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Towards a new classification of ectodermal dysplasias.

Ectodermal dysplasias (EDs) constitute a large and complex group of diseases characterized by various defects in hair, nails, teeth and sweat glands. Of the 170 EDs described so far, fewer than 30 have been explained at the molecular level with identification of the causative gene. This review proposes a new classification of EDs based on the function of the protein encoded by the mutated gene. The EDs are reviewed in light of the recent molecular and biochemical findings and an attempt is made to classify ED causative genes into four major functional subgroups: cell-cell communication and signalling; adhesion; transcription regulation; and development.

Cell Adhesion↗

Repuncturing the renal biopsy: strategies for molecular diagnosis in nephrology.

As has been exemplified by recent progress in the classification of cancer, future approaches to enhance the clinical diagnostic power of tissue biopsies may be based on gene expression profiles. A series of strategies to translate these approaches to the diagnosis of renal disease is here proposed. The theoretical and technical problems resulting from the small amount of starting material available from renal biopsies will be specifically addressed. A preliminary study with cDNA array-based expression data obtained from kidneys with tubulointerstitial inflammation and fibrosis suggests the feasibility of distinguishing molecular categories of renal disease. Finally, a combined conventional and molecular work-up of renal biopsies will be suggested. These approaches should add a new dimension to biopsy interpretation and provide novel information concerning renal pathogenesis, diagnosis, prognosis, and differential therapy. A coordinated effort from nephrologists and pathologists in large multicenter trials will be required to achieve this goal. It is hoped that this outlook will lead to stimulating discussions and the implementation of these innovative ideas in nephrology.

Biopsy↗

Aphid biology: expressed genes from alate Toxoptera citricida, the brown citrus aphid.

The brown citrus aphid, Toxoptera citricida (Kirkaldy), is considered the primary vector of citrus tristeza virus, a severe pathogen which causes losses to citrus industries worldwide. The alate (winged) form of this aphid can readily fly long distances with the wind, thus spreading citrus tristeza virus in citrus growing regions. To better understand the biology of the brown citrus aphid and the emergence of genes expressed during wing development, we undertook a large-scale 5' end sequencing project of cDNA clones from alate aphids. Similar large-scale expressed sequence tag (EST) sequencing projects from other insects have provided a vehicle for answering biological questions relating to development and physiology. Although there is a growing database in GenBank of ESTs from insects, most are from Drosophila melanogaster and Anopheles gambiae, with relatively few specifically derived from aphids. However, important morphogenetic processes are exclusively associated with piercing-sucking insect development and sap feeding insect metabolism. In this paper, we describe the first public data set of ESTs from the brown citrus aphid, T. citricida. The cDNA library was derived from alate adults due to their significance in spreading viruses (e.g., citrus tristeza virus). Over 5180 cDNA clones were sequenced, resulting in 4263 high-quality ESTs. Contig alignment of these ESTs resulted in 2124 total assembled sequences, including both contiguous sequences and singlets. Approximately 33% of the ESTs currently have no significant match in either the non-redundant protein or nucleic acid databases. Sequences returning matches with an E-value of < or = -10 using BLASTX, BLASTN, or TBLASTX were annotated based on their putative molecular function and biological process using the Gene Ontology classification system. These data will aid research efforts in the identification of important genes within insects, specifically aphids and other sap feeding insects within the Order Hemiptera.

Animals↗

What makes biochemical networks tick?

In view of the increasing number of reported concentration oscillations in living cells, methods are needed that can identify the causes of these oscillations. These causes always derive from the influences that concentrations have on reaction rates. The influences reach over many molecular reaction steps and are defined by the detailed molecular topology of the network. So-called 'autoinfluence paths', which quantify the influence of one molecular species upon itself through a particular path through the network, can have positive or negative values. The former bring a tendency towards instability. In this molecular context a new graphical approach is presented that enables the classification of network topologies into oscillophoretic and nonoscillophoretic, i.e. into ones that can and ones that cannot induce concentration oscillations. The network topologies are formulated in terms of a set of uni-molecular and bi-molecular reactions, organized into branched cycles of directed reactions, and presented as graphs. Subgraphs of the network topologies are then classified as negative ones (which can) and positive ones (which cannot) give rise to oscillations. A subgraph is oscillophoretic (negative) when it contains more positive than negative autoinfluence paths. Whether the former generates oscillations depends on the values of the other subgraphs, which again depend on the kinetic parameters. An example shows how this can be established. By following the rules of our new approach, various oscillatory kinetic models can be constructed and analyzed, starting from the classified simplest topologies and then working towards desirable complications. Realistic biochemical examples are analyzed with the new method, illustrating two new main classes of oscillophore topologies.

