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PubMed2006

Hydrogen multicentre bonds.

The concept of a chemical bond stands out as a major development in the process of understanding how atoms are held together in molecules and solids. Lewis' classical picture of chemical bonds as shared-electron pairs evolved to the quantum-mechanical valence-bond and molecular-orbital theories, and the classification of molecules and solids in terms of their bonding type: covalent, ionic, van der Waals and metallic. Along with the more complex hydrogen bonds and three-centre bonds, they form a paradigm within which the structure of almost all molecules and solids can be understood. Here, we present evidence for hydrogen multicentre bonds-a generalization of three-centre bonds-in which a hydrogen atom equally bonds to four or more other atoms. When substituting for oxygen in metal oxides, hydrogen bonds equally to all the surrounding metal atoms, becoming fourfold coordinated in ZnO, and sixfold coordinated in MgO. These multicentre bonds are remarkably strong despite their large hydrogen-metal distances. The calculated local vibration mode frequency in MgO agrees with infrared spectroscopy measurements. Multicoordinated hydrogen also explains the dependence of electrical conductivity on oxygen partial pressure, resolving a long-standing controversy on the role of point defects in unintentional n-type conductivity of ZnO (refs 8-10).

Journal Article↗
PubMed2000

Heritable disorders of connective tissue.

This chapter seeks to draw readers' attention to the importance of the heritable disorders of connective tissue in clinical practice. It describes the principal features of the Marfan and Ehlers-Danlos syndromes, osteogenesis imperfecta and benign joint hypermobility syndrome, their clinical and prognostic similarities and differences, and their distinguishing features. Recently revised international classifications drawing on advances in molecular genetics are described in detail. Wherever possible, patients' symptoms are explained on the basis of the altered biomechanics of genetically aberrant connective tissue matrix proteins. Finally, the chapter draws attention to the often unrecognized burden of chronic pain borne by patients with these conditions, a feature of which many rheumatologists seem unaware, and sets out a rational and holistic approach to treatment and management that is based on the best currently available evidence.

Ehlers-Danlos Syndrome↗
PubMed2002

DOLOP--database of bacterial lipoproteins.

UNLABELLED: Bacterial lipoproteins and lipid modification are gaining importance owing to their essential nature, roles in pathogenesis and interesting commercial applications. We have created an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. AVAILABILITY: The website called Database Of bacterial LipOProteins (DOLOP) is available at http://www.mrc-lmb.cam.ac.uk/genomes/dolop along with additional information on the biosynthetic pathway, supplementary material and other related figures.

Algorithms↗
PubMed2006

Genetic variation and relationships among eight Indian riverine buffalo breeds.

Twenty-seven microsatellite loci were used to define genetic variation and relationships among eight Indian riverine buffalo breeds. The total number of alleles ranged from 166 in the Toda breed to 194 each in the Mehsana and the Murrah. Significant departures from the Hardy-Weinberg equilibrium were observed for 26 locus-breed combinations due to heterozygote deficiency. Breed differentiation was analysed by estimation of F(ST) index (values ranging from 0.75% to 6.00%) for various breed combinations. The neighbour-joining tree constructed from chord distances, multidimensional scaling (MDS) display of F(ST) values and Bayesian clustering approach consistently identified the Toda, Jaffarabadi, and Pandharpuri breeds as one lineage each, and the Bhadawari, Nagpuri, Surati, Mehsana and Murrah breeds as admixture. Analysis of molecular variance refuted the earlier classification of these breeds proposed on the basis of morphological and geographical parameters. The Toda buffaloes, reared by a tribe of the same name, represent an endangered breed from the Nilgiri hills in South India. Divergence time of the Toda buffaloes from the other main breeds, calculated from Nei's standard genetic distances based on genotyping data on seven breeds and 20 microsatellite loci, suggested separation of this breed approximately 1800-2700 years ago. The results of the present study will be useful for development of rational breeding and conservation strategies for Indian buffaloes.

