comparative Study of Feature Selection and Classification Methods for Gene Expression Data

    KAUST Repository

    Abusamra, Heba

    2013-05-01

    Microarray technology has enriched the study of gene expression in such a way that scientists are now able to measure the expression levels of thousands of genes in a single experiment. Microarray gene expression data gained great importance in recent years due to its role in disease diagnoses and prognoses which help to choose the appropriate treatment plan for patients. This technology has shifted a new era in molecular classification, interpreting gene expression data remains a difficult problem and an active research area due to their native nature of “high dimensional low sample size”. Such problems pose great challenges to existing classification methods. Thus, effective feature selection techniques are often needed in this case to aid to correctly classify different tumor types and consequently lead to a better understanding of genetic signatures as well as improve treatment strategies. This thesis aims on a comparative study of state-of-the-art feature selection methods, classification methods, and the combination of them, based on gene expression data. We compared the efficiency of three different classification methods including: support vector machines, k- nearest neighbor and random forest, and eight different feature selection methods, including: information gain, twoing rule, sum minority, max minority, gini index, sum of variances, t- statistics, and one-dimension support vector machine. Five-fold cross validation was used to evaluate the classification performance. Two publicly available gene expression data sets of glioma were used for this study. Different experiments have been applied to compare the performance of the classification methods with and without performing feature selection. Results revealed the important role of feature selection in classifying gene expression data. By performing feature selection, the classification accuracy can be significantly boosted by using a small number of genes. The relationship of features selected in

  15. Inferring Player Experiences Using Facial Expressions Analysis

    NARCIS (Netherlands)

    Tan, C.T.; Bakkes, S.; Pisan, Y.; Blackmore, K.; Nesbitt, K.; Smith, S.P.

    2014-01-01

    Understanding player experiences is central to game design. Video captures of players is a common practice for obtaining rich reviewable data for analysing these experiences. However, not enough has been done in investigating ways of preprocessing the video for a more efficient analysis process.

  16. Molecular characterization and expression analysis of chalcone ...

    African Journals Online (AJOL)

    The cDNA sequence of the CHS gene in P. suffruticosa (Ps-CHS1, genbank accession no. GQ483511) was 1475 bp in full length containing an opening reading frame (ORF) of 1185 bp that encoded a 394 amino acid polypeptide. Bioinformatic analysis showed that, Ps-CHS1 possessed all the conserved active sites for the ...

  17. Identification of Optimal Reference Genes for Expression Analysis in Radish (Raphanus sativus L. and Its Relatives Based on Expression Stability

    Directory of Open Access Journals (Sweden)

    Mengmeng Duan

    2017-09-01

    Full Text Available Radish (Raphanus sativus is an important cruciferous root crop with a close relationship to Chinese cabbage (Brassica rapa. RT-qPCR is used extensively to evaluate the expression levels of target genes, and accurate measurement of target gene expression with this method is determined by the valid reference genes used for data nomalization in different experimental conditions. Screening for appropriate reference genes with stable expression based on RT-qPCR data is important for gene expression and functional analysis research in radish and its relatives. However, many researches have thought that almost no single reference gene is widely suitable for all experimental conditions, and few researchers have paid attention to the validation of reference genes in radish gene expression analysis. In the present study, 12 candidate reference genes were selected for analysis. Their expression in 28 samples, including 20 radish samples from different organs and conditions, four Chinese cabbage organs and four organs of their distant hybrid, was assessed by RT-qPCR and then five software tools—ΔCt, geNorm, NormFinder, BestKeeper and RefFinder—were used to compare their expression stability. The results showed that the most suitable reference genes were different in different organs and conditions. GAPDH, DSS1, and UP2 were optimal reference genes for gene expression analysis in all organs and conditions in radish. UPR, GSNOR1, and ACTIN2/7 were the most stable reference genes in different radish organs. UP2 and GAPDH were suitable reference genes for radish pistil development studies. RPII, UBC9, and GAPDH had the most stable expression in radish under various stresses. DSS1, UP2, and TEF2 were the optimal reference genes for Chinese cabbage organs, whereas TUA was optimal for the distant hybrid. UP2, and TEF2 were appropriate reference genes for all of the samples together. The optimal reference genes we identified, UP2, GAPDH, UPR, and GSNOR1 were

  18. Emotional expression in oral history narratives: comparing results of automated verbal and nonverbal analyses

    NARCIS (Netherlands)

    F.M.G. de Jong (Franciska); K.P. Truong (Khiet); G.J. Westerhof (Gerben); S.M.A. Lamers (Sanne); A. Sools (Anneke)

    2013-01-01

    textabstractAudiovisual collections of narratives about war-traumas are rich in descriptions of personal and emotional experiences which can be expressed through verbal and nonverbal means. We complement a commonly used verbal analysis with a nonverbal one to study emotional developments in

  19. Emotional expression in oral history narratives: comparing results of automated verbal and nonverbal analyses

    NARCIS (Netherlands)

    Truong, Khiet Phuong; Westerhof, Gerben Johan; Lamers, S.M.A.; de Jong, Franciska M.G.; Sools, A.

    Audiovisual collections of narratives about war-traumas are rich in descriptions of personal and emotional experiences which can be expressed through verbal and nonverbal means. We complement a commonly used verbal analysis with a nonverbal one to study emotional developments in narratives. Using

  20. Emotional expression in oral history narratives: comparing results of automated verbal and nonverbal analyses

    NARCIS (Netherlands)

    Truong, Khiet Phuong; Westerhof, Gerben Johan; Lamers, S.M.A.; de Jong, Franciska M.G.; Sools, Anna Maria

    2013-01-01

    Audiovisual collections of narratives about war-traumas are rich in descriptions of personal and emotional experiences which can be expressed through verbal and nonverbal means. We complement a commonly used verbal analysis with a nonverbal one to study emotional developments in narratives. Using

  1. Comparative Analysis of Measles Morbidigf and Mortalityin Calabar ...

    African Journals Online (AJOL)

    Comparative Analysis of Measles Morbidigf and. Mortalityin Calabar during the Eaqaanded Programme. ' on Immunization and the National Programme on. Immunization Eras. IS Etuk*, EE Ekanem'h", JJ Udo*. Summary. Etuk IS, Ekanem EE, UdoJJ. Comparative Analysis of Measles Morbidity and Mortality in Calabar ...

  2. Taxation and Gender Equity : A Comparative Analysis of Direct and ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    10 juin 2010 ... Taxation and Gender Equity : A Comparative Analysis of Direct and Indirect Taxes in Developing and Developed Countries. Couverture du livre Taxation and Gender Equity : A Comparative Analysis of Direct and Indirect Taxes. Directeur(s) : Caren Grown et Imraan Valodia. Maison(s) d'édition : Routledge ...

  3. Reshaping Health Care in Latin America: A Comparative Analysis of ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2000-01-01

    Reshaping Health Care in Latin America: A Comparative Analysis of Health Care Reform in Argentina, Brazil, and Mexico. Book cover Reshaping Health Care in Latin America: A Comparative Analysis of Health Care Reform. Editor(s):. Sonia Fleury, Susana Belmartino, and Enis Baris. Publisher(s):. IDRC. January 1, 2000.

  4. Tissue Non-Specific Genes and Pathways Associated with Diabetes: An Expression Meta-Analysis.

    Science.gov (United States)

    Mei, Hao; Li, Lianna; Liu, Shijian; Jiang, Fan; Griswold, Michael; Mosley, Thomas

    2017-01-21

    We performed expression studies to identify tissue non-specific genes and pathways of diabetes by meta-analysis. We searched curated datasets of the Gene Expression Omnibus (GEO) database and identified 13 and five expression studies of diabetes and insulin responses at various tissues, respectively. We tested differential gene expression by empirical Bayes-based linear method and investigated gene set expression association by knowledge-based enrichment analysis. Meta-analysis by different methods was applied to identify tissue non-specific genes and gene sets. We also proposed pathway mapping analysis to infer functions of the identified gene sets, and correlation and independent analysis to evaluate expression association profile of genes and gene sets between studies and tissues. Our analysis showed that PGRMC1 and HADH genes were significant over diabetes studies, while IRS1 and MPST genes were significant over insulin response studies, and joint analysis showed that HADH and MPST genes were significant over all combined data sets. The pathway analysis identified six significant gene sets over all studies. The KEGG pathway mapping indicated that the significant gene sets are related to diabetes pathogenesis. The results also presented that 12.8% and 59.0% pairwise studies had significantly correlated expression association for genes and gene sets, respectively; moreover, 12.8% pairwise studies had independent expression association for genes, but no studies were observed significantly different for expression association of gene sets. Our analysis indicated that there are both tissue specific and non-specific genes and pathways associated with diabetes pathogenesis. Compared to the gene expression, pathway association tends to be tissue non-specific, and a common pathway influencing diabetes development is activated through different genes at different tissues.

  5. Comparative Analysis of the Concept of Shakespearean Tragedies

    Science.gov (United States)

    Sipra, Muhammad Aslam; Nasir, Muhammad Haseeb

    2014-01-01

    In this article, the analysis of Shakespearean tragedies is presented. It reveals that Shakespeare's plays are full of conflicting thoughts, and expression is so convincing that it is not possible to plan a system of philosophy out of them. Each character, from the king to the clown, from the most highly intellectual to the simpleton, judges life…

  6. Comparative analysis of mangrove species and seedlings in a ...

    African Journals Online (AJOL)

    Data collection was based on identification, enumeration and recording. Density of species and seedlings were analysis using number of stem wood per hectare while relative abundance was expressed in percentage. Mangrove species density was highest in Plots 4 and lowest in Plot 1. Rhizophora racemosa had highest ...

  7. Comparative proteomic analysis of the effects of dietary mugwort ...

    African Journals Online (AJOL)

    Proteomic analysis by 2-dimensional electrophoresis (2-DE) of the longissimus dorsi muscle in finishing pigs (LY × D) grown on a diet supplemented with mugwort powder found roughly 300 spots on a polyacrylamide gel image. Among them, the expression levels of 12 spots were higher than those of the control group.

  8. COMPARATIVE ANALYSIS BETWEEN THE FUNDAMENTAL AND TECHNICAL ANALYSIS OF STOCKS

    Directory of Open Access Journals (Sweden)

    Nada Petrusheva

    2016-04-01

    Full Text Available In the world of investing and trading, in order to have a definite advantage and constantly create profit, you need to have a strategic approach. Generally speaking, the two main schools of thought and strategies in financial markets are fundamental and technical analysis. Fundamental and technical analysis differ in several aspects, such as the way of functioning and execution, the time horizon used, the tools used and their objective. These differences lead to certain advantages and disadvantages of each of the analyses. Fundamental and technical analysis are also a subject of critical reviews by the academic and scientific community and many of these reviews concern the methods of their application, i.e. the possibility of combining the two analyses and using them complementarily to fully utilize their strengths and advantages.

  9. Comparative Proteomic Analysis of Human Lung Adenocarcinoma Cisplatin-resistant Cell Strain A549/CDDP

    Directory of Open Access Journals (Sweden)

    Sien SHI

    2009-11-01

    Full Text Available Background and objective Chemotherapy plays an important role in the comprehensive therapy of lung cancer. However, the drug-resistance often causes the failure of the chemotherapy. The aim of this study is to identify differently expressed protein before and after cisplatin resistance of human lung adenocarcinoma cell A549 by proteomic analysis. Methods Cisplatin-resistant cell strain A549/CDDP was established by combining gradually increasing concentration of cisplatin with large dosage impact. Comparative proteomic analysis of A549 and A549/CDDP were carried out by means of two-dimensional gel electrophoresis. The differentially expressed proteins were detected and identified by MALDI-TOF mass spectrometry. Results Eighty-two differentially expressed proteins were screened by analysis the electrophoretic maps of A549 and A549/CDDP. Six differential proteins were analyzed by peptide mass fingerprinting. Glucose regulating protein 75, ribosomal protein S4, mitochondrial ATP synthase F1 complex beta subunit and immunoglobulin heavy chain variable region were identified. All four differentially expressed proteins were over-expressed in A549/CDDP, whereas low-expressed or no-expressed in A549. Conclusion These differentially expressed proteins give some clues to elucidate the mechanism of lung cancer cell resistant of cisplatin, providing the basis of searching for potential target of chemotherapy of lung cancer.

  10. Integrating technologies for comparing 3D gene expression domains in the developing chick limb.

    Science.gov (United States)

    Fisher, Malcolm E; Clelland, Allyson K; Bain, Andrew; Baldock, Richard A; Murphy, Paula; Downie, Helen; Tickle, Cheryll; Davidson, Duncan R; Buckland, Richard A

    2008-05-01

    Chick embryos are good models for vertebrate development due to their accessibility and manipulability. Recent large increases in available genomic data from both whole genome sequencing and EST projects provide opportunities for identifying many new developmentally important chicken genes. Traditional methods of documenting when and where specific genes are expressed in embryos using whole amount and section in-situ hybridisation do not readily allow appreciation of 3-dimensional (3D) patterns of expression, but this can be accomplished by the recently developed microscopy technique, Optical Projection Tomography (OPT). Here we show that OPT data on the developing chick wing from different labs can be reliably integrated into a common database, that OPT is efficient in capturing 3D gene expression domains and that such domains can be meaningfully compared. Novel protocols are used to compare 3D expression domains of 7 genes known to be involved in chick wing development. This reveals previously unappreciated relationships and demonstrates the potential, using modern genomic resources, for building a large scale 3D atlas of gene expression. Such an atlas could be extended to include other types of data, such as fate maps, and the approach is also more generally applicable to embryos, organs and tissues.

  11. Comparative proteomic analysis of Saccharomyces cerevisiae under different nitrogen sources.

    Science.gov (United States)

    Zhao, Shaohui; Zhao, Xinrui; Zou, Huijun; Fu, Jianwei; Du, Guocheng; Zhou, Jingwen; Chen, Jian

    2014-04-14

    In cultures containing multiple sources of nitrogen, Saccharomyces cerevisiae exhibits a sequential use of nitrogen sources through a mechanism known as nitrogen catabolite repression (NCR). To identify proteins differentially expressed due to NCR, proteomic analysis of S. cerevisiae S288C under different nitrogen source conditions was performed using two-dimensional gel electrophoresis (2-DE), revealing 169 candidate protein spots. Among these 169 protein spots, 121 were identified by matrix assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF). The identified proteins were closely associated with four main biological processes through Gene Ontology (GO) categorical analysis. The identification of the potential proteins and cellular processes related to NCR offer a global overview of changes elicited by different nitrogen sources, providing clues into how yeast adapt to different nutritional conditions. Moreover, by comparing our proteomic data with corresponding mRNA data, proteins regulated at the transcriptional and post-transcriptional level could be distinguished. Biological significance In S. cerevisiae, different nitrogen sources provide different growth characteristics and generate different metabolites. The nitrogen catabolite repression (NCR) process plays an important role for S. cerevisiae in the ordinal utilization of different nitrogen sources. NCR process can result in significant shift of global metabolic networks. Previous works on NCR primarily focused on transcriptomic level. The results obtained in this study provided a global atlas of the proteome changes triggered by different nitrogen sources and would facilitate the understanding of mechanisms for how yeast could adapt to different nutritional conditions. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Comparative analysis of Acinetobacters: three genomes for three lifestyles.

    Science.gov (United States)

    Vallenet, David; Nordmann, Patrice; Barbe, Valérie; Poirel, Laurent; Mangenot, Sophie; Bataille, Elodie; Dossat, Carole; Gas, Shahinaz; Kreimeyer, Annett; Lenoble, Patricia; Oztas, Sophie; Poulain, Julie; Segurens, Béatrice; Robert, Catherine; Abergel, Chantal; Claverie, Jean-Michel; Raoult, Didier; Médigue, Claudine; Weissenbach, Jean; Cruveiller, Stéphane

    2008-03-19

    Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.

  13. Comparative analysis of Acinetobacters: three genomes for three lifestyles.

    Directory of Open Access Journals (Sweden)

    David Vallenet

    Full Text Available Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss; ii strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS. Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment, louse, soil.

  14. Plain faces are more expressive: comparative study of facial colour, mobility and musculature in primates.

    Science.gov (United States)

    Santana, Sharlene E; Dobson, Seth D; Diogo, Rui

    2014-05-01

    Facial colour patterns and facial expressions are among the most important phenotypic traits that primates use during social interactions. While colour patterns provide information about the sender's identity, expressions can communicate its behavioural intentions. Extrinsic factors, including social group size, have shaped the evolution of facial coloration and mobility, but intrinsic relationships and trade-offs likely operate in their evolution as well. We hypothesize that complex facial colour patterning could reduce how salient facial expressions appear to a receiver, and thus species with highly expressive faces would have evolved uniformly coloured faces. We test this hypothesis through a phylogenetic comparative study, and explore the underlying morphological factors of facial mobility. Supporting our hypothesis, we find that species with highly expressive faces have plain facial colour patterns. The number of facial muscles does not predict facial mobility; instead, species that are larger and have a larger facial nucleus have more expressive faces. This highlights a potential trade-off between facial mobility and colour patterning in primates and reveals complex relationships between facial features during primate evolution. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  15. ADAM15 expression is downregulated in melanoma metastasis compared to primary melanoma

    Energy Technology Data Exchange (ETDEWEB)

    Ungerer, Christopher; Doberstein, Kai [Pharmazentrum Frankfurt/ZAFES, University Hospital Goethe University Frankfurt, Frankfurt am Main (Germany); Buerger, Claudia; Hardt, Katja; Boehncke, Wolf-Henning [Department of Dermatology, Clinic of the Goethe-University, Theodor-Stern-Kai, Frankfurt (Germany); Boehm, Beate [Division of Rheumatology, Goethe University, Frankfurt am Main (Germany); Pfeilschifter, Josef [Pharmazentrum Frankfurt/ZAFES, University Hospital Goethe University Frankfurt, Frankfurt am Main (Germany); Dummer, Reinhard [Department of Pathology, Institute of Surgical Pathology, University Hospital, Zurich (Switzerland); Mihic-Probst, Daniela [Department of Dermatology, University Hospital Zurich (Switzerland); Gutwein, Paul, E-mail: p.gutwein@med.uni-frankfurt.de [Pharmazentrum Frankfurt/ZAFES, University Hospital Goethe University Frankfurt, Frankfurt am Main (Germany)

    2010-10-22

    Research highlights: {yields} Strong ADAM15 expression is found in normal melanocytes. {yields} ADAM15 expression is significantly downregulated in patients with melanoma metastasis. {yields} TGF-{beta} can downregulate ADAM15 expression in melanoma cells. {yields} Overexpression of ADAM15 in melanoma cells inhibits migration, proliferation and invasion of melanoma cells. {yields} Conclusion: ADAM15 represents an tumor suppressor protein in melanoma. -- Abstract: In a mouse melanoma metastasis model it has been recently shown that ADAM15 overexpression in melanoma cells significantly reduced the number of metastatic nodules on the lung. Unfortunately, the expression of ADAM15 in human melanoma tissue has not been determined so far. In our study, we characterized the expression of ADAM15 in tissue micro-arrays of patients with primary melanoma with melanoma metastasis. ADAM15 was expressed in melanocytes and endothelial cells of benign nevi and melanoma tissue. Importantly, ADAM15 was significantly downregulated in melanoma metastasis compared to primary melanoma. We further demonstrate that IFN-{gamma} and TGF-{beta} downregulate ADAM15 protein levels in melanoma cells. To investigate the role of ADAM15 in melanoma progression, we overexpressed ADAM15 in melanoma cells. Importantly, overexpression of ADAM15 in melanoma cells reduced the migration, invasion and the anchorage dependent and independent cell growth of melanoma cells. In summary, the downregulation of ADAM15 plays an important role in melanoma progression and ADAM15 act as a tumorsuppressor in melanoma.

  16. Transcriptomic analysis of gene expression in mice treated with troxerutin.

    Directory of Open Access Journals (Sweden)

    Yuerong Wang

    Full Text Available Troxerutin, a semi-synthetic derivative of the natural bioflavanoid rutin, has been reported to possess many beneficial effects in human bodies, such as vasoprotection, immune support, anti-inflammation and anti-aging. However, the effects of troxerutin on genome-wide transcription in blood cells are still unknown. In order to find out effects of troxerutin on gene transcription, a high-throughput RNA sequencing was employed to analysis differential gene expression in blood cells consisting of leucocytes, erythrocytes and platelets isolated from the mice received subcutaneous injection of troxerutin. Transcriptome analysis demonstrated that the expression of only fifteen genes was significantly changed by the treatment with troxerutin, among which 5 genes were up-regulated and 10 genes were down-regulated. Bioinformatic analysis of the fifteen differentially expressed genes was made by utilizing the Gene Ontology (GO, and the differential expression induced by troxerutin was further evaluated by real-time quantitative PCR (Q-PCR.

  17. comparative analysis of the growth performance and haemolymph

    African Journals Online (AJOL)

    Dr Osondu

    4 No.2 2011. COMPARATIVE ANALYSIS OF THE GROWTH PERFORMANCE AND HAEMOLYMPH .... Statistical Analysis. Data collected from the experiments were analyzed by one way analysis of variance. (ANOVA) and student- Newman kuel's test was used for the ... bigger and grow faster than albino snails. The lack of.

  18. Measuring populism: comparing two methods of content analysis

    NARCIS (Netherlands)

    Rooduijn, M.; Pauwels, T.

