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PubMed1989

Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences.

An analysis of molecular phylogeny was undertaken to examine whether the evolution of the hepadnavirus family is host-dependent. Using the nucleotide sequences of 18 strains, we constructed phylogenetic trees. The trees obtained show that all 12 strains of hepatitis B virus can be classified into four subgroups that are not compatible with conventional subtypes. We estimated the rate of synonymous (silent) substitution for hepatitis B virus to be 4.57 x 10(-5) per site per year. Applying this rate to the phylogenetic tree, we estimated that duck hepatitis B virus diverged from a common ancestor about 30,000 years ago at the earliest, that woodchuck hepatitis virus and ground squirrel hepatitis virus diverged about 10,000 years ago, and that hepatitis B virus diverged within the last 3000 years. Because these divergence times of the viruses are much more recent than those of the host species, it suggests that the hepadnavirus family evolved independently of host-species divergence.

Animals↗
PubMed2026

Comprehensive evaluation of ACMG/AMP-based variant classification tools.

MOTIVATION: The American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines represent the gold standard for clinical variant interpretation. Despite the widespread adoption of ACMG/AMP guidelines, a comprehensive comparison of the software tools designed to implement them has been lacking. This represents a significant gap, as clinicians require evidence-based guidance on which tools to use in their practice. RESULTS: We benchmarked four ACMG/AMP-based tools (Franklin, InterVar, TAPES, Genebe) selected from 22 tools, and compared their performance with LIRICAL, a top-performing phenotype-driven tool, using 151 expert-curated datasets from Mendelian disorders. Selection criteria included free availability, VCF compatibility, operational reliability, and not being disease-specific. Our evaluation framework assessed top-N accuracy (N = 1, 5, 10, 20, 50), retention rates, precision, recall, F1 scores, and area under the curve (AUC). Statistical validation employed bootstrap confidence intervals (n = 1000) and Friedman tests. LIRICAL (68.21%) and Franklin (61.59%) demonstrated superior top-10 variant prioritization accuracy in Mendelian disorders, significantly outperforming other tools (P = .0000). Results demonstrate that tools with advanced phenotypic integration significantly outperform those relying primarily on genomic features. AVAILABILITY AND IMPLEMENTATION: All data and source code required to reproduce the findings of this study are openly available in the Code Ocean repository at https://doi.org/10.24433/CO.6562438.v1.

Software↗
PubMed2001

Classification and phylogeny of hydrogenases.

Hydrogenases (H2ases) catalyze the reversible oxidation of molecular hydrogen and play a central role in microbial energy metabolism. Most of these enzymes are found in Archaea and Bacteria, but a few are present in Eucarya as well. They can be distributed into three classes: the [Fe]-H2ases, the [NiFe]-H2ases, and the metal-free H2ases. The vast majority of known H2ases belong to the first two classes, and over 100 of these enzymes have been characterized genetically and/or biochemically. Compelling evidence from sequences and structures indicates that the [NiFe]- and [Fe]-H2ases are phylogenetically distinct classes of proteins. The catalytic core of the [NiFe]-H2ases is a heterodimeric protein, although additional subunits are present in many of these enzymes. Functional classes of [NiFe]-H2ases have been defined, and they are consistent with categories defined by sequence similarity of the catalytic subunits. The catalytic core of the [Fe]-H2ases is a ca. 350-residue domain that accommodates the active site (H-cluster). A few monomeric [Fe]-H2ases are barely larger than the H-cluster domain. Many others are monomeric as well, but possess additional domains that contain redox centers, mostly iron-sulfur. Some [Fe]-H2ases are oligomeric. The modular structure of H2ases is strikingly illustrated in recently unveiled sequences and structures. It is also remarkable that most of the accessory domains and subunits of H2ases have counterparts in other redox complexes, in particular NADH-ubiquinone oxidoreductase (Complex I) of respiratory chains. Microbial genome sequences are bringing forth a significant body of additional H2ase sequence data and contribute to the understanding of H2ase distribution and evolution. Altogether, the available data suggest that [Fe]-H2ases are restricted to Bacteria and Eucarya, while [NiFe]-H2ases, with one possible exception, seem to be present only in Archaea and Bacteria. H2ase processing and maturation involve the products of several genes which have been identified and are currently being characterized in the case of the [NiFe]-H2ases. In contrast, near to nothing is known regarding the maturation of the [Fe]-H2ases. Inspection of the currently available genome sequences suggests that the [NiFe]-H2ase maturation proteins have no similar counterparts in the genomes of organisms possessing [Fe]-H2ases only. This observation, if confirmed, would be consistent with the phylogenetic distinctiveness of the two classes of H2ases. Sequence alignments of catalytic subunits of H2ases have been implemented to construct phylogenetic trees that were found to be consistent, in the main, with trees derived from other data. On the basis of the comparisons performed and discussed here, proposals are made to simplify and rationalize the nomenclature of H2ase-encoding genes.