Animals↗
PubMed2005

Distinct expression patterns of claudin-1 and claudin-4 in intraductal papillary-mucinous tumors of the pancreas.

The expression of claudin-4 was investigated in human pancreas, pancreatic ductal adenocarcinomas, and intraductal papillary-mucinous tumors of the pancreas (IPMT), and compared with that of claudin-1. In human adult pancreatic specimens, both claudin-1 and claudin-4 were immunohistochemically found in main and branching pancreatic ducts, terminal ductules and acinic cells, with the exception of endocrine cells. Of 12 cases of pancreatic ductal adenocarcinoma, 11 (92%) had positive immunostaining for claudin-4, and seven (58%) for claudin-1. In 44 lesions of 22 cases of IPMT, including six hyperplastic foci distant from the main lesions, clauidin-1 was positive in three out of six (50%) hyperplastic foci, 14 out of 17 (82%) adenomas, three out of 10 (30%) borderline tumors, two out of six (33%) non-invasive carcinomas, and one out of five (20%) invasive carcinomas, producing a statistically negative correlation with histological tumor grades. In contrast, claudin-4 was negative in the six hyperplastic foci, and positive in four out of the 17 (24%) adenomas, five out of the 10 (50%) borderline tumors, five out of the six (83%) non-invasive carcinomas, and four out of the five (80%) invasive carcinomas, producing a statistically positive correlation with histological tumor grades. On study of IPMT subtypes, claudin-1 was positive in nine out of 10 (90%) clear-cell types, seven out of 20 (35%) dark-cell types, and four out of eight (50%) compact-cell types. In contrast, claudin-4 was positive in two out of the 10 (20%) clear-cell types, 13 out of the 20 (65%) dark-cell types, and three out of the eight (38%) compact-cell types. These distinct expression patterns of claudin-1 and claudin-4 suggest that both claudins serve as useful molecular markers for the tumor classification of IPMT.

Adenocarcinoma, Mucinous↗
PubMedDate not supplied

Clinical applications of DNA microarray analysis.

Microarray technology provides a revolutionary macro-genetic and bioinformatic-rich platform for understanding human diseases. DNA microarrays facilitate the study of complex diseases, enabling several observations simultaneously that can become foundations for newer hypotheses-shifting us towards a non-reductionist approach to biological phenomenon. This appears of particular value for scientific and clinical dissection of tumor pathologies. Despite the tremendous potential presented by microarray technology for the investigation of disease, concrete insights and advances that translate to the clinical setting are only recently beginning to be tapped. Here, we discuss specific examples of how microarray technology is being integrated into our ever-evolving approach to clinical disease. We focus on molecular strategies for (a) disease classification, (b) disease outcome, and (c) disease mechanisms.

Gene Expression Profiling↗
PubMed2005

Genetics of the polymicrogyria syndromes.

Polymicrogyria is a relatively common malformation of cortical development, characterised by multiple small gyri with abnormal cortical lamination. The different forms of polymicrogyria encompass a wide range of clinical, aetiological, and histological findings. Advances in imaging have improved the diagnosis and classification of the condition. The molecular basis of polymicrogyria is beginning to be elucidated with the identification of a gene, GPR56, for bilateral frontoparietal polymicrogyria. Functional studies of the GPR56 gene product will yield insights not only into the causes of polymicrogyria but also into the mechanisms of normal cortical development and the regional patterning of the cerebral cortex. Based on imaging studies, several other region specific patterns of polymicrogyria have been identified, and there is increasing evidence that these may also have a significant genetic component to their aetiology. This paper reviews current knowledge of the different polymicrogyria syndromes, with discussion of clinical and imaging features, patterns of inheritance, currently mapped loci, candidate genes, chromosomal abnormalities, and implications for genetic counselling.

Cerebral Cortex↗
PubMed1999

HLA class II associations with rheumatic heart disease are more evident and consistent among clinically homogeneous patients.