    2011-01-01

    The measurement of populism - particularly over time and space - has received only scarce attention. In this research note two different ways to measure populism are compared: a classical content analysis and a computer-based content analysis. An analysis of political parties in the United Kingdom,

  19. Matrix metalloproteinases in the mouse retina: a comparative study of expression patterns and MMP antibodies.

    Science.gov (United States)

    De Groef, Lies; Andries, Lien; Lemmens, Kim; Van Hove, Inge; Moons, Lieve

    2015-12-29

    Matrix metalloproteinases (MMPs), a family of Zn(2+)-dependent endoproteases, have been shown to act as fine regulators of both health and disease. Limited research revealed that they are essential to maintaining ocular physiology and inordinate MMP activities have been linked to several neurodegenerative disorders of the retina, including age-related macular degeneration, proliferative diabetic retinopathy and glaucomatous optic neuropathies (GONs). Nevertheless, a clear definition of their pathology-exacerbating and/or -resolving actions is lacking, especially in the context of GONs, as most studies thus far merely focused on expression profiling in human patients. Therefore, in an initial step towards an improved understanding of MMP functions in the retina, we studied the spatial expression pattern of MMP-2, -3, -9 and MT1-MMP in the healthy mouse retina. The spatial expression pattern of MMP-2, -3, -9 and MT1-MMP was studied in the healthy mouse retina via immunohistochemical stainings, and immunoreactivity profiles were compared to existing literature. Moreover, we considered sensitivity and specificity issues with commercially available MMP antibodies via Western blot. Basal expression of MMP-2,-3, -9 and MT1-MMP was found in the retina of healthy, adult mice. MMP-2 expression was seen in Müller glia, predominantly in their end feet, which is in line with available literature. MMP-3 expression was described for the first time in the retina, and was observed in vesicle-like structures along the radial fibers of Müller glia. MMP-9 expression, about which still discords exists, was seen in microglia and in a sparse subset of (apoptosing) RGCs. MT1-MMP localization was for the first time studied in adult mice and was found in RGC axons and Müller glia, mimicking the MT1-MMP expression pattern seen in rabbits and neonatal mice. Moreover, one antibody was selected for each MMP, based on its staining pattern in Western blot. The present MMP immunoreactivity

  20. Microarray gene expression analysis of uterosacral ligaments in uterine prolapse.

    Science.gov (United States)

    Ak, Handan; Zeybek, Burak; Atay, Sevcan; Askar, Niyazi; Akdemir, Ali; Aydin, Hikmet Hakan

    2016-11-01

    Pelvic organ prolapse (POP) is a major health problem that impairs the quality of life with a wide clinical spectrum. Since the uterosacral ligaments provide primary support for the uterus and the upper vagina, we hypothesize that the disruption of these ligaments may lead to a loss of support and eventually contribute to POP. In this study, we therefore investigated whether there are any differences in the transcription profile of uterosacral ligaments in patients with POP when compared to those of the control samples. Seventeen women with POP and 8 non-POP controls undergoing hysterectomy for benign conditions were included in the study. Affymetrix® Gene Chip microarrays (Human Hu 133 plus 2.0) were used for whole genome gene expression profiling analysis. There was 1 significantly down-regulated gene, NKX2-3 in patients with POP compared to the controls (p=4.28464e-013). KIF11 gene was found to be significantly down-regulated in patients with ≥3 deliveries compared to patients with <3 deliveries (p=0.0156237). UGT1A1 (p=2.43388e-005), SCARB1 (p=1.19001e-006) and NKX2-3 (p=2.17966e-013) genes were found to be significantly down-regulated in the premenopausal patients compared to the premenopausal controls. UGT1A1 gene was also found to be significantly down-regulated in the post menopausal patients compared to the postmenopausal controls (p=0.0005). This study provides evidence for a significant down-regulation of the genes that take role in cell cycle, proliferation and embryonic development along with cell adhesion process on the development of POP for the first time. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  1. Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus

    Directory of Open Access Journals (Sweden)

    Xiaoxu Zhou

    2016-03-01

    Full Text Available Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 differentially expressed unigenes were not annotated with any database, 160 of which were apparently expressed at higher levels in papilla, 76 were expressed at higher levels in skin. We identified a total of 288 papilla-specific genes, 171 skin-specific genes and 600 co-expressed genes. Also, 40 genes in papilla-specific were not annotated with any database, 2 in skin-specific. Development-related genes were also enriched, such as fibroblast growth factor, transforming growth factor-β, collagen-α2 and Integrin-α2, which may be related to the formation of the papilla and skin in sea cucumber. Further pathway analysis identified ten KEGG pathways that were differently enriched between the papilla and skin. The findings on expression profiles between two key organs of the sea cucumber should be valuable to reveal molecular mechanisms involved in the development of organs that are related but with morphological differences in the sea cucumber.

  2. Molecular cloning, sequence analysis and tissue expression of ...

    African Journals Online (AJOL)

    Proofreader

    2017-10-01

    Oct 1, 2017 ... Molecular cloning, sequence analysis and tissue expression of bovine imprinted. ASCL2 gene. O. Bamidele1 ... The objectives of this study were to perform in silico analysis of the genomic messenger RNA (mRNA), and protein sequences ...... Non-linear dynamics of nonsynonymous (dN) and synonymous ...

  3. Cloning and expression analysis of dihydroxyflavonol 4-reductase ...

    African Journals Online (AJOL)

    Dihydroflavonol 4-reductase (DFR) gene is a key gene of anthocyanins biosynthesis pathway, which represent an importance pathway for orchid flower. In this study, cloning and expression analysis of DFR gene in Ascocenda spp. were carried out. Nucleotide analysis revealed that the Ascocenda DFR gene was 1,056 bp ...

  4. Pathway level analysis of gene expression using singular value decomposition

    Directory of Open Access Journals (Sweden)

    Kepler Thomas B

    2005-09-01

    Full Text Available Abstract Background A promising direction in the analysis of gene expression focuses on the changes in expression of specific predefined sets of genes that are known in advance to be related (e.g., genes coding for proteins involved in cellular pathways or complexes. Such an analysis can reveal features that are not easily visible from the variations in the individual genes and can lead to a picture of expression that is more biologically transparent and accessible to interpretation. In this article, we present a new method of this kind that operates by quantifying the level of 'activity' of each pathway in different samples. The activity levels, which are derived from singular value decompositions, form the basis for statistical comparisons and other applications. Results We demonstrate our approach using expression data from a study of type 2 diabetes and another of the influence of cigarette smoke on gene expression in airway epithelia. A number of interesting pathways are identified in comparisons between smokers and non-smokers including ones related to nicotine metabolism, mucus production, and glutathione metabolism. A comparison with results from the related approach, 'gene-set enrichment analysis', is also provided. Conclusion Our method offers a flexible basis for identifying differentially expressed pathways from gene expression data. The results of a pathway-based analysis can be complementary to those obtained from one more focused on individual genes. A web program PLAGE (Pathway Level Analysis of Gene Expression for performing the kinds of analyses described here is accessible at http://dulci.biostat.duke.edu/pathways.

  5. Comparative Study of Human Age Estimation with or without Preclassification of Gender and Facial Expression

    Science.gov (United States)

    Cho, So Ra; Shin, Kwang Yong; Bang, Jae Won; Park, Kang Ryoung

    2014-01-01

    Age estimation has many useful applications, such as age-based face classification, finding lost children, surveillance monitoring, and face recognition invariant to age progression. Among many factors affecting age estimation accuracy, gender and facial expression can have negative effects. In our research, the effects of gender and facial expression on age estimation using support vector regression (SVR) method are investigated. Our research is novel in the following four ways. First, the accuracies of age estimation using a single-level local binary pattern (LBP) and a multilevel LBP (MLBP) are compared, and MLBP shows better performance as an extractor of texture features globally. Second, we compare the accuracies of age estimation using global features extracted by MLBP, local features extracted by Gabor filtering, and the combination of the two methods. Results show that the third approach is the most accurate. Third, the accuracies of age estimation with and without preclassification of facial expression are compared and analyzed. Fourth, those with and without preclassification of gender are compared and analyzed. The experimental results show the effectiveness of gender preclassification in age estimation. PMID:25295308

  6. Comparative Transcriptional Profiling of Contrasting Rice Genotypes Shows Expression Differences during Arsenic Stress

    Directory of Open Access Journals (Sweden)

    Arti Rai

    2015-07-01

    Full Text Available Accumulation of arsenic (As in rice ( L. grain is a serious concern worldwide. Long-term exposure to As affects nutritional status in rice grain and is associated with higher rates of skin, bladder, and lung cancers, and heart disease. Genotypic variations in rice for As accumulation or tolerance are prevalent and are regulated by genetic and environmental factors. To understand molecular networks involved in As accumulation, genome-wide expression analysis was performed in roots of low- and high-As accumulating rice genotypes (LARGs and HARGs. Six rice genotypes with contrasting As accumulation potential and tolerance were used in this study. Genome-wide expression analysis suggested their differential response against As stress. This study suggests up- and downregulation of a number of unique genes involved in various pathways and biological processes in response to As stress in rice genotypes. A comparison of gene expression profiles, principal component analysis, and -means clustering suggests that an independent pathway is operating during As stress tolerance or accumulation in contrasting genotypes. It was also observed that the differential behavior of genotype, Nayanmoni, from other LARGs might be due to its different genetic background. -motif profiling of As-induced coexpressed genes in diverse rice genotypes led to the identification of unique -motifs present in differentially expressed genes. This study suggests that the genetic mechanism regulating the differential As accumulation in different genotypes may not be dependent on gene expression at the transcriptional level. However, many genes identified in this study can be analyzed and used for marker–trait associations related to As accumulation in diverse genotypes around the world.

  7. Gene expression and cell differentiation in matrix-associated chondrocyte transplantation grafts: a comparative study.

    Science.gov (United States)

    Albrecht, C; Tichy, B; Nürnberger, S; Hosiner, S; Zak, L; Aldrian, S; Marlovits, S

    2011-10-01

    Although scaffold composition and architecture are considered to be important parameters for tissue engineering, their influence on gene expression and cell differentiation is rarely investigated in scaffolds used for matrix-associated autologous chondrocyte transplantation (MACT). In this study we have therefore comparatively analyzed the gene expression of important chondrogenic markers in four clinical applied cell-graft systems with very different scaffold characteristics. Residuals (n=165) of four different transplant types (MACI®, Hyalograft®C, CaReS® and Novocart®3D) were collected during surgery and analyzed for Col1, Col2, aggrecan, versican, melanoma inhibitory activity (MIA) and IL-1β by real-time PCR. Scaffold and cell morphology were evaluated by histology and electron microscopy. Despite the cultivation on 3D scaffolds, the cell differentiation on all transplant types didn't reach the levels of native cartilage. Gene expression highly differed between the transplant types. The highest differentiation of cells (Col2/Col1 ratio) was found in CaReS®, followed by Novocart®3D, Hyalograft®C and MACI®. IL-1β expression also exhibited high differences between the scaffolds showing low expression levels in Novocart®3D and CaReS® and higher expression levels in MACI® and Hyalograft®C. Our data indicate that scaffold characteristics as well as culture conditions highly influence gene expression in cartilage transplants and that these parameters may have profound impact on the tissue regeneration after MACT. Copyright © 2011 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

  8. Comparative immunohistochemical expression of RANK, RANKL and OPG in radicular and dentigerous cysts.

    Science.gov (United States)

    de Moraes, Maiara; de Lucena, Hévio Freitas; de Azevedo, Paulo Roberto Medeiros; Queiroz, Lélia Maria Guedes; Costa, Antonio de Lisboa Lopes

    2011-11-01

    Receptor activator of nuclear factor-κB (RANK), RANK ligand (RANKL) and osteoprotegerin (OPG) are members of the superfamily of ligands and receptors of tumour necrosis factor family involved in bone metabolism. The formation, differentiation and activity of osteoclasts are regulated by these proteins. To clarify the roles of osteoclast regulatory factors in cystic expansion of odontogenic cysts, expression of these proteins were analysed in radicular and dentigerous cysts. The immunohistochemistry expression of these biomarkers were evaluated and measured in lining epithelium and fibrous capsule of the radicular (n=20) and dentigerous cysts (n=20). A similar expression in lining epithelium was observed in the lesions. The fibrous capsule of dentigerous cyst showed a higher content of RANK-positive and RANKL-positive cells than fibrous capsule of radicular cyst. In the lining epithelium the RANKL/OPG ratio showed higher numbers of OPG-positive than RANKL-positive cells, whereas fibrous capsule of the cysts had a tendency to present a similar expression (OPG=RANKL). Ours findings indicate the presence of RANK, RANKL and OPG in cysts. Moreover, increased expression of OPG compared to RANKL in the lining epithelium could contribute to the differential bone resorption activity in theses lesions. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. A comparative study between release analysis and column flotation

    Energy Technology Data Exchange (ETDEWEB)

    Jorge Pineres; Juan Barraza [Universidad del Valle, Cali (Colombia)

    2007-07-01

    This paper shows the results of a comparative study between release analysis and column flotation of three Colombian coals: Guachinte (South West), Cerrejon (North) and Nech (Midlands). Analysis release was used in order to evaluate the coal potential cleaning in terms of both low ash and high organic recovery of froth. Results from release analysis were compared with those from a column flotation and showed that the froth from Nechi coal had the highest recovery and the lowest ash, followed by Cerrejon and then by Guachinte. Results of release analysis were in agreement with the column flotation. 10 refs., 4 figs., 1 tab.

  10. Global gene expression analysis for evaluation and design of biomaterials

    Directory of Open Access Journals (Sweden)

    Nobutaka Hanagata, Taro Takemura and Takashi Minowa

    2010-01-01

    Full Text Available Comprehensive gene expression analysis using DNA microarrays has become a widespread technique in molecular biological research. In the biomaterials field, it is used to evaluate the biocompatibility or cellular toxicity of metals, polymers and ceramics. Studies in this field have extracted differentially expressed genes in the context of differences in cellular responses among multiple materials. Based on these genes, the effects of materials on cells at the molecular level have been examined. Expression data ranging from several to tens of thousands of genes can be obtained from DNA microarrays. For this reason, several tens or hundreds of differentially expressed genes are often present in different materials. In this review, we outline the principles of DNA microarrays, and provide an introduction to methods of extracting information which is useful for evaluating and designing biomaterials from comprehensive gene expression data.

  11. Global gene expression analysis for evaluation and design of biomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Hanagata, Nobutaka; Takemura, Taro; Minowa, Takashi, E-mail: HANAGATA.Nobutaka@nims.go.j [Nanotechnology Innovation Center and Biomaterials Center, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 (Japan)

    2010-02-15

    Comprehensive gene expression analysis using DNA microarrays has become a widespread technique in molecular biological research. In the biomaterials field, it is used to evaluate the biocompatibility or cellular toxicity of metals, polymers and ceramics. Studies in this field have extracted differentially expressed genes in the context of differences in cellular responses among multiple materials. Based on these genes, the effects of materials on cells at the molecular level have been examined. Expression data ranging from several to tens of thousands of genes can be obtained from DNA microarrays. For this reason, several tens or hundreds of differentially expressed genes are often present in different materials. In this review, we outline the principles of DNA microarrays, and provide an introduction to methods of extracting information which is useful for evaluating and designing biomaterials from comprehensive gene expression data. (topical review)

  12. Comparative nutritional compositions and proteomics analysis of transgenic Xa21 rice seeds compared to conventional rice.

    Science.gov (United States)

    Gayen, Dipak; Paul, Soumitra; Sarkar, Sailendra Nath; Datta, Swapan K; Datta, Karabi

    2016-07-15

    Transgenic rice expressing the Xa21 gene have enhanced resistant to most devastating bacterial blight diseases caused by Xanthomonas oryzae pv. oryzae (Xoo). However, identification of unintended modifications, owing to the genetic modification, is an important aspect of transgenic crop safety assessment. In this study, the nutritional compositions of seeds from transgenic rice plants expressing the Xa21 gene were compared against non-transgenic rice seeds. In addition, to detect any changes in protein translation levels as a result of Xa21 gene expression, rice seed proteome analyses were also performed by two-dimensional gel electrophoresis. No significant differences were found in the nutritional compositions (proximate components, amino acids, minerals, vitamins and anti-nutrients) of the transgenic and non-transgenic rice seeds. Although gel electrophoresis identified 11 proteins that were differentially expressed between the transgenic and non-transgenic seed, only one of these (with a 20-fold up-regulation in the transgenic seed) shows nutrient reservoir activity. No new toxins or allergens were detected in the transgenic seeds. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Semi-supervised consensus clustering for gene expression data analysis

    OpenAIRE

    Wang, Yunli; Pan, Youlian

    2014-01-01

    Background Simple clustering methods such as hierarchical clustering and k-means are widely used for gene expression data analysis; but they are unable to deal with noise and high dimensionality associated with the microarray gene expression data. Consensus clustering appears to improve the robustness and quality of clustering results. Incorporating prior knowledge in clustering process (semi-supervised clustering) has been shown to improve the consistency between the data partitioning and do...

  14. New tools for comparing microscopy images: quantitative analysis of cell types in Bacillus subtilis.

    Science.gov (United States)

    van Gestel, Jordi; Vlamakis, Hera; Kolter, Roberto

    2015-02-15

    Fluorescence microscopy is a method commonly used to examine individual differences between bacterial cells, yet many studies still lack a quantitative analysis of fluorescence microscopy data. Here we introduce some simple tools that microbiologists can use to analyze and compare their microscopy images. We show how image data can be converted to distribution data. These data can be subjected to a cluster analysis that makes it possible to objectively compare microscopy images. The distribution data can further be analyzed using distribution fitting. We illustrate our methods by scrutinizing two independently acquired data sets, each containing microscopy images of a doubly labeled Bacillus subtilis strain. For the first data set, we examined the expression of srfA and tapA, two genes which are expressed in surfactin-producing and matrix-producing cells, respectively. For the second data set, we examined the expression of eps and tapA; these genes are expressed in matrix-producing cells. We show that srfA is expressed by all cells in the population, a finding which contrasts with a previously reported bimodal distribution of srfA expression. In addition, we show that eps and tapA do not always have the same expression profiles, despite being expressed in the same cell type: both operons are expressed in cell chains, while single cells mainly express eps. These findings exemplify that the quantification and comparison of microscopy data can yield insights that otherwise would go unnoticed. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  15. Comparative Proteomic Analysis of Yak Follicular Fluid during Estrus

    Directory of Open Access Journals (Sweden)

    Xian Guo

    2016-09-01

    Full Text Available The breeding of yaks is highly seasonal, there are many crucial proteins involved in the reproduction control program, especially in follicular development. In order to isolate differential proteins between mature and immature follicular fluid (FF of yak, the FF from yak follicles with different sizes were sampled respectively, and two-dimensional gel electrophoresis (2-DE of the proteins was carried out. After silver staining, the Image Master 2D platinum software was used for protein analysis and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS was performed for differential protein identification. The expression level of transferrin and enolase superfamily member 1 (ENOSF1 was determined by Western blotting for verification analysis. The results showed that 2-DE obtained an electrophoresis map of proteins from mature and immature yak FF with high resolution and repeatability. A comparison of protein profiles identified 12 differently expressed proteins, out of which 10 of them were upregulated while 2 were downregulated. Western blotting showed that the expression of transferrin and ENOSF1 was enhanced with follicular development. Both the obtained protein profiles and the differently expressed proteins identified in this study provided experimental data related to follicular development during yak breeding seasons. This study also laid the foundation for understanding the microenvironment during oocyte development.

  16. Comparative Transcriptome Profiling Reveals Different Expression Patterns in Xanthomonas oryzae pv. oryzae Strains with Putative Virulence-Relevant Genes

    Science.gov (United States)

    Zhang, Fan; Du, Zhenglin; Huang, Liyu; Cruz, Casiana Vera; Zhou, Yongli; Li, Zhikang

    2013-01-01

    Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of rice bacterial blight, which is a major rice disease in tropical Asian countries. An attempt has been made to investigate gene expression patterns of three Xoo strains on the minimal medium XOM2, PXO99 (P6) and PXO86 (P2) from the Philippines, and GD1358 (C5) from China, which exhibited different virulence in 30 rice varieties, with putative virulence factors using deep sequencing. In total, 4,781 transcripts were identified in this study, and 1,151 and 3,076 genes were differentially expressed when P6 was compared with P2 and with C5, respectively. Our results indicated that Xoo strains from different regions exhibited distinctly different expression patterns of putative virulence-relevant genes. Interestingly, 40 and 44 genes involved in chemotaxis and motility exhibited higher transcript alterations in C5 compared with P6 and P2, respectively. Most other genes associated with virulence, including exopolysaccharide (EPS) synthesis, Hrp genes and type III effectors, including Xanthomonas outer protein (Xop) effectors and transcription activator-like (TAL) effectors, were down-regulated in C5 compared with P6 and P2. The data were confirmed by real-time quantitative RT-PCR, tests of bacterial motility, and enzyme activity analysis of EPS and xylanase. These results highlight the complexity of Xoo and offer new avenues for improving our understanding of Xoo-rice interactions and the evolution of Xoo virulence. PMID:23734193

  17. Comparative Analysis of Kernel Methods for Statistical Shape Learning

    National Research Council Canada - National Science Library

    Rathi, Yogesh; Dambreville, Samuel; Tannenbaum, Allen

    2006-01-01

    .... In this work, we perform a comparative analysis of shape learning techniques such as linear PCA, kernel PCA, locally linear embedding and propose a new method, kernelized locally linear embedding...

  18. Comparative analysis of myocardial revascularization methods for ischemic heart disease

    Directory of Open Access Journals (Sweden)

    Sinkeev M.S.

    2012-09-01

    Full Text Available The review of literature is devoted to the comparative analysis of clinical researches of efficiency and frequency of complications after application of surgical and medicamentous methods of treatment of coronary heart disease.

  19. A comparative analysis of the characteristics of the wines produced ...

    African Journals Online (AJOL)

    A comparative analysis of the characteristics of the wines produced from the fruit juices of vitis vinifera (Grapevine), Citrus sinensis sweet orange) and Ananos comosus (pineapple)using pure cultured brewer's yeast.

  20. Bluetooth security attacks comparative analysis, attacks, and countermeasures

    CERN Document Server

    Haataja, Keijo; Pasanen, Sanna; Toivanen, Pekka

    2013-01-01

    This overview of Bluetooth security examines network vulnerabilities and offers a comparative analysis of recent security attacks. It also examines related countermeasures and proposes a novel attack that works against all existing Bluetooth versions.

  1. Analogy of ISSR and RAPD markers for comparative analysis of ...

    African Journals Online (AJOL)

    Analogy of ISSR and RAPD markers for comparative analysis of genetic diversity among different Jatropha curcas genotypes. S Gupta, M Srivastava, GP Mishra, PK Naik, RS Chauhan, SK Tiwari, M Kumar, R Singh ...

