Genomics insights最新文献_第3页

Cloning and Initial Functional Characterization of Mlk4α and Mlk4β. Mlk4α和Mlk4β基因的克隆及初步功能鉴定

Genomics insights Pub Date : 2011-03-22 eCollection Date: 2011-01-01 DOI: 10.4137/GEI.S6092

Vladimir I Kashuba, Elvira V Grigorieva, Sergei M Kvasha, Tatiana V Pavlova, Vladimir Grigoriev, Alexei Protopopov, Olga Kharchenko, Rinat Gizatullin, Alla V Rynditch, Eugene R Zabarovsky

{"title":"Cloning and Initial Functional Characterization of Mlk4α and Mlk4β.","authors":"Vladimir I Kashuba, Elvira V Grigorieva, Sergei M Kvasha, Tatiana V Pavlova, Vladimir Grigoriev, Alexei Protopopov, Olga Kharchenko, Rinat Gizatullin, Alla V Rynditch, Eugene R Zabarovsky","doi":"10.4137/GEI.S6092","DOIUrl":"https://doi.org/10.4137/GEI.S6092","url":null,"abstract":"We have cloned a novel human mixed-lineage kinase gene, MLK4. Two alternatively spliced forms, MLK4α (580 aa) and MLK4β (1036 aa), have been identified and mapped to chromosomal band 1q42. MLK4 shows high amino acid homology to the kinase catalytic domain of MLK3 (72%), MLK1 (71%) and MLK2 (69%). Strong expression of MLK4 was detected in the human pancreas and kidneys. pCMV-MLK4β c-myc-tagged protein (human) was expressed in the cytoplasm and nucleus of transiently transfected COS-1 cells, while pCMV-MLK4α c-myc-tagged protein (human) was expressed in cytoplasm only. Both MLK4 isoforms reduced the colony formation ability of MCF7 cells by 85%-95% and almost totally suppressed cell proliferation in the CyQUANT cell proliferation assay. Human pCMV-MLK4β transgenic mice expressed the MLK4β in all tissues examined but no phenotypic abnormalities were observed. Thus, in this work, we present the cloning and sequencing of MLK4α and MLK4β for the first time; the data obtained suggest that MLK4 may function as a MAP kinase. ","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"4 ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2011-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GEI.S6092","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33941237","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: 10

ESTs from Seeds to Assist the Selective Breeding of Jatropha curcas L. for Oil and Active Compounds. 麻疯树种子est辅助麻疯树油脂和活性成分的选择性育种

Genomics insights Pub Date : 2010-10-28 eCollection Date: 2010-01-01 DOI: 10.4137/GEI.S4340

Kleber A Gomes, Tiago C Almeida, Abelmon S Gesteira, Ivon P Lôbo, Ana Carolina R Guimarães, Antonio B de Miranda, Marie-Anne Van Sluys, Rosenira S da Cruz, Júlio Cm Cascardo, Nicolas Carels

{"title":"ESTs from Seeds to Assist the Selective Breeding of Jatropha curcas L. for Oil and Active Compounds.","authors":"Kleber A Gomes, Tiago C Almeida, Abelmon S Gesteira, Ivon P Lôbo, Ana Carolina R Guimarães, Antonio B de Miranda, Marie-Anne Van Sluys, Rosenira S da Cruz, Júlio Cm Cascardo, Nicolas Carels","doi":"10.4137/GEI.S4340","DOIUrl":"https://doi.org/10.4137/GEI.S4340","url":null,"abstract":"We report here on the characterization of a cDNA library from seeds of Jatropha curcas L. at three stages of fruit maturation before yellowing. We sequenced a total of 2200 clones and obtained a set of 931 non-redundant sequences (unigenes) after trimming and quality control, ie, 140 contigs and 791 singlets with PHRED quality ≥10. We found low levels of sequence redundancy and extensive metabolic coverage by homology comparison to GO. After comparison of 5841 non-redundant ESTs from a total of 13193 reads from GenBank with KEGG, we identified tags with nucleotide variations among J. curcas accessions for genes of fatty acid, terpene, alkaloid, quinone and hormone pathways of biosynthesis. More specifically, the expression level of four genes (palmitoyl-acyl carrier protein thioesterase, 3-ketoacyl-CoA thiolase B, lysophosphatidic acid acyltransferase and geranyl pyrophosphate synthase) measured by real-time PCR proved to be significantly different between leaves and fruits. Since the nucleotide polymorphism of these tags is associated to higher level of gene expression in fruits compared to leaves, we propose this approach to speed up the search for quantitative traits in selective breeding of J. curcas. We also discuss its potential utility for the selective breeding of economically important traits in J. curcas. ","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"3 ","pages":"29-56"},"PeriodicalIF":0.0,"publicationDate":"2010-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GEI.S4340","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33941236","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: 30

