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Tissue Expression Profiles of 5 Putative Imprinted Genes in Bovine Chromosome 29  [PDF]
Oladeji Bamidele, Ofelia G. Omitogun, Ikhide G. Imumorin
Open Journal of Animal Sciences (OJAS) , 2016, DOI: 10.4236/ojas.2016.64033
Genomic imprinting is an epigenetic process that regulates gene expression in the mammalian genome. Although there are specific imprinting differences between the mammalian species, cattle present unique opportunity for characterizing imprinted genes because of its sub-species classification. Five putative imprinted genes (TSSC4, CDKN1C, KCNQ1, PHLDA2 and NAP1L4) on bovine chromosome 29 (Bta 29) which had been characterized to have promoter CGI were quantitatively assayed for their relative expression across eight tissues (muscle, brain, liver, kidney, spinal cord, heart, lymph and skin) sampled in Angus cattle. The differential abundance of these genes in muscle and skin tissues of Angus, White Fulani and N’Dama cattle breeds was comparatively analyzed. These three breeds are representative of the Bos taurus and Bos indicus cattle sub-species while the two tissues are selected based on their strategic economic importance in cattle production. All the genes, except TSSC4, were relatively expressed across all the tissues. It was observed that Angus had the highest differential abundance in muscle tissues for TSSC4, PHLDA2 and NAP1L4 while N’Dama and White Fulani were the most abundant for KCNQ1 and NAP1L4 in skin tissues. The study identified marked differences in the expression profiles of the genes in both muscle and skin tissues of the three breeds that were characteristics of their genetics, environment and nutrition.
Classification of Genes and Putative Biomarker Identification Using Distribution Metrics on Expression Profiles  [PDF]
Hung-Chung Huang,Daniel Jupiter,Vincent VanBuren
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009056
Abstract: Identification of genes with switch-like properties will facilitate discovery of regulatory mechanisms that underlie these properties, and will provide knowledge for the appropriate application of Boolean networks in gene regulatory models. As switch-like behavior is likely associated with tissue-specific expression, these gene products are expected to be plausible candidates as tissue-specific biomarkers.
Phylogenetically informed logic relationships improve detection of biological network organization
Jike Cui, Todd F DeLuca, Jae-Yoon Jung, Dennis P Wall
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-476
Abstract: Taking advantage of a phylogenetic matrix constructed from the large orthologs database Roundup, we invented a method to create balanced profiles for individual triplets of genes that guarantee equal weight on the different phylogenetic scenarios of coevolution between genes. When we applied this idea to LAPP, the method to search for logic triplets of genes, the balanced profiles resulted in significant performance improvement and the discovery of hundreds of thousands more putative triplets than unadjusted profiles. We found that logic triplets detected biological network organization and identified key proteins and their functions, ranging from neighbouring proteins in local pathways, to well separated proteins in the whole pathway, and to the interactions among different pathways at the system level. Finally, our case study suggested that the directionality in a logic relationship and the profile of a triplet could disclose the connectivity between the triplet and surrounding networks.Balanced profiles are superior to the raw profiles employed by traditional methods of phylogenetic profiling in searching for high order gene sets. Gene triplets can provide valuable information in detection of biological network organization and identification of key genes at different levels of cellular interaction.Phylogenetic relationships among gene sequences have been used to reconstruct the evolution and organization of gene functional networks in cells. Profiles of orthologous relationships among genomes, specifically the presence or absence of genes across a set of organisms, have proved to be valuable for understanding functional relationships and network organization [1].The practice of "phylogentic profiling" has successfully penetrated many efforts in comparative genomics including genome annotation and functional coevolution [2-6]. The accuracy and predictive power tends to be modest unless the profiles are reconstructed in a way that accounts for phylogenetic relatio
Putative Genes Involved in Saikosaponin Biosynthesis in Bupleurum Species  [PDF]
Tsai-Yun Lin,Chung-Yi Chiou,Shu-Jiau Chiou
International Journal of Molecular Sciences , 2013, DOI: 10.3390/ijms140612806
Abstract: Alternative medicinal agents, such as the herb Bupleurum, are increasingly used in modern medicine to supplement synthetic drugs. First, we present a review of the currently known effects of triterpene saponins-saikosaponins of Bupleurum species. The putative biosynthetic pathway of saikosaponins in Bupleurum species is summarized, followed by discussions on identification and characterization of genes involved in the biosynthesis of saikosaponins. The purpose is to provide a brief review of gene extraction, functional characterization of isolated genes and assessment of expression patterns of genes encoding enzymes in the process of saikosaponin production in Bupleurum species, mainly B. kaoi. We focus on the effects of MeJA on saikosaponin production, transcription patterns of genes involved in biosynthesis and on functional depiction.