Algorithms↗

A molecular phylogeny for the large African orchid genus Disa.

Phylogenetic relationships were inferred for the African subtribe Disinae (Orchidoideae, Orchidaceae), which include the large genus Disa and the small genus Schizodium. One nuclear (ITS) gene region and two plastid (trnLF and matK) gene regions were sequenced for 136 ingroup, representing 70% of all known Disinae species, as well as for 7 outgroup taxa. The combined data matrix contained 4094 characters and was analysed using parsimony and Bayesian inference. Our results show that the generic status of Schizodium can no longer be supported, as it is deeply embedded within the genus Disa. Furthermore, the currently recognised subgenera do not reflect the phylogenetic relationships and should be rejected. Several of the currently recognised sections are monophyletic, others contain misplaced elements, while some are polyphyletic. Morphological divergence, rather than convergence, has hampered previous attempts at a phylogenetic classification of the Disinae. On the basis of our molecular phylogenetic hypothesis, we propose a monotypic subtribe Disinae and a subdivision of the genus Disa into 18 sections.

Africa↗

IntEnz, the integrated relational enzyme database.

IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at http://www.ebi.ac.uk/intenz.

Animals↗

Meperidine and lidocaine block of recombinant voltage-dependent Na+ channels: evidence that meperidine is a local anesthetic.

BACKGROUND: The opioid meperidine induces spinal anesthesia and blocks nerve action potentials, suggesting it is a local anesthetic. However, whether it produces effective clinical local anesthesia in peripheral nerves remains unclear. Classification as a local anesthetic requires clinical local anesthesia but also blockade of voltage-dependent Na+ channels with characteristic features (tonic and phasic blockade and a negative shift in the voltage-dependence of steady-state inactivation) involving an intrapore receptor. The authors tested for these molecular pharmacologic features to explore whether meperidine is a local anesthetic. METHODS: The authors studied rat skeletal muscle mu1 (RSkM1) voltage-dependent Na+ channels or a mutant form heterologously coexpressed with rat brain Na+ channel accessory beta1, subunit in Xenopus oocytes. Polymerase chain reaction was used for mutagenesis, and mutations were confirmed by sequencing. Na+ currents were measured using a two-microelectrode voltage clamp. Meperidine and the commonly used local anesthetic lidocaine were applied to oocytes in saline solution at room temperature. RESULTS: Meperidine and lidocaine produced tonic current inhibition with comparable concentration dependence. Meperidine caused phasic current inhibition in which the concentration-response relationship was shifted to fivefold greater concentration relative to lidocaine. Meperidine and lidocaine negatively shifted the voltage dependence of steady-state inactivation. Mutation of a putative local anesthetic receptor reduced phasic inhibition by meperidine and lidocaine and tonic inhibition by lidocaine, but not meperidine tonic inhibition. CONCLUSIONS: Meperidine blocks Na+ channels with molecular pharmacologic features of a local anesthetic. The findings support classification of meperidine as a local anesthetic but with less overall potency than lidocaine.

Algorithms↗

Determination of tumour marker genes from gene expression data.

Cancer classification has traditionally been based on the morphological study of tumours. However, tumours with similar histological appearances can exhibit different responses to therapy, indicating differences in tumour characteristics on the molecular level. Thus, development of a novel, reliable and precise method for classification of tumours is essential for more successful diagnosis and treatment. The high-throughput gene expression data obtained using microarray technology are currently being investigated for diagnostic applications. However, these large datasets introduce a range of challenges, making data analysis a major part of every experiment for any application, including cancer classification and diagnosis. One of the major concerns in the application of microarrays to tumour diagnostics is the fact that the expression levels of many genes are not measurably affected by carcinogenic changes in the cells. Thus, a crucial step in the application of microarrays to cancer diagnostics is the selection of diagnostic marker genes from the gene expression profiles. These molecular markers give valuable additional information for tumour diagnosis, prognosis and therapy development.

Biomarkers, Tumor↗

Circumscription and phylogeny of the Laurales: evidence from molecular and morphological data.