  2. Dynamic association rules for gene expression data analysis.

    Science.gov (United States)

    Chen, Shu-Chuan; Tsai, Tsung-Hsien; Chung, Cheng-Han; Li, Wen-Hsiung

    2015-10-14

    The purpose of gene expression analysis is to look for the association between regulation of gene expression levels and phenotypic variations. This association based on gene expression profile has been used to determine whether the induction/repression of genes correspond to phenotypic variations including cell regulations, clinical diagnoses and drug development. Statistical analyses on microarray data have been developed to resolve gene selection issue. However, these methods do not inform us of causality between genes and phenotypes. In this paper, we propose the dynamic association rule algorithm (DAR algorithm) which helps ones to efficiently select a subset of significant genes for subsequent analysis. The DAR algorithm is based on association rules from market basket analysis in marketing. We first propose a statistical way, based on constructing a one-sided confidence interval and hypothesis testing, to determine if an association rule is meaningful. Based on the proposed statistical method, we then developed the DAR algorithm for gene expression data analysis. The method was applied to analyze four microarray datasets and one Next Generation Sequencing (NGS) dataset: the Mice Apo A1 dataset, the whole genome expression dataset of mouse embryonic stem cells, expression profiling of the bone marrow of Leukemia patients, Microarray Quality Control (MAQC) data set and the RNA-seq dataset of a mouse genomic imprinting study. A comparison of the proposed method with the t-test on the expression profiling of the bone marrow of Leukemia patients was conducted. We developed a statistical way, based on the concept of confidence interval, to determine the minimum support and minimum confidence for mining association relationships among items. With the minimum support and minimum confidence, one can find significant rules in one single step. The DAR algorithm was then developed for gene expression data analysis. Four gene expression datasets showed that the proposed

  3. SIGNATURE: A workbench for gene expression signature analysis

    Directory of Open Access Journals (Sweden)

    Chang Jeffrey T

    2011-11-01

    Full Text Available Abstract Background The biological phenotype of a cell, such as a characteristic visual image or behavior, reflects activities derived from the expression of collections of genes. As such, an ability to measure the expression of these genes provides an opportunity to develop more precise and varied sets of phenotypes. However, to use this approach requires computational methods that are difficult to implement and apply, and thus there is a critical need for intelligent software tools that can reduce the technical burden of the analysis. Tools for gene expression analyses are unusually difficult to implement in a user-friendly way because their application requires a combination of biological data curation, statistical computational methods, and database expertise. Results We have developed SIGNATURE, a web-based resource that simplifies gene expression signature analysis by providing software, data, and protocols to perform the analysis successfully. This resource uses Bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures, all carried out within a GenePattern web interface for easy use and access. Conclusions SIGNATURE is available for public use at http://genepattern.genome.duke.edu/signature/.

  4. Comparative analysis of two acetylcholinesterase genes of Bombyx ...

    African Journals Online (AJOL)

    To compare the sequences and tissue expressions of the two aces between the two species, cDNAs encoding two ace genes were cloned and designated as Bmm-ace1 and Bmm-ace2 from the larvae of the B. mandarina. The amino acid sequence of Bmm-ace1 shared 99.71% homology with its homolog, Bm-ace1, in B.

  5. A Comparative Study of Feature Selection and Classification Methods for Gene Expression Data of Glioma

    KAUST Repository

    Abusamra, Heba

    2013-11-01

    Microarray gene expression data gained great importance in recent years due to its role in disease diagnoses and prognoses which help to choose the appropriate treatment plan for patients. This technology has shifted a new era in molecular classification. Interpreting gene expression data remains a difficult problem and an active research area due to their native nature of “high dimensional low sample size”. Such problems pose great challenges to existing classification methods. Thus, effective feature selection techniques are often needed in this case to aid to correctly classify different tumor types and consequently lead to a better understanding of genetic signatures as well as improve treatment strategies. This paper aims on a comparative study of state-of-the- art feature selection methods, classification methods, and the combination of them, based on gene expression data. We compared the efficiency of three different classification methods including: support vector machines, k-nearest neighbor and random forest, and eight different feature selection methods, including: information gain, twoing rule, sum minority, max minority, gini index, sum of variances, t-statistics, and one-dimension support vector machine. Five-fold cross validation was used to evaluate the classification performance. Two publicly available gene expression data sets of glioma were used in the experiments. Results revealed the important role of feature selection in classifying gene expression data. By performing feature selection, the classification accuracy can be significantly boosted by using a small number of genes. The relationship of features selected in different feature selection methods is investigated and the most frequent features selected in each fold among all methods for both datasets are evaluated.

  6. Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression

    DEFF Research Database (Denmark)

    Hustinx, Steven R; Cao, Dengfeng; Maitra, Anirban

    2004-01-01

    Serial analysis of gene expression (SAGE) is a powerful tool for the discovery of novel tumor markers. The publicly available online SAGE libraries of normal and neoplastic tissues (http://www.ncbi.nlm.nih.gov/SAGE/) have recently been expanded; in addition, a more complete annotation of the human...... 16 additional differentially expressed genes. The differential expression of seven genes, involved in multiple cellular processes such as signal transduction (MIC-1), differentiation (DMBT1 and Neugrin), immune response (CD74), inflammation (CXCL2), cell cycle (CEB1) and enzymatic activity...... of this program. Novel differentially expressed genes in a cancer type can be identified by revisiting updated and expanded SAGE databases. TAGmapper should prove to be a powerful tool for the discovery of novel tumor markers through assignment of uncharacterized SAGE tags....

  7. Caco-2 cells - expression, regulation and function of drug transporters compared with human jejunal tissue.

    Science.gov (United States)

    Brück, S; Strohmeier, J; Busch, D; Drozdzik, M; Oswald, S

    2017-03-01

    Induction or inhibition of drug transporting proteins by concomitantly administered drugs can cause serious drug-drug interactions (DDIs). However, in vitro assays currently available are mostly for studying the inhibitory potential of drugs on intestinal transporter proteins, rather than induction. Therefore, this study investigated the suitability of the frequently used intestinal Caco-2 cell line to predict transporter-mediated DDIs as caused by induction via activation of nuclear receptors. TaqMan® low density arrays and LC-MS/MS based targeted proteomics were used to evaluate transporter expression in Caco-2 cells in comparison with jejunal tissue, in culture-time dependence studies and after incubation with different known inducers of drug metabolism and transport. Additionally, studies on ABCB1 function were performed using Transwell® assays with [3 H]-digoxin and [3 H]-talinolol as substrates after incubation with the prototypical inducers rifampicin, St John's wort, carbamazepine and efavirenz. The gene and protein expression pattern of drug transporters in Caco-2 cells and jejunal tissue differed considerably. For some transporters culture-time dependent differences in mRNA expression and/or protein abundance could be determined. Finally, none of the studied prototypical inducers showed an effect either on mRNA expression and protein abundance or on the function of ABCB1. Differences in transporter expression in Caco-2 cells compared with jejunal tissue, as well as expression dependence on culture time must be considered in in vitro studies to avoid under- or overestimation of certain transporters. The Caco-2 cell model is not suitable for the evaluation of DDIs caused by transporter induction. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  8. Comparative tissue expression of American lobster (Homarus americanus) immune genes during bacterial and scuticociliate challenge.

    Science.gov (United States)

    Clark, K Fraser; Acorn, Adam R; Wang, Haili; Greenwood, Spencer J

    2015-12-01

    The American lobster (Homarus americanus) fishery is the most economically significant fishery in Canada; although comparatively little is known about the lobsters' response to pathogenic challenge. This is the first study to investigate the expression of immune genes in tissues outside of the lobster hepatopancreas in response to challenges by the Gram-positive bacteria, Aerococcus viridans var. homari or the scuticociliate parasite, Anophryoides haemophila. The hepatopancreas has been regarded as the major humoral immune organ in crustaceans, but the contribution of other organs and tissues to the molecular immune response has largely been overlooked. This study used RT-qPCR to monitor the gene expression of several immune genes including three anti-lipopolysaccharide isoforms (ALF) Homame ALF-B1, Homame ALF-C1 and ALFHa-1, acute phase serum amyloid protein A (SAA), as well as thioredoxin and hexokinase, in antennal gland and gill tissues. Our findings indicate that the gene expression of the SAA and all ALF isoforms in the antennal gland and gill tissues increased in response to pathogenic challenge. However, there was differential expression of individual ALF isoforms that were dependent on both the tissue, and the pathogen used in the challenge. The gene expression changes of several immune genes were found to be higher in the antennal gland than have been previously reported for the hepatopancreas. This study demonstrates that increased immune gene expression from the gill and antennal gland over the course of pathogen induced disease contributes to the immune response of H. americanus. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. A comparative analysis of watershed and edge based segmentation ...

    African Journals Online (AJOL)

    MJP

    2015-03-17

    Mar 17, 2015 ... Background: Useful information which is helpful in the diagnosis of various disorders is obtained from the analysis of individual blood cells. Aim: To perform a comparative analysis between edge-based segmentation and watershed segmentation on images of the red blood cells. Method: The images.

  10. Comparative Analysis of Termiteria and Surrounding Soil Properties ...

    African Journals Online (AJOL)

    Comparative Analysis of Termiteria and Surrounding Soil Properties in the University of Agriculture, Makurdi, Nigeria. IS Eneji, R Sha'Ato, SE Ejembi. Abstract. Variations in the properties of termitaria and their surrounding soil properties within the University of Agriculture Makurdi were investigated using routine soil analysis ...

  11. A comparative analysis of watershed and edge based segmentation ...

    African Journals Online (AJOL)

    Background: Useful information which is helpful in the diagnosis of various disorders is obtained from the analysis of individual blood cells. Aim: To perform a comparative analysis between edge-based segmentation and watershed segmentation on images of the red blood cells. Method: The images to be used for the ...

  12. A Comparative Analysis of Fuzzy Inference Engines in Context of ...

    African Journals Online (AJOL)

    Fuzzy inference engine has found successful applications in a wide variety of fields, such as automatic control, data classification, decision analysis, expert engines, time series prediction, robotics, pattern recognition, etc. This paper presents a comparative analysis of three fuzzy inference engines, max-product, max-min ...

  13. The Constant Comparative Analysis Method Outside of Grounded Theory

    Science.gov (United States)

    Fram, Sheila M.

    2013-01-01

    This commentary addresses the gap in the literature regarding discussion of the legitimate use of Constant Comparative Analysis Method (CCA) outside of Grounded Theory. The purpose is to show the strength of using CCA to maintain the emic perspective and how theoretical frameworks can maintain the etic perspective throughout the analysis. My…

  14. Comparative analysis and relationships of six important crop ...

    African Journals Online (AJOL)

    Using informatics tools to compare important species is now feasible as structural genomics continue in importance and establishment of structure-function relationships become a common way of comparative analysis. Currently, many of the technical issues involved in sequencing complete genomes have been solved.

  15. A Comparative Analysis of Charter Schools and Traditional Public Schools

    Science.gov (United States)

    Smith, Jodi Renee Abbott

    2014-01-01

    The focus of this descriptive research study was to compare charter and traditional public schools on the academic knowledge of fifth grade students as measured by Arizona's Instrument to Measure Standards (AIMS) in a suburb of a large southwestern city. This analysis also compared charter and traditional public schools on AYP status. It was…

  16. Customer service on the Czech mobile telecommunication market. Comparative Analysis

    OpenAIRE

    Hanzlík, Radek

    2013-01-01

    The main goal of this thesis is to compare the quality of customer service between the Mobile Network Operators (MNOs) and Mobile Virtual Network Operators (MVNOs) on the Czech mobile telecommunication market. The mystery shopping method is used as the source of data for the comparative analysis.

  17. comparative cost and strength analysis of cement and aggregate

    African Journals Online (AJOL)

    2012-07-02

    Jul 2, 2012 ... Abstract. This research presents a comparative cost and strength analysis of cement and aggregate replace- ment materials which is aimed at reducing the cost of concrete production. Tests were performed to compare the strength and cost of seven various cement replacement materials(rice husk ash,.

  18. Comparative Cost and Strength Analysis of Cement and Aggregate ...

    African Journals Online (AJOL)

    This research presents a comparative cost and strength analysis of cement and aggregate replacement materials which is aimed at reducing the cost of concrete production. Tests were performed to compare the strength and cost of seven various cement replacement materials(rice husk ash, groundnut husk ash, palm oil ...

  19. COMPARATIVE ANALYSIS OF CELEBRITY AND NON-CELEBRITY ADVERTISEMENT

    OpenAIRE

    Ammar Asad; Muhammad Naseem Hayat; Shafaqat Mehmood

    2013-01-01

    This study is undertaken to make a comparative analysis of celebrity advertisement and non-celebrity advertisement with respect to attitude toward advertisement, attitude toward brand, purchase intentions, and advertising attributes. For this purpose, a simple random sample of 200 students studying four different disciplines was taken from the Private University in Lahore. For econometric proof, reliability analysis, descriptive analysis, and independent sample T-test was used to interpret th...

  20. Leaf proteome analysis of transgenic plants expressing antiviral antibodies.

    Science.gov (United States)

    Di Carli, Mariasole; Villani, Maria Elena; Renzone, Giovanni; Nardi, Luca; Pasquo, Alessandra; Franconi, Rosella; Scaloni, Andrea; Benvenuto, Eugenio; Desiderio, Angiola

    2009-02-01

    The expression of exogenous antibodies in plant is an effective strategy to confer protection against viral infection or to produce molecules with pharmaceutical interest. However, the acceptance of the transgenic technology to obtain self-protecting plants depends on the assessment of their substantial equivalence compared to non-modified crops with an established history of safe use. In fact, the possibility exists that the introduction of transgenes in plants may alter expression of endogenous genes and/or normal production of metabolites. In this study, we investigated whether the expression in plant of recombinant antibodies directed against viral proteins may influence the host leaf proteome. Two transgenic plant models, generated by Agrobacterium tumefaciens-mediated transformation, were analyzed for this purpose, namely, Lycopersicon esculentum cv. MicroTom and Nicotiana benthamiana, expressing recombinant antibodies against cucumber mosaic virus and tomato spotted wilt virus, respectively. To obtain a significant representation of plant proteomes, optimized extraction procedures have been devised for each plant species. The proteome repertoire of antibody-expressing and control plants was compared by 2-DE associated to DIGE technology. Among the 2000 spots detected within the gels, about 10 resulted differentially expressed in each transgenic model and were identified by MALDI-TOF PMF and muLC-ESI-IT-MS/MS procedures. Protein variations were restricted to a limited number of defined differences with an average ratio below 2.4. Most of the differentially expressed proteins were related to photosynthesis or defense function. The overall results suggest that the expression of recombinant antibodies in both systems does not significantly alter the leaf proteomic profile, contributing to assess the biosafety of resistant plants expressing antiviral antibodies.

  1. Global expression profiling applied to the analysis of Arabidopsis stamen development.

    Science.gov (United States)

    Alves-Ferreira, Márcio; Wellmer, Frank; Banhara, Aline; Kumar, Vijaya; Riechmann, José Luis; Meyerowitz, Elliot M

    2007-11-01

    To obtain detailed information about gene expression during stamen development in Arabidopsis (Arabidopsis thaliana), we compared, by microarray analysis, the gene expression profile of wild-type inflorescences to those of the floral mutants apetala3, sporocyteless/nozzle, and male sterile1 (ms1), in which different aspects of stamen formation are disrupted. These experiments led to the identification of groups of genes with predicted expression at early, intermediate, and late stages of stamen development. Validation experiments using in situ hybridization confirmed the predicted expression patterns. Additional experiments aimed at characterizing gene expression specifically during microspore formation. To this end, we compared the gene expression profiles of wild-type flowers of distinct developmental stages to those of the ms1 mutant. Computational analysis of the datasets derived from this experiment led to the identification of genes that are likely involved in the control of key developmental processes during microsporogenesis. We also identified a large number of genes whose expression is prolonged in ms1 mutant flowers compared to the wild type. This result suggests that MS1, which encodes a putative transcriptional regulator, is involved in the stage-specific repression of these genes. Lastly, we applied reverse genetics to characterize several of the genes identified in the microarray experiments and uncovered novel regulators of microsporogenesis, including the transcription factor MYB99 and a putative phosphatidylinositol 4-kinase.

  2. Global Expression Profiling Applied to the Analysis of Arabidopsis Stamen Development1[W][OA

    Science.gov (United States)

    Alves-Ferreira, Márcio; Wellmer, Frank; Banhara, Aline; Kumar, Vijaya; Riechmann, José Luis; Meyerowitz, Elliot M.

    2007-01-01

    To obtain detailed information about gene expression during stamen development in Arabidopsis (Arabidopsis thaliana), we compared, by microarray analysis, the gene expression profile of wild-type inflorescences to those of the floral mutants apetala3, sporocyteless/nozzle, and male sterile1 (ms1), in which different aspects of stamen formation are disrupted. These experiments led to the identification of groups of genes with predicted expression at early, intermediate, and late stages of stamen development. Validation experiments using in situ hybridization confirmed the predicted expression patterns. Additional experiments aimed at characterizing gene expression specifically during microspore formation. To this end, we compared the gene expression profiles of wild-type flowers of distinct developmental stages to those of the ms1 mutant. Computational analysis of the datasets derived from this experiment led to the identification of genes that are likely involved in the control of key developmental processes during microsporogenesis. We also identified a large number of genes whose expression is prolonged in ms1 mutant flowers compared to the wild type. This result suggests that MS1, which encodes a putative transcriptional regulator, is involved in the stage-specific repression of these genes. Lastly, we applied reverse genetics to characterize several of the genes identified in the microarray experiments and uncovered novel regulators of microsporogenesis, including the transcription factor MYB99 and a putative phosphatidylinositol 4-kinase. PMID:17905860

  3. Meta Analysis of Gene Expression Data within and Across Species.

    Science.gov (United States)

    Fierro, Ana C; Vandenbussche, Filip; Engelen, Kristof; Van de Peer, Yves; Marchal, Kathleen

    2008-12-01

    Since the second half of the 1990s, a large number of genome-wide analyses have been described that study gene expression at the transcript level. To this end, two major strategies have been adopted, a first one relying on hybridization techniques such as microarrays, and a second one based on sequencing techniques such as serial analysis of gene expression (SAGE), cDNA-AFLP, and analysis based on expressed sequence tags (ESTs). Despite both types of profiling experiments becoming routine techniques in many research groups, their application remains costly and laborious. As a result, the number of conditions profiled in individual studies is still relatively small and usually varies from only two to few hundreds of samples for the largest experiments. More and more, scientific journals require the deposit of these high throughput experiments in public databases upon publication. Mining the information present in these databases offers molecular biologists the possibility to view their own small-scale analysis in the light of what is already available. However, so far, the richness of the public information remains largely unexploited. Several obstacles such as the correct association between ESTs and microarray probes with the corresponding gene transcript, the incompleteness and inconsistency in the annotation of experimental conditions, and the lack of standardized experimental protocols to generate gene expression data, all impede the successful mining of these data. Here, we review the potential and difficulties of combining publicly available expression data from respectively EST analyses and microarray experiments. With examples from literature, we show how meta-analysis of expression profiling experiments can be used to study expression behavior in a single organism or between organisms, across a wide range of experimental conditions. We also provide an overview of the methods and tools that can aid molecular biologists in exploiting these public data.

  4. [Key technologies in image analysis of comparative genomic hybridization].

    Science.gov (United States)

    Ni, J; Ji, L; Wang, M

    2001-12-01

    Comparative genomic hybridization has become a new technique in molecular-cytogenetics, and it has found significant applications in tumor pathology. Image analysis is an important part of comparative genomic hybridization. It analyzes the fluorescent images by many steps and finally determines whether there is any abnormality in the copy number of the test tumor tissue. This paper expatiates on the key steps in the image analysis of comparative genomic hybridization, including background correction, chromosome segmentation, chromosome axis determination, karyotyping and determining ratio profile. The future trend is also discussed.

  5. Altered β-catenin expression in oral mucosal dysplasia: a comparative study

    Directory of Open Access Journals (Sweden)

    Brunno Santos de Freitas SILVA

    2015-10-01

    Full Text Available Objective The current study aimed to investigate the β-catenin expression in oral leukoplakia (OL with different degrees of epithelial dysplasia and normal oral mucosa.Material and Methods Formalin-fixed, paraffin-embedded tissue samples of 39 OL (mild dysplasia n=19, moderate dysplasia n=13, and severe dysplasia n=7, and 10 normal oral mucosa (control group were submitted to immunohistochemical reactions to anti-β-catenin primary antibody. A qualitative β-catenin analysis was performed based on the percentage of positive cells. The cellular location and the epithelial layer were also considered. The Chi-square test and the Fisher’s exact test were used to verify possible differences in the β-catenin expression among the OL groups. A p-value of <0.05 was considered statistically significant.Results Membranous expression of β-catenin in parabasal and basal layers was gradually lost in the higher degrees of epithelial dysplasia. In normal oral mucosa, β-catenin was detected only in the cytoplasmic membrane. However, a significant increase in cytoplasmic β-catenin could be observed between mild and moderate dysplasia (Fisher Exact test - p<0.001 and between mild and severe dysplasia (p<0.001.Conclusions The β-catenin cytoplasmic expression observed in this study may represent the initial stage of modifications in the E-cadherin-catenin complex, along with morphological cellular changes.

  6. Do Dynamic Compared to Static Facial Expressions of Happiness and Anger Reveal Enhanced Facial Mimicry?

    Directory of Open Access Journals (Sweden)

    Krystyna Rymarczyk

    Full Text Available Facial mimicry is the spontaneous response to others' facial expressions by mirroring or matching the interaction partner. Recent evidence suggested that mimicry may not be only an automatic reaction but could be dependent on many factors, including social context, type of task in which the participant is engaged, or stimulus properties (dynamic vs static presentation. In the present study, we investigated the impact of dynamic facial expression and sex differences on facial mimicry and judgment of emotional intensity. Electromyography recordings were recorded from the corrugator supercilii, zygomaticus major, and orbicularis oculi muscles during passive observation of static and dynamic images of happiness and anger. The ratings of the emotional intensity of facial expressions were also analysed. As predicted, dynamic expressions were rated as more intense than static ones. Compared to static images, dynamic displays of happiness also evoked stronger activity in the zygomaticus major and orbicularis oculi, suggesting that subjects experienced positive emotion. No muscles showed mimicry activity in response to angry faces. Moreover, we found that women exhibited greater zygomaticus major muscle activity in response to dynamic happiness stimuli than static stimuli. Our data support the hypothesis that people mimic positive emotions and confirm the importance of dynamic stimuli in some emotional processing.