Amino Acid Sequence↗
PubMedDate not supplied

[Morphological structure and classification of Muller mixed uterine tumors].

A review of the literature is presented which deals with modern aspects of Muller mixed tumors (MMT) classification and problems of their histo- and morphogenesis, immunohistochemical, ultrastructural and molecular-genetic peculiarities. Prognostic factors and survival rates are considered. Further study of MMT is necessary for verification of their histo- and morphogenesis and for development of their classification.

Female↗
PubMed2007

Nosology and classification of genetic skeletal disorders: 2006 revision.

The objective of the paper is to provide the revision of the Nosology of Constitutional Disorders of Bone that incorporates newly recognized disorders and reflects new molecular and pathogenetic concepts. Criteria for inclusion of disorders were (1) significant skeletal involvement corresponding to the definition of skeletal dysplasias, metabolic bone disorders, dysostoses, and skeletal malformation and/or reduction syndromes, (2) publication and/or MIM listing, (3) genetic basis proven or very likely, and (4) nosologic autonomy confirmed by molecular or linkage analysis and/or distinctive diagnostic features and observation in multiple individuals or families. Three hundred seventy-two different conditions were included and placed in 37 groups defined by molecular, biochemical and/or radiographic criteria. Of these conditions, 215 were associated with one or more of 140 different genes. Nosologic status was classified as final (mutations or locus identified), probable (pedigree evidence), or bona fide (multiple observations and clear diagnostic criteria, but no pedigree or locus evidence yet). The number of recognized genetic disorders with a significant skeletal component is growing and the distinction between dysplasias, metabolic bone disorders, dysostoses, and malformation syndromes is blurring. For classification purposes, pathogenetic and molecular criteria are integrating with morphological ones but disorders are still identified by clinical features and radiographic appearance. Molecular evidence leads to confirmation of individual entities and to the constitution of new groups, but also allows for delineation of related but distinct entities and indicates a previously unexpected heterogeneity of molecular mechanisms; thus, molecular evidence does not necessarily simplify the Nosology, and a further increase in the number of entities and growing complexity is expected. By providing an updated overview of recognized entities with skeletal involvement and of the underlying gene defects, the new Nosology can provide practical diagnostic help, facilitate the recognition of new entities, and foster and direct research in skeletal biology and genetic disorders.

Bone Diseases↗
PubMed2006

Drug excipients.

The therapeutical use of drugs involves the application of dosage forms, serving as carrier systems together with several excipients to deliver the active ingredient to the site of action. Drug delivery technology combines an understanding of medicinal chemistry and pharmacology with the skill of formulation, aiming the preparation of improved pharmaceuticals. The recently introduced Biopharmaceutical Classification System provides guidance for dosage form design, taking the molecular and physico-chemical properties of drugs into consideration through their solubility and permeability characteristics. Pharmaceutical excipients used for oral dosage form have been traditionally assumed as being inert. However, recent experience and new results have shown that they can interact with the active drug ingredient, affecting its dissolution, absorption and bioavailability. Classification of the excipients is based on their role in the pharmaceutical formulation and on their interactions influencing drug delivery, based on their chemical and physico-chemical properties. The main classes are the antioxidants, coating materials, emulgents, taste- and smell-improvers, ointment bases, conserving agents, consistency-improvers and disintegrating materials. Some of the excipients may serve multiple purposes; for example, methylcellulose is a coating material, is applied in the preparation of suspensions, to increase viscosity, as a disintegrating agent or binder in tablets. The aim of this paper is to review the drug-excipients with respect to their chemistry, importance and interactions altering the pharmacokinetics of the drug substances. Emphasis will be given to two major classes of excipients: the antioxidants and disintegrants (substances facilitating disintegration of the drug tablets in the gastro-intestinal tract). Details will be given on the mechanisms through which they can alter drug effectiveness and tolerance, and control their application. Examples and references will be given for their analysis.

