The open genomics journal最新文献

{"title":"Drosophila Orthologs, Expressed Specifically in Courting Zebra Finch Males, are Engaged in Courtship","authors":"Z. Villányi, Antal Mai, J. Szabad","doi":"10.2174/1875693X20131205002","DOIUrl":"https://doi.org/10.2174/1875693X20131205002","url":null,"abstract":"The comparison of transcriptomes generated from the brains of courting and caring zebra finch males revealed the excessive expression of seven genes in the courting males. Two of the encoded proteins (APPBP2 and CST3) appear to share function with the Amyloid Precursor Protein (APP), and two (ARL2 and GPM6A) are engaged in neurogenesis. The LOC100228889 gene is expressed in the brain, DLEC1 is a tumor suppressor gene, and UBE2O encodes a ubiquitin- conjugating enzyme. Five out of the seven genes - ARL2, CST3, GPM6A, APPBP2, and UBE2O - have Drosophila orthologs: Arf84F, Cys, M6, Pat1, and CG10254, respectively. We RNAi-silenced the function of Arf84F, Cys, M6, and Pat1- and also that of the APP homolog DmelAppl - in the nervous system of elav-Gal4; UAS-RNAi Drosophila males revealed that while their courting activities were severely reduced, the locomotor abilities and functions of the sensory system were not affected. It appears that the genes above represent evolutionally conserved gene functions in courtship.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"234 1","pages":"8-15"},"PeriodicalIF":0.0,"publicationDate":"2013-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68123434","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}

{"title":"Conserved Sequences and Secondary RNA Structures Confirm That H19 Functions as a Pri-miRNA and as an RNA-binding Protein Platform","authors":"E. Devor, Jillian N. De Mik, B. Schickling","doi":"10.2174/1875693X20130703001","DOIUrl":"https://doi.org/10.2174/1875693X20130703001","url":null,"abstract":"The imprinted non-coding RNA H19 was discovered nearly thirty years ago yet, to date, its function has not been ascertained. Recently, H19 has been shown to be the primary transcript of the microRNA miR-675. Both H19 and miR-675 are known to be highly expressed in early fetal development and in an array of solid tumors in humans. We ex- amined H19 sequence and secondary RNA structure in the context of therian evolution to begin to understand the rela- tionship between H19, miR-675, development and oncogenesis. Both H19 sequence and, to a somewhat greater extent, secondary RNA structure is conserved, particularly among eutherians. The pattern of secondary RNA structure conserva- tion in which not only is pre-miR-675 highly conserved but also a number of other, smaller hairpins and a stable fold, coupled with the presence several conserved poly-pyrimidine tracts that are putative binding sites for the RNA-binding protein IMP1, suggests that H19 has two functions compatible with a non-coding RNA. The first is as pri-miR-675 and the second is as a stable docking platform for a regulatory RNP composed of the 3' half of the H19 transcript and up to four molecules of IMP1.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"6 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2013-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68123424","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}

{"title":"Primary Lens Luxation in Australian Tenterfield and Miniature Bull Terriers is due to an old ADAMTS17 mutation and is an additive trait","authors":"P. Gharahkhani, C. O'Leary, D. Duffy, M. Bernays, M. Kyaw-Tanner","doi":"10.2174/1875693X01205010007","DOIUrl":"https://doi.org/10.2174/1875693X01205010007","url":null,"abstract":"Primary Lens Luxation (PLL) is an inherited disease common in Terrier breeds. A truncating mutation in the ADAMTS17 orthologue on CFA03 is reported to cause PLL in 17 breeds, mostly Terriers. This study investigated the mode of inheritance and penetrance of PLL, age of the ADAMTS17 mutation, and other possible causes of PLL in Australian Tenterfield Terriers and Miniature Bull Terriers. The ADAMTS17 mutation and 30 nearby microsatellites on CFA03 were genotyped in 66 Australian Tenterfield Terriers, and 74 Miniature Bull Terriers. Lifetime risk of developing clinical PLL in homozygote and heterozygous animals, penetrance of PLL in general population, and recurrence risk of the disease for offspring and siblings of an index case was estimated. The effect of the ADAMTS17 mutation on the risk of PLL was dose and age dependent, and best fitted an additive model. Primary lens luxation was fully penetrant in homozygotes over 6 years and incompletely penetrant with a significant risk of PLL in heterozygote animals. Microsatellite haplotype testing estimated the mutation to be an old mutation, consistent with its appearance on several different background haplotypes and suggesting it entered the tested Tenterfield Terrier population at least three times, and the tested Miniature Bull Terrier population once. Finite polygenic model and survival analyses suggested that the ADAMTS17 mutation is the main cause of PLL in these breeds, and if the PLL phenotype is controlled by factors other than this mutation, such as a second locus or an environmental effect, the effect is much less than that of this disease associated SNP.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"5 1","pages":"7-13"},"PeriodicalIF":0.0,"publicationDate":"2012-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68123245","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}