  7. Lack of repeatable differential expression patterns between MON810 and comparable commercial varieties of maize.

    Science.gov (United States)

    Coll, Anna; Nadal, Anna; Palaudelmàs, Montserrat; Messeguer, Joaquima; Melé, Enric; Puigdomènech, Pere; Pla, Maria

    2008-09-01

    The introduction of genetically modified organisms (GMO) in many countries follows strict regulations to assure that only products that have been safety tested in relation to human health and the environment are marketed. Thus, GMOs must be authorized before use. By complementing more targeted approaches, profiling methods can assess possible unintended effects of transformation. We used microarrays to compare the transcriptome profiles of widely commercialized maize MON810 varieties and their non-GM near-isogenic counterparts. The expression profiles of MON810 seedlings are more similar to those of their corresponding near-isogenic varieties than are the profiles of other lines produced by conventional breeding. However, differential expression of approximately 1.7 and approximately 0.1% of transcripts was identified in two variety pairs (AristisBt/Aristis and PR33P67/PR33P66) that had similar cryIA(b) mRNA levels, demonstrating that commercial varieties of the same event have different similarity levels to their near-isogenic counterparts without the transgene (note that these two pairs also show phenotypic differences). In the tissues, developmental stage and varieties analyzed, we could not identify any gene differentially expressed in all variety-pairs. However, a small set of sequences were differentially expressed in various pairs. Their relation to the transgenesis was not proven, although this is likely to be modulated by the genetic background of each variety.

  8. Do Dynamic Compared to Static Facial Expressions of Happiness and Anger Reveal Enhanced Facial Mimicry?

    Science.gov (United States)

    Rymarczyk, Krystyna; Żurawski, Łukasz; Jankowiak-Siuda, Kamila; Szatkowska, Iwona

    2016-01-01

    Facial mimicry is the spontaneous response to others' facial expressions by mirroring or matching the interaction partner. Recent evidence suggested that mimicry may not be only an automatic reaction but could be dependent on many factors, including social context, type of task in which the participant is engaged, or stimulus properties (dynamic vs static presentation). In the present study, we investigated the impact of dynamic facial expression and sex differences on facial mimicry and judgment of emotional intensity. Electromyography recordings were recorded from the corrugator supercilii, zygomaticus major, and orbicularis oculi muscles during passive observation of static and dynamic images of happiness and anger. The ratings of the emotional intensity of facial expressions were also analysed. As predicted, dynamic expressions were rated as more intense than static ones. Compared to static images, dynamic displays of happiness also evoked stronger activity in the zygomaticus major and orbicularis oculi, suggesting that subjects experienced positive emotion. No muscles showed mimicry activity in response to angry faces. Moreover, we found that women exhibited greater zygomaticus major muscle activity in response to dynamic happiness stimuli than static stimuli. Our data support the hypothesis that people mimic positive emotions and confirm the importance of dynamic stimuli in some emotional processing.

  9. Comparing anger, anger expression, life stress and social support between Korean female nursing and general university students.

    Science.gov (United States)

    Jun, Won Hee; Lee, Gyungjoo

    2017-12-01

    To compare anger, anger expression, life stress and social support among female students at a nursing university and a general university and to examine factors affecting anger in each group. University students typically experience constant stress resulting from factors like academic requirements, personal relationships and career decisions; this tends to promote anger. Particularly, nursing students' anger can negatively affect the quality of care that they provide, and also their mental health. Therefore, anger management of nursing students is very important in the training and development of future nurses. Nursing education needs to confirm factors associated with anger of nursing students compared with general university students to develop specific intervention programs for decreasing their anger levels. A descriptive, cross-sectional design was used. Participants were 286 female students (146 from a nursing university and 140 from a general university); they completed self-report surveys examining anger, anger expression, life stress and social support. A stepwise multiple regression analysis was done to identify factors affecting anger. Data were collected from 15 May-10 June 2016. In the stepwise multiple regression analysis, we entered three anger expression factors, eight life stress factors and social support as explanatory variables; factors affecting anger among nursing students were anger-out and same-sex peer relationship stress. In general university students, anger-out, anger-control and anger-in were identified as factors affecting anger. Becoming proficient in beneficial anger expression techniques and reducing stress from same-sex peer relationships will reduce anger among female nursing students. © 2017 John Wiley & Sons Ltd.

  10. Comparative Transcriptome Analysis of Hot Pepper (Capsicum annuum L. Leaf Heterosis by RNA-seq

    Directory of Open Access Journals (Sweden)

    Tao Li

    2015-12-01

    Full Text Available Heterosis has been mostly used in hot pepper breeding and production, but the molecular basis of heterosis has not been extensively studied. In this study, comparative transcriptomes analysis of parental lines (D6, D7 and F1 hybrids (D6×D7 and D7×D6 was performed. A total of 0.6 billion raw reads, and 0.44 billion high-quality reads were obtained after the filtering process. Statistical analysis of genes with presence/deletion variations showed that, there were 1068 (6.20% and 780 (4.56% genes in the "single parent express consistent type" in the direct (D6×D7 and reciprocal (D7×D6 F1 hybrids, respectively. More genes fit into the non-additive expression type in two F1 hybrids compared to the parents, and less than 8% of the genes belong to the additive expression type. 66.08% in direct and 62.96% in reciprocal F1 hybrids belong to the epistatic dominance expression pattern. There were more differentially expressed genes (DEGs between the two parental lines (351 than between the two hybrids (17. The results of gene ontology (GO analysis showed that there were obvious differences in electron transmission and photorespiration between two F1 hybrids. GO terms for regulating plant hypersensitive responses, and MAPK pathways were only enriched in the direct hybrid (D6×D7.

  11. Capturing heterogeneity in gene expression studies by surrogate variable analysis.

    Directory of Open Access Journals (Sweden)

    Jeffrey T Leek

    2007-09-01

    Full Text Available It has unambiguously been shown that genetic, environmental, demographic, and technical factors may have substantial effects on gene expression levels. In addition to the measured variable(s of interest, there will tend to be sources of signal due to factors that are unknown, unmeasured, or too complicated to capture through simple models. We show that failing to incorporate these sources of heterogeneity into an analysis can have widespread and detrimental effects on the study. Not only can this reduce power or induce unwanted dependence across genes, but it can also introduce sources of spurious signal to many genes. This phenomenon is true even for well-designed, randomized studies. We introduce "surrogate variable analysis" (SVA to overcome the problems caused by heterogeneity in expression studies. SVA can be applied in conjunction with standard analysis techniques to accurately capture the relationship between expression and any modeled variables of interest. We apply SVA to disease class, time course, and genetics of gene expression studies. We show that SVA increases the biological accuracy and reproducibility of analyses in genome-wide expression studies.

  12. Comparative transcriptomic analysis reveals similarities and dissimilarities in Saccharomyces cerevisiae wine strains response to nitrogen availability.

    Directory of Open Access Journals (Sweden)

    Catarina Barbosa

    Full Text Available Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23, under low (67 mg/L and high nitrogen (670 mg/L regimes, at three time points during fermentation (12 h, 24 h and 96 h. Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12 h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this

  13. Comparative Transcriptomic Analysis Reveals Similarities and Dissimilarities in Saccharomyces cerevisiae Wine Strains Response to Nitrogen Availability

    Science.gov (United States)

    Barbosa, Catarina; García-Martínez, José; Pérez-Ortín, José E.; Mendes-Ferreira, Ana

    2015-01-01

    Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23), under low (67 mg/L) and high nitrogen (670 mg/L) regimes, at three time points during fermentation (12h, 24h and 96h). Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this nutrient in the grape

  14. Facial expression analysis with AFFDEX and FACET: A validation study.

    Science.gov (United States)

    Stöckli, Sabrina; Schulte-Mecklenbeck, Michael; Borer, Stefan; Samson, Andrea C

    2017-12-07

    The goal of this study was to validate AFFDEX and FACET, two algorithms classifying emotions from facial expressions, in iMotions's software suite. In Study 1, pictures of standardized emotional facial expressions from three databases, the Warsaw Set of Emotional Facial Expression Pictures (WSEFEP), the Amsterdam Dynamic Facial Expression Set (ADFES), and the Radboud Faces Database (RaFD), were classified with both modules. Accuracy (Matching Scores) was computed to assess and compare the classification quality. Results show a large variance in accuracy across emotions and databases, with a performance advantage for FACET over AFFDEX. In Study 2, 110 participants' facial expressions were measured while being exposed to emotionally evocative pictures from the International Affective Picture System (IAPS), the Geneva Affective Picture Database (GAPED) and the Radboud Faces Database (RaFD). Accuracy again differed for distinct emotions, and FACET performed better. Overall, iMotions can achieve acceptable accuracy for standardized pictures of prototypical (vs. natural) facial expressions, but performs worse for more natural facial expressions. We discuss potential sources for limited validity and suggest research directions in the broader context of emotion research.

  15. Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress

    Directory of Open Access Journals (Sweden)

    Close Timothy J

    2009-08-01

    Full Text Available Abstract Background Rice and barley are both members of Poaceae (grass family but have a marked difference in salt tolerance. The molecular mechanism underlying this difference was previously unexplored. This study employs a comparative genomics approach to identify analogous and contrasting gene expression patterns between rice and barley. Results A hierarchical clustering approach identified several interesting expression trajectories among rice and barley genotypes. There were no major conserved expression patterns between the two species in response to salt stress. A wheat salt-stress dataset was queried for comparison with rice and barley. Roughly one-third of the salt-stress responses of barley were conserved with wheat while overlap between wheat and rice was minimal. These results demonstrate that, at transcriptome level, rice is strikingly different compared to the more closely related barley and wheat. This apparent lack of analogous transcriptional programs in response to salt stress is further highlighted through close examination of genes associated with root growth and development. Conclusion The analysis provides support for the hypothesis that conservation of transcriptional signatures in response to environmental cues depends on the genetic similarity among the genotypes within a species, and on the phylogenetic distance between the species.

  16. Systematic analysis of gene expression pattern in has-miR-197 over-expressed human uterine leiomyoma cells.

    Science.gov (United States)

    Ling, Jing; Wu, Xiaoli; Fu, Ziyi; Tan, Jie; Xu, Qing

    2015-10-01

    Our previous study showed that the expression of miR-197 in leiomyoma was down-regulated compared with myometrium. Further, miR-197 has been identified to affect uterine leiomyoma cell proliferation, apoptosis, and metastasis ability, though the responsible molecular mechanism has not been well elucidated. In this study, we sought to determine the expression patterns of miR-197 targeted genes and to explore their potential functions, participating Pathways and the networks that are involved in the biological behavior of human uterine leiomyoma. After transfection of human uterine leiomyoma cells with miR-197, we confirmed the expression level of miR-197 using quantitative real-time PCR (qRT-PCR), and we detected the gene expression profiles after miR-197 over-expression through DNA microarray analysis. Further, we performed GO and Pathway analysis. The dominantly dys-regulated genes, which were up- or down-regulated by more than 10-fold, compared with parental cells, were confirmed using qRT-PCR technology. Compared with the control group, miR-197 was up-regulated by 30-fold after miR-197 lentiviral transfection. The microarray data showed that 872 genes were dys-regulated by more than 2-fold in human uterine leiomyoma cells after miR-197 overexpression, including 537 up-regulated and 335 down-regulated genes. The GO analysis indicated that the dys-regulated genes were primarily involved in response to stimuli, multicellular organ processes, and the signaling of biological progression. Further, Pathway analysis data showed that these genes participated in regulating several signaling Pathways, including the JAK/STAT signaling Pathway, the Toll-like receptor signaling Pathway, and cytokine-cytokine receptor interaction. The qRT-PCR results confirmed that 17 of the 66 selected genes, which were up- or down-regulated more than 10-fold by miR-197, were consistent with the microarray results, including tumorigenesis-related genes, such as DRT7, SLC549, SFMBT2, FLJ37956

  17. Analysis of Expressed Sequence Tags (EST) in Date Palm.

    Science.gov (United States)

    Al-Faifi, Sulieman A; Migdadi, Hussein M; Algamdi, Salem S; Khan, Mohammad Altaf; Al-Obeed, Rashid S; Ammar, Megahed H; Jakse, Jerenj

    2017-01-01

    Expressed sequence tags (EST) were generated from a normalized cDNA library of the date palm Sukkari cv. to understand the high-quality and better field performance of this well-known commercial cultivar. A total of 6943 high-quality ESTs were generated, out of them 6671 are submitted to the GenBank dbEST (LIBEST_028537). The generated ESTs were assembled into 6362 unigenes, consisting of 494 (14.4%) contigs and 5868 (84.53%) singletons. The functional annotation shows that the majority of the ESTs are associated with binding (44%), catalytic (40%), transporter (5%), and structural molecular (5%) activities. The blastx results show that 73% of unigenes are significantly similar to known plant genes and 27% are novel. The latter could be of particular interest in date palm genetic studies. Further analysis shows that some ESTs are categorized as stress/defense- and fruit development-related genes. These newly generated ESTs could significantly enhance date palm EST databases in the public domain and are available to scientists and researchers across the globe. This knowledge will facilitate the discovery of candidate genes that govern important developmental and agronomical traits in date palm. It will provide important resources for developing genetic tools, comparative genomics, and genome evolution among date palm cultivars.

  18. Expression

    Directory of Open Access Journals (Sweden)

    Wang-Xia Wang

    2014-02-01

    Full Text Available The miR-15/107 family comprises a group of 10 paralogous microRNAs (miRNAs, sharing a 5′ AGCAGC sequence. These miRNAs have overlapping targets. In order to characterize the expression of miR-15/107 family miRNAs, we employed customized TaqMan Low-Density micro-fluid PCR-array to investigate the expression of miR-15/107 family members, and other selected miRNAs, in 11 human tissues obtained at autopsy including the cerebral cortex, frontal cortex, primary visual cortex, thalamus, heart, lung, liver, kidney, spleen, stomach and skeletal muscle. miR-103, miR-195 and miR-497 were expressed at similar levels across various tissues, whereas miR-107 is enriched in brain samples. We also examined the expression patterns of evolutionarily conserved miR-15/107 miRNAs in three distinct primary rat brain cell preparations (enriched for cortical neurons, astrocytes and microglia, respectively. In primary cultures of rat brain cells, several members of the miR-15/107 family are enriched in neurons compared to other cell types in the central nervous system (CNS. In addition to mature miRNAs, we also examined the expression of precursors (pri-miRNAs. Our data suggested a generally poor correlation between the expression of mature miRNAs and their precursors. In summary, we provide a detailed study of the tissue and cell type-specific expression profile of this highly expressed and phylogenetically conserved family of miRNA genes.

  19. Comparative proteomic analysis of genetically modified maize grown under different agroecosystems conditions in Brazil

    Science.gov (United States)

    2013-01-01

    Background Profiling technologies allow the simultaneous measurement and comparison of thousands of cell components without prior knowledge of their identity. In the present study, we used two-dimensional gel electrophoresis combined with mass spectrometry to evaluate protein expression of Brazilian genetically modified maize hybrid grown under different agroecosystems conditions. To this effect, leaf samples were subjected to comparative analysis using the near-isogenic non-GM hybrid as the comparator. Results In the first stage of the analysis, the main sources of variation in the dataset were identified by using Principal Components Analysis which correlated most of the variation to the different agroecosystems conditions. Comparative analysis within each field revealed a total of thirty two differentially expressed proteins between GM and non-GM samples that were identified and their molecular functions were mainly assigned to carbohydrate and energy metabolism, genetic information processing and stress response. Conclusions To the best of our knowledge this study represents the first evidence of protein identities with differentially expressed isoforms in Brazilian MON810 genetic background hybrid grown under field conditions. As global databases on outputs from “omics” analysis become available, these could provide a highly desirable benchmark for safety assessments. PMID:24304660

  20. Strong correlation between ASPM gene expression and HCV cirrhosis progression identified by co-expression analysis.

    Science.gov (United States)

    Wang, Fan; Chang, Ying; Li, Jin; Wang, Hongling; Zhou, Rui; Qi, Jian; Liu, Jing; Zhao, Qiu

    2017-01-01

    Hepatitis C virus (HCV) cirrhosis is at a high risk of hepatocellular carcinoma (HCC), and its progression is influenced by a complex network of gene interactions. A weighted gene co-expression network was constructed to identify gene modules associated with the seven-stage disease progression from HCV cirrhosis to HCV-related HCC (n=65). In the significant module (R2=0.86), a total of 25 network hub genes were identified, half of which were also hub nodes in the protein-protein interaction network of the module genes. In validation, most hub genes showed a moderate correlation with the disease progression, and only ASPM was highly correlated (R2=0.801). In the test set (n=63), ASPM was also more highly expressed in HCV cirrhosis with concomitant HCC than in those without HCC (P=0.0054). Gene set enrichment analysis (GSEA) demonstrated that the gene set of "regulation of protein amino acid phosphorylation" (n=20) was enriched in HCV cirrhosis samples with ASPM highly expressed (false discovery rate (FDR)=0.049). In gene ontology (GO) analysis, genes in the enriched set were associated with liver neoplasms and other neoplastic diseases. In conclusion, through co-expression analysis, ASPM was identified and validated in association with the progression of HCV cirrhosis probably by regulating tumor-related phosphorylation. Copyright © 2016 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

  1. Genome-wide expression analysis of transcription regulatory complexes

    NARCIS (Netherlands)

    Lenstra, T.L.

    2012-01-01

    Transcription regulation is important for nearly all cellular processes. To understand how transcription is regulated by different regulatory complexes, DNA microarray expression analysis is used to determine the genome-wide changes in mRNA levels upon deletion of individual factors that belong to

  2. Cloning and expression analysis of an anthocyanidin synthase gene ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 93; Issue 2. Cloning and expression analysis of an anthocyanidin synthase gene homologue from Brassica carinata. Mingli Yan Suping Ding Lili Liu Xiaoming Yin Jiabin Shu. Research Note Volume 93 Issue 2 August 2014 pp 513-516 ...

  3. Identification and expression analysis of vitellogenin from silk ...

    African Journals Online (AJOL)

    This study mainly shows the DNA sequence and expression analysis of vitellogenin in Actias selene (Ash-Vg). Specific primers were designed to amplify Ash-Vg gene by polymerase chain reaction (PCR) and the obtained DNA sequence was 7329 bp long, including 6 exons and 5 introns with an open reading frame ...

  4. Identification and expression analysis of primary auxin-responsive ...

    Indian Academy of Sciences (India)

    Keywords. auxin; Aux/IAA; bioinformatic analysis; cucumber; gene expression. Abstract. Aux/IAA is an important gene family involved in many aspects of growth and development. Aux/IAA proteins are short-lived nuclear proteins that are induced primarily by various phytohormones. In this study, 29 Aux/IAA family genes ...

  5. Molecular cloning, expression and computational analysis of a water ...

    African Journals Online (AJOL)

    UTR, 522 bp mORF and a polyA adenylational signal. It codes for a poly-peptide of 173 amino acids having predicted molecular weight and isoelectric point of 19 KDa and 7.75 respectively. Heterologous expression and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the protein in ...

  6. Iterated Process Analysis over Lattice-Valued Regular Expressions

    DEFF Research Database (Denmark)

    Midtgaard, Jan; Nielson, Flemming; Nielson, Hanne Riis

    2016-01-01

    We present an iterated approach to statically analyze programs of two processes communicating by message passing. Our analysis operates over a domain of lattice-valued regular expressions, and computes increasingly better approximations of each process's communication behavior. Overall the work...

  7. Spatial and temporal expression analysis of D- myo -inositol 3 ...

    African Journals Online (AJOL)

    1á (eukaryotic elongation factor 1-alpha) using SYBER-Green. The qRT-PCR data analysis indicated that the expression of the four highly conserved MIPS genes is both temporally and spatially regulated, information much needed for reverse ...

  8. Genomewide identification and expression analysis of the ARF gene ...

    Indian Academy of Sciences (India)

    Genomewide identification and expression analysis of the ARF gene family in apple. Xiao-Cui Luo, Mei-Hong Sun, Rui-Rui Xu, Huai-Rui Shu, Jia-Wei Wang and Shi-Zhong Zhang. J. Genet. 93, 785–797. Figure 1. Phylogenetic relation of apple ARF genes. The phylogenetic tree was constructed based on a complete protein ...

  9. Evolution and expression analysis of the soybean glutamate ...

    Indian Academy of Sciences (India)

    Evolution and expression analysis of the soybean glutamate decarboxylase gene family. TAE KYUNG HYUN, SEUNG HEE EOM, XIAO HAN and JU-SUNG KIM http://www.ias.ac.in/jbiosci. J. Biosci. 39(5), December 2014, 899–907, © Indian Academy of Sciences. Supplementary material. Supplementary figure 1.

  10. Cloning, expression and functional analysis of MAP30 from ...

    African Journals Online (AJOL)

    The apoptosis percentage and the mitochondria membrane potential level was displayed by flow cytometry analysis and JC-1 fluorescent probe assay, respectively. The mRNA expression of caspase-9 and Apaf-1 was investigated by reverse transcription polymerase chain reaction (RT-PCR). The content of Cyt C and the ...

  11. Molecular cloning and expression analysis of a zeta-class ...

    African Journals Online (AJOL)

    It encoded the 206 amino acid residues with a molecular mass of 23.1 KD and isoelectric point of 6.10. ... Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis and enzyme activity assay indicated that the prokaryotic expression product was a fusion protein with a molecular weight of about 30 KD ...

  12. Genome-wide identification, functional analysis and expression ...

    African Journals Online (AJOL)

    Fuyou Fu

    2013-07-24

    Jul 24, 2013 ... RH89-039-16 referred to as RH and from a heterozygous diploid breeding line. All PDR genes expression was analyzed, using Mev. 4.8 version (Saeed et al., 2003). RESULTS. Identification of 76 potato PDR proteins by sequence analysis. Potato genome annotation files were downloaded. Then. Mapman ...

  13. Molecular cloning, sequence analysis and tissue expression of ...

    African Journals Online (AJOL)

    Achaete-scute like-2 (ASCL2) gene is a maternally expressed gene that encodes a lineage-specific transcription factor that is essential for neurectoderm and trophectoderm development and is implicated in pre-natal and post-natal development in mammals. Using comparative genomics, various in silico sequence ...

  14. Analysis and visualization of gene expression data using ...

    African Journals Online (AJOL)

    Several clustering and biclustering methods have been introduced to analyze the gene expression data by identifying the similar patterns and grouping genes into subsets that share biological significance. However, it is not clear how the different methods compare with each other with respect to the biological relevance of ...

