Genomics insights最新文献_第2页

MicroRNAs Circulate in the Hemolymph of Drosophila and Accumulate Relative to Tissue microRNAs in an Age-Dependent Manner 微rna在果蝇的血淋巴中循环，并以年龄依赖的方式相对于组织微rna积累

Genomics insights Pub Date : 2016-03-28 DOI: 10.4137/GEI.S38147

J. Dhahbi, H. Atamna, Rui Li, A. Yamakawa, Noel Guerrero, Hanh T Lam, P. Mote, S. Spindler

{"title":"MicroRNAs Circulate in the Hemolymph of Drosophila and Accumulate Relative to Tissue microRNAs in an Age-Dependent Manner","authors":"J. Dhahbi, H. Atamna, Rui Li, A. Yamakawa, Noel Guerrero, Hanh T Lam, P. Mote, S. Spindler","doi":"10.4137/GEI.S38147","DOIUrl":"https://doi.org/10.4137/GEI.S38147","url":null,"abstract":"In mammals, extracellular miRNAs circulate in biofluids as stable entities that are secreted by normal and diseased tissues, and can enter cells and regulate gene expression. Drosophila melanogaster is a proven system for the study of human diseases. They have an open circulatory system in which hemolymph (HL) circulates in direct contact with all internal organs, in a manner analogous to vertebrate blood plasma. Here, we show using deep sequencing that Drosophila HL contains RNase-resistant circulating miRNAs (HL-miRNAs). Limited subsets of body tissue miRNAs (BT-miRNAs) accumulated in HL, suggesting that they may be specifically released from cells or particularly stable in HL. Alternatively, they might arise from specific cells, such as hemocytes, that are in intimate contact with HL. Young and old flies accumulated unique populations of HL-miRNAs, suggesting that their accumulation is responsive to the physiological status of the fly. These HL-miRNAs in flies may function similar to the miRNAs circulating in mammalian biofluids. The discovery of these HL-miRNAs will provide a new venue for health and disease-related research in Drosophila.","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"9 1","pages":"29 - 39"},"PeriodicalIF":0.0,"publicationDate":"2016-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GEI.S38147","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70701176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 15

Inferring Orthologs: Open Questions and Perspectives 推断同源物:开放的问题和观点

Genomics insights Pub Date : 2016-02-25 DOI: 10.4137/GEI.S37925

F. Tekaia

引用次数: 51

Identification of Potential Anticancer Activities of Novel Ganoderma lucidum Extracts Using Gene Expression and Pathway Network Analysis. 利用基因表达和通路网络分析鉴定新型灵芝提取物的潜在抗癌活性

Genomics insights Pub Date : 2016-02-16 eCollection Date: 2016-01-01 DOI: 10.4137/GEI.S32477

Chi H J Kao, Karen S Bishop, Yuanye Xu, Dug Yeo Han, Pamela M Murray, Gareth J Marlow, Lynnette R Ferguson

{"title":"Identification of Potential Anticancer Activities of Novel Ganoderma lucidum Extracts Using Gene Expression and Pathway Network Analysis.","authors":"Chi H J Kao, Karen S Bishop, Yuanye Xu, Dug Yeo Han, Pamela M Murray, Gareth J Marlow, Lynnette R Ferguson","doi":"10.4137/GEI.S32477","DOIUrl":"10.4137/GEI.S32477","url":null,"abstract":"Ganoderma lucidum (lingzhi) has been used for the general promotion of health in Asia for many centuries. The common method of consumption is to boil lingzhi in water and then drink the liquid. In this study, we examined the potential anticancer activities of G. lucidum submerged in two commonly consumed forms of alcohol in East Asia: malt whiskey and rice wine. The anticancer effect of G. lucidum, using whiskey and rice wine-based extraction methods, has not been previously reported. The growth inhibition of G. lucidum whiskey and rice wine extracts on the prostate cancer cell lines, PC3 and DU145, was determined. Using Affymetrix gene expression assays, several biologically active pathways associated with the anticancer activities of G. lucidum extracts were identified. Using gene expression analysis (real-time polymerase chain reaction [RT-PCR]) and protein analysis (Western blotting), we confirmed the expression of key genes and their associated proteins that were initially identified with Affymetrix gene expression analysis. ","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"9 1","pages":"1-16"},"PeriodicalIF":0.0,"publicationDate":"2016-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70701468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Applying Side-chain Flexibility in Motifs for Protein Docking. 基序侧链柔韧性在蛋白质对接中的应用。

Genomics insights Pub Date : 2015-10-15 eCollection Date: 2015-01-01 DOI: 10.4137/GEI.S29821

