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Genetic variation among different populations of Aster tripolium grown on naturally and anthropogenic salt-contaminated habitats: implications for conservation strategies.

The sea aster, Aster tripolium L., grows naturally in temperate regions, mainly in the salt meadows close to the coast. The species is also found in naturally and anthropogenically salt-contaminated inland habitats, such as potash mine dumps. The genetic relationships among populations from different habitats and correlations of the genotype with physiological and vegetational parameters were investigated. A. tripolium plants from five different sites close to the seashore on the North Sea island Baltrum, from five different potash mine dumps and, as an outgroup, from the seashore in Japan were probed. DNA was extracted from five plants from each of the 11 A. tripolium populations and analyzed for random amplified polymorphic DNA (RAPD). Altogether 35 polymorphic bands in 51 individuals and 45 different detectable genotypes could be identified. For evaluation of the genetic variation using RAPD bands, the neighbor-joining method, the principal coordinate analysis, and the analysis of molecular variance were applied, resulting in the classification into three genetic groups. A. tripolium plants from different ecological habitats on Baltrum were closely related while the plants growing at the deposit dumps showed a higher genetic diversity. The Japanese population was genetically very different from the German populations. Correlations between phytosociological and soil parameters and the respective genotype were not significant. The results argue for a conservation of anthropogenically salt-contaminated habitats to maintain genetic variability not only on the species level, but also within a species.

Adaptation, Physiological↗

Alpha-L-arabinofuranosidases: the potential applications in biotechnology.

Recently, alpha-L-arabinofuranosidases (EC3.2.1.55) have received increased attention primarily due to their role in the degradation of lignocelluloses as well as their positive effect on the activity of other enzymes acting on lignocelluloses. As a result, these enzymes are used in many biotechnological applications including wine industry, clarification of fruit juices, digestion enhancement of animal feedstuffs and as a natural improver for bread. Moreover, these enzymes could be used to improve existing technologies and to develop new technologies. The production, mechanisms of action, classification, synergistic role, biochemical properties, substrate specificities, molecular biology and biotechnological applications of these enzymes have been reviewed in this article.

Biotechnology↗

Nociceptors for the 21st century.

This review summarizes recent developments in the context of the neurochemical classification of nociceptors and explores the relationships between functionally and neurochemically defined subgroups. Although the complete picture is not yet available, several lines of intriguing evidence suggest that despite the complexity and diversity of nociceptor properties, a relatively "simple" neurochemical classification fits well with several recently identified molecular characteristics.

Animals↗

Emerging intracellular bacterial infections.

Human infections by intracellular bacteria have been recognized for many years, but much of what we know about the pathogenesis of these diseases and their etiologic organisms has emerged within the past few years as a result of improved molecular-based means for their detection and classification. New insights concerning the epidemiology and pathogenesis of intracellular bacterial infections and methods for the detection of Chlamydophila pneumoniae, Ehrlichia chaffeensis, Anaplasma phagocytophilum, and Rickettsia species have made an impact on how we view them as agents of human disease. Emerging evidence suggesting a possible intracellular existence for another organism, Mycoplasma pneumoniae, may explain how this organism interacts with the host to induce chronic inflammatory conditions of the respiratory tract.

Chlamydia Infections↗

Genome-based identification of diagnostic molecular markers for human lung carcinomas by PLS-DA.

Partial least squares discriminant analysis (PLS-DA) provides a sound statistical basis for the selection of a limited number of gene transcripts most effective in discriminating different lung tumoral histotypes. The potentialities of the PLS-DA approach are pointed out by its ability to identify genes which, according to current knowledge, are considered molecular markers for colon cancer diagnostics and classification. Indeed application of PLS-DA to in vivo data allowed identification of a set of genes able to discriminate primary lung tumours from colon metastases.

Biomarkers, Tumor↗

Diabetic neuropathy.

