A meeting at the gene. Biodiversity and natural history.
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The Gene Ontology (GO) database and informatics resource.
The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.
Animals↗
Update on hemangiomas and vascular malformations.
Hemangiomas and vascular malformations are frequently encountered in pediatric practice, especially hemangiomas and port-wine stains. These lesions may cause physical and psychological complications and it is important to recognize which lesions need to be treated and how. Great progress has been made in the classification of vascular anomalies. Angiogenesis and molecular genetics are areas of active research; recent findings relating to hemangiomas and vascular malformations are presented. New clinical features of hemangiomas are described, such as association of extensive facial hemangiomas with various malformations and the occurrence of Kasabach-Merritt phenomenon, not with common hemangiomas, but with other vascular tumors (Kaposiform hemangioendothelioma and tufted angioma). Interferon alfa is effective for treatment of complicated hemangiomas but may cause serious neurological side effects. It is to be hoped that early diagnosis of Sturge-Weber syndrome will soon be possible with new, noninvasive, functional imaging techniques. New issues surrounding pulsed dye laser therapy for port-wine stains are also discussed in this article.
Child↗
The nucleotide sequence of coxsackievirus A9; implications for receptor binding and enterovirus classification.
The complete nucleotide sequence of the genome of coxsackievirus A9 (CAV-9) has been determined from cDNA cloned in Escherichia coli. Excluding the 3' poly(A) stretch, the RNA genome is 7452 nucleotides long and encodes a single polyprotein of 2201 amino acids. Comparison of the nucleotide and predicted amino acid sequences with those of the coxsackieviruses B1, B3 and B4 reveals a surprising degree of homology, with overall amino acid homologies of 86.9%, 86.2% and 87.0%, respectively. In contrast, there is much less homology to another coxsackie A virus, CAV-21, 60.4% overall amino acid homology. This demonstrates the high degree of diversity within the CAV group and indicates that the current classification does not directly correlate with molecular genetic properties. One major feature of CAV-9 is an insertion, relative to all other enteroviruses sequenced to date, which is located at the C terminus of VP1, and includes an arginine-glycine-aspartic acid tripeptide. Such sequences in a number of other proteins are known to have activity in promoting attachment to cell receptors and the implications for CAV-9 receptor binding are discussed.
Amino Acid Sequence↗
A sequence-based classifier distinguishes phenotype-associated genes from other gene models in plants.
Only a small fraction of annotated plant genes possess experimentally validated associations with specific phenotypes. Phenotype-associated genes have distinct structural, molecular, and evolutionary characteristics compared with nonvalidated gene models. Here, we develop a simple classifier that uses sequence and evolutionary features, which can be generated for any species with an annotated reference genome assembly, to accurately distinguish phenotype-associated genes from both the overall population of annotated gene models and a specific set of genes identified as being tolerant of premature stop mutations. A model trained solely on genes from maize (Zea mays) identifies and prioritizes rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) genes that are highly enriched in genes with experimentally validated links to phenotypes in both of these evolutionarily distant species. Gene models predicted to have a higher probability of being linked to phenotypes display patterns consistent with known biological properties of phenotype-associated genes. Notably, the sets of genes predicted to have a high probability of being linked to phenotype variation do not consist exclusively of well-characterized gene families but included many uncharacterized gene families carrying domains of unknown function. The quantitative scores generated by this model offer a valuable resource for prioritizing and exploring the vast number of uncharacterized gene models in plants, reducing the risk of failure in future reverse genetic efforts and potentially accelerating gene discovery and functional annotation in crops.
Phenotype↗
Metabolic functions of duplicate genes in Saccharomyces cerevisiae.
The roles of duplicate genes and their contribution to the phenomenon of enzyme dispensability are a central issue in molecular and genome evolution. A comprehensive classification of the mechanisms that may have led to their preservation, however, is currently lacking. In a systems biology approach, we classify here back-up, regulatory, and gene dosage functions for the 105 duplicate gene families of Saccharomyces cerevisiae metabolism. The key tool was the reconciled genome-scale metabolic model iLL672, which was based on the older iFF708. Computational predictions of all metabolic gene knockouts were validated with the experimentally determined phenotypes of the entire singleton yeast library of 4658 mutants under five environmental conditions. iLL672 correctly identified 96%-98% and 73%-80% of the viable and lethal singleton phenotypes, respectively. Functional roles for each duplicate family were identified by integrating the iLL672-predicted in silico duplicate knockout phenotypes, genome-scale carbon-flux distributions, singleton mutant phenotypes, and network topology analysis. The results provide no evidence for a particular dominant function that maintains duplicate genes in the genome. In particular, the back-up function is not favored by evolutionary selection because duplicates do not occur more frequently in essential reactions than singleton genes. Instead of a prevailing role, multigene-encoded enzymes cover different functions. Thus, at least for metabolism, persistence of the paralog fraction in the genome can be better explained with an array of different, often overlapping functional roles.
