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At least 757 records · Page 42Linked to original sources

PubMed2002

Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns.

All protein sequences from 19 complete chloroplast genomes (cpDNA) have been studied using a new computational method able to analyze functional correlations among series of protein sequences contained in complete proteomes. First, all open reading frames (ORFs) from the cpDNAs, comprising a total of 2266 protein sequences, were compared against the 3168 proteins from Synechocystis PCC6803 complete genome to find functionally related orthologous proteins. Additionally, all cpDNA genomes were pairwise compared to find orthologous groups not present in cyanobacteria. Annotations in the cluster of othologous proteins database and CyanoBase were used as reference for the functional assignments. Following this protocol, new functional assignments were made for ORFs of unknown function and for ycfs (hypothetical chloroplast frames), which still lack a functional assignment. Using this information, a matrix of functional relationships was derived from profiles of the presence and/or absence of orthologous proteins; the matrix included 1837 proteins in 277 orthologous clusters. A factor analysis study of this matrix, followed by cluster analysis, allowed us to obtain accurate phylogenetic reconstructions and the detection of genes probably involved in speciation as phylogenetic correlates. Finally, by grouping common evolutionary patterns, we show that it is possible to determine functionally linked protein networks. This has allowed us to suggest putative associations for some unknown ORFs.

Bacterial Proteins↗

PubMed2003

The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

Gene Ontology Annotation (GOA) is a project run by the European Bioinformatics Institute (EBI) that aims to provide assignments of terms from the Gene Ontology (GO) resource to gene products in a number of its databases (http://www.ebi.ac.uk/GOA). In the first stage of this project, GO assignments have been applied to a data set representing the complete human proteome by a combination of electronic mappings and manual curation. This vocabulary has also been applied to the nonredundant proteome sets for all other completely sequenced organisms as well as to proteins from a wide range of organisms where the proteome is not yet complete.

Computational Biology↗

PubMed2006

Iterative gene prediction and pseudogene removal improves genome annotation.

Correct gene prediction is impaired by the presence of processed pseudogenes: nonfunctional, intronless copies of real genes found elsewhere in the genome. Gene prediction programs frequently mistake processed pseudogenes for real genes or exons, leading to biologically irrelevant gene predictions. While methods exist to identify processed pseudogenes in genomes, no attempt has been made to integrate pseudogene removal with gene prediction, or even to provide a freestanding tool that identifies such erroneous gene predictions. We have created PPFINDER (for Processed Pseudogene finder), a program that integrates several methods of processed pseudogene finding in mammalian gene annotations. We used PPFINDER to remove pseudogenes from N-SCAN gene predictions, and show that gene prediction improves substantially when gene prediction and pseudogene masking are interleaved. In addition, we used PPFINDER with gene predictions as a parent database, eliminating the need for libraries of known genes. This allows us to run the gene prediction/PPFINDER procedure on newly sequenced genomes for which few genes are known.

Animals↗

PubMed2006

Gene discovery and annotation using LCM-454 transcriptome sequencing.

454 DNA sequencing technology achieves significant throughput relative to traditional approaches. More than 261,000 ESTs were generated by 454 Life Sciences from cDNA isolated using laser capture microdissection (LCM) from the developmentally important shoot apical meristem (SAM) of maize (Zea mays L.). This single sequencing run annotated >25,000 maize genomic sequences and also captured approximately 400 expressed transcripts for which homologous sequences have not yet been identified in other species. Approximately 70% of the ESTs generated in this study had not been captured during a previous EST project conducted using a cDNA library constructed from hand-dissected apex tissue that is highly enriched for SAMs. In addition, at least 30% of the 454-ESTs do not align to any of the approximately 648,000 extant maize ESTs using conservative alignment criteria. These results indicate that the combination of LCM and the deep sequencing possible with 454 technology enriches for SAM transcripts not present in current EST collections. RT-PCR was used to validate the expression of 27 genes whose expression had been detected in the SAM via LCM-454 technology, but that lacked orthologs in GenBank. Significantly, transcripts from approximately 74% (20/27) of these validated SAM-expressed "orphans" were not detected in meristem-rich immature ears. We conclude that the coupling of LCM and 454 sequencing technologies facilitates the discovery of rare, possibly cell-type-specific transcripts.

Base Sequence↗

PubMed2002

Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee.

