The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine-guanine dinucleotides, DNA methylation ...is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of such methylation variable positions will significantly improve our understanding of genome biology and our ability to diagnose disease. Here, we report the results of the pilot study for the Human Epigenome Project entailing the methylation analysis of the human major histocompatibility complex. This study involved the development of an integrated pipeline for high-throughput methylation analysis using bisulphite DNA sequencing, discovery of methylation variable positions, epigenotyping by matrix-assisted laser desorption/ionisation mass spectrometry, and development of an integrated public database available at http://www.epigenome.org. Our analysis of DNA methylation levels within the major histocompatibility complex, including regulatory exonic and intronic regions associated with 90 genes in multiple tissues and individuals, reveals a bimodal distribution of methylation profiles (i.e., the vast majority of the analysed regions were either hypo- or hypermethylated), tissue specificity, inter-individual variation, and correlation with independent gene expression data.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Human cancers often carry many somatically acquired genomic rearrangements, some of which may be implicated in cancer development. However, conventional strategies for characterizing rearrangements ...are laborious and low-throughput and have low sensitivity or poor resolution. We used massively parallel sequencing to generate sequence reads from both ends of short DNA fragments derived from the genomes of two individuals with lung cancer. By investigating read pairs that did not align correctly with respect to each other on the reference human genome, we characterized 306 germline structural variants and 103 somatic rearrangements to the base-pair level of resolution. The patterns of germline and somatic rearrangement were markedly different. Many somatic rearrangements were from amplicons, although rearrangements outside these regions, notably including tandem duplications, were also observed. Some somatic rearrangements led to abnormal transcripts, including two from internal tandem duplications and two fusion transcripts created by interchromosomal rearrangements. Germline variants were predominantly mediated by retrotransposition, often involving AluY and LINE elements. The results demonstrate the feasibility of systematic, genome-wide characterization of rearrangements in complex human cancer genomes, raising the prospect of a new harvest of genes associated with cancer using this strategy.
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Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (approximately 2.5 million hits) per week, ...providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species.
A new method of silicon surface texturing is reported, which is based on thin silica layer electrochemical reduction in molten salts. A thermal silica layer grown on p-type silicon was ...potentiostatically reduced in molten calcium chloride at 850
°C. Typical nano–micro-formations obtained at different stages of electrolysis were demonstrated by SEM. X-ray diffraction measurements confirmed conversion of the amorphous thermal silica layer into crystalline silicon. The proposed approach shows promise in photovoltaic applications, for instance, for production of antireflection coatings in silicon solar cells.
A population of 16,235 children aged 18 months was screened using the Checklist for Autism in Toddlers (CHAT) to identify childhood autism (CA). Two further screening procedures were conducted at age ...3 and 5 years. The population was followed up at age 7 years in order to establish the sensitivity, specificity, and positive predictive value of the instrument.
A brief checklist assessing joint attention and pretend play behaviors was administered by primary health care practitioners when the children were 18 months old. Follow-up methods included screening through parents and health practitioners and checking medical and educational records.
Nineteen cases of CA were successfully identified by the CHAT at 18 months. At follow-up a total of 50 cases of CA were identified via all surveillance methods. Thus, the CHAT has a sensitivity of 38% and a specificity of 98% for identifying CA. The positive predictive value of the instrument was maximized by concentration on the highest-risk group. Repeated screening 1 month later increased the positive predictive value to 75% for identification of CA but reduced the sensitivity to 20%, although the specificity was close to 100%. The screen also identified cases of pervasive developmental disorder as well as children with language and other developmental disorders.
The CHAT can be used to identify cases of autism and related pervasive developmental disorders at 18 months of age. It is emphasized that the CHAT is not a diagnostic instrument but can identify potential cases of autism spectrum disorders for a full diagnostic assessment.
Phylogenetic relationships in the genus Nicotiana were investigated using parsimony analyses of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrDNA). In addition, origins of ...some amphidiploid taxa in Nicotiana were investigated using the techniques of genomic in situ hybridization (GISH), and the results of both sets of analyses were used to evaluate previous hypotheses about the origins of these taxa. Phylogenetic analyses of the ITS nrDNA data were performed on the entire genus (66 of 77 naturally occurring species, plus three artificial hybrids), comprising both diploid and polyploid taxa, and on the diploid taxa only (35 species) to examine the effects of amphidiploids on estimates of relationships. All taxa, regardless of ploidy, produced clean, single copies of the ITS region, even though some taxa are hybrids. Results are compared with a published plastid (matK) phylogeny using fewer, but many of the same, taxa. The patterns of relationships in Nicotiana, as seen in both analyses, are largely congruent with each other and previous evolutionary ideas based on morphology and cytology, but some important differences are apparent. None of the currently recognized subgenera of Nicotiana is monophyletic and, although most of the currently recognized sections are coherent, others are clearly polyphyletic. Relying solely upon ITS nrDNA analysis to reveal phylogenetic patterns in a complex genus such as Nicotiana is insufficient, and it is clear that conventional analysis of single data sets, such as ITS, is likely to be misleading in at least some respects about evolutionary history. ITS sequences of natural and well‐documented amphidiploids are similar or identical to one of their two parents—usually, but not always, the maternal parent—and are not in any sense themselves ‘hybrid’. Knowing how ITS evolves in artificial amphidiploids gives insight into what ITS analysis might reveal about naturally occurring amphidiploids of unknown origin, and it is in this perspective that analysis of ITS sequences is highly informative.