Molecular Cloning of a Novel Bradykinin-Related Peptide from the Skin of Indian Bronzed Frog Hylarana Temporalis. 一种新型缓激肽相关肽的克隆(英文)

Genomics insights Pub Date : 2010-10-18 eCollection Date: 2010-01-01 DOI: 10.4137/GEI.S5409

V Reshmy, V Preeji, A Parvin, K Santhoshkumar, S George

引用次数: 3

Design, Construction and Validation of Targeted BAC Array-Based CGH Test for Detecting the Most Commons Chromosomal Abnormalities. 靶向BAC阵列CGH检测最常见染色体异常的设计、构建与验证

Genomics insights Pub Date : 2010-03-11 eCollection Date: 2010-01-01 DOI: 10.4137/GEI.S3683

Stefano Gambardella, Erika Ciabattoni, Francesca Motta, Giusy Stoico, Francesca Gullotta, Michela Biancolella, Anna Maria Nardone, Antonio Novelli, Ercole Brunetti, Laura Bernardini, Giuseppe Novelli

{"title":"Design, Construction and Validation of Targeted BAC Array-Based CGH Test for Detecting the Most Commons Chromosomal Abnormalities.","authors":"Stefano Gambardella, Erika Ciabattoni, Francesca Motta, Giusy Stoico, Francesca Gullotta, Michela Biancolella, Anna Maria Nardone, Antonio Novelli, Ercole Brunetti, Laura Bernardini, Giuseppe Novelli","doi":"10.4137/GEI.S3683","DOIUrl":"https://doi.org/10.4137/GEI.S3683","url":null,"abstract":"We designed a targeted-array called GOLD (Gain or Loss Detection) Chip consisting of 900 FISH-mapped non-overlapping BAC clones spanning the whole genome to enhance the coverage of 66 unique human genomic regions involved in well known microdeletion/microduplication syndromes. The array has a 10 Mb backbone to guarantee the detection of the aneuploidies, and has an implemented resolution for telomeres, and for regions involved in common genomic diseases. In order to evaluate clinical diagnostic applicability of GOLDChip, analytical validity was carried-out via retrospective analysis of DNA isolated from a series of cytogenetically normal amniocytes and cytogenetically abnormal DNA obtained from cultured amniocytes, peripheral blood and/or cell lines. We recruited 47 DNA samples corresponding to pathologies with significant frequencies (Cri du Chat syndrome, Williams syndrome, Prader Willi/Angelman syndromes, Smith-Magenis syndrome, DiGeorge syndrome, Miller-Dieker syndrome, chromosomes 13, 18 and 21 trisomies). We set up an experimental protocol that allowed to identify chromosomal rearrangements in all the DNA samples analyzed. Our results provide evidence that our targeted BAC array can be used for the identification of the most common microdeletion syndromes and common aneuploidies. ","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"3 ","pages":"9-21"},"PeriodicalIF":0.0,"publicationDate":"2010-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GEI.S3683","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33928058","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: 2

Single Nucleotide Polymorphisms Caused by Assembly Errors. 组装错误引起的单核苷酸多态性。

Genomics insights Pub Date : 2010-02-04 eCollection Date: 2010-01-01 DOI: 10.4137/GEI.S3653

Jürgen Kleffe, Robert Weißmann, Florian F Schmitzberger

{"title":"Single Nucleotide Polymorphisms Caused by Assembly Errors.","authors":"Jürgen Kleffe, Robert Weißmann, Florian F Schmitzberger","doi":"10.4137/GEI.S3653","DOIUrl":"https://doi.org/10.4137/GEI.S3653","url":null,"abstract":"We compare the results of three different assembler programs, Celera, Phrap and Mira2, for the same set of about a hundred thousand Sanger reads derived from an unknown bacterial genome. In difference to previous assembly comparisons we do not focus on speed of computation and numbers of assembled contigs but on how the different sequence assemblies agree by content. Threefold consistently assembled genome regions are identified in order to estimate a lower bound of erroneously identified single nucleotide polymorphisms (SNP) caused by nothing but the process of mathematical sequence assembly. We identified 509 sequence triplets common to all three de-novo assemblies spanning only 34% (3.3 Mb) of the bacterial genome with 175 of these regions (~1.5 Mb) including erroneous SNPs and insertion/deletions. Within these triplets this on average leads to one error per 7,155 base pairs. Replacing the assembler Mira2 by the most recent version Mira3, the letter number even drops to 5,923. Our results therefore suggest that a considerably high number of erroneous SNPs may be present in current sequence data and mathematicians should urgently take up research on numerical stability of sequence assembly algorithms. Furthermore, even the latest versions of currently used assemblers produce erroneous SNPs that depend on the order reads are used as input. Such errors will severely hamper molecular diagnostics as well as relating genome variation and disease. This issue needs to be addressed urgently as the field is moving fast into clinical applications. ","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"3 ","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2010-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GEI.S3653","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33928057","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