To accelerate the molecular analysis of behavior in the honey bee (Apis mellifera), we created expressed sequence tag (EST) and cDNA microarray resources for the bee brain. Over 20,000 cDNA clones were partially sequenced from a normalized (and subsequently subtracted) library generated from adult A. mellifera brains. These sequences were processed to identify 15,311 high-quality ESTs representing 8912 putative transcripts. Putative transcripts were functionally annotated (using the Gene Ontology classification system) based on matching gene sequences in Drosophila melanogaster. The brain ESTs represent a broad range of molecular functions and biological processes, with neurobiological classifications particularly well represented. Roughly half of Drosophila genes currently implicated in synaptic transmission and/or behavior are represented in the Apis EST set. Of Apis sequences with open reading frames of at least 450 bp, 24% are highly diverged with no matches to known protein sequences. Additionally, over 100 Apis transcript sequences conserved with other organisms appear to have been lost from the Drosophila genome. DNA microarrays were fabricated with over 7000 EST cDNA clones putatively representing different transcripts. Using probe derived from single bee brain mRNA, microarrays detected gene expression for 90% of Apis cDNAs two standard deviations greater than exogenous control cDNAs. [The sequence data described in this paper have been submitted to Genbank data library under accession nos. BI502708-BI517278. The sequences are also available at http://titan.biotec.uiuc.edu/bee/honeybee_project.htm.]

Animals↗

PubMed2003

GALA, a database for genomic sequence alignments and annotations.

We have developed a relational database to contain whole genome sequence alignments between human and mouse with extensive annotations of the human sequence. Complex queries are supported on recorded features, both directly and on proximity among them. Searches can reveal a wide variety of relationships, such as finding all genes expressed in a designated tissue that have a highly conserved noncoding sequence 5' to the start site. Other examples are finding single nucleotide polymorphisms that occur in conserved noncoding regions upstream of genes and identifying CpG islands that overlap the 5' ends of divergently transcribed genes. The database is available online at http://globin.cse.psu.edu/ and http://bio.cse.psu.edu/.

5' Untranslated Regions↗

PubMed2002

Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set.

A set of 7407 cDNA clones (NIA mouse 7.4K) was assembled from >20 cDNA libraries constructed mainly from early mouse embryos, including several stem cell libraries. The clone set was assembled from embryonic and newborn organ libraries consisting of ~120,000 cDNA clones, which were initially re-arrayed into a set of ~11,000 unique cDNA clones. A set of tubes was constructed from the racks in this set to prevent contamination and potential mishandling errors in all further re-arrays. Sequences from this set (11K) were analyzed further for quality and clone identity, and high-quality clones with verified identity were re-arrayed into the final set (7.4K). The set is freely available, and a corresponding database was built to provide comprehensive annotation for those clones with known identity or homology, and has been made available through an extensive Web site that includes many link-outs to external databases and analysis servers.

Animals↗

PubMed2003

Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping.

Expressed sequence tags (ESTs) currently encompass more entries in the public databases than any other form of sequence data. Thus, EST data sets provide a vast resource for gene identification and expression profiling. We have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring. About 96% of the available ESTs could be properly aligned with a genomic locus, with the remaining ESTs deriving from organelle genomes and non-Arabidopsis sources or displaying insufficient sequence quality for alignment. The mapping provides verified sets of EST clusters for evaluation of EST clustering programs. Analysis of the spliced alignments suggests corrections to current gene structure annotation and provides examples of alternative and non-canonical pre-mRNA splicing. All results of this study were parsed into a database and are accessible via a flexible Web interface at http://www.plantgdb.org/AtGDB/.

Alternative Splicing↗

PubMed2005

Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists.

We introduce a tool for text mining, Dragon Plant Biology Explorer (DPBE) that integrates information on Arabidopsis (Arabidopsis thaliana) genes with their functions, based on gene ontologies and biochemical entity vocabularies, and presents the associations as interactive networks. The associations are based on (1) user-provided PubMed abstracts; (2) a list of Arabidopsis genes compiled by The Arabidopsis Information Resource; (3) user-defined combinations of four vocabulary lists based on the ones developed by the general, plant, and Arabidopsis GO consortia; and (4) three lists developed here based on metabolic pathways, enzymes, and metabolites derived from AraCyc, BRENDA, and other metabolism databases. We demonstrate how various combinations can be applied to fields of (1) gene function and gene interaction analyses, (2) plant development, (3) biochemistry and metabolism, and (4) pharmacology of bioactive compounds. Furthermore, we show the suitability of DPBE for systems approaches by integration with "omics" platform outputs. Using a list of abiotic stress-related genes identified by microarray experiments, we show how this tool can be used to rapidly build an information base on the previously reported relationships. This tool complements the existing biological resources for systems biology by identifying potentially novel associations using text analysis between cellular entities based on genome annotation terms. Thus, it allows researchers to efficiently summarize existing information for a group of genes or pathways, so as to make better informed choices for designing validation experiments. Last, DPBE can be helpful for beginning researchers and graduate students to summarize vast information in an unfamiliar area. DPBE is freely available for academic and nonprofit users at http://research.i2r.a-star.edu.sg/DRAGON/ME2/.