  15. Suppressed inflammatory gene expression during human hypertrophic scar compared to normotrophic scar formation.

    Science.gov (United States)

    van den Broek, Lenie J; van der Veer, Willem M; de Jong, Etty H; Gibbs, Susan; Niessen, Frank B

    2015-08-01

    Hypertrophic scar formation is a result of adverse cutaneous wound healing. The pathogenesis of hypertrophic scar formation is still poorly understood. A problem next to the lack of suitable animal models is that often normal skin is compared to hypertrophic scar (HTscar) and not to normotrophic scar (NTscar) tissue. Another drawback is that often only one time period after wounding is studied, while scar formation is a dynamic process over a period of several months. In this study, we compared the expression of genes involved in inflammation, angiogenesis and extracellular matrix (ECM) formation and also macrophage infiltration in biopsies obtained before and up to 52 weeks after standard surgery in five patients who developed HTscar and six patients who developed NTscar. It was found that HTscar formation coincided with a prolonged decreased expression of inflammatory genes (TNFα, IL-1α, IL-1RN, CCL2, CCL3, CXCL2, CXCR2, C3 and IL-10) and an extended increased expression of ECM-related genes (PLAU, Col3A1, TGFβ3). This coincided with a delayed but prolonged infiltration of macrophages (type 2) in HTscar tissue compared to NTscar tissue. These findings were supported by immunohistochemical localization of proteins coding for select genes named above. Our study emphasizes that human cutaneous wound healing is a dynamic process that is needed to be studied over a period of time rather than a single point of time. Taken together, our results suggest innate immune stimulatory therapies may be a better option for improving scar quality than the currently used anti-inflammatory scar therapies. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. In silico analysis of stomach lineage specific gene set expression pattern in gastric cancer.

    Science.gov (United States)

    Pandi, Narayanan Sathiya; Suganya, Sivagurunathan; Rajendran, Suriliyandi

    2013-10-04

    Stomach lineage specific gene products act as a protective barrier in the normal stomach and their expression maintains the normal physiological processes, cellular integrity and morphology of the gastric wall. However, the regulation of stomach lineage specific genes in gastric cancer (GC) is far less clear. In the present study, we sought to investigate the role and regulation of stomach lineage specific gene set (SLSGS) in GC. SLSGS was identified by comparing the mRNA expression profiles of normal stomach tissue with other organ tissue. The obtained SLSGS was found to be under expressed in gastric tumors. Functional annotation analysis revealed that the SLSGS was enriched for digestive function and gastric epithelial maintenance. Employing a single sample prediction method across GC mRNA expression profiles identified the under expression of SLSGS in proliferative type and invasive type gastric tumors compared to the metabolic type gastric tumors. Integrative pathway activation prediction analysis revealed a close association between estrogen-α signaling and SLSGS expression pattern in GC. Elevated expression of SLSGS in GC is associated with an overall increase in the survival of GC patients. In conclusion, our results highlight that estrogen mediated regulation of SLSGS in gastric tumor is a molecular predictor of metabolic type GC and prognostic factor in GC. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Genome-wide comparative analysis of four Indian Drosophila species.

    Science.gov (United States)

    Mohanty, Sujata; Khanna, Radhika

    2017-12-01

    Comparative analysis of multiple genomes of closely or distantly related Drosophila species undoubtedly creates excitement among evolutionary biologists in exploring the genomic changes with an ecology and evolutionary perspective. We present herewith the de novo assembled whole genome sequences of four Drosophila species, D. bipectinata, D. takahashii, D. biarmipes and D. nasuta of Indian origin using Next Generation Sequencing technology on an Illumina platform along with their detailed assembly statistics. The comparative genomics analysis, e.g. gene predictions and annotations, functional and orthogroup analysis of coding sequences and genome wide SNP distribution were performed. The whole genome of Zaprionus indianus of Indian origin published earlier by us and the genome sequences of previously sequenced 12 Drosophila species available in the NCBI database were included in the analysis. The present work is a part of our ongoing genomics project of Indian Drosophila species.

  18. Expression Sensitivity Analysis of Human Disease Related Genes

    Directory of Open Access Journals (Sweden)

    Liang-Xiao Ma

    2013-01-01

    Full Text Available Background. Genome-wide association studies (GWAS have shown its revolutionary power in seeking the influenced loci on complex diseases genetically. Thousands of replicated loci for common traits are helpful in diseases risk assessment. However it is still difficult to elucidate the variations in these loci that directly cause susceptibility to diseases by disrupting the expression or function of a protein currently. Results. We evaluate the expression features of disease related genes and find that different diseases related genes show different expression perturbation sensitivities in various conditions. It is worth noting that the expression of some robust disease-genes doesn’t show significant change in their corresponding diseases, these genes might be easily ignored in the expression profile analysis. Conclusion. Gene ontology enrichment analysis indicates that robust disease-genes execute essential function in comparison with sensitive disease-genes. The diseases associated with robust genes seem to be relatively lethal like cancer and aging. On the other hand, the diseases associated with sensitive genes are apparently nonlethal like psych and chemical dependency diseases.

  19. Fast method for skeletal tissue gene expression analysis.

    Science.gov (United States)

    Dalle Carbonare, Luca; Vilei, Maria Teresa; Stranieri, Chiara; Innamorati, Giulio; Rosato, Antonio; Boldrin, Elisa; Sella, Stefania; Giannini, Sandro; Valenti, Maria Teresa

    2016-08-01

    Several chronic diseases have been associated with bone alteration in the last few years. Despite the wealth of information provided by the analysis of the transcriptome in affected tissues, only a limited number of studies evaluated gene expression in bone tissue due to the difficulty to obtain high quality RNA. Therefore, skeletal pathologies have been often associated to a defective maturation process that occurs during recruitment of progenitor stem cells. In order to explore the possibility of analysing the gene expression during osteogenic differentiation in skeletal tissue, a single-step method to extract well-preserved RNA from bone specimens was performed. A comparison between this technique and a traditional method was made by analysing the quality and yield of RNA obtained. In addition, RNAs were assayed by reverse transcription-quantitative polymerase chain reaction to analyse the expression levels of the bone genes associated with the differentiation process in a mouse model. The present data showed that good quality RNA can be obtained from bone tissue by a simple single-step method allowing the expression analysis of the genes encoded by skeletal tissue. In conclusion, the present study allows the possibility to easily obtain good quality RNA from bone tissue that is suitable for gene expression studies of bone diseases.

  20. Mycobacterial species as case-study of comparative genome analysis

    DEFF Research Database (Denmark)

    Zakham, F.; Belayachi, L.; Ussery, David

    2011-01-01

    The genus Mycobacterium represents more than 120 species including important pathogens of human and cause major public health problems and illnesses. Further, with more than 100 genome sequences from this genus, comparative genome analysis can provide new insights for better understanding...... the evolutionary events of these species and improving drugs, vaccines, and diagnostics tools for controlling Mycobacterial diseases. In this present study we aim to outline a comparative genome analysis of fourteen Mycobacterial genomes: M. avium subsp. paratuberculosis K—10, M. bovis AF2122/97, M. bovis BCG str...

  1. Analysis of multiplex gene expression maps obtained by voxelation

    Directory of Open Access Journals (Sweden)

    Smith Desmond J

    2009-04-01

    Full Text Available Abstract Background Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. Results To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in

  2. Independent component analysis of Alzheimer's DNA microarray gene expression data

    Directory of Open Access Journals (Sweden)

    Vanderburg Charles R

    2009-01-01

    Full Text Available Abstract Background Gene microarray technology is an effective tool to investigate the simultaneous activity of multiple cellular pathways from hundreds to thousands of genes. However, because data in the colossal amounts generated by DNA microarray technology are usually complex, noisy, high-dimensional, and often hindered by low statistical power, their exploitation is difficult. To overcome these problems, two kinds of unsupervised analysis methods for microarray data: principal component analysis (PCA and independent component analysis (ICA have been developed to accomplish the task. PCA projects the data into a new space spanned by the principal components that are mutually orthonormal to each other. The constraint of mutual orthogonality and second-order statistics technique within PCA algorithms, however, may not be applied to the biological systems studied. Extracting and characterizing the most informative features of the biological signals, however, require higher-order statistics. Results ICA is one of the unsupervised algorithms that can extract higher-order statistical structures from data and has been applied to DNA microarray gene expression data analysis. We performed FastICA method on DNA microarray gene expression data from Alzheimer's disease (AD hippocampal tissue samples and consequential gene clustering. Experimental results showed that the ICA method can improve the clustering results of AD samples and identify significant genes. More than 50 significant genes with high expression levels in severe AD were extracted, representing immunity-related protein, metal-related protein, membrane protein, lipoprotein, neuropeptide, cytoskeleton protein, cellular binding protein, and ribosomal protein. Within the aforementioned categories, our method also found 37 significant genes with low expression levels. Moreover, it is worth noting that some oncogenes and phosphorylation-related proteins are expressed in low levels. In

  3. Comparative analysis of land cadastral system in Macedonia and Slovenia

    OpenAIRE

    Stojčeska, Viktorija

    2015-01-01

    In the graduation thesis the topic of cadastral systems in Macedonia and Slovenia is discussed. The historical development, organization and functioning of today's cadastral systems in both countries is presented and compared. The development of cadastre of real property in Macedonia is presented in detail, where the land recording is presented from the title deeds system (tapija) to today's unified cadastre. The thesis comprises a comparative analysis of land administration syste...

  4. Comparative Analysis of the Concept of Shakespearean Tragedies

    OpenAIRE

    Muhammad Aslam Sipra; Muhammad Haseeb Nasir

    2014-01-01

    In this article, the analysis of Shakespearean tragedies is presented. It reveals that Shakespeare’s plays are full of conflicting thoughts, and expression is so convincing that it is not possible to plan a system of philosophy out of them. Each character, from the king to the clown, from the most highly intellectual to the simpleton, judges life from his own point of view and says something that is so deep and appropriate at the playwright’s versatility of genius. So is the case ...

  5. Integrative sparse principal component analysis of gene expression data.

    Science.gov (United States)

    Liu, Mengque; Fan, Xinyan; Fang, Kuangnan; Zhang, Qingzhao; Ma, Shuangge

    2017-12-01

    In the analysis of gene expression data, dimension reduction techniques have been extensively adopted. The most popular one is perhaps the PCA (principal component analysis). To generate more reliable and more interpretable results, the SPCA (sparse PCA) technique has been developed. With the "small sample size, high dimensionality" characteristic of gene expression data, the analysis results generated from a single dataset are often unsatisfactory. Under contexts other than dimension reduction, integrative analysis techniques, which jointly analyze the raw data of multiple independent datasets, have been developed and shown to outperform "classic" meta-analysis and other multidatasets techniques and single-dataset analysis. In this study, we conduct integrative analysis by developing the iSPCA (integrative SPCA) method. iSPCA achieves the selection and estimation of sparse loadings using a group penalty. To take advantage of the similarity across datasets and generate more accurate results, we further impose contrasted penalties. Different penalties are proposed to accommodate different data conditions. Extensive simulations show that iSPCA outperforms the alternatives under a wide spectrum of settings. The analysis of breast cancer and pancreatic cancer data further shows iSPCA's satisfactory performance. © 2017 WILEY PERIODICALS, INC.

  6. DSGeo: software tools for cross-platform analysis of gene expression data in GEO.

    Science.gov (United States)

    Lacson, Ronilda; Pitzer, Erik; Kim, Jihoon; Galante, Pedro; Hinske, Christian; Ohno-Machado, Lucila

    2010-10-01

    The Gene Expression Omnibus (GEO) is the largest resource of public gene expression data. While GEO enables data browsing, query and retrieval, additional tools can help realize its potential for aggregating and comparing data across multiple studies and platforms. This paper describes DSGeo-a collection of valuable tools that were developed for annotating, aggregating, integrating, and analyzing data deposited in GEO. The core set of tools include a Relational Database, a Data Loader, a Data Browser, and an Expression Combiner and Analyzer. The application enables querying for specific sample characteristics and identifying studies containing samples that match the query. The Expression Combiner application enables normalization and aggregation of data from these samples and returns these data to the user after filtering, according to the user's preferences. The Expression Analyzer allows simple statistical comparisons between groups of data. This seamless integration makes annotated cross-platform data directly available for analysis.

  7. Analysis of the expression of putatively imprinted genes in bovine peri-implantation embryos

    DEFF Research Database (Denmark)

    Tveden-Nyborg, Pernille Yde; Alexopoulos, N.I.; Cooney, M.A.

    2008-01-01

    imprinted genes (Ata3, Dlk1, Gnas, Grb10, Magel2, Mest-1, Ndn and Sgce) in bovine peri-implantation embryos. Two embryonic developmental stages were examined, Day 14 and Day 21. The gene expression pattern of single embryos was recorded for in vivo, in vitro produced (IVP) and parthenogenetic embryos....... The IVP embryos allow us to estimate the effect of in vitro procedures and the analysis of parthenogenetic embryos provides provisional information on maternal genomic imprinting. Among the 8 genes investigated, only Mest-1 showed differential expression in Day 21 parthenogenetic embryos compared...... to in vivo and IVP counterparts, indicating maternal imprinting of this gene. In addition, our expression analysis of single embryos revealed a more heterogeneous gene expression in IVP than in in vivo developed embryos, adding further to the hypothesis of transcriptional dysregulation induced by in vitro...

  8. A high efficiency cloning and expression system for proteomic analysis.

    Science.gov (United States)

    Ding, Xuan Z; Paulsen, Ian T; Bhattacharjee, Apurba K; Nikolich, Mikeljon P; Myers, Gary; Hoover, David L

    2006-07-01

    The recent description of the complete genomes of the two most pathogenic species of Brucella opens the way for genome-based analysis of the antigenicity of their proteins. In the present report, we describe a bench-level high-efficiency cloning and expression system (HECES) that allow expression of large numbers of Brucella proteins based on genomic sequence information. Purified proteins are produced with high efficiency in a microarray format conducive to analysis of their sero-reactivity against serum from immunized animals. This method is applicable at either small or large scale of protein processing. While it does not require robotics, the format is amenable to robotic implementation for all aspects of the process and subsequent analysis of protein characteristics. This method will allow selection of new reagents for diagnosis of brucellosis and development of vaccine against Brucella, an important zoonotic disease and biothreat agent.

  9. Comparative gene expression profiling of placentas from patients with severe pre-eclampsia and unexplained fetal growth restriction

    Directory of Open Access Journals (Sweden)

    Kurahashi Hiroki

    2011-08-01

    Full Text Available Abstract Background It has been well documented that pre-eclampsia and unexplained fetal growth restriction (FGR have a common etiological background, but little is known about their linkage at the molecular level. The aim of this study was to further investigate the mechanisms underlying pre-eclampsia and unexplained FGR. Methods We analyzed differentially expressed genes in placental tissue from severe pre-eclamptic pregnancies (n = 8 and normotensive pregnancies with or (n = 8 without FGR (n = 8 using a microarray method. Results A subset of the FGR samples showed a high correlation coefficient overall in the microarray data from the pre-eclampsia samples. Many genes that are known to be up-regulated in pre-eclampsia are also up-regulated in FGR, including the anti-angiogenic factors, FLT1 and ENG, believed to be associated with the onset of maternal symptoms of pre-eclampsia. A total of 62 genes were found to be differentially expressed in both disorders. However, gene set enrichment analysis for these differentially expressed genes further revealed higher expression of TP53-downstream genes in pre-eclampsia compared with FGR. TP53-downstream apoptosis-related genes, such as BCL6 and BAX, were found to be significantly more up-regulated in pre-eclampsia than in FGR, although the caspases are expressed at equivalent levels. Conclusions Our current data indicate a common pathophysiology for FGR and pre-eclampsia, leading to an up-regulation of placental anti-angiogenic factors. However, our findings also suggest that it may possibly be the excretion of these factors into the maternal circulation through the TP53-mediated early-stage apoptosis of trophoblasts that leads to the maternal symptoms of pre-eclampsia.

  10. Cloning, characterization and expression analysis of porcine microRNAs

    Directory of Open Access Journals (Sweden)

    Desilva Udaya

    2009-02-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are small ~22-nt regulatory RNAs that can silence target genes, by blocking their protein production or degrading the mRNAs. Pig is an important animal in the agriculture industry because of its utility in the meat production. Besides, pig has tremendous biomedical importance as a model organism because of its closer proximity to humans than the mouse model. Several hundreds of miRNAs have been identified from mammals, humans, mice and rats, but little is known about the miRNA component in the pig genome. Here, we adopted an experimental approach to identify conserved and unique miRNAs and characterize their expression patterns in diverse tissues of pig. Results By sequencing a small RNA library generated using pooled RNA from the pig heart, liver and thymus; we identified a total of 120 conserved miRNA homologs in pig. Expression analysis of conserved miRNAs in 14 different tissue types revealed heart-specific expression of miR-499 and miR-208 and liver-specific expression of miR-122. Additionally, miR-1 and miR-133 in the heart, miR-181a and miR-142-3p in the thymus, miR-194 in the liver, and miR-143 in the stomach showed the highest levels of expression. miR-22, miR-26b, miR-29c and miR-30c showed ubiquitous expression in diverse tissues. The expression patterns of pig-specific miRNAs also varied among the tissues examined. Conclusion Identification of 120 miRNAs and determination of the spatial expression patterns of a sub-set of these in the pig is a valuable resource for molecular biologists, breeders, and biomedical investigators interested in post-transcriptional gene regulation in pig and in related mammals, including humans.

  11. ADAGE signature analysis: differential expression analysis with data-defined gene sets.

    Science.gov (United States)

    Tan, Jie; Huyck, Matthew; Hu, Dongbo; Zelaya, René A; Hogan, Deborah A; Greene, Casey S

    2017-11-22

    Gene set enrichment analysis and overrepresentation analyses are commonly used methods to determine the biological processes affected by a differential expression experiment. This approach requires biologically relevant gene sets, which are currently curated manually, limiting their availability and accuracy in many organisms without extensively curated resources. New feature learning approaches can now be paired with existing data collections to directly extract functional gene sets from big data. Here we introduce a method to identify perturbed processes. In contrast with methods that use curated gene sets, this approach uses signatures extracted from public expression data. We first extract expression signatures from public data using ADAGE, a neural network-based feature extraction approach. We next identify signatures that are differentially active under a given treatment. Our results demonstrate that these signatures represent biological processes that are perturbed by the experiment. Because these signatures are directly learned from data without supervision, they can identify uncurated or novel biological processes. We implemented ADAGE signature analysis for the bacterial pathogen Pseudomonas aeruginosa. For the convenience of different user groups, we implemented both an R package (ADAGEpath) and a web server ( http://adage.greenelab.com ) to run these analyses. Both are open-source to allow easy expansion to other organisms or signature generation methods. We applied ADAGE signature analysis to an example dataset in which wild-type and ∆anr mutant cells were grown as biofilms on the Cystic Fibrosis genotype bronchial epithelial cells. We mapped active signatures in the dataset to KEGG pathways and compared with pathways identified using GSEA. The two approaches generally return consistent results; however, ADAGE signature analysis also identified a signature that revealed the molecularly supported link between the MexT regulon and Anr. We designed

  12. GECKO: a complete large-scale gene expression analysis platform.

    Science.gov (United States)

    Theilhaber, Joachim; Ulyanov, Anatoly; Malanthara, Anish; Cole, Jack; Xu, Dapeng; Nahf, Robert; Heuer, Michael; Brockel, Christoph; Bushnell, Steven

    2004-12-10

    Gecko (Gene Expression: Computation and Knowledge Organization) is a complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community. Based on a client-server architecture, with a centralized repository of typically many tens of thousands of Affymetrix scans, Gecko includes automatic processing pipelines for uploading data from remote sites, a data base, a computational engine implementing approximately 50 different analysis tools, and a client application. Among available analysis tools are clustering methods, principal component analysis, supervised classification including feature selection and cross-validation, multi-factorial ANOVA, statistical contrast calculations, and various post-processing tools for extracting data at given error rates or significance levels. On account of its open architecture, Gecko also allows for the integration of new algorithms. The Gecko framework is very general: non-Affymetrix and non-gene expression data can be analyzed as well. A unique feature of the Gecko architecture is the concept of the Analysis Tree (actually, a directed acyclic graph), in which all successive results in ongoing analyses are saved. This approach has proven invaluable in allowing a large (approximately 100 users) and distributed community to share results, and to repeatedly return over a span of years to older and potentially very complex analyses of gene expression data. The Gecko system is being made publicly available as free software http://sourceforge.net/projects/geckoe. In totality or in parts, the Gecko framework should prove useful to users and system developers with a broad range of analysis needs.

  13. GECKO: a complete large-scale gene expression analysis platform

    Directory of Open Access Journals (Sweden)

    Heuer Michael

    2004-12-01

    Full Text Available Abstract Background Gecko (Gene Expression: Computation and Knowledge Organization is a complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community. Results Based on a client-server architecture, with a centralized repository of typically many tens of thousands of Affymetrix scans, Gecko includes automatic processing pipelines for uploading data from remote sites, a data base, a computational engine implementing ~ 50 different analysis tools, and a client application. Among available analysis tools are clustering methods, principal component analysis, supervised classification including feature selection and cross-validation, multi-factorial ANOVA, statistical contrast calculations, and various post-processing tools for extracting data at given error rates or significance levels. On account of its open architecture, Gecko also allows for the integration of new algorithms. The Gecko framework is very general: non-Affymetrix and non-gene expression data can be analyzed as well. A unique feature of the Gecko architecture is the concept of the Analysis Tree (actually, a directed acyclic graph, in which all successive results in ongoing analyses are saved. This approach has proven invaluable in allowing a large (~ 100 users and distributed community to share results, and to repeatedly return over a span of years to older and potentially very complex analyses of gene expression data. Conclusions The Gecko system is being made publicly available as free software http://sourceforge.net/projects/geckoe. In totality or in parts, the Gecko framework should prove useful to users and system developers with a broad range of analysis needs.

  14. Comparing Different Classes of Reinforcement to Increase Expressive Language for Individuals with Autism

    Science.gov (United States)

    Leaf, Justin B.; Dale, Stephanie; Kassardjian, Alyne; Tsuji, Kathleen H.; Taubman, Mitchell; McEachin, John J.; Leaf, Ronald B.; Oppenheim-Leaf, Misty L.