Gene Duplication↗
Cutaneous malignant lymphomas: update 2006.
Cutaneous lymphomas represent a unique group of lymphomas and are the second most frequent extranodal lymphomas. As with other neoplasias, the pathogenesis is based mainly on a stepwise accumulation of mutations of suppressor genes and oncogenes caused by genetic, environmental or infectious factors. The diagnostic work-up includes clinical, histological, imaging and hematological investigations and in many cases immunohistochemical and molecular biological analyses. The current WHO/EORTC classification of cutaneous lymphomas differentiates "mature T-cell and NK-cell lymphomas", "mature B-cell lymphomas" and "immature hematopoietic malignancies", their variants and subgroups. It is compatible with the WHO classification for neoplasias of the hematopoietic and lymphoid tissue and respects the organ-specific peculiarities of primary cutaneous lymphomas. The assignment of the various types of cutaneous lymphomas into prognostic categories (pre-lymphomatous "abortive" disorders; definite malignant lymphomas of low-grade malignancy; definite malignant lymphomas of high-grade malignancy) provides essential information on the biological behavior and allows an appropriate planning of the therapeutic strategy, which may be topical or systemic and aggressive or non-aggressive. Besides the classical options for therapy, there are new and "experimental" strategies, the efficacy of which has to be studied in clinical trials.
Dermatology↗
The Sicilian gambit. A new approach to the classification of antiarrhythmic drugs based on their actions on arrhythmogenic mechanisms. Task Force of the Working Group on Arrhythmias of the European Society of Cardiology.
The Queen's Gambit is an opening move in chess that provides a variety of aggressive options to the player electing it. This report represents a similar gambit (the Sicilian Gambit) on the part of a group of basic and clinical investigators who met in Taormina, Sicily to consider the classification of antiarrhythmic drugs. Paramount to their considerations were 1) dissatisfaction with the options offered by existing classification systems for inspiring and directing research, development, and therapy, 2) the disarray in the field of antiarrhythmic drug development and testing in this post-Cardiac Arrhythmia Suppression Trial (CAST) era, and 3) the desire to provide an operational framework for consideration of antiarrhythmic drugs that will both encourage advancement and have the plasticity to grow as a result of the advances that occur. The multifaceted approach suggested is, like the title of the article, a gambit. It is an opening rather than a compendium and is intended to challenge thought and investigation rather than to resolve issues. The article incorporates first, a discussion of the shortcomings of the present system for drug classification; second, a review of the molecular targets on which drugs act (including channels and receptors); third, a consideration of the mechanisms responsible for arrhythmias, including the identification of "vulnerable parameter" that might be most accessible to drug effect; and finally, clinical considerations with respect to antiarrhythmic drugs. Information relating to the various levels of information is correlated across categories (i.e., clinical arrhythmias, cellular mechanisms, and molecular targets), and a "spread sheet" approach to antiarrhythmic action is presented that considers each drug as a unit, with similarities to and dissimilarities from other drugs being highlighted. A complete reference list for this work would require as many pages as the text itself. For this reason, referencing is selective and incomplete. It is designed, in fact, to provide sufficient background information to give the interested reader a starting frame of reference rather than to recognize the complete body of literature that is the basis for this article.
Animals↗
Further understanding human disease genes by comparing with housekeeping genes and other genes.
BACKGROUND: Several studies have compared various features of heritable disease genes with other so called non-disease genes, but they have yielded some conflicting results. A potential problem in those studies is that the non-disease genes contained a large number of essential genes--genes which are indispensable for humans to survive and reproduce. Since a functional disruption of an essential gene has fatal consequences, it's more reasonable to regard essential genes as extremely severe "disease" genes. Here we perform a comparative study on the features of human essential, disease, and other genes. RESULTS: In the absence of a set of well defined human essential genes, we consider a set of 1,789 ubiquitously expressed human genes (UEHGs), also known as housekeeping genes, as an approximation. We demonstrate that UEHGs are very likely to contain a large proportion of essential genes. We show that the UEHGs, disease genes and other genes are different in their evolutionary conservation rates, DNA coding lengths, gene functions, etc. Our findings systematically confirm that disease genes have an intermediate essentiality which is less than housekeeping genes but greater than other human genes. CONCLUSION: The human genome may contain thousands of essential genes having features which differ significantly from disease and other genes. We propose to classify them as a unique group for comparisons of disease genes with non-disease genes. This new way of classification and comparison enables us to have a clearer understanding of disease genes.