Excipients↗
PubMed1992

Analysis of gene expression in single live neurons.

We present here a method for broadly characterizing single cells at the molecular level beyond the more common morphological and transmitter/receptor classifications. The RNA from defined single cells is amplified by microinjecting primer, nucleotides, and enzyme into acutely dissociated cells from a defined region of rat brain. Further processing yields amplified antisense RNA. A second round of amplification results in greater than 10(6)-fold amplification of the original starting material, which is adequate for analysis--e.g., use as a probe, making of cDNA libraries, etc. We demonstrate this method by constructing expression profiles of single live cells from rat hippocampus. This profiling suggests that cells that appear to be morphologically similar may show marked differences in patterns of expression. In addition, we characterize several mRNAs from a single cell, some of which were previously undescribed, perhaps due to "rarity" when averaged over many cell types. Electrophysiological analysis coupled with molecular biology within the same cell will facilitate a better understanding of how changes at the molecular level are manifested in functional properties. This approach should be applicable to a wide variety of studies, including development, mutant models, aging, and neurodegenerative disease.

Animals↗
PubMed2003

Semiquantitative evaluation of mRNAs for the membranous form of immunoglobulin heavy chain is useful for investigating the etiology in CVID.

Common variable immunodeficiency (CVID) is a primary antibody deficiency syndrome characterized by defective B-cell maturation and antibody formation resulting in low serum antibody levels of all immunoglobulin (Ig) isotypes. To investigate the pathogenesis of CVID, we developed a set of competitive polymerase chain reaction for membrane-bound Ig heavy chain (mHC) mRNAs for IgM, IgG and IgA. Data on three children with CVID in group A of Bryant's classification were analysed. All the three mHC mRNA levels in Patient 1 were almost same as those in healthy controls. In Patient 2, mHC mRNA for IgM was detected at a level similar to that in controls, but mHC mRNAs for IgG and IgA heavy chains were not detected. In Patient 3, all the three mHC mRNAs were undetectable. Our data suggest that a different molecular basis exists in these patients with CVID even though all belong to group A of Bryant's classification. Use of our method facilitates a better understanding of molecular events in CVID patients and may be useful for precise classifications of CVID.

Child↗
PubMed2000

Multi-minicore disease--searching for boundaries: phenotype analysis of 38 cases.

Multi-minicore disease (MmD) is a congenital myopathy morphologically defined by the presence of multiple small zones of sarcomeric disorganization and lack of oxidative activity ("minicores") in muscle fibers. The dinical expression of MmD is considered to be greatly variable, and the morphological lesions are nonspecific; therefore, its boundaries are poorly defined, and its molecular bases are not known. To better define the phenotypic characteristics of MmD, we analyzed a large series of 38 patients with multiple minicores in muscle fibers in the absence of any other potential cause. According to clinical features, 4 subgroups were identified. Most patients (30 cases) shared a common highly consistent phenotype marked by the axial predominance of muscle weakness and a high occurrence of severe respiratory insufficiency and scoliosis ("classical" form). Other forms were characterized by pharyngolaryngeal involvement and total lack of head control (2 cases), antenatal onset with arthrogryposis (3 cases), and slowly progressive weakness with marked hand amyotrophy (3 cases). Type 1 fiber predominance and hypotrophy as well as centrally located nuclei were found in every subgroup. MmD is thus phenotypically heterogeneous, but a typical recognizable phenotype does exist. This phenotype classification should be helpful when undertaking research into the molecular defects that cause MmD.

Biopsy↗
PubMedDate not supplied

Molecular phylogeny of labyrinthulids and thraustochytrids based on the sequencing of 18S ribosomal RNA gene.