Various theoretical accounts propose that an important developmental relation exists between joint attention, play, and imitation abilities, and later theory of mind ability. However, very little ...direct empirical evidence supports these claims for putative “precursor” theory of mind status. A small sample (
N=13) of infants, for whom measures of play, joint attention, and imitation had been collected at 20 months of age, was followed-up longitudinally at 44 months and a battery of theory of mind measures was conducted. Language and IQ were measured at both timepoints. Imitation ability at 20 months was longitudinally associated with expressive, but not receptive, language ability at 44 months. In contrast, only the joint attention behaviours of gaze switches between an adult and an active toy and looking to an adult during an ambiguous goal detection task at 20 months were longitudinally associated with theory of mind ability at 44 months. It is argued that joint attention, play, and imitation, and language and theory of mind, might form part of a shared social–communicative representational system in infancy that becomes increasingly specialised and differentiated as development progresses.
Gene trapping is a method of generating murine embryonic stem (ES) cell lines containing insertional mutations in known and novel genes. A number of international groups have used this approach to ...create sizeable public cell line repositories available to the scientific community for the generation of mutant mouse strains. The major gene trapping groups worldwide have recently joined together to centralize access to all publicly available gene trap lines by developing a user-oriented Website for the International Gene Trap Consortium (IGTC). This collaboration provides an impressive public informatics resource comprising ∼45 000 well-characterized ES cell lines which currently represent ∼40% of known mouse genes, all freely available for the creation of knockout mice on a non-collaborative basis. To standardize annotation and provide high confidence data for gene trap lines, a rigorous identification and annotation pipeline has been developed combining genomic localization and transcript alignment of gene trap sequence tags to identify trapped loci. This information is stored in a new bioinformatics database accessible through the IGTC Website interface. The IGTC Website (www.genetrap.org) allows users to browse and search the database for trapped genes, BLAST sequences against gene trap sequence tags, and view trapped genes within biological pathways. In addition, IGTC data have been integrated into major genome browsers and bioinformatics sites to provide users with outside portals for viewing this data. The development of the IGTC Website marks a major advance by providing the research community with the data and tools necessary to effectively use public gene trap resources for the large-scale characterization of mammalian gene function.
The association between, and stability of, clinical diagnosis and diagnosis derived
from the Autism Diagnostic Interview-Revised (ADI-R; Lord, Rutter, & Le Couteur, 1994) was
examined in a sample of ...prospectively identified children with childhood autism and other
pervasive developmental disorders assessed at the age of 20 months and 42 months. Clinical
diagnosis of autism was stable, with all children diagnosed with childhood autism at age 20
months receiving a diagnosis of childhood autism or a related pervasive developmental
disorder (PDD) at age 42 months. Clinical diagnosis of childhood autism was also
reasonably sensitive, with all children who went on to receive a clinical diagnosis of
childhood autism at 42 months being identified as having autism or PDD at 20 months.
However, clinical diagnosis for PDD and Asperger's syndrome lacked sensitivity at 20
months, with several children who subsequently received these diagnoses at 42 months
receiving diagnoses of language disorder or general developmental delay, as well as in two
cases being considered clinically normal, at the earlier timepoint. The ADI-R was found to
have good specificity but poor sensitivity at detecting childhood autism at 20 months;
however, the stability of diagnosis from 20 to 42 months was good. In addition, the ADI-R
at age 20 months was not sensitive to the detection of related PDDs or Asperger's syndrome.
The continuity and discontinuity between behavioural abnormalities identified at both
timepoints in the three domains of impairment in autism was examined, both in children who
met final clinical criteria for an autistic spectrum disorder, and for children with language
disorder who did not, as well as for a small sample of typically developing children.
Investigation to see if there are key psychological risk indicators for autism in a random population study of children at 18 months of age; and to assess how well these discriminate children who ...receive a diagnosis of autism from other forms of developmental delay.
Sixteen thousand children in the southeast of England were screened for autism by their health visitor or GP, during their routine 18-month-old developmental check-up, using the CHAT (Checklist for Autism in Toddlers). From a previous high-risk study we predicted that children at 18 months of age who failed three items ('protodeclarative pointing', 'gaze-monitoring', and 'pretend play') would be at risk for receiving a diagnosis of autism. From other evidence, we further predicted that those 18-month-olds who failed one or two of the key items (either pretend play, or protodeclarative pointing and pretend play) would be at risk for developmental delay without autism.
Twelve children out of the total population of 16,000 consistently failed the three key items. Of these, 10 (83.3%) received a diagnosis of autism. Thus, the false positive rate was 16.6% (2 out of 12 cases), and even these 2 cases were not normal. When the 10 children with autism were reassessed at 3.5 years of age, their diagnosis remained the same. Thus the false positive rate among the cases diagnosed with autism was zero. In contrast, of 22 children who consistently failed either protodeclarative pointing and/or pretend play, none received a diagnosis of autism, but 15 (68.2%) received a diagnosis of language delay.
Consistent failure of the three key items from the CHAT at 18 months of age carries an 83.3% risk of autism; and this pattern of risk indicator is specific to autism when compared to other forms of developmental delay.
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