    2014-01-01

    One of the basic principles of applied behavior analysis is that behavior change is largely due to that behavior being reinforced. Therefore the use of positive reinforcement is a key component of most behavioral programs for individuals diagnosed with autism. In this study we compared four different classes of reinforcers (i.e., food, praise,…

  15. Gene expression profile of cervical tissue compared to exfoliated cells: Impact on biomarker discovery

    Directory of Open Access Journals (Sweden)

    Vernon Suzanne D

    2005-05-01

    Full Text Available Abstract Background Exfoliated cervical cells are used in cytology-based cancer screening and may also be a source for molecular biomarkers indicative of neoplastic changes in the underlying tissue. However, because of keratinization and terminal differentiation it is not clear that these cells have an mRNA profile representative of cervical tissue, and that the profile can distinguish the lesions targeted for early detection. Results We used whole genome microarrays (25,353 unique genes to compare the transcription profiles from seven samples of normal exfoliated cells and one cervical tissue. We detected 10,158 genes in exfoliated cells, 14,544 in the tissue and 7320 genes in both samples. For both sample types the genes grouped into the same major gene ontology (GO categories in the same order, with exfoliated cells, having on average 20% fewer genes in each category. We also compared microarray results of samples from women with cervical intraepithelial neoplasia grade 3 (CIN3, n = 15 to those from age and race matched women without significant abnormalities (CIN1, CIN0; n = 15. We used three microarray-adapted statistical packages to identify differential gene expression. The six genes identified in common were two to four fold upregulated in CIN3 samples. One of these genes, the ubiquitin-conjugating enzyme E2 variant 1, participates in the degradation of p53 through interaction with the oncogenic HPV E6 protein. Conclusion The findings encourage further exploration of gene expression using exfoliated cells to identify and validate applicable biomarkers. We conclude that the gene expression profile of exfoliated cervical cells partially represents that of tissue and is complex enough to provide potential differentiation between disease and non-disease.

  16. Comparative study of expression of smad3 in oral lichen planus and normal oral mucosa.

    Science.gov (United States)

    Nafarzadeh, Shima; Ejtehadi, Samad; Amini Shakib, Pouyan; Fereidooni, Majid; Bijani, Ali

    2013-01-01

    Oral lichen planus (OLP) is a chronic inflammatory disease of the oral mucosa which is considered by the World Health Organization (WHO) as a premalignant condition. One step in malignant development is so called epithelial mesenchymal transition (EMT), a process whereby epithelial cells acquire mesenchymal characteristics. A factor known to induce EMT is the transforming growth factor-β (TGF-β), which uses the Smad proteins as mediators for its signaling. The aim of this study was to compare the expression of Smad 3 in Oral Lichen Planus and normal oral mucosa. This descriptive analytic study was performed on 30 patients with OLP (21 women and 9 men with mean age of 45.23± 2.44 years) and 20 normal oral mucosa (14 women and 6 men with mean age of 46.95± 2.21 years). The samples were studied by immunohistochemical staining. Data were analyzed with paired T-test and Wilcoxon test by SPSS software. Expression of Smad3 in OLP samples and normal oral mucosa was different. This difference was statistically significant (Poral lichen planus compared to normal oral mucosa might help to discuss its higher potential for malignant transition.

  17. PCR Expression Analysis Of the Estrogeninducible Gene Bcei in Gastrointestinal and Other Human Tumors

    Directory of Open Access Journals (Sweden)

    Iris Wundrack

    1994-01-01

    Full Text Available A polymerase chain reaction (PCR assay was developed to test for tumor cell specific expression of the BCEI gene. This new marker gene, reported at first for human breast cancer, was found specifically active in various gastrointestinal carcinomas by previously applying immunohistochemistry and RNA (Northern blot analysis. Presently, by using reverse transcription -PCR analysis, a series of primary tumor tissues and established tumor cell lines were testcd for BCEI transcription. This approach was compared to immunostaining achieved by an antibody directed against the BCEI gene’s product. The result demonstrate the superior sensitivity of PCR by indicating the gene’ s expression in cases where immunohistochemical testing remained negative.

  18. Gene expression analysis of endometrium reveals progesterone resistance and candidate susceptibility genes in women with endometriosis.

    Science.gov (United States)

    Burney, Richard O; Talbi, Said; Hamilton, Amy E; Vo, Kim Chi; Nyegaard, Mette; Nezhat, Camran R; Lessey, Bruce A; Giudice, Linda C

    2007-08-01

    The identification of molecular differences in the endometrium of women with endometriosis is an important step toward understanding the pathogenesis of this condition and toward developing novel strategies for the treatment of associated infertility and pain. In this study, we conducted global gene expression analysis of endometrium from women with and without moderate/severe stage endometriosis and compared the gene expression signatures across various phases of the menstrual cycle. The transcriptome analysis revealed molecular dysregulation of the proliferative-to-secretory transition in endometrium of women with endometriosis. Paralleled gene expression analysis of endometrial specimens obtained during the early secretory phase demonstrated a signature of enhanced cellular survival and persistent expression of genes involved in DNA synthesis and cellular mitosis in the setting of endometriosis. Comparative gene expression analysis of progesterone-regulated genes in secretory phase endometrium confirmed the observation of attenuated progesterone response. Additionally, interesting candidate susceptibility genes were identified that may be associated with this disorder, including FOXO1A, MIG6, and CYP26A1. Collectively these findings provide a framework for further investigations on causality and mechanisms underlying attenuated progesterone response in endometrium of women with endometriosis.

  19. Microarray gene expression profiling and analysis in renal cell carcinoma

    Directory of Open Access Journals (Sweden)

    Sadhukhan Provash

    2004-06-01

    Full Text Available Abstract Background Renal cell carcinoma (RCC is the most common cancer in adult kidney. The accuracy of current diagnosis and prognosis of the disease and the effectiveness of the treatment for the disease are limited by the poor understanding of the disease at the molecular level. To better understand the genetics and biology of RCC, we profiled the expression of 7,129 genes in both clear cell RCC tissue and cell lines using oligonucleotide arrays. Methods Total RNAs isolated from renal cell tumors, adjacent normal tissue and metastatic RCC cell lines were hybridized to affymatrix HuFL oligonucleotide arrays. Genes were categorized into different functional groups based on the description of the Gene Ontology Consortium and analyzed based on the gene expression levels. Gene expression profiles of the tissue and cell line samples were visualized and classified by singular value decomposition. Reverse transcription polymerase chain reaction was performed to confirm the expression alterations of selected genes in RCC. Results Selected genes were annotated based on biological processes and clustered into functional groups. The expression levels of genes in each group were also analyzed. Seventy-four commonly differentially expressed genes with more than five-fold changes in RCC tissues were identified. The expression alterations of selected genes from these seventy-four genes were further verified using reverse transcription polymerase chain reaction (RT-PCR. Detailed comparison of gene expression patterns in RCC tissue and RCC cell lines shows significant differences between the two types of samples, but many important expression patterns were preserved. Conclusions This is one of the initial studies that examine the functional ontology of a large number of genes in RCC. Extensive annotation, clustering and analysis of a large number of genes based on the gene functional ontology revealed many interesting gene expression patterns in RCC. Most

  20. Genome Expression Pathway Analysis Tool – Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context

    Directory of Open Access Journals (Sweden)

    Engelmann Julia C

    2007-06-01

    Full Text Available Abstract Background Regulation of gene expression is relevant to many areas of biology and medicine, in the study of treatments, diseases, and developmental stages. Microarrays can be used to measure the expression level of thousands of mRNAs at the same time, allowing insight into or comparison of different cellular conditions. The data derived out of microarray experiments is highly dimensional and often noisy, and interpretation of the results can get intricate. Although programs for the statistical analysis of microarray data exist, most of them lack an integration of analysis results and biological interpretation. Results We have developed GEPAT, Genome Expression Pathway Analysis Tool, offering an analysis of gene expression data under genomic, proteomic and metabolic context. We provide an integration of statistical methods for data import and data analysis together with a biological interpretation for subsets of probes or single probes on the chip. GEPAT imports various types of oligonucleotide and cDNA array data formats. Different normalization methods can be applied to the data, afterwards data annotation is performed. After import, GEPAT offers various statistical data analysis methods, as hierarchical, k-means and PCA clustering, a linear model based t-test or chromosomal profile comparison. The results of the analysis can be interpreted by enrichment of biological terms, pathway analysis or interaction networks. Different biological databases are included, to give various information for each probe on the chip. GEPAT offers no linear work flow, but allows the usage of any subset of probes and samples as a start for a new data analysis. GEPAT relies on established data analysis packages, offers a modular approach for an easy extension, and can be run on a computer grid to allow a large number of users. It is freely available under the LGPL open source license for academic and commercial users at http

  1. Gene expression analysis in human breast cancer associated blood vessels.

    Directory of Open Access Journals (Sweden)

    Dylan T Jones

    Full Text Available Angiogenesis is essential for solid tumour growth, whilst the molecular profiles of tumour blood vessels have been reported to be different between cancer types. Although presently available anti-angiogenic strategies are providing some promise for the treatment of some cancers it is perhaps not surprisingly that, none of the anti-angiogenic agents available work on all tumours. Thus, the discovery of novel anti-angiogenic targets, relevant to individual cancer types, is required. Using Affymetrix microarray analysis of laser-captured, CD31-positive blood vessels we have identified 63 genes that are upregulated significantly (5-72 fold in angiogenic blood vessels associated with human invasive ductal carcinoma (IDC of the breast as compared with blood vessels in normal human breast. We tested the angiogenic capacity of a subset of these genes. Genes were selected based on either their known cellular functions, their enriched expression in endothelial cells and/or their sensitivity to anti-VEGF treatment; all features implicating their involvement in angiogenesis. For example, RRM2, a ribonucleotide reductase involved in DNA synthesis, was upregulated 32-fold in IDC-associated blood vessels; ATF1, a nuclear activating transcription factor involved in cellular growth and survival was upregulated 23-fold in IDC-associated blood vessels and HEX-B, a hexosaminidase involved in the breakdown of GM2 gangliosides, was upregulated 8-fold in IDC-associated blood vessels. Furthermore, in silico analysis confirmed that AFT1 and HEX-B also were enriched in endothelial cells when compared with non-endothelial cells. None of these genes have been reported previously to be involved in neovascularisation. However, our data establish that siRNA depletion of Rrm2, Atf1 or Hex-B had significant anti-angiogenic effects in VEGF-stimulated ex vivo mouse aortic ring assays. Overall, our results provide proof-of-principle that our approach can identify a cohort of

  2. comparative analysis of some existing kinetic models with proposed ...

    African Journals Online (AJOL)

    IGNATIUS NWIDI

    But based on values of ARE%, first proposed kinetic model accounted for 93.3% while pseudo second-order kinetic model accounted for 6.7% of the results for biosorption of the three heavy metals by the five microbes. Keynotes: Heavy metals, Biosorption, Kinetics Models, Comparative analysis, Average Relative Error. 1.

  3. A comparative analysis of returns of various financial asset classes ...

    African Journals Online (AJOL)

    A comparative analysis of returns of various financial asset classes in South Africa: a triumph of bonds? ... Southern African Business Review ... The PDF file you selected should load here if your Web browser has a PDF reader plug-in ...

  4. Comparative analysis of the Proximate composition and Sensory ...

    African Journals Online (AJOL)

    Comparative analysis of the Proximate composition and Sensory properties of dokuwa produced in Niger State Metropolis. ... Sensory evaluation of the samples on the basis of colour, texture, aroma, taste and overall acceptability showed that significant difference (p<0.05) existed between the samples. The sample from ...

  5. A Comparative Analysis of Administrative Competencies of Male ...

    African Journals Online (AJOL)

    Nekky Umera

    Comparative Analysis of Admin. Competencies of Male & Female Principals leadership roles of supervisors as well. Explaining each of these skills,. Sergiovanni and Starrat (1979) argued that technical skills assume ability to use knowledge, methods and techniques to perform specific tasks. The mechanics associated with ...

  6. a comparative analysis of first day neonatal mortality between

    African Journals Online (AJOL)

    2013-11-11

    Nov 11, 2013 ... A COMPARATIVE ANALYSIS OF FIRST DAY NEONATAL MORTALITY BETWEEN ADOLESCENTS AND ADULT. FEMALES GIVING BIRTH ..... Multivariable logistic regression on predictors of neonatal mortality and maternal age5. Number of .... Provision of low cost special care units for LBW neonates to ...

  7. Comparative analysis of acon- Plasmodium falciparum rapid malaria ...

    African Journals Online (AJOL)

    Comparative analysis of acon- Plasmodium falciparum rapid malaria diagnostic test with routine microscopy among school children and pregnant women in a rural community in Enugu State, ... The following parameters were determined: intrinsic validity, predictive values, species diagnostic power and logistic factors.

  8. Comparative Analysis of VLF Signal Variation along Trajectory ...

    Indian Academy of Sciences (India)

    Comparative qualitative analysis of amplitude and phase delay variations was carried out along the trajectory of GQD/22.1 kHz and NAA/24.0 kHz VLF signal traces, propagating from Skelton (UK) and Maine (USA) toward Belgrade, induced by four isolated solar X-ray flare events occurred during the period from September ...

  9. Comparative demand analysis for rice in Edo, delta and Lagos ...

    African Journals Online (AJOL)

    The study examined the comparative demand analysis for rice types in Edo, Delta and Lagos states of Nigeria. A multi-stage sampling procedure, involving four stages, was used to select eight hundred and twelve (812) households. Data collected were analysed using both descriptive and inferential statistics. The results of ...

  10. Comparative Demand Analysis for Rice in Three States of South ...

    African Journals Online (AJOL)

    Dauda Omoba

    2013-01-01

    Jan 1, 2013 ... The study examined the comparative demand analysis for rice types in Edo, Delta and Lagos states of .... variables, such as age, education level, household ..... Variable. Entire sample Mean Lagos. Delta. Edo. Income. Rural. Urban Rural Urban Rural Urban Rural Urban Low Middle High. Expenditure.

  11. Comparative analysis of accident potiential of priority junction with ...

    African Journals Online (AJOL)

    Comparative analysis of accident potiential of priority junction with different layouts and controls. M Salifu. Abstract. No Abstract. Journal of the Ghana Institution of Engineers Vol. 3 (1) 2005: pp. 42-53. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT · AJOL African ...

  12. Indian Ocean surface winds from NCMRWF analysis as compared to ...

    Indian Academy of Sciences (India)

    The quality of the surface wind analysis at the National Centre for Medium Range Weather Forecasts (NCMRWF), New Delhi over the tropical Indian Ocean and its improvement in 2001 are examined by comparing it with in situ buoy measurements and satellite derived surface winds from NASA QuikSCAT satellite (QSCT) ...

  13. Comparative and Familial Analysis of Handedness in Great Apes

    Science.gov (United States)

    Hopkins, William D.

    2006-01-01

    Historically, population-level handedness has been considered a hallmark of human evolution. Whether nonhuman primates exhibit population-level handedness remains a topic of considerable debate. This paper summarizes published data on handedness in great apes. Comparative analysis indicated that chimpanzees and bonobos show population-level right…

  14. A comparative analysis of strategy disclosure reporting trends in ...

    African Journals Online (AJOL)

    A comparative analysis of strategy disclosure reporting trends in South Africa in 2010. ... Southern African Business Review ... In South Africa, the King II Report on Corporate Governance recommended that organisations should produce a sustainability report some time during the reporting cycle (IOD 2009: 13). The latest ...

  15. Comparative analysis of crayfish marketing in selected markets of ...

    African Journals Online (AJOL)

    The study was on comparative analysis of crayfish marketing in some selected markets of Akwa Ibom and Abia states of Nigeria. It specifically looked at market integration, costs and return, marketing margin, marketing efficiency and factors influencing marketing efficiency in both states. Data were collected from 60 ...

  16. A comparative analysis of strategy disclosure reporting trends in ...

    African Journals Online (AJOL)

    chestt

    A comparative analysis of strategy disclosure reporting trends in South Africa in 2010. 29 the strategy ... M. Ungerer. 30 could result in a competitive advantage for the organisation (Lazarus & McManus. 2006: 925). Table 1: The advantages and disadvantages of transparency in disclosure of strategic information.

  17. Comparative analysis of transformed potato microtubers and its non ...

    African Journals Online (AJOL)

    The rapid progress of transgenic biotechnology has significantly promoted the development and production of genetically modified (GM) crops. The aim of this study was to compare some compositional analysis and genetic variation of transformed potato microtubers (Solanum tuberosum L. Desiree) line (which harbor ...

  18. A comparative analysis of the perception and understanding of ...

    African Journals Online (AJOL)

    A comparative analysis of the perception and understanding of physical education and school sport among South African children aged 6-15 years. ... PE teachers are qualified in some cases and grossly unqualified in many others. PE programmes in white schools and urban cities offer a wide and balanced variety of ...

  19. Comparative Analysis of the Effects of Organization Development ...

    African Journals Online (AJOL)

    Comparative Analysis of the Effects of Organization Development Interventions on Organizational Leadership and Management Practice: A Case Of Green Earth Program ... A pre- assessment of leadership and management practice at Green Earth was conducted which identified six problem areas or improvement issues.

  20. Comparative Analysis on Chemical Composition of Bentonite Clays ...

    African Journals Online (AJOL)

    2017-09-12

    Sep 12, 2017 ... Abdullahi and Audu. 35. Comparative Analysis on Chemical Composition of Bentonite Clays. Obtained from Ashaka and Tango Deposits in Gombe State, Nigeria. Abdullahi S.L1 and Audu A.A2. 1Kano State Polytechnic, Kano - Nigeria. 2Department of Pure and Industrial Chemistry, Bayero University Kano ...

  1. Comparative Life-Cycle Cost Analysis Of Solar Photovoltaic Power ...

    African Journals Online (AJOL)

    Many homes in Nigeria are in remote locations where grid electricity supply could not be extended. This paper attempts to present a concise life-cycle-cost comparison of diesel generator power supply system and photovoltaic power system for a remote rural application. In this comparative analysis, conceptual designs ...

  2. comparative analysis of salivary glucose and electrolytes in diabetic ...

    African Journals Online (AJOL)

    periodontitis. COMPARATIVE ANALYSIS OF SALIVARY GLUCOSE AND ELECTROLYTES IN. DIABETIC INDIVIDUALS WITH PERIODONTITIS. 1. Department of Physiology, University of Ibadan, Ibadan. 2. Department of Medicine, Endocrinology Unit, University College Hospital, Ibadan. T.J. Lasisi1 and A.A. Fasanmade2.

  3. Indian Ocean surface winds from NCMRWF analysis as compared to ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    The quality of the surface wind analysis at the National Centre for Medium Range Weather Fore- casts (NCMRWF), New Delhi over the tropical Indian Ocean and its improvement in 2001 are examined by comparing it with in situ buoy measurements and satellite derived surface winds from. NASA QuikSCAT satellite (QSCT) ...

  4. A comparative analysis of Numerov and Nystrom methods | Unanam ...

    African Journals Online (AJOL)

    In this paper, two test problems were used to study the behaviour and performance of two numerical methods (Numerov and Nystrom) of solving second order initial value problem (IVP) of ordinary differential equation without the first order term. A test implementation of each of the methods and a comparative analysis of the ...

  5. A comparative analysis of cohesion in academic and newspaper texts

    African Journals Online (AJOL)

    This article presents findings on a comparative analysis of cohesion in academic and newspaper texts on road traffic accidents. Cohesive devices are the surface structure features that link different parts of a text and make it flow logically. They are the necessary reins that hold the clauses of a text together. Coherence, on ...

  6. A Comparative Analysis of the Caracteristics of Authors in Four ...

    African Journals Online (AJOL)

    A comparative analysis of the characteristics of Nigerian s of articles published in the African Journal of Library, Archives and Information Science (AJLAIS), the Nigerian Libraries (NL), Lagos Librarian (LL) and the Nigerian Library and Information Science Review (NLISR), between 1994 and 2000 was carried out.

  7. A Comparative Analysis of Fuzzy Inference Engines in Context of ...

    African Journals Online (AJOL)

    PROF. O. E. OSUAGWU

    robotics, pattern recognition, etc. This paper presents a comparative analysis of three fuzzy inference engines, max-product, max-min and root sum in fuzzy controllers using profitability control data. The presented results shows that RSS inference engine gives largest output membership function, while the product inference ...

  8. Comparative economic analysis of yam minisett and ware yam ...

    African Journals Online (AJOL)

    This study on comparative economic analysis of yam minisett and ware yam production was conducted using 150 yam farmers as respondents. A structured questionnaire was used in collecting data from the yam farmers. Statistical tools such as frequency distribution, percentages, means and gross margin were used for ...

  9. A Comparative Analysis of Three Unique Theories of Organizational Learning

    Science.gov (United States)

    Leavitt, Carol C.

    2011-01-01

    The purpose of this paper is to present three classical theories on organizational learning and conduct a comparative analysis that highlights their strengths, similarities, and differences. Two of the theories -- experiential learning theory and adaptive -- generative learning theory -- represent the thinking of the cognitive perspective, while…

  10. Comparative analysis of the chemical composition of three spices ...

    African Journals Online (AJOL)

    Comparative analysis of the chemical composition of three spices – Allium sativum L. Zingiber officinale Rosc. and Capsicum frutescens L. commonly consumed in Nigeria. ... Phytochemical screening indicated that these spices are also rich in phytonutrients including alkaloid, tannin, carotenoids, saponin and flavonoids.

  11. Genome-wide comparative analysis of tonoplast intrinsic protein (TIP) genes in plants.

    Science.gov (United States)

    Regon, Preetom; Panda, Piyalee; Kshetrimayum, Erina; Panda, Sanjib Kumar

    2014-12-01

    Tonoplast intrinsic proteins (TIPs) play a vital role in water transport across membranes. In the present study, we performed a comparative analysis of TIP genes in ten plant species including both monocots and dicots. A total of 100 TIP aquaporin genes were identified, and their relationships among the plant species were analyzed. Phylogenetic analysis was performed to evaluate the relationship of these genes within the plant species. Based on the phylogenetic analysis results, TIPs were classified into five distinct arbitrary groups (group I to group V), which represented TIP2, TIP5, TIP4, TIP1, and TIP3, respectively. Group I represented the largest arbitrary group, followed by group IV, in the phylogenetic tree. The result clearly indicates that TIP2 and TIP1 are abundant aquaporins and highly related among the species. In the present review, a comparative study of gene structure analysis between dicots and monocots has been performed to analyze their structural variation. Most of the predicted motifs are conserved among the species, signifying an evolutionary relationship. The gene expression analysis indicated that the expression of TIP genes varies during different developmental stages and also during stressed conditions. The results indicated a great degree of evolutionary relationship and variation in the expression levels of TIPs in plants.