The Discovery of Putative Urine Markers for the Specific Detection of Prostate Tumor by Integrative Mining of Public Genomic Profiles  [PDF]
Min Chen, Kai Wang, Liang Zhang, Cheng Li, Yongliang Yang
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0028552
Abstract: Urine has emerged as an attractive biofluid for the noninvasive detection of prostate cancer (PCa). There is a strong imperative to discover candidate urinary markers for the clinical diagnosis and prognosis of PCa. The rising flood of various omics profiles presents immense opportunities for the identification of prospective biomarkers. Here we present a simple and efficient strategy to derive candidate urine markers for prostate tumor by mining cancer genomic profiles from public databases. Prostate, bladder and kidney are three major tissues from which cellular matters could be released into urine. To identify urinary markers specific for PCa, upregulated entities that might be shed in exosomes of bladder cancer and kidney cancer are first excluded. Through the ontology-based filtering and further assessment, a reduced list of 19 entities encoding urinary proteins was derived as putative PCa markers. Among them, we have found 10 entities closely associated with the process of tumor cell growth and development by pathway enrichment analysis. Further, using the 10 entities as seeds, we have constructed a protein-protein interaction (PPI) subnetwork and suggested a few urine markers as preferred prognostic markers to monitor the invasion and progression of PCa. Our approach is amenable to discover and prioritize potential markers present in a variety of body fluids for a spectrum of human diseases.
Adult midgut expressed sequence tags from the tsetse fly Glossina morsitans morsitans and expression analysis of putative immune response genes
M J Lehane, S Aksoy, W Gibson, A Kerhornou, M Berriman, J Hamilton, M B Soares, M F Bonaldo, S Lehane, N Hall
Genome Biology , 2003, DOI: 10.1186/gb-2003-4-10-r63
Abstract: A total of 21,427 ESTs were produced from the midgut of adult Glossina morsitans morsitans and grouped into 8,876 clusters or singletons potentially representing unique genes. Putative functions were ascribed to 4,035 of these by homology. Of these, a remarkable 3,884 had their most significant matches in the Drosophila protein database. We selected 68 genes with putative immune-related functions, macroarrayed them and determined their expression profiles following bacterial or trypanosome challenge. In both infections many genes are downregulated, suggesting a malaise response in the midgut. Trypanosome and bacterial challenge result in upregulation of different genes, suggesting that different recognition pathways are involved in the two responses. The most notable block of genes upregulated in response to trypanosome challenge are a series of Toll and Imd genes and a series of genes involved in oxidative stress responses.The project increases the number of known Glossina genes by two orders of magnitude. Identification of putative immunity genes and their preliminary characterization provides a resource for the experimental dissection of tsetse-trypanosome interactions.The African trypanosomes that cause sleeping sickness in humans and nagana in livestock are cyclically transmitted by tsetse flies (Glossinidae). Tsetse flies are obligate blood feeders and ingest trypanosomes along with the blood meal from infected animals. In the fly, the trypanosomes undergo complex cycles of growth and development all of which occur within the lumen of the alimentary canal of the fly and, in the case of the brucei group trypanosomes, the salivary glands [1]. Tsetse flies are normally refractory to trypanosome infection with typically less than half the fly population becoming infected, even under ideal conditions in the laboratory. This is reflected in field infection rates which often fail to exceed 10% of the fly population. In addition, many of those that become infected fai
An interactive tool for visualization of relationships between gene expression profiles
Peter Ruzanov, Steven JM Jones
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-193
Abstract: We designed and built TreeBuilder3D, an interactive viewer for visualizing the hierarchical relationships between expression profiles such as SAGE libraries or microarrays. The program allows loading expression data as plain text files and visualizing the relative differences of the analyzed datasets in 3-dimensional space using various distance metrics.TreeBuilder3D provides a simple interface and has a small size. Written in Java, TreeBuilder3D is a platform-independent, open source application, which may be useful in analysis of large-scale gene expression data.Development of high throughput transcription profiling techniques such as microarrays and SAGE [2] has made it possible to evaluate the expression levels of genes on a genome wide scale. The ability to look at expression profiles of different cellular states has the potential to provide knowledge about the mechanisms driving such important events as