Hui Liu, Feng Lin, Jian-Li Yang, Hong-Rui Wang, Xiu-Ling Liu

{"title":"Applying Side-chain Flexibility in Motifs for Protein Docking.","authors":"Hui Liu, Feng Lin, Jian-Li Yang, Hong-Rui Wang, Xiu-Ling Liu","doi":"10.4137/GEI.S29821","DOIUrl":"https://doi.org/10.4137/GEI.S29821","url":null,"abstract":"Conventional rigid docking algorithms have been unsatisfactory in their computational results, largely due to the fact that protein structures are flexible in live environments. In response, we propose to introduce the side-chain flexibility in protein motif into the docking. First, the Morse theory is applied to curvature labeling and surface region growing, for segmentation of the protein surface into smaller patches. Then, the protein is described by an ensemble of conformations that incorporate the flexibility of interface side chains and are sampled using rotamers. Next, a 3D rotation invariant shape descriptor is proposed to deal with the flexible motifs and surface patches; thus, pairwise complementarity matching is needed only between the convex patches of ligand and the concave patches of receptor. The iterative closest point (ICP) algorithm is implemented for geometric alignment of the two 3D protein surface patches. Compared with the fast Fourier transform-based global geometric matching algorithm and other methods, our FlexDock system generates much less false-positive docking results, which benefits identification of the complementary candidates. Our computational experiments show the advantages of the proposed flexible docking algorithm over its counterparts. ","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"8 ","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2015-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GEI.S29821","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34124487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Reassessment of the Genome Size in Elaeis guineensis and Elaeis oleifera, and Its Interspecific Hybrid. 对 Elaeis guineensis 和 Elaeis oleifera 及其种间杂交种基因组大小的重新评估。

Genomics insights Pub Date : 2014-09-03 eCollection Date: 2014-01-01 DOI: 10.4137/GEI.S15522

Julceia Camillo, André P Leão, Alexandre A Alves, Eduardo F Formighieri, Ana Ls Azevedo, Juliana D Nunes, Guy de Capdeville, Jean K de A Mattos, Manoel T Souza

{"title":"Reassessment of the Genome Size in Elaeis guineensis and Elaeis oleifera, and Its Interspecific Hybrid.","authors":"Julceia Camillo, André P Leão, Alexandre A Alves, Eduardo F Formighieri, Ana Ls Azevedo, Juliana D Nunes, Guy de Capdeville, Jean K de A Mattos, Manoel T Souza","doi":"10.4137/GEI.S15522","DOIUrl":"10.4137/GEI.S15522","url":null,"abstract":"Aiming at generating a comprehensive genomic database on Elaeis spp., our group is leading several R&D initiatives with Elaeis guineensis (African oil palm) and Elaeis oleifera (American oil palm), including the whole-genome sequencing of the last. Genome size estimates currently available for this genus are controversial, as they indicate that American oil palm genome is about half the size of the African oil palm genome and that the genome of the interspecific hybrid is bigger than both the parental species genomes. We estimated the genome size of three E. guineensis genotypes, five E. oleifera genotypes, and two interspecific hybrids genotypes. On average, the genome size of E. guineensis is 4.32 ± 0.173 pg, while that of E. oleifera is 4.43 ± 0.018 pg. This indicates that both genomes are similar in size, even though E. oleifera is in fact bigger. As expected, the hybrid genome size is around the average of the two genomes, 4.40 ± 0.016 pg. Additionally, we demonstrate that both species present around 38% of GC content. As our results contradict the currently available data on Elaeis spp. genome sizes, we propose that the actual genome size of the Elaeis species is around 4 pg and that American oil palm possesses a larger genome than African oil palm. ","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"7 ","pages":"13-22"},"PeriodicalIF":0.0,"publicationDate":"2014-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34031207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Application of Machine Learning to Development of Copy Number Variation-based Prediction of Cancer Risk. 机器学习在基于拷贝数变化的癌症风险预测中的应用。

Genomics insights Pub Date : 2014-06-26 eCollection Date: 2014-01-01 DOI: 10.4137/GEI.S15002

Xiaofan Ding, Shui-Ying Tsang, Siu-Kin Ng, Hong Xue

引用次数: 18

Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology. 芽孢杆菌的比较基因组学及其在工业微生物学中的应用。

Genomics insights Pub Date : 2013-08-18 eCollection Date: 2013-01-01 DOI: 10.4137/GEI.S12732

Archana Sharma, T Satyanarayana

引用次数: 19

Inter-Laboratory Variability in Array-Based RNA Quantification Methods. 基于阵列的RNA定量方法的实验室间变异。

Genomics insights Pub Date : 2013-05-06 eCollection Date: 2013-01-01 DOI: 10.4137/GEI.S11909