  12. Plant Reactome: a resource for plant pathways and comparative analysis.

    Science.gov (United States)

    Naithani, Sushma; Preece, Justin; D'Eustachio, Peter; Gupta, Parul; Amarasinghe, Vindhya; Dharmawardhana, Palitha D; Wu, Guanming; Fabregat, Antonio; Elser, Justin L; Weiser, Joel; Keays, Maria; Fuentes, Alfonso Munoz-Pomer; Petryszak, Robert; Stein, Lincoln D; Ware, Doreen; Jaiswal, Pankaj

    2017-01-04

    Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Comparative analysis of cation/proton antiporter superfamily in plants

    Energy Technology Data Exchange (ETDEWEB)

    Ye, Chuyu [ORNL; Yang, Xiaohan [ORNL; Xia, Xinli [Beijing Forestry University, China; Yin, Weilun [Beijing Forestry University, China

    2013-01-01

    The cation/proton antiporter superfamily is associated with the transport of monovalent cations across membranes. This superfamily was annotated in the Arabidopsis genome and some members were functionally characterized. In the present study, a systematic analysis of the cation/proton antiporter genes in diverse plant specieswas reported.We identified 240 cation/proton antiporters in alga, moss, and angiosperm. A phylogenetic tree was constructed showing these 240members are separated into three families, i.e., Na+/H+ exchangers, K+ efflux antiporters, and cation/H+ exchangers. Our analysis revealed that tandem and/or segmental duplications contribute to the expansion of cation/H+ exchangers in the examined angiospermspecies. Sliding windowanalysis of the nonsynonymous/synonymous substitution ratios showed some differences in the evolutionary fate of cation/proton antiporter paralogs. Furthermore, we identified over-represented motifs among these 240 proteins and foundmostmotifs are family specific, demonstrating diverse evolution of the cation/proton antiporters among three families. In addition, we investigated the co-expressed genes of the cation/proton antiporters in Arabidopsis thaliana. The results showed some biological processes are enriched in the co-expressed genes, suggesting the cation/proton antiporters may be involved in these biological processes. Taken together, this study furthers our knowledge on cation/proton antiporters in plants.

  14. Gene expression analysis in RA: towards personalized medicine

    Science.gov (United States)

    Burska, A N; Roget, K; Blits, M; Soto Gomez, L; van de Loo, F; Hazelwood, L D; Verweij, C L; Rowe, A; Goulielmos, G N; van Baarsen, L G M; Ponchel, F

    2014-01-01

    Gene expression has recently been at the forefront of advance in personalized medicine, notably in the field of cancer and transplantation, providing a rational for a similar approach in rheumatoid arthritis (RA). RA is a prototypic inflammatory autoimmune disease with a poorly understood etiopathogenesis. Inflammation is the main feature of RA; however, many biological processes are involved at different stages of the disease. Gene expression signatures offer management tools to meet the current needs for personalization of RA patient's care. This review analyses currently available information with respect to RA diagnostic, prognostic and prediction of response to therapy with a view to highlight the abundance of data, whose comparison is often inconclusive due to the mixed use of material source, experimental methodologies and analysis tools, reinforcing the need for harmonization if gene expression signatures are to become a useful clinical tool in personalized medicine for RA patients. PMID:24589910

  15. Comparative proteomics analysis suggests that placental mitochondria are involved in the development of pre-eclampsia.

    Directory of Open Access Journals (Sweden)

    Zhonghua Shi

    Full Text Available INTRODUCTION: Pre-eclampsia (PE, a severe pregnancy-specific disease characterized by the new onset of hypertension, proteinuria, edema, and a series of other systematic disorders, is a state of widespread mitochondrial dysfunction of the placenta. METHODS: We compared the morphology of mitochondria in pre-eclamptic and normotensive placentae using electron microscopy. To reveal the systematic protein expression changes of placental mitochondria that might explain the pathogenesis of PE, we performed iTRAQ analysis combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS on differentially expressed placental mitochondria proteins from 4 normotensive and 4 pre-eclamptic pregnancies. Bioinformatics analysis was used to find the relative processes that these differentially expressed proteins were involved in. Three differentially expressed proteins were chosen to confirm by Western blotting and immunohistochemistry. RESULTS: Morphological data demonstrated degenerative and apoptotic changes in the mitochondria of pre-eclamptic placentae. We found four proteins were upregulated and 22 proteins were downregulated in pre-eclamptic placentae compared with normotensive placentae. Bioinformatics analysis showed that these proteins were involved in many critical processes in the development of pre-eclampsia such as apoptosis, fatty acid oxidation, the respiratory chain, reactive oxygen species generation, the tricarboxylic acid cycle and oxidative stress. CONCLUSIONS: This preliminary work provides a better understanding of the proteomic alterations of mitochondria from pre-eclamptic placentae and may aid in our understanding of the importance of mitochondria in the development of pre-eclampsia.

  16. Influence of Androgen Receptor Expression on the Survival Outcomes in Breast Cancer: A Meta-Analysis.

    Science.gov (United States)

    Kim, Yoonseok; Jae, Eunae; Yoon, Myunghee

    2015-06-01

    Despite the fact that the androgen receptor (AR) is known to be involved in the pathogenesis of breast cancer, its prognostic effect remains controversial. In this meta-analysis, we explored AR expression and its impact on survival outcomes in breast cancer. We searched PubMed, EMBASE, Cochrane Library, ScienceDirect, SpringerLink, and Ovid databases and references of articles to identify studies reporting data until December 2013. Disease-free survival (DFS) and overall survival (OS) were analyzed by extracting the number of patients with recurrence and survival according to AR expression. There were 16 articles that met the criteria for inclusion in our meta-analysis. DFS and OS were significantly longer in patients with AR expression compared with patients without AR expression (odds ratio [OR], 0.60; 95% confidence interval [CI], 0.40-0.90; OR, 0.53; 95% CI, 0.38-0.73, respectively). In addition, hormone receptor (HR) positive patients had a longer DFS when AR was also expressed (OR, 0.63; 95% CI, 0.41-0.98). For patients with triple negative breast cancer (TNBC), AR expression was also associated with longer DFS and OS (OR, 0.44, 95% CI, 0.26-0.75; OR, 0.26, 95% CI, 0.12-0.55, respectively). Furthermore, AR expression was associated with a longer DFS and OS in women (OR, 0.42, 95% CI, 0.27-0.64; OR, 0.47, 95% CI, 0.38-0.59, respectively). However, in men, AR expression was associated with a worse DFS (OR, 6.00; 95% CI, 1.46-24.73). Expression of AR in breast cancer might be associated with better survival outcomes, especially in patients with HR-positive tumors and TNBC, and women. Based on this meta-analysis, we propose that AR expression might be related to prognostic features and contribute to clinical outcomes.

  17. Comparison of linear discriminant analysis methods for the classification of cancer based on gene expression data.

    Science.gov (United States)

    Huang, Desheng; Quan, Yu; He, Miao; Zhou, Baosen

    2009-12-10

    More studies based on gene expression data have been reported in great detail, however, one major challenge for the methodologists is the choice of classification methods. The main purpose of this research was to compare the performance of linear discriminant analysis (LDA) and its modification methods for the classification of cancer based on gene expression data. The classification performance of linear discriminant analysis (LDA) and its modification methods was evaluated by applying these methods to six public cancer gene expression datasets. These methods included linear discriminant analysis (LDA), prediction analysis for microarrays (PAM), shrinkage centroid regularized discriminant analysis (SCRDA), shrinkage linear discriminant analysis (SLDA) and shrinkage diagonal discriminant analysis (SDDA). The procedures were performed by software R 2.80. PAM picked out fewer feature genes than other methods from most datasets except from Brain dataset. For the two methods of shrinkage discriminant analysis, SLDA selected more genes than SDDA from most datasets except from 2-class lung cancer dataset. When comparing SLDA with SCRDA, SLDA selected more genes than SCRDA from 2-class lung cancer, SRBCT and Brain dataset, the result was opposite for the rest datasets. The average test error of LDA modification methods was lower than LDA method. The classification performance of LDA modification methods was superior to that of traditional LDA with respect to the average error and there was no significant difference between theses modification methods.

  18. Comparative analysis of equalization methods for SC-FDMA

    DEFF Research Database (Denmark)

    Dogadaev, Anton Konstantinovich; Kozlov, Alexander; Ukhanova, Ann

    2010-01-01

    In this paper we introduce comparative analysis for different types of equalization schemes, based on the minimum mean square error (MMSE) optimization. The following types of equalizers were compared: linear equalization, decision feedback equalization (DFE) and turbo equalization. Performance...... and complexity of these schemes were tested for Single Carrier Frequency Division Multiple Access (SC-FDMA) system with Single Input Single Output (SISO) antenna configuration. SC-FDMA is a common technique, which is used in the UTRA LTE Uplink, so the results of complexity and performance analysis could...... be applied to find the appropriate equalization algorithm to be used in the Uplink channel of the LTE – the famous standard in 4G telecommunications. Simulation results in the end in this paper show bit error ratio (BER) and modulation error ratio (MER) for compared schemes....

  19. Gene expression changes in response to aging compared to heat stress, oxidative stress and ionizing radiation in Drosophila melanogaster

    Science.gov (United States)

    Landis, Gary; Shen, Jie; Tower, John

    2012-01-01

    Gene expression changes in response to aging, heat stress, hyperoxia, hydrogen peroxide, and ionizing radiation were compared using microarrays. A set of 18 genes were up-regulated across all conditions, indicating a general stress response shared with aging, including the heat shock protein (Hsp) genes Hsp70, Hsp83 and l(2)efl, the glutathione-S-transferase gene GstD2, and the mitochondrial unfolded protein response (mUPR) gene ref(2)P. Selected gene expression changes were confirmed using quantitative PCR, Northern analysis and GstD-GFP reporter constructs. Certain genes were altered in only a subset of the conditions, for example, up-regulation of numerous developmental pathway and signaling genes in response to hydrogen peroxide. While aging shared features with each stress, aging was more similar to the stresses most associated with oxidative stress (hyperoxia, hydrogen peroxide, ionizing radiation) than to heat stress. Aging is associated with down-regulation of numerous mitochondrial genes, including electron-transport-chain (ETC) genes and mitochondrial metabolism genes, and a sub-set of these changes was also observed upon hydrogen peroxide stress and ionizing radiation stress. Aging shared the largest number of gene expression changes with hyperoxia. The extensive down-regulation of mitochondrial and ETC genes during aging is consistent with an aging-associated failure in mitochondrial maintenance, which may underlie the oxidative stress-like and proteotoxic stress-like responses observed during aging. PMID:23211361

  20. Gene expression changes in response to aging compared to heat stress, oxidative stress and ionizing radiation in Drosophila melanogaster.

    Science.gov (United States)

    Landis, Gary; Shen, Jie; Tower, John

    2012-11-01

    Gene expression changes in response to aging, heat stress, hyperoxia, hydrogen peroxide, and ionizing radiation were compared using microarrays. A set of 18 genes were up-regulated across all conditions, indicating a general stress response shared with aging, including the heat shock protein (Hsp) genes Hsp70, Hsp83 and l(2)efl, the glutathione-S-transferase gene GstD2, and the mitochondrial unfolded protein response (mUPR) gene ref(2)P. Selected gene expression changes were confirmed using quantitative PCR, Northern analysis and GstD-GFP reporter constructs. Certain genes were altered in only a subset of the conditions, for example, up-regulation of numerous developmental pathway and signaling genes in response to hydrogen peroxide. While aging shared features with each stress, aging was more similar to the stresses most associated with oxidative stress (hyperoxia, hydrogen peroxide, ionizing radiation) than to heat stress. Aging is associated with down-regulation of numerous mitochondrial genes, including electron-transport-chain (ETC) genes and mitochondrial metabolism genes, and a sub-set of these changes was also observed upon hydrogen peroxide stress and ionizing radiation stress. Aging shared the largest number of gene expression changes with hyperoxia. The extensive down-regulation of mitochondrial and ETC genes during aging is consistent with an aging-associated failure in mitochondrial maintenance, which may underlie the oxidative stress-like and proteotoxic stress-like responses observed during aging.

  1. Immunohistochemical expression of vascular endothelial growth factor in keratocystic odontogenic tumor, dentigerous cyst, and radicular cyst: A comparative study.

    Science.gov (United States)

    Khajuria, Nidhi; Metgud, Rashmi; Naik, Smitha; Lerra, Sahul; Tiwari, Priya; Mamta; Katakwar, Payal; Tak, Anirudh

    2016-01-01

    Cyst and tumors arise from tissue remains of odontogenesis, these interactions have been considered to play an important role in the tumorigenesis of odontogenic lesions. The connective tissue stroma has an essential role in the preservation of epithelial tissues and minor alterations in the epithelium are followed by corresponding changes in the stroma, such as angiogenesis. Vascular endothelial growth factor (VEGF) is considered the first factor which maintains its position as the most critical driver of vascular formation and is required to initiate the formation of immature vessels, with this aim, present study was executed to evaluate VEGF expression in kertocystic odontogenic tumor, dentigerous cyst and radicular cyst (RC). A retrospective study was carried out comprising a total of 31 cases; 13 cases of keratocystic odontogenic tumor (KCOT), nine cases of dentigerous cyst (DC) and nine cases of RC. The sections were stained immunohistochemically with VEGF antibody and were evaluated for the presence and intensity of the immuno reactive cells. Statistical analysis was carried out using Chi-square test to inter-compare the VEGF expression between KCOT, DC, and RC. VEGF expression in the epithelium and connective tissue was significantly higher in KCOT compared to dentigerous and RC. One case of KCOT with carcinomatous change also revealed positive results for the VEGF expression in the dysplastic epithelium, tumor islands, and connective tissue. The significant difference was observed on inter-comparison of the VEGF expression in the connective tissue of KCOT and DC, whereas no significant difference was observed in the VEGF expression in the connective tissue of KCOT and DC. The present study data supports the literature finding that angiogenesis can be important in the progression and enlargement of odontogenic cysts similarly to what occurs in neoplastic conditions and further it can be concluded that the higher positivity for VEGF of KCOT could help to

  2. Microarray analysis of female- and larval-specific gene expression in the horn fly (Diptera: Muscidae).

    Science.gov (United States)

    Guerrero, Felix D; Dowd, Scot E; Sun, Yan; Saldivar, Leonel; Wiley, Graham B; Macmil, Simone L; Najar, Fares; Roe, Bruce A; Foil, Lane D

    2009-03-01

    The horn fly, Haematobia irritans L., is an obligate blood-feeding parasite of cattle, and control of this pest is a continuing problem because the fly is becoming resistant to pesticides. Dominant conditional lethal gene systems are being studied as population control technologies against agricultural pests. One of the components of these systems is a female-specific gene promoter that drives expression of a lethality-inducing gene. To identify candidate genes to supply this promoter, microarrays were designed from a horn fly expressed sequence tag (EST) database and probed to identify female-specific and larval-specific gene expression. Analysis of dye swap experiments found 432 and 417 transcripts whose expression levels were higher or lower in adult female flies, respectively, compared with adult male flies. Additionally, 419 and 871 transcripts were identified whose expression levels were higher or lower in first-instar larvae compared with adult flies, respectively. Three transcripts were expressed more highly in adult females flies compared with adult males and also higher in the first-instar larval lifestage compared with adult flies. One of these transcripts, a putative nanos ortholog, has a high female-to-male expression ratio, a moderate expression level in first-instar larvae, and has been well characterized in Drosophila. melanogaster (Meigen). In conclusion, we used microarray technology, verified by reverse transcriptase-polymerase chain reaction and massively parallel pyrosequencing, to study life stage- and sex-specific gene expression in the horn fly and identified three gene candidates for detailed evaluation as a gene promoter source for the development of a female-specific conditional lethality system.

  3. Analysis of meniscal degeneration and meniscal gene expression

    Directory of Open Access Journals (Sweden)

    Norton James H

    2010-01-01

    Full Text Available Abstract Background Menisci play a vital role in load transmission, shock absorption and joint stability. There is increasing evidence suggesting that OA menisci may not merely be bystanders in the disease process of OA. This study sought: 1 to determine the prevalence of meniscal degeneration in OA patients, and 2 to examine gene expression in OA meniscal cells compared to normal meniscal cells. Methods Studies were approved by our human subjects Institutional Review Board. Menisci and articular cartilage were collected during joint replacement surgery for OA patients and lower limb amputation surgery for osteosarcoma patients (normal control specimens, and graded. Meniscal cells were prepared from these meniscal tissues and expanded in monolayer culture. Differential gene expression in OA meniscal cells and normal meniscal cells was examined using Affymetrix microarray and real time RT-PCR. Results The grades of meniscal degeneration correlated with the grades of articular cartilage degeneration (r = 0.672; P HLA-DPA1, integrin, beta 2 (ITGB2, ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1, ankylosis, progressive homolog (ANKH and fibroblast growth factor 7 (FGF7, were expressed at significantly higher levels in OA meniscal cells compared to normal meniscal cells. Importantly, many of the genes that have been shown to be differentially expressed in other OA cell types/tissues, including ADAM metallopeptidase with thrombospondin type 1 motif 5 (ADAMTS5 and prostaglandin E synthase (PTGES, were found to be expressed at significantly higher levels in OA meniscal cells. This consistency suggests that many of the genes detected in our study are disease-specific. Conclusion Our findings suggest that OA is a whole joint disease. Meniscal cells may play an active role in the development of OA. Investigation of the gene expression profiles of OA meniscal cells may reveal new therapeutic targets for OA therapy and also may uncover novel

  4. A comparative approach to understanding tissue-specific expression of uncoupling protein 1 expression in adipose tissue

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    Andrew eShore

    2013-01-01

    Full Text Available The thermoregulatory function of brown adipose tissue (BAT is due to the tissue-specific expression of uncoupling protein 1 (UCP1 which is thought to have evolved in early mammals. We report that a CpG island close to the UCP1 transcription start site is highly conserved in all 29 vertebrates examined apart from the mouse and xenopus. Using methylation sensitive restriction digest and bisulphite mapping we show that the CpG island in both the bovine and human is largely un-methylated and is not related to differences in UCP1 expression between white and brown adipose tissue. Tissue-specific expression of UCP1 has been proposed to be regulated by a conserved 5’ distal enhancer which has been reported to be absent in marsupials. We demonstrate that the enhancer, is also absent in 5 eutherians as well as marsupials, monotremes, amphibians and fish, is present in pigs despite UCP1 having become a pseudogene, and that absence of the enhancer element does not relate to brown adipose tissue-specific UCP1 expression. We identify an additional putative 5’ regulatory unit which is conserved in 14 eutherian species but absent in other eutherians and vertebrates, but again unrelated to UCP1 expression. We conclude that despite clear evidence of conservation of regulatory elements in the UCP1 5’ untranslated region, this does not appear to be related to species or tissues-specific expression of UCP1.

  5. Molecular Characterization and Expression Analysis of Equine ( Gene in Horse (

    Directory of Open Access Journals (Sweden)

    Ki-Duk Song

    2014-05-01

    Full Text Available The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene (VEGFα by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog, we constructed a phylogenetic tree which showed that equine VEGFα belonged to the same clade of the pig VEGFα. Analysis for synonymous (Ks and non-synonymous substitution ratios (Ka revealed that the horse VEGFα underwent positive selection. RNA was extracted from blood samples before and after exercise and different tissue samples of three horses. Expression analyses using reverse transcription-polymerase chain reaction (RT-PCR and quantitative-polymerase chain reaction (qPCR showed ubiquitous expression of VEGFα mRNA in skeletal muscle, kidney, thyroid, lung, appendix, colon, spinal cord, and heart tissues. Analysis of differential expression of VEGFα gene in blood leukocytes after exercise indicated a unimodal pattern. These results will be useful in developing biomarkers that can predict the recovery capacity of racing horses.

  6. IDIOMS CONTAINING THE COMPONENT BLACK / SCHWARZ IN THE ENGLISH AND GERMAN LANGUAGES: COMPARATIVE ANALYSIS

    Directory of Open Access Journals (Sweden)

    Yakovleva, S.L.

    2016-06-01

    Full Text Available The article presents a comparative analysis of English and German idiomatic expressions containing the component of colour in their structure. It has been revealed that black dominates in the English linguistic idiomatic view of the world. The core centre of the focal colours in the German culture is also schwarz / black. General and specific features of black / schwarz as a part of national linguistic views of the world of the English and German languages are considered in the article.

  7. A unified censored normal regression model for qPCR differential gene expression analysis.

    Directory of Open Access Journals (Sweden)

    Peter Pipelers

    Full Text Available Reverse transcription quantitative polymerase chain reaction (RT-qPCR is considered as the gold standard for accurate, sensitive, and fast measurement of gene expression. Prior to downstream statistical analysis, RT-qPCR fluorescence amplification curves are summarized into one single value, the quantification cycle (Cq. When RT-qPCR does not reach the limit of detection, the Cq is labeled as "undetermined". Current state of the art qPCR data analysis pipelines acknowledge the importance of normalization for removing non-biological sample to sample variation in the Cq values. However, their strategies for handling undetermined Cq values are very ad hoc. We show that popular methods for handling undetermined values can have a severe impact on the downstream differential expression analysis. They introduce a considerable bias and suffer from a lower precision. We propose a novel method that unites preprocessing and differential expression analysis in a single statistical model that provides a rigorous way for handling undetermined Cq values. We compare our method with existing approaches in a simulation study and on published microRNA and mRNA gene expression datasets. We show that our method outperforms traditional RT-qPCR differential expression analysis pipelines in the presence of undetermined values, both in terms of accuracy and precision.

  8. Methods to increase reproducibility in differential gene expression via meta-analysis.

    Science.gov (United States)

    Sweeney, Timothy E; Haynes, Winston A; Vallania, Francesco; Ioannidis, John P; Khatri, Purvesh

    2017-01-09

    Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, gene expression meta-analysis can improve reproducibility by integrating data from multiple studies. However, there are multiple choices in designing and carrying out a meta-analysis. Yet, clear guidelines on best practices are scarce. Here, we hypothesized that studying subsets of very large meta-analyses would allow for systematic identification of best practices to improve reproducibility. We therefore constructed three very large gene expression meta-analyses from clinical samples, and then examined meta-analyses of subsets of the datasets (all combinations of datasets with up to N/2 samples and K/2 datasets) compared to a 'silver standard' of differentially expressed genes found in the entire cohort. We tested three random-effects meta-analysis models using this procedure. We showed relatively greater reproducibility with more-stringent effect size thresholds with relaxed significance thresholds; relatively lower reproducibility when imposing extraneous constraints on residual heterogeneity; and an underestimation of actual false positive rate by Benjamini-Hochberg correction. In addition, multivariate regression showed that the accuracy of a meta-analysis increased significantly with more included datasets even when controlling for sample size. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Comparative secretome analysis of rat stomach under different nutritional status

    Directory of Open Access Journals (Sweden)

    Lucia L. Senin

    2015-06-01

    Full Text Available The fact that gastric surgery is at the moment the most effective treatment to fight against obesity highlights the relevance of gastric derived proteins as potential targets to treat this pathology. Taking advantage of a previously established gastric explant model for endocrine studies, the proteomic analysis of gastric secretome was performed. To validate this gastric explant system for proteomic analysis, the identification of ghrelin, a classical gastric derived peptide, was performed by MS. In addition, the differential analysis of gastric secretomes under differential nutritional status (control feeding vs fasting vs re-feeding was performed. The MS identified proteins are showed in the present manuscript. The data supplied in this article is related to the research article entitled “Comparative secretome analysis of rat stomach under different nutritional status” [1].