Arabidopsis↗

PubMed2002

From information management to protein annotation: preparing protein structures for drug discovery.

In contrast to academic pursuits of structural genomics, Structural GenomiX (SGX) solves protein structures at high throughput for the main purpose of enhancing drug-discovery projects, either internally or in partnership with pharmaceutical/biotechnology companies. This involves a radical redesign of the pipeline of methods that turn a gene sequence into a three-dimensional protein structure. The various processes all report electronically to a Laboratory Information Management System (LIMS) to make sure all the parameters of the experiment are recorded in an accessible and 'mineable' form, helping guarantee reproducibility of results. Quality control at several key points keeps the process from branching out on a wrong hypothesis. Protein annotation, in a broad sense, takes care of the interpretation of a protein crystal structure or the crystal structure of one or several protein-ligand complexes. This interpretation both gathers all necessary biological information (protein function, mechanism, specific features within a protein family etc.) and hands over this information in a form accessible to medicinal chemistry teams designing specific small-molecule agonists or antagonists.

Crystallization↗

PubMed2002

Annotation: The 'effects' of parenting reconsidered: findings, challenges, and applications.

BACKGROUND: Questions remain concerning the 'effects' of parenting on behavioural/emotional problems in children. This annotation discusses recent findings concerning the parenting 'effects' literature and identifies areas in need of further research. METHOD: The review begins by examining theories and definitions of parenting, and then considers research findings on the predictors of parent-child relationships and their effects on behavioural/emotional adjustment in children. Evidence for causal processes are then examined in light of findings emphasizing the need to consider the impact of larger systems on child's well-being, bi-directional processes in parent-child interactions, and alternative hypotheses suggested by behavioural genetics. RESULTS: Different kinds of evidence suggest strong links between parent-child relationship quality and children's well-being, but difficulties remain for drawing causal connections. The need for greater integration among research traditions and the need for theory development are highlighted. In addition, although a substantial and robust research base exists on parent-child relationships, the applicability of these findings to clinical settings is uncertain. CONCLUSIONS: Substantial progress has been made in our understanding of the nature of parent-child relationships and their developmental effects, but a number of basic conceptual and methodological and clinical questions continue to need rigorous study.

Affective Symptoms↗

PubMed2002

Annotation: randomised trials.

BACKGROUND: This annotation describes the uses of randomised controlled trials (RCTs) in clinical child psychology and psychiatry. METHOD: It explores the scientific basis for randomised designs, the conceptual and methodological issues that can arise when using them, alternative methods, and future directions. RESULTS: There are many issues that have to be tackled when using randomised trials to answer questions about the effectiveness of interventions used by child mental health professionals. The most important are conceptual issues concerning the design of these studies, practical issues, and issues about the interpretation of the results. There are some situations in which randomised trials are not possible or ideal and alternative strategies may therefore be needed. Future RCTs should be more explicit about whether their primary purpose is to further scientific knowledge or to evaluate the benefit of a treatment in routine clinical practice. Future trials should also have outcomes of unequivocal significance and be reported in accordance with standardised guidelines. CONCLUSIONS: Well-designed and unambiguously reported RCTs usually provide the best possible evidence about the effectiveness of an intervention. RCTs are not, however, the only way of establishing cause and effect and their results should always be interpreted in the light of other evidence.

Humans↗

PubMed2001

Annotation: the cognitive neuroscience of face recognition: implications for developmental disorders.

Face recognition is often considered to be a modular (encapsulated) function. This annotation supports the proposal that faces are special, but suggests that their identification makes use of general-purpose cortical systems that are implicated in high-level vision and also in memory and learning more generally. These systems can be considered to function within two distinct cortical streams: a medial stream (for learning and salience of faces encountered) and a lateral stream (for distributed representations of visual properties and identities of faces). Function in the lateral stream, especially, may be critically dependent on the normal development of magnocellular vision. The relevance of face recognition anomalies in three developmental syndromes (Autism, Williams syndrome, and Turner syndrome) and the two-route model sketched above is considered.

Autistic Disorder↗

PubMed2005

Expressed sequence tags from the midgut and an epithelial cell line of Chironomus tentans: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels.

Expressed sequence tags (ESTs) were generated from two Chironomus tentans cDNA libraries, constructed from an embryo epithelial cell line and from larva midgut tissue. 8584 5'-end ESTs were generated and assembled into 3110 tentative unique transcripts, providing the largest contribution of C. tentans sequences to public databases to date. Annotation using Blast gave 1975 (63.5%) transcripts with a significant match in the major gene/protein databases, 1170 with a best match to Anopheles gambiae and 480 to Drosophila melanogaster. 1091 transcripts (35.1%) had no match to any database. Studies of open reading frames suggest that at least 323 of these contain a coding sequence, indicating that a large proportion of the genes in C. tentans belong to previously unknown gene families.