{"title":"Letter: High-level of Heteroplasmy in the Mitochondrial Cox1-Minichromosome of the Human Body Louse, Pediculus humanus, and the Human Head Louse, Pediculus capitis","authors":"Kate E. Herd, S. Barker, R. Shao","doi":"10.2174/1875693X01205010014","DOIUrl":"https://doi.org/10.2174/1875693X01205010014","url":null,"abstract":"The mitochondrial (mt) genome of bilateral animals typically consists of a single chromosome, ~16 kb long, and contains 37 genes. Variation in mt gene sequence within an individual, i.e. heteroplasmy, is common in bilateral animals but usually occurs at very low levels. In the lineage that led to the human body louse, the typical mt chromosome has fragmented into 18 minichromosomes: each minichromosome is 3 to 4 kb long and contains 1 to 3 genes and a non- coding region. To understand the presence and the level of heteroplasmy in fragmented mt genomes, we cloned and sequenced seven copies of full-length cox1-minichromosome of a human body louse and a human head louse. We found 17 heteroplasmic sites in the coding region and 118 heteroplasmic sites in the non-coding region of the cox1- minichromosome. The level of heteroplasmy in the human lice appears to be much higher than that in other animals that have the typical mt genome. We propose that recombination between different minichromosomes of the fragmented mt genome may contribute to the high-level of heteroplasmy in the human lice.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"5 1","pages":"14-17"},"PeriodicalIF":0.0,"publicationDate":"2012-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68123293","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}

{"title":"Repeated Template Switching: Obstacles in cDNA Libraries and Ways to Avoid Them","authors":"Z. Villányi, Antal Mai, J. Szabad","doi":"10.2174/1875693X01205010001","DOIUrl":"https://doi.org/10.2174/1875693X01205010001","url":null,"abstract":"We screened zebra finch cDNA libraries with the plaque-based competitive hybridization technique for genes differentially expressed in the brains of courting and non-courting males. The cDNA libraries were generated by the SMART TM cDNA Library Construction Kit. Sixty-six percent (35/53) of the isolated clones possessed high homology to sequences present in the cDNA libraries of species ranging from Arabidopsis to humans. The clones had to be false positives since the corresponding sequences are absent in genomic libraries. The false positive clones were tandem repeats of different lengths of the SMART IV TM oligonucleotide and originated through repeated template switching during reverse transcription. We report here based on in silico data that multiple template switching and subsequent repeated incorporation of primers at 3`end of first strand cDNA is a common event during the generation of cDNA libraries created by the template switching strategy. We demonstrate that the repeat containing clones disturbs hybridization procedures aimed to identify differentially expressed genes. We propose an additional hybridization step with repeat containing clones to avoid the identification of false positives, and recommend the use of switch primers without palindrome sequences to avoid the formation of tandem repeats during cDNA library construction.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"5 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2012-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68123236","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}