  10. Emotional prosody expression in acoustic analysis in patients with right hemisphere ischemic stroke.

    Science.gov (United States)

    Guranski, Konstanty; Podemski, Ryszard

    2015-01-01

    The role of the right cerebral hemisphere in nonverbal speech activities remains controversial. Most research supports the dominant role of the right hemisphere in the control of emotional prosody. There has been significant discussion of the participation of cortical and subcortical structures of the right hemisphere in the processing of various acoustic speech parameters. The aim of this study was an acoustic analysis of the speech parameters during emotional expression in right hemisphere ischemic strokes with an attempt to reference the results to lesion location. Acoustic speech analysis was conducted on forty-six right-handed patients with right-middle cerebral artery stroke, together with 34 age-matched people in the control group. We compared the results of acoustic studies between patients with varying infarct locations and the control group. Variations in fundamental frequency during verbal expression of joy, anger and sadness were significantly smaller in the patient group than in the control group. Cortical lesion caused more restrictions in fundamental frequency variation in the expression of joy and a lower voice intensity in expressions of anger and joy compared to those patients with subcortical lesions. Cortical lesion was associated with a more impaired expression of emotional prosody than subcortical lesion. The results indicate the leading role of the cortical structures of the right hemisphere in the expression of emotional prosody. Copyright © 2015 Polish Neurological Society. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

  11. MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.

    Science.gov (United States)

    Zhai, Peng; Yang, Longshu; Guo, Xiao; Wang, Zhe; Guo, Jiangtao; Wang, Xiaoqi; Zhu, Huaiqiu

    2017-10-02

    During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatranscriptomics, metaproteomics and metabolomics data. To reveal the diversity of microbial communities and interactions between living conditions and microbes, it is necessary to introduce comparative analysis based upon integration of all four types of data mentioned above. Comparative meta-omics, especially comparative metageomics, has been established as a routine process to highlight the significant differences in taxon composition and functional gene abundance among microbiota samples. Meanwhile, biologists are increasingly concerning about the correlations between meta-omics features and environmental factors, which may further decipher the adaptation strategy of a microbial community. We developed a graphical comprehensive analysis software named MetaComp comprising a series of statistical analysis approaches with visualized results for metagenomics and other meta-omics data comparison. This software is capable to read files generated by a variety of upstream programs. After data loading, analyses such as multivariate statistics, hypothesis testing of two-sample, multi-sample as well as two-group sample and a novel function-regression analysis of environmental factors are offered. Here, regression analysis regards meta-omic features as independent variable and environmental factors as dependent variables. Moreover, MetaComp is capable to automatically choose an appropriate two-group sample test based upon the traits of input abundance profiles. We further evaluate the performance of its choice, and exhibit applications for metagenomics, metaproteomics and metabolomics samples. MetaComp, an integrative software capable for applying to all meta-omics data, originally distills the influence of living environment on microbial community by regression analysis

  12. Comparative Efficacy Profile Between Ex-Press Miniature Shunt and Trabeculectomy

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    Osman Ondas

    2016-01-01

    Full Text Available Aim: The purpose of this study is, to compare the efficacy profile between Ex-Press Miniature Shunt and trabeculectomy on intraocular pressure (IOP in primary open angle glaucoma (POAG patients. Material and Method: 40 POAG patients were retrospectively analyzed between March 2012 and April 2014. Group 1 consist of 20 eyes of 20 patients who underwent Ex-Press Miniature Shunt, group 2 consist of 20 eyes of 20 patients who underwent trabeculectomy. Postoperative 7th day, 1st month, 2nd month, 3rd month and 6th month opthalmologic examination was fully implemented. Other types of glaucoma, patients with other diseases and with complications were excluded from the study. IOP was measured by applanation tonometer. Results: Postoperative 7th day, 1st month, 2nd month and 3rd month; there was no statistically significant difference between the two groups in mean IOP (p>0.05. Increase in visual acuity at the 6th month was; 19.41% in group 1, 17.32% in group 2 and there was no change in visual acuity by 80.59% in group 1, by % 82.68 in group 2. The mean IOP at the 6th month was; 13.00±5.33 (9-23 mmHg in group 1, 14.03±5.79 (7-24 mmHg in group 2 and no statistically significant difference was found between the two groups (p=0.730. The mean IOP decrease at the 6th month was; 16.09±4.97 mmHg in group 1, 15.06 ±3.11 mmHg in group 2 and no statistically significant difference was found between the two groups (p>0.05. Discussion: Unlike trabeculectomy; sclera and iris tissue is not removed in application of Ex-Press Miniature Shunt. Its as effective as trabeculectomy and its complication rate is low.

  13. Evaluating the risks of clinical research: direct comparative analysis.

    Science.gov (United States)

    Rid, Annette; Abdoler, Emily; Roberson-Nay, Roxann; Pine, Daniel S; Wendler, David

    2014-09-01

    Many guidelines and regulations allow children and adolescents to be enrolled in research without the prospect of clinical benefit when it poses minimal risk. However, few systematic methods exist to determine when research risks are minimal. This situation has led to significant variation in minimal risk judgments, raising concern that some children are not being adequately protected. To address this concern, we describe a new method for implementing the widely endorsed "risks of daily life" standard for minimal risk. This standard defines research risks as minimal when they do not exceed the risks posed by daily life activities or routine examinations. This study employed a conceptual and normative analysis, and use of an illustrative example. Different risks are composed of the same basic elements: Type, likelihood, and magnitude of harm. Hence, one can compare the risks of research and the risks of daily life by comparing the respective basic elements with each other. We use this insight to develop a systematic method, direct comparative analysis, for implementing the "risks of daily life" standard for minimal risk. The method offers a way of evaluating research procedures that pose the same types of risk as daily life activities, such as the risk of experiencing anxiety, stress, or other psychological harm. We thus illustrate how direct comparative analysis can be applied in practice by using it to evaluate whether the anxiety induced by a respiratory CO2 challenge poses minimal or greater than minimal risks in children and adolescents. Direct comparative analysis is a systematic method for applying the "risks of daily life" standard for minimal risk to research procedures that pose the same types of risk as daily life activities. It thereby offers a method to protect children and adolescents in research, while ensuring that important studies are not blocked because of unwarranted concerns about research risks.

  14. Analysis of the differences in whole-genome expression related to asthma and obesity.

    Science.gov (United States)

    Gruchała-Niedoszytko, Marta; Niedoszytko, Marek; Sanjabi, Bahram; van der Vlies, Pieter; Niedoszytko, Piotr; Jassem, Ewa; Małgorzewicz, Sylwia

    2015-01-01

    Concomitant obesity significantly impairs asthma control. Obese asthmatics show more severe symptoms and an increased use of medications. The primary aim of the study was to identify genes that are differentially expressed in the peripheral blood of asthmatic patients with obesity, asthmatic patients with normal body mass, and obese patients without asthma. Secondly, we investigated whether the analysis of gene expression in peripheral blood may be helpful in the differential diagnosis of obese patients who present with symptoms similar to asthma. The study group included 15 patients with asthma (9 obese and 6 normal-weight patients), while the control group-13 obese patients in whom asthma was excluded. The analysis of whole-genome expression was performed on RNA samples isolated from peripheral blood. The comparison of gene expression profiles between asthmatic patients with obesity and those with normal body mass revealed a significant difference in 6 genes. The comparison of the expression between controls and normal-weight patients with asthma showed a significant difference in 23 genes. The analysis of genes with a different expression revealed a group of transcripts that may be related to an increased body mass (PI3, LOC100008589, RPS6KA3, LOC441763, IFIT1, and LOC100133565). Based on gene expression results, a prediction model was constructed, which allowed to correctly classify 92% of obese controls and 89% of obese asthmatic patients, resulting in the overall accuracy of the model of 90.9%. The results of our study showed significant differences in gene expression between obese asthmatic patients compared with asthmatic patients with normal body mass as well as in obese patients without asthma compared with asthmatic patients with normal body mass.

  15. Host gene expression analysis in Sri Lankan melioidosis patients.

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    Shivankari Krishnananthasivam

    2017-06-01

    Full Text Available Melioidosis is a life threatening infectious disease caused by the gram-negative bacillus Burkholderia pseudomallei predominantly found in southeast Asia and northern Australia. Studying the host transcription profiles in response to infection is crucial for understanding disease pathogenesis and correlates of disease severity, which may help improve therapeutic intervention and survival. The aim of this study was to analyze gene expression levels of human host factors in melioidosis patients and establish useful correlation with disease biomarkers, compared to healthy individuals and patients with sepsis caused by other pathogens.The study population consisted of 30 melioidosis cases, 10 healthy controls and 10 sepsis cases caused by other pathogens. Total RNA was extracted from peripheral blood mononuclear cells (PBMC's of study subjects. Gene expression profiles of 25 gene targets including 19 immune response genes and 6 epigenetic factors were analyzed by real time quantitative polymerase chain reaction (RT-qPCR.Inflammatory response genes; TLR4, late onset inflammatory mediator HMGB1, genes associated with antigen presentation; MICB, PSMB2, PSMB8, PSME2, epigenetic regulators; DNMT3B, HDAC1, HDAC2 were significantly down regulated, whereas the anti-inflammatory gene; IL4 was up regulated in melioidosis patients compared to sepsis cases caused by other pathogens. Septicaemic melioidosis cases showed significant down regulation of IL8 compared to sepsis cases caused by other pathogens. HMGB1, MICB, PSMB8, PSMB2, PSME2, HDAC1, HDAC2 and DNMT3B showed consistent down regulation of gene expression in melioidosis patients compared to other sepsis infection, irrespective of comorbidities such as diabetes, duration of clinical symptoms and antibiotic treatment.Specific immune response genes and epigenetic regulators are differentially expressed among melioidosis patients and patients with sepsis caused by other pathogens. Therefore, these genes may

  16. Behavioral analysis of Drosophila transformants expressing human taste receptor genes in the gustatory receptor neurons.

    Science.gov (United States)

    Adachi, Ryota; Sasaki, Yuko; Morita, Hiromi; Komai, Michio; Shirakawa, Hitoshi; Goto, Tomoko; Furuyama, Akira; Isono, Kunio

    2012-06-01

    Transgenic Drosophila expressing human T2R4 and T2R38 bitter-taste receptors or PKD2L1 sour-taste receptor in the fly gustatory receptor neurons and other tissues were prepared using conventional Gal4/UAS binary system. Molecular analysis showed that the transgene mRNAs are expressed according to the tissue specificity of the Gal4 drivers. Transformants expressing the transgene taste receptors in the fly taste neurons were then studied by a behavioral assay to analyze whether transgene chemoreceptors are functional and coupled to the cell response. Since wild-type flies show strong aversion against the T2R ligands as in mammals, the authors analyzed the transformants where the transgenes are expressed in the fly sugar receptor neurons so that they promote feeding ligand-dependently if they are functional and activate the neurons. Although the feeding preference varied considerably among different strains and individuals, statistical analysis using large numbers of transformants indicated that transformants expressing T2R4 showed a small but significant increase in the preference for denatonium and quinine, the T2R4 ligands, as compared to the control flies, whereas transformants expressing T2R38 did not. Similarly, transformants expressing T2R38 and PKD2L1 also showed a similar preference increase for T2R38-specific ligand phenylthiocarbamide (PTC) and a sour-taste ligand, citric acid, respectively. Taken together, the transformants expressing mammalian taste receptors showed a small but significant increase in the feeding preference that is taste receptor and also ligand dependent. Although future improvements are required to attain performance comparable to the endogenous robust response, Drosophila taste neurons may serve as a potential in vivo heterologous expression system for analyzing chemoreceptor function.

  17. Comparative gene expression profiling of P. falciparum malaria parasites exposed to three different histone deacetylase inhibitors.

    Directory of Open Access Journals (Sweden)

    Katherine T Andrews

    Full Text Available Histone deacetylase (HDAC inhibitors are being intensively pursued as potential new drugs for a range of diseases, including malaria. HDAC inhibitors are also important tools for the study of epigenetic mechanisms, transcriptional control, and other important cellular processes. In this study the effects of three structurally related antimalarial HDAC inhibitors on P. falciparum malaria parasite gene expression were compared. The three hydroxamate-based compounds, trichostatin A (TSA, suberoylanilide hydroxamic acid (SAHA; Vorinostat® and a 2-aminosuberic acid derivative (2-ASA-9, all caused profound transcriptional effects, with ~2-21% of genes having >2-fold altered expression following 2 h exposure to the compounds. Only two genes, alpha tubulin II and a hydrolase, were up-regulated by all three compounds after 2 h exposure in all biological replicates examined. The transcriptional changes observed after 2 h exposure to HDAC inhibitors were found to be largely transitory, with only 1-5% of genes being regulated after removing the compounds and culturing for a further 2 h. Despite some structural similarity, the three inhibitors caused quite diverse transcriptional effects, possibly reflecting subtle differences in mode of action or cellular distribution. This dataset represents an important contribution to our understanding of how HDAC inhibitors act on malaria parasites and identifies alpha tubulin II as a potential transcriptional marker of HDAC inhibition in malaria parasites that may be able to be exploited for future development of HDAC inhibitors as new antimalarial agents.

  18. Bioinformatics microarray analysis and identification of gene expression profiles associated with cirrhotic liver

    Directory of Open Access Journals (Sweden)

    Kun-Ming Chan

    2016-04-01

    Full Text Available Cirrhosis is the endpoint of liver fibrosis that is accompanied by limited regeneration capacity and complications and is the ultimate cause of death in many patients. Despite this, few studies have thoroughly looked at the gene expression profiles in the cirrhotic liver. Hence, this study aims to identify the genes that were differentially expressed in the cirrhotic liver and to explore the putative related signaling pathway and interaction networks. The gene expression profiles of cirrhotic livers and noncirrhotic livers were examined and compared using microarray gene analysis. Proteins encoded by the differentially expressed genes were analyzed for functional clustering and signaling pathway involvement using MetaCore bioinformatics analyses. The Gene Ontology analysis as well as the Kyoto encyclopedia of Genes and Genomes pathway analysis were also performed. A total of 213 significant genes were differentially expressed at more than a two-fold change in cirrhotic livers as compared to noncirrhotic livers. Of these, 105 upregulated genes and 63 downregulated genes were validated through MetaCore bioinformatics analyses. The signaling pathways and major functions of proteins encoded by these differentially expressed genes were further analyzed; results showed that the cirrhotic liver has a unique gene expression pattern related to inflammatory reaction, immune response, and cell growth, and is potentially cancer related. Our findings suggest that the microarray analysis may provide clues to the molecular mechanisms of liver cirrhosis for future experimental studies. However, further exploration of areas regarding therapeutic strategy might be possible to support metabolic activity, decrease inflammation, or enhance regeneration for liver cirrhosis.

  19. How to normalize metatranscriptomic count data for differential expression analysis.

    Science.gov (United States)

    Klingenberg, Heiner; Meinicke, Peter

    2017-01-01

    Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count data. For taxon-specific scaling and recombination of scaled counts we provide a simple R script. When applying transcriptomic tools for differential expression analysis directly to metatranscriptomic data with an organism-independent (global) scaling of counts the resulting differences may be difficult to interpret. The differences may correspond to changing functional profiles of the contributing organisms but may also result from a variation of taxonomic abundances. Taxon-specific scaling eliminates this variation and therefore the resulting differences actually reflect a different behavior of organisms under changing conditions. In simulation studies we show that the divergence between results from global and taxon-specific scaling can be drastic. In particular, the variation of organism abundances can imply a considerable increase of significant differences with global scaling. Also, on real metatranscriptomic data, the predictions from taxon-specific and global scaling can differ

  20. Comparative analysis of special preparedness young water-slalom

    Directory of Open Access Journals (Sweden)

    Daria Okun

    2016-02-01

    Full Text Available Purpose: to identify indicators is specially trained water-slalom aged 10–12 years. Material & Methods: methods of theoretical analysis, synthesis and synthesis of information, pedagogical control tests (tests, methods of mathematical statistics. Results: presented materials research performance technical readiness of 60 young water-slalom groups of initial training. A comparative analysis of the results and regulatory requirements, the proposed curriculum for youth sports schools. Conclusions: the results of the study suggest lagging performance testing young athletes behind the standards of the program requirements, indicating insufficient specially trained water-slaloms.

  1. Comparative Analysis of Resonant Converters for Energy Storage Systems

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    Vuchev Stoyan

    2017-01-01

    Full Text Available The following paperwork presents a comparative analysis of multiphase resonant converters for applications in energy storage systems. Models of the examined converters are developed in the software environments of MATLAB and LTspice. Results from the simulation examination of the converters during charging of supercapacitors and rechargeable batteries are presented. These results are compared to results obtained from experimental examination of the converters via a laboratory stand. For the purposes of the experimental examination, a control system is developed on the base of a virtual instrument in LabVIEW. The advantages and disadvantages of the different converters are discussed.

  2. Analysis of DNA strand-specific differential expression with high density tiling microarrays

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    Antequera Francisco

    2010-03-01

    Full Text Available Abstract Background DNA microarray technology allows the analysis of genome structure and dynamics at genome-wide scale. Expression microarrays (EMA contain probes for annotated open reading frames (ORF and are widely used for the analysis of differential gene expression. By contrast, tiling microarrays (TMA have a much higher probe density and provide unbiased genome-wide coverage. The purpose of this study was to develop a protocol to exploit the high resolution of TMAs for quantitative measurement of DNA strand-specific differential expression of annotated and non-annotated transcripts. Results We extensively filtered probes present in Affymetrix Genechip Yeast Genome 2.0 expression and GeneChip S. pombe 1.0FR tiling microarrays to generate custom Chip Description Files (CDF in order to compare their efficiency. We experimentally tested the potential of our approach by measuring the differential expression of 4904 genes in the yeast Schizosaccharomyces pombe growing under conditions of oxidative stress. The results showed a Pearson correlation coefficient of 0.943 between both platforms, indicating that TMAs are as reliable as EMAs for quantitative expression analysis. A significant advantage of TMAs over EMAs is the possibility of detecting non-annotated transcripts generated only under specific physiological conditions. To take full advantage of this property, we have used a target-labelling protocol that preserves the original polarity of the transcripts and, therefore, allows the strand-specific differential expression of non-annotated transcripts to be determined. By using a segmentation algorithm prior to generating the corresponding custom CDFs, we identified and quantitatively measured the expression of 510 transcripts longer than 180 nucleotides and not overlapping previously annotated ORFs that were differentially expressed at least 2-fold under oxidative stress. Conclusions We show that the information derived from TMA

  3. Comparative transcriptome analysis to investigate the high starch accumulation of duckweed (Landoltia punctata) under nutrient starvation.

    Science.gov (United States)

    Tao, Xiang; Fang, Yang; Xiao, Yao; Jin, Yan-Ling; Ma, Xin-Rong; Zhao, Yun; He, Kai-Ze; Zhao, Hai; Wang, Hai-Yan

    2013-05-08

    Duckweed can thrive on anthropogenic wastewater and produce tremendous biomass production. Due to its relatively high starch and low lignin percentage, duckweed is a good candidate for bioethanol fermentation. Previous studies have observed that water devoid of nutrients is good for starch accumulation, but its molecular mechanism remains unrevealed. This study globally analyzed the response to nutrient starvation in order to investigate the starch accumulation in duckweed (Landoltia punctata). L. punctata was transferred from nutrient-rich solution to distilled water and sampled at different time points. Physiological measurements demonstrated that the activity of ADP-glucose pyrophosphorylase, the key enzyme of starch synthesis, as well as the starch percentage in duckweed, increased continuously under nutrient starvation. Samples collected at 0 h, 2 h and 24 h time points respectively were used for comparative gene expression analysis using RNA-Seq. A comprehensive transcriptome, comprising of 74,797 contigs, was constructed by a de novo assembly of the RNA-Seq reads. Gene expression profiling results showed that the expression of some transcripts encoding key enzymes involved in starch biosynthesis was up-regulated, while the expression of transcripts encoding enzymes involved in starch consumption were down-regulated, the expression of some photosynthesis-related transcripts were down-regulated during the first 24 h, and the expression of some transporter transcripts were up-regulated within the first 2 h. Very interestingly, most transcripts encoding key enzymes involved in flavonoid biosynthesis were highly expressed regardless of starvation, while transcripts encoding laccase, the last rate-limiting enzyme of lignifications, exhibited very low expression abundance in all three samples. Our study provides a comprehensive expression profiling of L. punctata under nutrient starvation, which indicates that nutrient starvation down-regulated the global metabolic

  4. Comparative analysis of tax administration system in Russian regions

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    Aleksey Sergeevich Naydenov

    2011-09-01

    Full Text Available This paper presents the results of the study on tax administration attractiveness for taxpayers in the Russian Federation. The authors provide an overview of existing approaches to understanding the nature of the tax administration. To solve the problem of estimating the attractiveness of the tax administration in this study, we proposed a methodological approach based on comparative analysis of the rank of territorial systems of tax administration. In the basis of comparative analysis is the calculation of a set of indicators that characterize the tax administration system attractiveness from the standpoint of the taxpayer, with subsequent calculation of integral indexes and rankings of the Russian Federation. The results assessing the attractiveness of the tax administration system in the regions are shown. In this paper, we attempt to assess modern tax administration as one of the key economic institutions, as well as to obtain quantitative data on the status of the tax administration in Russia's regions.

  5. Comparative analysis about dynamic performances of grid synchronization schemes

    DEFF Research Database (Denmark)

    Yi, Hao; Wang, Xiongfei; Blaabjerg, Frede

    2017-01-01

    For a grid-connected Voltage-Source Converter (VSC), dynamics of the grid synchronization plays an important role in affecting the converter performances and stability. Due to its significance, this paper gives a comparative analysis about some basic grid synchronization schemes, through viewpoint...... of dynamic performances, which appeared as the impacts of voltage pe