Animals↗

PubMedDate not supplied

An annotated historical account of canine parvovirus.

A brief annotated history of canine parvovirus-type 2 (CPV-2) and its variants is summarized with emphasis on the most significant contributions of individuals involved in the initial recognition of CPV-2 and subsequent discoveries that have advanced our knowledge of the nature and evolution of this novel canine virus. Time has obscured the observations of many veterinary clinicians and researchers throughout the world who sensed the presence of a new disease when CPV-2 first made its appearance in 1978 and then, within 1-2 years, spread worldwide. Since 1979, nearly 600 articles, papers, numerous text chapters and monographs have been published on the subject of CPV-2. The early history is well known by veterinary infectious diseases specialists and noteworthy publications are recorded on the National Library of Medicine (USA) website, PubMed and in review articles. Because of the great number of publications, it is not practicable to cite them individually; however, reference is made to certain individuals, reviews and selected papers that I consider particularly relevant to the history of progress in the understanding of CPV-2 and the disease it causes. The clinical disease caused by CPV-2 and its variants, the immune response to infection or vaccines, host range and the development of practical diagnostic assays are noted in historical context. The basic biological properties and the physical, molecular and antigenic structure of CPV-2 and its variants are also discussed briefly. Finally, key players who have contributed to the antigenic and DNA sequence (evolutionary) relationships between CPV-2 and the other autonomous parvoviruses of carnivores are noted and hypotheses regarding the origin and evolution of CPV-2 and its variants are mentioned.

Animals↗

PubMed1997

Annotation: on the grandmothers' role in the adjustment and maladjustment of grandchildren.

The present annotation explores the impact of grandmother involvement on their grandchildren's adjustment. A review of relevant research suggests that the impact of such involvement is conditional on a range of factors, including (a) the level of need experienced by the mother and child, (b) the mother-grandmother relationship history, (c) the developmental stage and life circumstances of the grandmother, (d) the levels of disagreement between mother and grandmother over child-related issues, and (e) the perceived appropriateness of involvement in cultural and interpersonal terms. Under most circumstances grandmother involvement is not a pre-requisite for grandchild adjustment. Where a genuine need for support exists and the support offered is tailored to meet that need, then grandmother involvement can represent a protective feature of the family environment. However, in situations where no such need exists, or the grandmother-mother relationship history precludes a harmonious relationship, then grandmother involvement can represent a risk factor and have a negative effect on family functioning and child adjustment.

Adjustment Disorders↗

PubMed2004

Annotation: childhood-onset schizophrenia: clinical and treatment issues.

BACKGROUND: In the past 10 years, there has been increased research on childhood-onset schizophrenia and clear advances have been achieved. METHOD: This annotation reviews the recent clinical and treatment literature on childhood-onset schizophrenia. RESULTS: There is now strong evidence that the syndrome of childhood-onset schizophrenia exists and there are several similarities between childhood- and later-onset schizophrenia. Schizophrenia in youth can be reliably diagnosed using the same criteria employed with adults, and childhood-onset schizophrenia is predictive of schizophrenia or schizophrenia spectrum disorders in adulthood. Data is accumulating to guide pharmacological treatment strategies, and practice parameters have been developed to guide clinical care. CONCLUSIONS: Despite significant advances, there remains an urgent need for additional research on treatment and service delivery strategies. Promising work with adults highlights the importance of attending to psychosocial as well as pharmacologic treatment strategies, and the potential value of preventive interventions.

Antipsychotic Agents↗

PubMed2004

Annotation: children's relationships with their non-resident fathers.

BACKGROUND: The frequency of parental separation means that increasing numbers of children have fathers who live in different households from mother-and-child; the significance of contact and relationships between children and their non-resident fathers for children's adjustment is receiving growing attention. Lessons from this research are considered. METHODS: Recent meta-analyses and overviews of research, and key research projects, are discussed. Findings related to contact and relationship quality are the main focus of the annotation. RESULTS: Economic support from non-resident fathers is related to children's well-being, and continues to be a key factor. Findings on contact are more mixed, especially from early studies; the effect size of associations between contact and positive child outcome has increased in recent research. Quality of child-father relationships is consistently related to adjustment outcome. Authoritative parenting, involvement and feelings of closeness are of particular importance in relation to adjustment, and these links are related to the quality of mother-non-resident father relations, and the mother-child relationship. Age differences, patterns over time, and gender are discussed; the perspectives of fathers and the problems they face in maintaining authoritative relationships are considered. CONCLUSIONS: The significance of child-non-resident father relationships for children's and fathers' well-being is clear and merits further research; fruitful new directions for such research, within the framework of other family relationships, are outlined.

Adaptation, Psychological↗