{"title":"An In-Solution Hybridisation Method for the Isolation of Pathogen DNA from Human DNA-rich Clinical Samples for Analysis by NGS.","authors":"Miriam Smith, Susana Campino, Yong Gu, Taane G Clark, Thomas D Otto, Gareth Maslen, Magnus Manske, Mallika Imwong, Arjen M Dondorp, Dominic P Kwiatkowski, Michael A Quail, Harold Swerdlow","doi":"10.2174/1875693X01205010018","DOIUrl":"10.2174/1875693X01205010018","url":null,"abstract":"<p><p>Studies on DNA from pathogenic organisms, within clinical samples, are often complicated by the presence of large amounts of host, e.g., human DNA. Isolation of pathogen DNA from these samples would improve the efficiency of next-generation sequencing (NGS) and pathogen identification. Here we describe a solution-based hybridisation method for isolation of pathogen DNA from a mixed population. This straightforward and inexpensive technique uses probes made from whole-genome DNA and off-the-shelf reagents. In this study, <i>Escherichia coli</i> DNA was successfully enriched from a mixture of <i>E.coli</i> and human DNA. After enrichment, genome coverage following NGS was significantly higher and the evenness of coverage and GC content were unaffected. This technique was also applied to samples containing a mixture of human and <i>Plasmodium falciparum</i> DNA. The <i>P.falciparum</i> genome is particularly difficult to sequence due to its high AT content (80.6%) and repetitive nature. Post enrichment, a bias in the recovered DNA was observed, with a poorer representation of the AT-rich non-coding regions. This uneven coverage was also observed in pre-enrichment samples, but to a lesser degree. Despite the coverage bias in enriched samples, SNP (single-nucleotide polymorphism) calling in coding regions was unaffected and the majority of samples had over 90% of their coding region covered at 5× depth. This technique shows significant promise as an effective method to enrich pathogen DNA from samples with heavy human contamination, particularly when applied to GC-neutral genomes.</p>","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"5 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837216/pdf/emss-54177.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31899421","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}

{"title":"LETTER TO THE EDITOR The Mysterious Case of the Reverse Sequences","authors":"G. Gutiérrez","doi":"10.2174/1875693X01104010016","DOIUrl":"https://doi.org/10.2174/1875693X01104010016","url":null,"abstract":"I would like you to do a little experiment with me. Let’s suppose we get a bacterial SSU rRNA and we blast it at the NCBI [1]. The result we get is obvious: a large number of homologous sequences of many bacteria. Now let's do something else, we are going to reverse the same sequence. It is easy to do with the EMBOSS program Revseq [2]. The reverse sequence is written in the direction 3'-5'. For example 5’AGTC3’ becomes 3’CTGA5’. If we blast with the reverse sequence, what would we get? The answer is nothing. We should not get any significant result because the reverse sequence is meaningless, sequences are always written in the 5 '-3' direction in the databases. Well, have you already done the blast with the reverse sequence? You are surprised because there are significant results! How is it possible? By this method I have detected more than 300 SSU rRNA reversed sequences in the NCBI non-redundant nucleotide database (Table 1). I think researchers who sent the sequences were wrong and sent the sequences in 3'-5' direction, but why? One explanation is that people make mistakes. The rRNA sequences are commonly used in identification and phylogeny of species. It is unavoidable, If you do one thing many times, sooner or later you make a mistake. This may explain the abundance but not why people makes mistakes. I want to propose two explanations that are not mutually exclusive. The first one says that it depends on the language of the researcher who submitted the sequence to the database. Genetics was developed in western culture, where texts are read and written horizontally left-to-right (LFT), for that reason we write DNA sequences in the 5’-3’ direction, the 5’ end on the left, the 3’ end on the right. Some oriental languages are written right-to-left (RTL). Muslims and jews write horizontally in the RTL direction. The chinese and japanese write top-to-bottom (TTB) but they can both read the columns LFT or RTL. My guess is that researchers who mother-tongue is not LFT use RTL and/or TTB text editors that change the direction of the sequences. Table 1 shows the places of origin of the sequences, 57% of them belong to non-LFT countries. I have not included the sequences from","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"4 1","pages":"16-17"},"PeriodicalIF":0.0,"publicationDate":"2011-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68123200","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}