In this review, an in-depth anatomic and molecular pathogenesis of diabetic neuropathy is provided. Classifications and clinical manifestations of diabetic neuropathy are discussed. The current modalities of treatment and clinical research on this disorder are summarized.

Anticonvulsants↗

Regulation of GABAA receptor trafficking, channel activity, and functional plasticity of inhibitory synapses.

Neural inhibition in the brain is mainly mediated by ionotropic gamma-aminobutyric acid type A (GABA(A)) receptors. Different subtypes of these receptors, distinguished by their subunit composition, are either concentrated at postsynaptic sites where they mediate phasic inhibition or found at perisynaptic and extrasynaptic locations where they prolong phasic inhibition and mediate tonic inhibition, respectively. Of special interest are mechanisms that modulate the stability and function of postsynaptic GABA(A) receptor subtypes and that are implicated in functional plasticity of inhibitory transmission in the brain. We will summarize recent progress on the classification of synaptic versus extrasynaptic receptors, the molecular composition of the postsynaptic cytoskeleton, the function of receptor-associated proteins in trafficking of GABA(A) receptors to and from synapses, and their role in post-translational signaling mechanisms that modulate the stability, density, and function of GABA(A) receptors in the postsynaptic membrane.

Carrier Proteins↗

Extremely high conservation in the untranslated region as well as the coding region of CNP mRNAs throughout elasmobranch species.

C-type natriuretic peptide (CNP) is a crucial osmoregulatory hormone in elasmobranchs, participating in salt secretion and drinking. In contrast to teleosts and tetrapods in which the NP family is composed of a group of structurally related peptides, we have shown that CNP is the sole NP in sharks. In the present study, CNP cDNAs were cloned from four species of batoids, another group of elasmobranchs. The cloned batoid CNP precursors contained a plausible mature peptide of 22 amino acid residues that is identical to most shark CNP-22s, but five successive amino acids were consistently deleted in the prosegment compared with shark precursors, supporting the diphyletic classification of sharks and rays. In addition, molecular phylogenetic trees of CNP precursors were consistent with a diphyletic interpretation. Except for the deletion, the nucleotide and deduced amino acid sequences of the CNP cDNAs are extremely well-conserved among all elasmobranch species, even between sharks and rays. Surprisingly, high conservation is evident not only for the coding region, but also for the untranslated regions. It is most likely that the high conservation is due to the low nucleotide substitution rate in the elasmobranch genome, and high selection pressure. The 3'-untranslated region of the elasmobranch CNP cDNAs contained three to six repeats of the ATTTA motif that is associated with the regulation of mRNA stability and translation efficiency. Alternative polyadenylation sites were also found; the long 3'-untranslated region contains a core of ATTTA motifs while the short form has only one or no ATTTA motif, indicating that the post-transcriptional modification of mRNA is important for regulation of CNP synthesis. These characteristics in the 3'-untranslated region were conserved among all elasmobranch CNP cDNAs. Since CNP has been implicated as a fast-acting hormone to facilitate salt secretion from the rectal gland, the conserved 3'-untranslated region most likely contributes to rapid regulation of CNP synthesis in elasmobranchs in response to acute changes in internal and external environments.

Amino Acid Sequence↗

Non-Hodgkin lymphoma.

Non-Hodgkin lymphoma is a non-specific term that includes several lymphoproliferative malignant diseases with different clinical and histological appearances. Here, we concentrate on adult lymphomas. We look at their molecular basis, at the development of a classification system based on a better understanding of the biology of the various subgroups, and at how refinement of adverse prognostic factor groupings helps in clinical management. Lymphomas can present in various ways and be difficult to diagnose. About a quarter of cases arise extranodally and might present special problems. Developments in cytotoxic chemotherapy have led to good long-term survival prospects for aggressive lymphoma; introduction of novel approaches, including monoclonal antibody therapy, offers promise for indolent lymphoma, and should further improve prognosis for aggressive tumours.