differentiation, aging and tumorogenesis. In addition to understanding transcription profiles of individual genes, the ability to visualize relationships between whole sets of gene expression data provides the means to infer higher-order relationships between the sampled biological conditions [8]. In this paper, we describe the design and usage of an interactive viewer, which builds hypothetical phenetic networks from SAGE expression data. These networks may help to associate analyzed SAGE libraries with some intermediate stages in the development of different cellular states or progress of disease, such as cancer. As an example, we have used our program to analyze publicly available SAGE data, but our application is also applicable to microarray data analysis.Traditionally, hierarchical data are presented as a rooted or unrooted tree with bifurcating branches connecting different data points (nodes). Generally, only the distances along the edges of the tree are shown proportionally. In a non-reticulated tree, the distance between nodes that are not directly co
The Turkish Online Journal of Distance Education , 2011,
Abstract: The study aims to identify the economic profiles of Open Education Faculty students and to determine the relationship between their economic profiles and the following of online courses using Internet. In the study survey model was used. The population of the study was composed of 4652 Anadolu University Open Education Faculty students who live in Bolu. Sample of the study consisted of 361 students randomly selected from research population. Data were obtained by surveys. Some of the research findings are as follows: the income levels of parents for both unemployed and single and employed students are in the range of 0-1300 TL. Since almost all the mothers are housewives, they do not have separate incomes. Fathers for both unemployed and single and employed students are commonly workers, retired individuals, self employed indibviduals and public officials. Meaningful relationships were observed between the economic profiles of employed students which include opportunities such as having access to a computer at the workplace or owning one at home and following the classes through Internet.
Polymerase Chain Reaction and Cloning of Burkholderia pseudomallei Putative Genes
Nagi A. AL-Haj,Lai L. Suang,Mariana N. Shamsudin,Rasedee Abdullah,Rahmah Mohamed,Zamberi Sekawi
Research Journal of Medical Sciences , 2012,
Abstract: Total of 23 putative Open Read Farms from B. pseudomallei strain D286 was successfully cloned and the nucleotide sequence analysis of the putative genes showed the homologue (98-100%) to strain K96243. The high similarity in gene sequences between these strains is confirmed for presence of the necessary ORF for LPS biosynthesis through PCR amplification the application of the ORFs in the PCR amplification and expression method. The findings of this study have contributed to some information on the molecular bases of the LPS biosynthesis genes in B. pseudomallei specifically for strain D286. PCR amplification, a specific pair of primer for each ORFs was proving specific for amplification of genes in B. pseudomallei strain D286. The PCR mixture with addition of DMSO, formamide and glycerol could ease the PCR optimization where different pairs of primers were involved. The specific primer pairs with the PCR mixture could be used in developing a PCR diagnosis of melioidosis.
Transcriptome Analysis Reveals Putative Genes Involved in Iridoid Biosynthesis in Rehmannia glutinosa  [PDF]
Peng Sun,Shuhui Song,Lili Zhou,Bing Zhang,Jianjun Qi,Xianen Li
International Journal of Molecular Sciences , 2012, DOI: 10.3390/ijms131013748
Abstract: Rehmannia glutinosa, one of the most widely used herbal medicines in the Orient, is rich in biologically active iridoids. Despite their medicinal importance, no molecular information about the iridoid biosynthesis in this plant is presently available. To explore the transcriptome of R. glutinosa and investigate genes involved in iridoid biosynthesis, we used massively parallel pyrosequencing on the 454 GS FLX Titanium platform to generate a substantial EST dataset. Based on sequence similarity searches against the public sequence databases, the sequences were first annotated and then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) based analysis. Bioinformatic analysis indicated that the 454 assembly contained a set of genes putatively involved in iridoid biosynthesis. Significantly, homologues of the secoiridoid pathway genes that were only identified in terpenoid indole alkaloid producing plants were also identified, whose presence implied that route II iridoids and route I iridoids share common enzyme steps in the early stage of biosynthesis. The gene expression patterns of four prenyltransferase transcripts were analyzed using qRT-PCR, which shed light on their putative functions in tissues of R. glutinosa. The data explored in this study will provide valuable information for further studies concerning iridoid biosynthesis.
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