The order Laurales comprises a few indisputed core constituents, namely Gomortegaceae, Hernandiaceae, Lauraceae, and Monimiaceae sensu lato, and an equal number of families that have recently been included in, or excluded from, the order, namely Amborellaceae, Calycanthaceae, Chloranthaceae, Idiospermaceae, and Trimeniaceae. In addition, the circumscription of the second largest family in the order, the Monimiaceae, has been problematic. I conducted two analyses, one on 82 rbcL sequences representing all putative Laurales and major lineages of basal angiosperms to clarify the composition of the order and to determine the relationships of the controversal families, and the other on a concatenated matrix of sequences from 28 taxa and six plastid genome regions (rbcL, rpl16, trnT-trnL, trnL-trnF, atpB-rbcL, and psbA-trnH) that together yielded 898 parsimony-informative characters. Fifteen morphological characters that play a key role in the evolution and classification of Laurales were analyzed on the most parsimonious molecular trees as well as being included directly in the analysis in a total evidence approach. The resulting trees strongly support the monophyly of the core Laurales (as listed above) plus Calycanthaceae and Idiospermaceae. Trimeniaceae form a clade with Illiciaceae, Schisandraceae, and Austrobaileyaceae, whereas Amborellaceae and Chloranthaceae represent isolated clades that cannot be placed securely based on rbcL alone. Within Laurales, the deepest split is between Calycanthaceae (including Idiospermaceae) and the remaining six families, which in turn form two clades, the Siparunaceae (Atherospermataceae-Gomortegaceae) and the Hernandiaceae (Monimiaceae s.str. [sensu stricto]-Lauraceae). Monimiaceae clearly are polyphyletic as long as they include Atherospermataceae and Siparunaceae. Several morphological character state changes are congruent with the molecular tree: (1) Calycanthaceae have disulculate tectate-columellate pollen, while their sister clade has inaperturate thin-exined pollen, with the exception of Atherospermataceae, which have columellate but meridionosulcate or disulcate pollen. (2) Calycanthaceae have two ventral ovules while their sister clade has solitary ovules. Within this sister clade, the Hernandiaceae (Lauraceae-Monimiaceae) have apical ovules, while the Siparunaceae (Atherospermataceae-Gomortegaceae) are inferred to ancestrally have basal ovules, a condition lost in Gomortega, the only lauralean genus with a syncarpous ovary. (3) Calycanthaceae lack floral nectaries (except for isolated nectarogeneous fields on the inner tepals), while their sister clade ancestrally has paired nectar glands on the filaments. Filament glands were independently lost in higher Monimiaceae and in Siparunaceae concomitant with pollinator changes away from nectar-foraging flies and bees to non-nectar feeding beetles and gall midges. (4) Disporangiate stamens with anthers dehiscing by two apically hinged valves are ancestral in Siparunaceae-(Atherospermataceae-Gomortegaceae) and evolved independently within Hernandiaceae and Lauraceae. Depending on the correct placement of Calycanthaceae-like fossil flowers, tetrasporangiate anthers with valvate dehiscence (with the valves laterally hinged) may be ancestral in Laurales and lost in modern Calycanthaceae and Monimiaceae.

Journal Article↗

Genotype of GB virus C/hepatitis G virus by molecular evolutionary analysis.

GB virus C/hepatitis G virus is a newly described virus. Classification of GB virus C/hepatitis G virus into genotypes has not been established. We analyzed nucleotide sequences within the 5' untranslated region of GB virus C/hepatitis G virus isolates and segregated these isolates into genotypes. Twenty serum samples with GB virus C/hepatitis G virus RNA from Australia, Cameroon, the Congo, Japan, Mongolia, and Bangladesh were studied. Reverse transcription and polymerase chain reaction were used to obtain GB virus C/hepatitis G virus RNA. After nucleotide sequences from the 5' untranslated region were determined, 68 nucleotide sequences, including 48 previously reported sequences, were analyzed by molecular evolutionary methods. The phylogenetic tree of the 5' untranslated region showed that all strains could be divided into three major genotypes, GB type (type 1), HG type (type 2), and Asian type (type 3). Bootstrap analysis indicated that the strains could be divided into three major genotypes but could not be further subdivided. Moreover, frequency histograms of pairwise distances between nucleotide sequences demonstrated only one peak. These result indicated that GB virus C/hepatitis G virus can be classified into three major genotypes, GB type (type 1), HG type (type 2), and Asian type (type 3), and should not be divided into minor subtypes.

Base Sequence↗

Molecular phylogeny of microsporidians with particular reference to species that infect the muscles of fish.