Adolescent↗
Megakaryoblastic disorders in children.
Acute leukemia is the most common neoplasm in children, of which approximately one fourth of cases are acute myeloid leukemia. To a large extent, the clinicopathologic spectrum of acute myeloid leukemia seen in the pediatric age group is similar to that in adults. However, megakaryoblastic proliferations, including transient myeloproliferative disorder and acute megakaryoblastic leukemia, occur exclusively or predominantly in children. Although the clinical and pathologic features of these disorders have been well characterized, until recently their pathogenetic mechanisms have remained poorly understood. Recent advances have provided important insight into the pathogenesis of these disorders, and they provide a molecular basis for a clinically meaningful classification of primary megakaryoblastic disorders in the pediatric age group.
Acute Disease↗
A mouse stromal response to tumor invasion predicts prostate and breast cancer patient survival.
Primary and metastatic tumor growth induces host tissue responses that are believed to support tumor progression. Understanding the molecular changes within the tumor microenvironment during tumor progression may therefore be relevant not only for discovering potential therapeutic targets, but also for identifying putative molecular signatures that may improve tumor classification and predict clinical outcome. To selectively address stromal gene expression changes during cancer progression, we performed cDNA microarray analysis of laser-microdissected stromal cells derived from prostate intraepithelial neoplasia (PIN) and invasive cancer in a multistage model of prostate carcinogenesis. Human orthologs of genes identified in the stromal reaction to tumor progression in this mouse model were observed to be expressed in several human cancers, and to cluster prostate and breast cancer patients into groups with statistically different clinical outcomes. Univariate Cox analysis showed that overexpression of these genes is associated with shorter survival and recurrence-free periods. Taken together, our observations provide evidence that the expression signature of the stromal response to tumor invasion in a mouse tumor model can be used to probe human cancer, and to provide a powerful prognostic indicator for some of the most frequent human malignancies.
Animals↗
The classification of personality disorders should be rooted in biology.
As scientific classifications develop over time, they become based less on observations and more on mechanisms. Existing dimensional schema are limited by being overly broad and by being rooted in self-report rather than theory. Future models should be consistent with a scientific hierarchy, leading to a bottom-up classification of traits and disorders, linking molecular genetics, neurobiological markers, and temperamental variations.
Genetic Predisposition to Disease↗
Bullera koratensis sp. nov. and Bullera lagerstroemiae sp. nov., two new ballistoconidium-forming yeast species in the Trichosporonales clade isolated from plant leaves in Thailand.
Seven strains of ballistoconidiogenous yeasts that contain xylose, form Q-10 ubiquinone, propagate by budding and don't produce stalk conidia were isolated from plant leaves collected in Thailand and were found to represent two new species. The taxonomic properties of the two species coincided with the genus Bullera so they are described as Bullera koratensis sp. nov. and Bullera lagerstroemiae sp. nov. In phylogenetic trees based on the nucleotide sequences of 18S ribosomal DNA and the D1/D2 domain of 26S rDNA, these two species are located in the Trichosporonales clade (Cryptococcus humicola-Trichosporon lineage).
Base Sequence↗
Klippel-Feil anomaly with Sprengel anomaly, omovertebral bone, thumb abnormalities, and flexion-crease changes: novel association or syndrome?
We report on a family with Klippel-Feil anomaly (KF), Sprengel anomaly, omovertebral bone, thumb abnormalities, and flexion-crease abnormalities. This combination of abnormalities does not fit into Holt-Oram syndrome, Wildervanck syndrome, oculo-auriculo-vertebral (Goldenhar) anomaly, or the VATER complex. Clinical aspects of a KF classification are discussed. The state of molecular research on KF is briefly reported. We conclude that this set of anomalies is a novel combination, probably representing pleiotropy of a single Mendelian gene.
Abnormalities, Multiple↗
Clinically potential subclasses of retinoid synergists revealed by gene expression profiling.