Humans↗

Clinical, histologic, and ultrastructural features of the corneal dystrophy caused by the R124L mutation of the BIGH3 gene.

OBJECTIVE: This study was designed to describe the clinical, histologic, and ultrastructural features of the corneal dystrophy associated with the R124L mutation of the BIGH3 gene. DESIGN: Retrospective clinical and histologic review of a new genetic mutation. PARTICIPANTS: Thirty-four patients from five unrelated French families with corneal dystrophy caused by the R124L mutation of the BIGH3 gene were studied at the clinical, histologic, and ultrastructural levels. Records of patients carrying this mutation were compared with those from three unrelated patients with corneal dystrophy of Bowman's layer (CDB) type 2 (R555Q mutation) and from three unrelated patients with classic corneal granular dystrophy (R555W mutation). INTERVENTION: The mutational genetic status of the BIGH3 gene was determined for each patient, and the histologic and ultrastructural data available after corneal graft were analyzed. MAIN OUTCOMES MEASURES: Genomic DNA was extracted from peripheral blood leukocytes. Exons 4 and 12 of the BIGH3 gene were amplified by the polymerase chain reaction (PCR), and the PCR products were directly sequenced. RESULTS: All 34 patients with the R124L mutation displayed the clinical, histologic, and electron microscopic features of the dystrophy previously described as a superficial variant of corneal granular dystrophy. Combining molecular genetics with clinical and histologic findings established a clear distinction between the R555Q and R555W dystrophies. CONCLUSIONS: The R124L mutation of the BIGH3 gene is associated with specific clinical and morphologic criteria. This indicates that molecular studies are needed for an adequate classification of corneal dystrophies. All criteria are presently available to segregate the dystrophy caused by the R124L mutation (known as CDB1) from the dystrophy caused by the R555Q mutation (known as CDB2).

Adult↗

[Pathological and clinical correlations in primary cutaneous B-cell lymphomas: a series of 44 cases].

AIMS: histological and clinical relationship study of 44 cases of primary cutaneous B cell lymphoma, classified according to WHO classification. MATERIALS AND METHODS: histological, immunological and molecular analysis was correlated with clinical data. RESULTS: 33 cases (75%) were marginal zone B-cell lymphomas (MZL), with head and trunk predominance (median age = 54 years). Relapses in other mucosa-related sites occurred in 3 patients. Histological transformation implied a more aggressive treatment in 3 cases. A favorable outcome was observed in most cases. 9 (20%) diffuse large B-cell lymphomas (DLBCL) appeared as a unique nodule, with female predominance (median age = 74 years) and 4 lymphoma-related deaths which seemed age-related (> 70 years) with only one lower limb localization. Histological aggressive features were present in 3 patients with a fatal outcome. 2 (5%) WHO grade 3 follicular lymphomas (FL) had an heterogeneous phenotype, with head localization, cutaneous relapses and good outcome. CONCLUSIONS: MZL, the predominant type, has a good prognosis, although transformation can occur, needing a more aggressive treatment. DLBCL, observed in older patients, has clinical and histological prognostic factors identical to extra-cutaneous lymphomas. FL appears rare and has an heterogeneous phenotype. Relationships with its nodal counterpart remains unclear.

Adult↗

Triple Philadelphia chromosomes with major-bcr rearrangement in hypotriploid erythroleukaemia.