Sickle Cell Disease in the Post Genomic Era: A Monogenic Disease with a Polygenic Phenotype 后基因组时代的镰状细胞病:一种多基因表型的单基因疾病

Genomics insights Pub Date : 2009-07-30 DOI: 10.4137/GEI.S2626

Adel Driss, Kwaku Asare, J. Hibbert, Beatrice E. Gee, Tom Adamkiewicz, Jonathan K. Stiles

{"title":"Sickle Cell Disease in the Post Genomic Era: A Monogenic Disease with a Polygenic Phenotype","authors":"Adel Driss, Kwaku Asare, J. Hibbert, Beatrice E. Gee, Tom Adamkiewicz, Jonathan K. Stiles","doi":"10.4137/GEI.S2626","DOIUrl":"https://doi.org/10.4137/GEI.S2626","url":null,"abstract":"More than half a century after the discovery of the molecular basis of Sickle Cell Disease (SCD), the causes of the phenotypic heterogeneity of the disease remain unclear. This heterogeneity manifests with different clinical outcomes such as stroke, vaso-occlusive episodes, acute chest syndrome, avascular necrosis, leg ulcers, priapism and retinopathy. These outcomes cannot be explained by the single mutation in the beta-globin gene alone but may be attributed to genetic modifiers and environmental effects. Recent advances in the post human genome sequence era have opened the door for the identification of novel genetic modifiers in SCD. Studies are showing that phenotypes of SCD seem to be modulated by polymorphisms in genes that are involved in inflammation, cell–cell interaction and modulators of oxidant injury and nitric oxide biology. The discovery of genes implicated in different phenotypes will help understanding of the physiopathology of the disease and aid in establishing targeted cures. However, caution is needed in asserting that genetic modifiers are the cause of all SCD phenotypes, because there are other factors such as genetic background of the population, environmental components, socio-economics and psychology that can play significant roles in the clinical heterogeneity.","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"2 1","pages":"23 - 48"},"PeriodicalIF":0.0,"publicationDate":"2009-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GEI.S2626","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70701565","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: 101

Sickle Cell Disease in the Post Genomic Era: A Monogenic Disease with a Polygenic Phenotype. 后基因组时代的镰状细胞病:一种多基因表型的单基因疾病。

Genomics insights Pub Date : 2009-07-30

A Driss, K O Asare, J M Hibbert, B E Gee, T V Adamkiewicz, J K Stiles

{"title":"Sickle Cell Disease in the Post Genomic Era: A Monogenic Disease with a Polygenic Phenotype.","authors":"A Driss, K O Asare, J M Hibbert, B E Gee, T V Adamkiewicz, J K Stiles","doi":"","DOIUrl":"","url":null,"abstract":"More than half a century after the discovery of the molecular basis of Sickle Cell Disease (SCD), the causes of the phenotypic heterogeneity of the disease remain unclear. This heterogeneity manifests with different clinical outcomes such as stroke, vaso-occlusive episodes, acute chest syndrome, avascular necrosis, leg ulcers, priapism and retinopathy. These outcomes cannot be explained by the single mutation in the beta-globin gene alone but may be attributed to genetic modifiers and environmental effects. Recent advances in the post human genome sequence era have opened the door for the identification of novel genetic modifiers in SCD. Studies are showing that phenotypes of SCD seem to be modulated by polymorphisms in genes that are involved in inflammation, cell-cell interaction and modulators of oxidant injury and nitric oxide biology. The discovery of genes implicated in different phenotypes will help understanding of the physiopathology of the disease and aid in establishing targeted cures. However, caution is needed in asserting that genetic modifiers are the cause of all SCD phenotypes, because there are other factors such as genetic background of the population, environmental components, socio-economics and psychology that can play significant roles in the clinical heterogeneity.","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"2009 2","pages":"23-48"},"PeriodicalIF":0.0,"publicationDate":"2009-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28931289","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