Ribosomal DNA from eight species of microsporidians infecting fish have been sequenced. Seven of these species infect the skeletal muscle of fish (Pleistophora spp.) and one species infects migratory mesenchyma cells (Glugea anomala). These sequences, in addition to other available microsporidian rDNA sequences from a broad range of host taxa, have been used in phylogenetic analysis. This analysis revealed that muscle-infecting microsporidians from fish are a polyphyletic group, indicating that characters supposed to be important in the classification of the genus Pleistophora have to be re-evaluated. One character that probably has a polyphyletic origin is the amorphous coat, which has been extensively used in the definition of this genus. Furthermore, our results showed that the insect parasitizing Pleistophora spp. are not related to the true pleistophorans parasitic in skeletal muscle of fish. Phylogenetic analysis of small subunit rDNA sequences revealed disagreements between the molecular phylogeny and classifications based upon ultrastructure. Many of the morphological characters claimed to be important in microsporidian classifications appeared to have arisen several times during evolution: for example, the diplokaryon and sporophorous vesicles.

Animals↗

Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling.

We analyzed global gene expression patterns of 91 human hepatocellular carcinomas (HCCs) to define the molecular characteristics of the tumors and to test the prognostic value of the expression profiles. Unsupervised classification methods revealed two distinctive subclasses of HCC that are highly associated with patient survival. This association was validated via 5 independent supervised learning methods. We also identified the genes most strongly associated with survival by using the Cox proportional hazards survival analysis. This approach identified a limited number of genes that accurately predicted the length of survival and provides new molecular insight into the pathogenesis of HCC. Tumors from the low survival subclass have strong cell proliferation and antiapoptosis gene expression signatures. In addition, the low survival subclass displayed higher expression of genes involved in ubiquitination and histone modification, suggesting an etiological involvement of these processes in accelerating the progression of HCC. In conclusion, the biological differences identified in the HCC subclasses should provide an attractive source for the development of therapeutic targets (e.g., HIF1a) for selective treatment of HCC patients. Supplementary material for this article can be found on the HEPATOLOGY Web site (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html)

Carcinoma, Hepatocellular↗

Applications of biotechnological methods to studies of protozoan parasites.

Biotechnology applies and extends the concepts and techniques of molecular biology. An overview of the applications and potential uses of the technology is presented for selected protozoan parasites. The areas reviewed include the characterization of protozoa, the production of their antigens, and the uses of hybridomas for studies of the antigens and host responses. In addition to the traditional methods of classification, parasitic protozoa are identified and characterized according to stable molecular markers. Peptidemes, zymodemes, antigens, schizodemes, and chromosomal complements define isolates and correlate with biological activities of the parasites. While antigens are typically extracted from parasites obtained from infected hosts or grown in vitro, they may be produced with in vitro translation systems, recombinant procedures with bacteria, or more recently developed techniques such as co-transformation and electroporation with eucaryotic cells. Monoclonal antibodies produced by B-cell hybridomas are used to identify parasites, antigens, epitopes, and the locations and functions of specific antigens. T-cell hybridomas may provide insights into cell-mediated immunity and interactions with the parasites.

Animals↗

Origin and classification of neocortical interneurons.

Neocortical interneurons are very diverse in morphological, physiological, molecular, and developmental characteristics. Recent work is discovering strong correlations between these phenotypic features, confirming the intuition of Cajal and Lorente that distinct classes of interneurons exist, each presumably mediating a different circuit function. A paper by Butt et al. in this issue of Neuron describes correlations between the developmental origin of interneurons and their anatomical, electrophysiological, and molecular properties. An effort to standardize the nomenclature of interneurons is underway. Because different interneuron subtypes have different ontogenic origin, they could be classified based on their developmental specification by transcription factors.

Animals↗

Molecular cloning of prepro-thyrotropin-releasing hormone cDNA from medaka (Oryzias latipes).

The cDNA encoding prepro-thyrotropin-releasing hormone (ppTRH) in a teleost, medaka (Oryzias latipes) was isolated and characterized. The medaka ppTRH cDNA codes for 270 amino acid residues including eight TRH progenitor sequences (-Lys/Arg-Arg-Gln-His-Pro-Gly-Lys/Arg-Arg-). In silico analyses of the medaka genome database predicted that the structure of the medaka ppTRH gene is similar to the ppTRH genes of the other vertebrate species studied to date; consisting of three exons and two introns. Identity of the medaka ppTRH with the other vertebrates is rather low except the sockeye salmon. A molecular phylogenic tree showed that the ppTRH sequences reflected the predicted pattern of species classification. RT-PCR analysis demonstrated ppTRH gene expression in the brain and retina. These results gave some insight into the molecular evolution of ppTRH and physiological functions of TRH in vertebrates.