Labyrinthulids and thraustochytrids are unicellular heterotrophs, formerly considered as fungi, but presently are recognized as members in the stramenopiles of the kingdom Protista sensu lato. We determined the 18S ribosomal RNA gene sequences of 14 strains from different species of the six genera and analyzed the molecular phylogenetic relationships. The results conflict with the current classification based on morphology, at the genus and species levels. These organisms are separated, based on signature sequences and unique inserted sequences, into two major groups, which were named the labyrinthulid phylogenetic group and the thraustochytrid phylogenetic group. Although these groupings are in disagreement with many conventional taxonomic characters, they correlated better with the sugar composition of the cell wall. Thus, the currently used taxonomic criteria need serious reconsideration.

Animals↗
PubMed2001

Molecular pathogenesis of hereditary motor, sensory and autonomic neuropathies.

The hereditary motor, sensory and autonomic neuropathies are a heterogeneous group of neurological diseases. The classification of such is presently in a state of change. The original classification system was based on clinical findings whose limitations are being unfurled with increasing insights into the molecular basis of these disorders. In particular, much progress has been achieved in understanding the demyelinating forms of Charcot-Marie-Tooth (type 1), for which at least a dozen loci have been delineated and six genes identified. As anticipated, these genes play predominant roles in myelin biology. Four separate loci for the axonal Charcot-Marie-Tooth neuropathies (type 2) have been identified and only now are researchers beginning to tease out the responsible genes and the underlying molecular mechanisms. Similarly, progress is being made with the pure hereditary motor neuropathies. This review presents an updated list of genes responsible for inherited peripheral neuropathies and explores the underlying molecular mechanisms actively being investigated.

Autonomic Nervous System Diseases↗
PubMed1996

Molecular genetics of small round cell tumors.

The small round cell tumors of children and young adults constitute part of a group of undifferentiated tumors, the precise diagnosis of which is often a challenge for the pathologist because of their uniform morphological appearance. Diagnostic cytogenetic analysis and identification of specific chromosomal abnormalities have been especially useful for the classification of some of these tumors. The cloning of the genes and molecular characterization of the associated genetic anomalies have led to the discovery of the mechanisms involved in their neoplastic transformation and identified a variety of tumor-specific molecular genetic markers. Information has also been provided regarding the histogenetic origin and mechanisms of differentiation in these tumors. This review focuses on the tumor-specific genetic markers, particularly those of clinical relevance, and the recently identified genes and deregulation mechanisms associated with them. The availability of these markers provides auxiliary methods with increasingly improved resolution for primary diagnosis and classification of histologically similar tumors and tools for monitoring patients and identifying potential antineoplastic therapy targets.

Adolescent↗
PubMed2004

Post-transplant lymphoproliferative disorders. Molecular analysis of histogenesis and pathogenesis.

AIM: Post-transplant lymphoproliferative disorders (PTLD) represent a serious complication of solid organ transplantation. Despite several advances in the biological categorization of PTLD, current classifications are not fully predictive of the clinical behavior of the disease. This study assessed a comprehensive molecular analysis of the clinico-pathologic spectrum of PTLD in order to better clarify the physiopathology of these disorders. METHODS: Fifty-two monoclonal PTLD were investigated for: 1). somatic hypermutation of IgV genes by direct sequencing of IgV rearrangements; 2). expression of BCL6, MUM1 and CD138 proteins by immunohistochemistry; 3). aberrant hypermethylation of DAP-kinase gene by methylation-specific polymerase chain reaction (PCR); 4). genotypic characterization of Epstein Barr virus (EBV) in EBV infected PTLD by PCR analysis of the prevalence of deletions in the carboxyterminal portion of the LMP1 gene and for the definition of type-1/type-2 EBV infection. RESULTS: We report that virtually all monoclonal PTLD originate from B cells that have experienced the germinal center (GC) reaction reflecting different stages of mature B cell differentiation and that tumor development seems frequently associated with EBV and/or other molecular lesions preventing apoptosis of cells that have failed the physiological process of germinal center reaction. CONCLUSION: To date, classification of PTLD is mainly based on morphology and conventional immunophenotyping. Because current classification schemes are not fully predictive of prognosis, knowledge of PTLD histogenesis and pathogenesis may potentially contribute to refine the distinction of PTLD into more homogeneous categories with prognostic relevance.