The Philadelphia (Ph) chromosome is observed in approximately 1% of patients with acute myeloblastic leukaemia (AML), especially subtypes M1 and M2 in the French-American-British classification. We describe here a cytogenetic and molecular investigation of a rare case with Ph-positive AML M6 (erythroleukaemia). A 63-yr-old woman was diagnosed as having erythroleukaemia. Leukaemic cells were positive for CD4 and CD7 as well as CD13, CD33, CD34 and HLA-DR. They were analyzed by G-banding, fluorescence in situ hybridization (FISH), Southern blot and reverse transcriptase polymerase chain reaction analyses. The karyotypes at diagnosis were as follows: 61, XX, -X, -1, -2, -3, -4, -5, -7, t(9;22)(q34;q11)x 2, -15, -16, -17, -18, + 19, +21, +22 [3]/61, idem, -22, +der(22)t(9;22) [36]. FISH with BCR/ABL probes showed that 39% and 57% of interphase nuclei had double and triple BCR/ABL fusion signals, respectively. Chromosome analysis in complete remission showed a normal karyotype in all 20 metaphases, confirming the diagnosis as Ph positive-acute leukaemia. FISH at relapse showed that 92% of interphase nuclei had triple fusion signals. Rearrangement of major breakpoint cluster region (M-bcr) in the BCR gene and coexpression of p210-type (b2a2) and p190-type (e1a2) BCR/ABL fusion transcripts due to alternative splicing were also detected. We conclude that clonal evolution from double to triple Ph chromosomes may be implicated in the disease progression. Considering other two reported cases, Ph-positive erythroleukaemia appears to be correlated with coexpression of myeloid/T-lymphoid markers and hyperdiploidy with double or triple Ph chromosomes, although breakpoints in the BCR gene are heterogenous.

Aneuploidy↗

Exclusion of the dymeclin and PAPSS2 genes in a novel form of spondyloepimetaphyseal dysplasia and mental retardation.

Spondyloepimetaphyseal dysplasias (SEMD) represent a heterogeneous group of conditions composed of at least 15 well-defined entities. The classification is based on clinical, radiological and molecular findings. Among them, several conditions also include a mental retardation (MR) syndrome, namely Wolcott-Rallison syndrome, Dyggve-Melchior-Clausen syndrome (DMC) and lysosomal storage disorders. Here, we report on a novel form of SEMD with MR in two Pakistani sisters born to first-cousin parents. SEMD, MR, microcephaly, ataxia, facial dysmorphism and hirsutism of back and legs were noted in the two children. Skeletal findings included flat vertebral bodies with irregular vertebral plates, irregular and flared metaphyses with vertical striations, small and irregular epiphyses, small carpal bones and narrow iliac wings without lacy pelvis iliac crest. Similarities with DMC prompted us to test and eventually exclude the DMC gene, dymeclin, by direct sequencing. Similarly, we excluded the PAPSS2 gene (3'-alpha phosphoadenosine 5'-phosphosulphate synthase 2) responsible for SEMD Pakistani type. The combination of features observed in the two sisters does not fit with any previously reported SEMD and represents therefore a novel form of autosomal recessive SEMD with MR.

Abnormalities, Multiple↗

Chemotaxonomic characterisation of Sphingomonas.

Based on published results and investigations done for this study, chemotaxonomic characteristics of all validly described species of the genus Sphingomonas, as well as unnamed strains of this genus and related genera such as Rhizomonas and Blastomonas, are presented. All representatives of this group, here designated as sphingomonads, contain ubiquinone (Q-10). The two different polyamine patterns characterized either by the predominant polyamine sym-homospermidine or spermidine separate the sphingomonads into two major groups. Complex polar lipid profiles were found in sphingomonads in addition to the characteristic compound sphingoglycolipid. Identical profiles were found only in a few phylogenetically highly related species. Common to all sphingomonads is a fatty acid composition with 2-hydroxy fatty acids (14:0 2OH in all currently recognized species) and the lack of 3-hydroxy acids, which distinguishes them from taxa outside this group. Qualitative and quantitative differences in the fatty acid compositions, in several cases, were also suitable for identification at the species level. Thus, the differences in the chemotaxonomic characteristics demonstrate that the analyses of these low molecular weight cell compounds are suitable for classification of sphingomonads.

Journal Article↗

Molecular biology of gastric carcinoma: from laboratory to bedside.