{"title":"Sensitivity Analysis of Protein Role Prediction Methods: Which are the Relevant Data?","authors":"L. López-Kleine, A. Trubuil, V. Monnet","doi":"10.2174/1875693X01104010001","DOIUrl":"https://doi.org/10.2174/1875693X01104010001","url":null,"abstract":"Genome sequencing has allowed the generation of genomic and high-throughput post-genomic data. The avail- ability of huge amounts of this data has, in turn, led to the development of protein role inference methods. Some of these methods allow the use of heterogeneous data of varying quality which are more or less informative. However, only limited research has been devoted to finding relevant data in terms of the inference of protein roles. In this study, we identified relevant subsets of data for the prediction of protein roles within the framework of a kernel method (KCCA) used to pre- dict the role of a bacterial protein. We carried out a sensitivity analysis based on a fractional factorial design in order to study the influence of different microarray experiments, as well as of bacterial orders (groups of families) used to con- struct the phylogenetic profiles, on the prediction of a protein role. The results of this analysis showed to be useful for in- terpreting biological predictions highlighting specific data that should be investigated. The method is not restricted to KCCA, nor to the organism or to the data we used here.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"4 1","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2011-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68123143","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}

{"title":"Proceedings of the First Study Day on 4q Deletion Syndrome in Coventry, United Kingdom","authors":"P. Middlemiss, E. Strehle, D. Gurudutt, S. Wynn, B. Searle","doi":"10.2174/1875693X01104010010","DOIUrl":"https://doi.org/10.2174/1875693X01104010010","url":null,"abstract":"q deletions are rare chromosome disorders (RCD), with an estimated incidence of 1:50,000-100,000 that is rising as a result of routine introduction of chromosomal microarray testing. The diagnosis of a 4q deletion, as of any RCD, confers a sense of exclusion, isolation and guilt on families with an affected child. Reliable information available to a lay audience is scant. To address these issues, Unique, the Rare Chromosome Disorder Support Group, hosted the first international meeting on 4q deletions. Families valued the opportunity to meet genetics and medical professionals with an interest in 4q deletions and to exchange information with each other. In this paper, we intend to summarize all the information presented in this study meeting.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"57 1","pages":"10-15"},"PeriodicalIF":0.0,"publicationDate":"2011-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68123187","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}

{"title":"Genome Organization of the Three Identical ATP1 Genes on the Left Arm of Chromosome II of Saccharomyces cerevisiae: Sequence Analysis of the 35-kb Region Containing Three ATP1 Genes","authors":"M. Takeda, Shohei Nakamura, S. Matsushita","doi":"10.2174/1875693X01003010009","DOIUrl":"https://doi.org/10.2174/1875693X01003010009","url":null,"abstract":"The ATP1 gene (YBL099w) encoding the F1F0-ATPase complex  subunit of Saccharomyces cerevisiae is present on the left arm close to the telomere of chromosome II, and only one copy was reported by the Genome Project. Recently, we reported that three ATP1s designated ATP1a, ATP1b and ATP1c are located on chromosome II, with different distances between ATP1a and ATP1b, and ATP1b and ATP1c as identified previously. To elucidate the ATP1 repetition and their junction sites, we report here the complete nucleotide sequence of this region (approximately 35 kb) on the left arm of chromosome II in Saccharomyces cerevisiae using the prime clones 70113 and 70804 from ATCC, and genomic DNAs from various yeast strains S288C, DC5, W303-1A and those of the gene copy-specific ATP1-disruptants. The nucleotide sequences of the three ATP1s were identical, and they were repeated along with differing amounts of neighboring DNA sequences. The nucleotide sequence of the ATP1 repeat region has been deposited to DDBJ (AB304259, 20070511181828.08607). Keyword: ATP1, Nucleotide sequence, Repetitive genes, Junction, Saccharomyces cerevisiae.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"3 1","pages":"9-17"},"PeriodicalIF":0.0,"publicationDate":"2010-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68123131","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}