Gene Expression Analysis of Four Radiation-resistant Bacteria. 四种抗辐射细菌的基因表达分析。

Genomics insights Pub Date : 2009-06-16 eCollection Date: 2009-01-01 DOI: 10.4137/gei.s2380

Na Gao, Bin-Guang Ma, Yu-Sheng Zhang, Qin Song, Ling-Ling Chen, Hong-Yu Zhang

{"title":"Gene Expression Analysis of Four Radiation-resistant Bacteria.","authors":"Na Gao, Bin-Guang Ma, Yu-Sheng Zhang, Qin Song, Ling-Ling Chen, Hong-Yu Zhang","doi":"10.4137/gei.s2380","DOIUrl":"https://doi.org/10.4137/gei.s2380","url":null,"abstract":"To investigate the general radiation-resistant mechanisms of bacteria, bioinformatic method was employed to predict highly expressed genes for four radiation-resistant bacteria, i.e. Deinococcus geothermalis (D. geo), Deinococcus radiodurans (D. rad), Kineococcus radiotolerans (K. rad) and Rubrobacter xylanophilus (R. xyl). It is revealed that most of the three reference gene sets, i.e. ribosomal proteins, transcription factors and major chaperones, are generally highly expressed in the four bacteria. Recombinase A (recA), a key enzyme in recombinational repair, is predicted to be highly or marginally highly expressed in the four bacteria. However, most proteins associated with other repair systems show low expression levels. Some genes participating in 'information storage and processing,' 'cellular processes and signaling' and 'metabolism' are among the top twenty predicted highly expressed (PHX) genes in the four genomes. Many antioxidant enzymes and proteases are commonly highly expressed in the four bacteria, indicating that these enzymes play important roles in resisting irradiation. Finally, a number of 'hypothetical genes' are among the top twenty PHX genes in each genome, some of them might contribute vitally to resist irradiation. Some of the prediction results are supported by experimental evidence. All the above information not only helps to understand the radiation-resistant mechanisms but also provides clues for identifying new radiation-resistant genes from these bacteria. ","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"2 ","pages":"11-22"},"PeriodicalIF":0.0,"publicationDate":"2009-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/gei.s2380","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34066532","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: 10

Low Serum Alpha-Antitrypsin Associated with Anti-PR-3 ANCA in Autistic Children with GI Disease. 患有消化道疾病的自闭症儿童血清α-抗胰蛋白酶低与抗PR-3 ANCA相关。

Genomics insights Pub Date : 2009-06-04 eCollection Date: 2009-01-01 DOI: 10.4137/gei.s2918

A J Russo, A Krigsman, B Jepson, Andrew Wakefield

{"title":"Low Serum Alpha-Antitrypsin Associated with Anti-PR-3 ANCA in Autistic Children with GI Disease.","authors":"A J Russo, A Krigsman, B Jepson, Andrew Wakefield","doi":"10.4137/gei.s2918","DOIUrl":"10.4137/gei.s2918","url":null,"abstract":"Aim: To assess the possible relationship between serum alpha-1 antitrypsin (AAT) levels and anti-neutrophil cytoplasmic antibodies (ANCA) in autistic children with severe GI disease and to test the hypothesis that there is an association between low serum AAT levels, the presence of ANCA and inflammatory GI disease seen in some autistic children.Subjects and methods: Serum from 40 autistic children with chronic digestive disease (many with ileo-colonic lymphoid nodular hyperplasia (LNH) and inflammation of the colorectum, small bowel and/or stomach), and 41 controls (21 age matched autistic children with no GI disease and 20 age matched children without autism or GI disease) were tested using ELISAs designed to quantitate ANCA (anti-PR3), AAT and PR3 levels.Results: We found that a significant number of autistic children with chronic digestive disease had anti-PR3 ANCA, high serum PR3 and high severity of disease when compared to controls. This same group of autistic children had low serum levels of AAT compared to controls, which also correlated with the presence of anti-PR3 ANCA, high serum PR3, as well as the severity of intestinal disease, particularly LNH and severe erythema.Discussion: These results suggest a relationship between low AAT levels, ANCA and severity of GI disease seen in a subpopulation of ASD individuals. We suggest that low AAT levels may result in high levels of PR3, which may, in turn be associated with the presence of ANCA.","PeriodicalId":88494,"journal":{"name":"Genomics insights","volume":"2 ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2009-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34066531","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