Although the advancement of molecular oncology in gastric cancer lags behind that of colorectal cancer, the rapid developments witnessed in recent years have improved our understanding of the carcinogenesis, aetiology, progression and metastasis of gastric cancer. The different molecular genetic alterations in intestinal and diffuse types of gastric cancer have further supported the concept that these two pathological types are different disease entities. The association of telomerase and cadherin changes with Helicobacter pylori infection reinforces its aetiological role. The mutated cadherin gene identified in familial gastric cancer has shone light onto the pathogenesis. Adhesion molecules have already been applied to daily clinical practice as prognostic markers. Future molecular studies will contribute to the screening, classification, disease monitoring and therapeutics of gastric cancer.

Disease Progression↗

The epidemiology of gastric cancer.

The epidemiology of gastric cancer is remarkable for both its dramatic decline in incidence over the past century and its continuing presence as the second leading cause of cancer deaths worldwide despite this decline. Factors including increased consumption of fruits and vegetables, and decreased intake of salty foods have largely been credited for the decline. Epidemiologic studies continue to provide data on other gastric cancer risk factors, including associations with Helicobacter pylori infection, as well as dietary factors, tobacco, and alcohol intake. In response to the opposing trends of decreasing distal gastric cancer and increasing gastric cardia adenocarcinoma, studies are beginning to identify gastric cancer risk factors separately by tumor subsite. Future epidemiologic studies that include information on site of origin as well as molecular markers promise to yield more homogeneous classification of case groups, which will enhance identification of underlying disease processes.

Adenocarcinoma↗

Profiling the global tyrosine phosphorylation state by Src homology 2 domain binding.

Reversible tyrosine phosphorylation plays a crucial role in signal transduction, regulating many biological functions including proliferation, differentiation, and motility. The comprehensive characterization of the tyrosine phosphorylation state of a cell is of great interest for understanding the mechanisms that underlie signaling; however, current methods for analyzing tyrosine-phosphorylated proteins in crude protein extracts provide limited information, or are laborious and require relatively large amounts of protein. We have developed a simple, rapid, and flexible competitive binding assay based on the far-Western blot technique, in which a battery of Src homology 2 domain probes is used to detect patterns of specific tyrosine-phosphorylated sites. We demonstrate that distinct profiles of tyrosine phosphorylation can be detected with high sensitivity and specificity and low background. This proteomic approach can be used to rapidly profile the global tyrosine phosphorylation state of any cell of interest and has obvious applications as a molecular diagnostic tool, for example in the classification of tumors. The general strategy we describe here is not limited to Src homology 2 domains and could be used to profile the binding sites for any class of protein interaction domain.

Animals↗

Monitoring pollution in Tunisian coasts: application of a classification scale based on biochemical markers.

Over the past decade, molecular, biochemical and cellular markers have been extensively used in pollution monitoring of aquatic environments. Biochemical markers have been selected among early molecular events occurring in the toxicological mechanisms of main contaminants. This paper assesses the marine environment quality along the Tunisian coasts using a statistical approach. Clams (Ruditapes decussatus) were collected during the four seasons of 2003 on seven different sites from the Tunisian coasts. Oxidative stress was evaluated in gills using catalase activity (Cat), neutral lipids and malonedialdehyde accumulation. Glutathione S-transferase activity is related to the conjugation of organic compounds and was evaluated in both, gills and digestive glands. Acetylcholinesterase activity was evaluated as the biomarker of exposure to organophosphorous, carbamate pesticides and heavy metals. For each biomarker, a discriminatory factor was calculated and a response index allocated. For each site, a global response index was calculated as the sum of the response index of each biomarker. Discriminant analysis shows significant differences between sites and seasons compared with control sample. Faroua (site 1) and Menzel Jemile (site 2) seem to be the less polluted with respect to the other sites for all seasons. Gargour (site 6) shows the highest Multimarker Pollution Index during the four seasons, indicating higher contamination level.

Acetylcholinesterase↗