Amino Acid Sequence↗

Four new postsynaptic neurotoxins from Naja naja sputatrix venom: cDNA cloning, protein expression, and phylogenetic analysis.

cDNAs encoding 4 short chain alpha-neurotoxins from Malayan spitting cobra (Naja naja sputatrix) venom were cloned and expressed in Escherichia coli. The recombinant toxins possessed identical amino acid sequences to alpha-neurotoxins. This is the first report on cloning and expression of isoforms of neurotoxins from a species of spitting cobra. Two of these isoforms were also identified in the crude venom by reverse phase-high performance liquid chromatography (RP-HPLC), capillary electrophoresis followed by mass spectrometry and characterized by protein sequencing. Based on the variable amino acid residues, the neurotoxins in N. n. sputatrix could be assigned to 2 major groups, 10E11T and 10Q11A, which could be further subdivided into 10E11T28S: 10E11T28G and 10Q11A28S; 10Q11A28G respectively. These substitutions were also found to be unique to N. n. sputatrix neurotoxins. Phylogenetic analysis based on molecular properties of the toxins provided further support for the classification of N. n. sputatrix neurotoxin into 2 fundamental groups.

Amino Acid Sequence↗

The cone dystrophies.

The cone dystrophies are a heterogeneous group of inherited disorders that result in dysfunction of the cone photoreceptors and sometimes their post-receptoral pathways. The major clinical features of cone dystrophy are photophobia, reduced visual acuity and abnormal colour vision. Ganzfeld electroretinography shows reduced or absent cone responses. On the basis of their natural history, the cone dystrophies may be broadly divided into two groups: stationary and progressive cone dystrophies. The stationary cone dystrophies have received more attention, and subsequently our knowledge of their molecular genetic, psychophysical and clinical characteristics is better developed. Various methods of classification have been proposed for the progressive cone dystrophies, but none is entirely satisfactory, largely because the underlying disease mechanisms are poorly understood. Multidisciplinary studies involving clinical assessment, molecular genetics, electrophysiology and psychophysics should lead to an improved understanding of the pathogenesis of these disorders.

Color Vision Defects↗

Lipopolysaccharide structures of Helicobacter pylori genomic strains 26695 and J99, mouse model H. pylori Sydney strain, H. pylori P466 carrying sialyl Lewis X, and H. pylori UA915 expressing Lewis B classification of H. pylori lipopolysaccharides into glycotype families.

This study describes the molecular makeup of the cell-wall lipopolysaccharides (LPSs) (O-chain polysaccharide-->core oligosaccharide-->lipid A) from five Helicobacter pylori strains: H. pylori 26695 and J99, the complete genome sequences of which have been published, the established mouse model Sydney strain (SS1), and the symptomatic strains P466 and UA915. All chemical and serological experiments were performed on the intact LPSs. H. pylori 26695 and SS1 possessed either a low-Mr semi-rough-form LPS carrying mostly a single Ley type-2 blood-group determinant in the O-chain region covalently attached to the core oligosaccharide or a high-Mr smooth-form LPS, as did strain J99, with an elongated partially fucosylated type-2 N-acetyllactosamine (polyLacNAc) O-chain polymer, terminated mainly by a Lex blood-group determinant, connected to the core oligosaccharide. In the midst of semi-rough-form LPS glycoforms, H. pylori 26695 and SS1 also expressed in the O-chain region a difucosylated antigen, alpha-L-Fucp(1-3)-alpha-L-Fucp(1-4)-beta-D-GlcpNAc, and the cancer-cell-related type-1 or type-2 linear B-blood-group antigen, alpha-D-Galp(1-3)-beta-D-Galp(1-3 or 4)-beta-D-GlcpNAc. The LPS of H. pylori strain P466 carried the cancer-associated type-2 sialyl Lex blood-group antigen, and the LPS from strain UA915 expressed a type-1 Leb blood-group unit. These findings should aid investigations that focus on identifying and characterizing genes responsible for LPS biosynthesis in genomic strains 26695 and J99, and in understanding the role of H. pylori LPS in animal model studies. The LPSs from the H. pylori strains studied to date were grouped into specific glycotype families.

Animals↗