Victoria Y Wong, Manuel X Duval

{"title":"Inter-Laboratory Variability in Array-Based RNA Quantification Methods.","authors":"Victoria Y Wong, Manuel X Duval","doi":"10.4137/GEI.S11909","DOIUrl":"https://doi.org/10.4137/GEI.S11909","url":null,"abstract":"Ribonucleic acids (RNA) are hypothesized to have preceded their derivatives, deoxyribonucleic acids (DNA), as the molecular media of genetic information when life emerged on earth. Molecular biologists are accustomed to the dramatic effects a subtle variation in the ribose moiety composition between RNA and DNA can have on the stability of these molecules. While DNA is very stable after extraction from biological samples and subsequent treatment, RNA is notoriously labile. The short half-life property, inherent to RNA, benefits cells that do not need to express their entire repertoire of proteins. The cellular machinery turns off the production of a given protein by shutting down the transcription of its cognate coding gene and by either actively degrading the remaining mRNA or allowing it to decay on its own. The steady-state level of each mRNA in a given cell varies continuously and is specified by changing kinetics of synthesis and degradation. Because it is technically possible to simultaneously measure thousands of nucleic acid molecules, these quantities have been studied by the life sciences community to investigate a range of biological problems. Since the RNA abundance can change according to a wide range of perturbations, this makes it the molecule of choice for exploring biological systems; its instability, on the other hand, could be an underestimated source of technical variability. We found that a large fraction of the RNA abundance originally present in the biological system prior to extraction was masked by the RNA labeling and measurement procedure. The method used to extract RNA molecules from cells and to label them prior to hybridization operations on DNA arrays affects the original distribution of RNA. Only if RNA measurements are performed according to the same procedure can biological information be inferred from the assay read out. ","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"6 ","pages":"13-24"},"PeriodicalIF":0.0,"publicationDate":"2013-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GEI.S11909","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33873041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The DNA Habitat and its RNA Inhabitants: At the Dawn of RNA Sociology. DNA栖息地及其RNA居民:RNA社会学的开端。

Genomics insights Pub Date : 2013-03-04 eCollection Date: 2013-01-01 DOI: 10.4137/GEI.S11490

Luis P Villarreal, Guenther Witzany

{"title":"The DNA Habitat and its RNA Inhabitants: At the Dawn of RNA Sociology.","authors":"Luis P Villarreal, Guenther Witzany","doi":"10.4137/GEI.S11490","DOIUrl":"10.4137/GEI.S11490","url":null,"abstract":"Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code compositions and rearrangements by mobile genetic elements and noncoding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts and compel a reexamination. In this review, we try to find an alternate hypothesis. It seems plausible now that if we look at the abundance of regulatory RNAs and persistent viruses in host genomes, we will find more and more evidence that the key players that edit the genetic codes of host genomes are consortia of RNA agents and viruses that drive evolutionary novelty and regulation of cellular processes in all steps of development. This agent-based approach may lead to a qualitative RNA sociology that investigates and identifies relevant behavioral motifs of cooperative RNA consortia. In addition to molecular biological perspectives, this may lead to a better understanding of genetic code evolution and dynamics. ","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"6 ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2013-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GEI.S11490","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33941238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 35

Transcriptional Changes of Blood Eosinophils After Methacholine Inhalation Challenge in Asthmatics. 哮喘患者吸入甲胆碱后血嗜酸性粒细胞转录的变化。

Genomics insights Pub Date : 2012-01-30 eCollection Date: 2012-01-01 DOI: 10.4137/GEI.S9125

Scott J Tebbutt, Jian-Qing He, Amrit Singh, Casey P Shannon, Jian Ruan, Chris Carlsten

{"title":"Transcriptional Changes of Blood Eosinophils After Methacholine Inhalation Challenge in Asthmatics.","authors":"Scott J Tebbutt, Jian-Qing He, Amrit Singh, Casey P Shannon, Jian Ruan, Chris Carlsten","doi":"10.4137/GEI.S9125","DOIUrl":"https://doi.org/10.4137/GEI.S9125","url":null,"abstract":"Background: Methacholine challenge is commonly used within the asthma diagnostic algorithm. Methacholine challenge has recently been shown to induce airway remodelling in asthma via bronchoconstriction, without additional airway inflammation. We evaluated the effect of methacholine-induced bronchoconstriction on the peripheral whole-blood transcriptome.Methods: Fourteen males with adult-onset, occupational asthma, 26-77 years of age, underwent methacholine inhalation challenges. The concentration of methacholine eliciting a ≥20% fall in FEV1 (PC20) was determined. Blood was collected immediately prior to and two hours after challenge. Complete blood counts and leukocyte differentials were obtained. Transcriptome analysis was performed using Affymetrix GeneChip(®) Human Gene 1.0 ST arrays. Data were analyzed using robust LIMMA and SAM. The cell-specific Significance Analysis of Microarrays (csSAM) algorithm was used to deconvolute the gene expression data according to cell type.Results: Microarray pathway analysis indicated that inflammatory processes were differentially affected. CsSAM identified 1,559 transcripts differentially expressed (all down-regulated) between pre- and post-methacholine in eosinophils at a false discovery cutoff of 10%. Notable changes included the GOLGA5 and METTL2B genes and the protein ubiquitination and CCR3 pathways.Conclusions: We demonstrated significant changes in the peripheral blood eosinophil-specific transcriptome of asthmatics two hours after methacholine challenge. CCR3 and protein ubiquitination pathways are both significantly down-regulated.","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"5 ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2012-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GEI.S9125","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33941239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3