Retinoids have chemopreventive and therapeutic potency in oncology and dermatology, although their application is restricted by many undesirable side effects. For the development of more effective and less toxic retinoids, gene expression analyses using DNA microarrays have the potential to supplement conventional screening methods, which are based on the changes in cell morphology and/or function. In this study, we applied the class prediction algorithm, which was used in the molecular phenotyping of tumors, for the classification of synthetic retinoids (Am80 and Tp80) and retinoid synergists (HX630, TZ335, and PA024) as all-trans retinoic acid-like, 9-cis retinoic acid-like, and control-like classes. By analyzing the effects of all-trans retinoic acid and 9-cis retinoic acid on the gene expressions in a human promyelocytic leukemia cell line, HL60, we successfully selected 50 marker genes whose expression pattern could distinguish these classes. Moreover, the classification revealed the existence of two subclasses among the retinoid synergists used with Am80. Close inspection of the DNA microarray analyses indicated that these two subclasses had different effects on the apoptosis of HL60 cells, and this was confirmed by in vivo experiments. These results indicate that the retinoidal activity of Am80, which has already been used in clinical trials, could be modulated differently by the two classes of retinoid synergists. Thus, these two subclasses of retinoid synergists have the potency to widen the usage of Am80. Our analyses demonstrated that the gene expression profiling could provide important information for developing useful retinoid synergists by compensating conventional screening methods.
Alitretinoin↗
[Gene expression profiling of multiple myeloma].
Despite the fact that multiple myeloma is a unique entity, defined by the accumulation of malignant plasma cells, a marked heterogeneity is observed among patients (regarding biological and clinical presentation, response to treatment, or survival). Current prognostic parameters are poor predictors of response to therapy and of survival in individual patients. The application and analysis of DNA microarrays to plasma cells provide an overview of gene expression programs generated by these cells in normal and pathological conditions. Genes potentially involved in transformation process have been identified by gene profiles comparison between myeloma samples, normal plasma cells from various tissues, pretumoral plasma cells and immortalized plasma cells. We can speculate that in a near future gene expression-based classification will be used as a molecular prognostic indicator.
Antigens, CD↗
[Hereditary neuropathies].
BACKGROUND: Hereditary neuropathies constitute a heterogeneous group of diseases that make up a significant proportion of peripheral nerve disease cases. MATERIAL AND METHODS: The paper is based on a review of recent literature, including searches on Medline, and our own clinical and research experience. RESULTS: Charcot-Marie-Tooth disease, itself a heterogeneous disease, is the most common hereditary neuropathy. Several variants of neuropathy are associated with hereditary metabolic disorders. Diagnostic methods include nerve conduction velocity studies and electromyography, quantitative sensory testing, molecular genetic diagnostic testing, and in selected cases processing of nerve biopsies and skin biopsies for determination of epidermal nerve fibre densities. INTERPRETATION: A thorough family history of neuropathic symptoms and signs, and preferably clinical and electrophysiological examination of relatives is essential for the diagnosis of hereditary neuropathy. Molecular genetic analysis is promising for accurate classification of these diseases. Nerve biopsy is only helpful in selected cases.
Charcot-Marie-Tooth Disease↗
The 'Sicilian Gambit'. A new approach to the classification of antiarrhythmic drugs based on their actions on arrhythmogenic mechanisms. The Task Force of the Working Group on Arrhythmias of the European Society of Cardiology.
The Queen's Gambit is an opening move in chess that provides a variety of aggressive options to the player electing it. This report represents a similar gambit (the 'Sicilian Gambit') on the part of a group of basic and clinical investigators who met in Taormina, Sicily, to consider the classification of antiarrhythmic drugs. Paramount to their considerations were (1) dissatisfaction with the options offered by existing classification systems for inspiring and directing research, development and therapy, (2) the disarray in the field of antiarrhythmic drug development and testing in this post-CAST era, and (3) the desire to provide an operational framework for consideration of antiarrhythmic drugs that will both encourage advancement and have the plasticity to grow as a result of the advances that occur. The multifaceted approach suggested is, like the title of the manuscript, a gambit. It is an opening rather than a compendium, and is intended to challenge thought and investigation rather than to resolve issues. The manuscript incorporates first, a discussion of the shortcomings of the present system for drug classification; second, a review of the molecular targets on which drugs act (including channels and receptors); third, a consideration of the mechanisms responsible for arrhythmias, including the identification of 'vulnerable parameters' that might be most accessible to drug effect; and finally, clinical considerations with respect to antiarrhythmic drugs. Information relating to the various levels of information is correlated across categories (i.e., clinical arrhythmias, cellular mechanisms and molecular targets), and a 'spread sheet' approach to antiarrhythmic action is presented that considers each drug as a unit, with similarities to and dissimilarities from other drugs being highlighted. A complete reference list for this work would require as many pages as the text itself. For this reason, referencing is selective and incomplete. It is designed, in fact, to provide sufficient background information to give the interested reader a starting frame of reference, rather than to recognize the complete body of literature that is the basis for this paper.
Animals↗