Adolescent↗
PubMed1997

Immunohistochemical and molecular genetic approaches to soft tissue tumor diagnosis: a primer.

During the past two decades we have witnessed the identification of an expanding list of immunohistochemical and molecular markers linked to histopathologically defined subtypes of tumors. These markers offer new insights and approaches to the classification of tumors with important prognostic and/or therapeutic implications. We review the potentially diagnostic immunohistochemical and molecular markers of soft tissue tumors (STTs). The immunohistochemical markers reviewed include vimentin, cytokeratin, desmin, HHF35, S100, myoD1, alpha1-antitrypsin, vascular markers (factor VIII, CD31, CD34), MIC2, and others. The potentially diagnostic chromosomal translocations and associated genes identified in STT include Ewing's/PNET t(11;22)(q24;q12)(FLI1;EWS), t(21;22)(q22;q12)(ERG; EWS); t(7;22)(p22;q12)(ETV1;EWS); desmoplastic small round cell tumor t(11;22)(p13;q12)(WT1;EWS); extraskeletal myxoid chondrosarcoma t(9;22)(q22;q12) (TEC(CHN);EWS); malignant ectomesenchymoma t(11;22)(q24;q12)(FLI1;EWS); alveolar rhabdomyosarcoma t(2;13)(q35;q14)(PAX-3;FKHR); t(1;13) (p36;q14)(PAX-7;FKHR); myxoid and round cell liposarcoma t(12;16)(q13;p11)(CHOP;TLS(FUS)); synovial sarcoma t(X;18)(p11;q11)(SSX1&2;SYT), and others. The nature, utility, and limitations of these markers in diagnostic settings are explored.

Biomarkers, Tumor↗
PubMed2006

Timing and tempo of primate speciation.

Published molecular clocks for primates are used to estimate typical divergence times for phylogroups (1.6 Ma), species (3.3 Ma), sister species (2.7 Ma), genera (8.9 Ma) and sister genera (8.6 Ma). Significant median differences exist between major groups (infraorders and superfamilies) for various divergence times. These data are employed to estimate typical maximum duration of speciation. Typical primate values (1.1 Ma) suggest this process to be faster than is characteristic of many vertebrates. However, after considering divergence times for hybridizing congeneric and confamilial primates, this value is likely only to estimate the commencement of prezygotic isolating mechanisms, rather than the completion of reproductive isolation. Thus, speciation typically takes around 1.0 Ma to more than 4.0 Ma to occur, depending on whether prezygotic or post-zygotic isolating mechanisms are emphasized. Typical primate genus age is around 5.3 Ma, but we note differences among major groups. In light of these estimates, the classification of humans and chimpanzees is reconsidered using a molecular yardstick approach. Three taxonomic frameworks may flow from molecular analyses, all of them having major implications for understanding the evolution of humans and chimpanzees.

Animals↗
PubMed2006

Primary immunodeficiency diseases: an update from the International Union of Immunological Societies Primary Immunodeficiency Diseases Classification Committee Meeting in Budapest, 2005.

Although relatively rare, primary immunodeficiency diseases (PIDs) provide an excellent window into the functioning of the immune system. In the late 1960s, observations on these diseases, with their associated infections and genetics, bisected the immune system into humoral immunity and cell-mediated immunity. These diseases also represent a challenge in their diagnosis and treatment. Beginning in 1970, a unified nomenclature for the then-known PIDs was created by a committee convoked by the World Health Organization. Since then, and later under the aegis of the International Union of Immunological Societies, an international committee of experts has met every 2 to 3 years to update the classification of PIDs. During the past 15 years, the molecular basis of more than 120 PIDs has been elucidated. This update results from the latest meeting of this committee in Budapest, Hungary, in June 2005, which followed 2 1/2 days of scientific discussions. As a result of this work, new entities have been included, and the nomenclature of some PIDs (specifically of the various forms of class-switch recombination defects, previously known as hyper-IgM syndromes) has been changed.

B-Lymphocytes↗