BACKGROUND: Discrepancies in reported HLA class II associations with rheumatic heart disease (RHD) may have been due to inaccuracies of serological typing reagents and/or lack of defined clinical classification of patients analyzed. The molecular association between HLA and RHD was investigated in patients with defined clinical outcome. METHODS AND RESULTS: Class II allele/haplotype distribution was determined in 2 groups of RHD patients (n=88) and a control group (n=59). Patients were divided into the mitral valve disease (MVD) category (ie, those with mitral regurgitation with or without mitral stenosis) and the multivalvular lesions (MVL) category, with impairment of aortic and/or tricuspid valves in addition to mitral valve damage. The MVD category (n=65) accounted for 74% of patients and included significantly fewer recurrent RF episodes compared with MVL patients (P=0.002). CONCLUSIONS: Significant increases in DRB1*0701 and DQA1*0201 alleles and DRB1*0701-DQA1*0201 haplotypes were found in patients. Removal of the MVL patients from analysis increased the strength of HLA associations among the MVD sample. The frequency of DQA1*0103 allele was decreased and the DQB1*0603 allele was absent from the patient group, suggesting that these alleles may confer protective effects against RHD. DQ alleles in linkage disequilibrium with DR alleles appear to influence risk/protection effect: whereas the DRB1*13-DQA1*0501-3-DQB1*0301 haplotype showed a trend toward risk, the DRB1*13-DQA1*0103-DQB1*0603 haplotype was absent in the RHD sample. Our data indicate that certain class II alleles/haplotypes are associated with risk or protection from RHD and that these associations appear to be stronger and more consistent when analyzed in patients with relatively more homogeneous clinical manifestations.

Adolescent↗
PubMed1995

Binding-, intracellular transport-, and biosynthesis-defective mutants of vasopressin type 2 receptor in patients with X-linked nephrogenic diabetes insipidus.

Nephrogenic diabetes insipidus (NDI) is most often an X-linked disorder in which urine is not concentrated due to renal resistance to arginine vasopressin. We recently identified four vasopressin type 2 receptor gene mutations in unrelated X-linked NDI families, including R143P, delta V278, R202C, and 804insG. All these mutations reduced ligand binding activity to < 10% of the normal without affecting mRNA accumulation. To elucidate whether the receptors are expressed on the cell surface, we analyzed biosynthesis and localization of tagged or untagged receptors stably expressed in Chinese hamster ovary (CHO) cells, using two antibodies directed against distinct termini. Whole-cell and surface labeling studies revealed that the R202C clone had both surface-localized (50-55 kD) and intracellular proteins (40 and 75 kD), similar to the wild-type AVPR2 clone, whereas the R143P and delta V278 clones lacked the surface receptors, despite relatively increased intracellular components. The 804insG mutant cell produced no proteins despite an adequate mRNA level. Immunofluorescence staining confirmed that the R202C mutant reaches the cell surface, whereas the R143P and delta V278 mutants are retained within the cytoplasmic compartment. Thus, R202C, R143P/delta V278, and 804insG result in three distinct phenotypes, that is, a simple binding impairment at the cell surface, blocked intracellular transport, and ineffective biosynthesis or/and accelerated degradation of the receptor, respectively, and therefore are responsible for NDI. This phenotypic classification will help understanding of molecular pathophysiology of this disorder.

Amino Acid Sequence↗
PubMed2003

A two-centre evaluation of the human organotypic skin explant culture model for screening contact allergens.

Animal models are considered to be the "gold standard" for determining the potential contact allergenicity of low molecular weight chemicals. However, governmental regulations and ethical considerations limit the use of animals for such purposes. There is therefore a need for in vitro alternative models. The human organotypic skin explant culture (HOSEC) model is reported to be a promising alternative method for the predictive testing of contact allergens. The accelerated migration of Langerhans cells from the epidermis upon exposure to contact allergens is used to identify chemicals that are potentially capable of inducing a delayed-type hypersensitivity. In the study described in this paper, the model was further refined, and used, in two independent laboratories, to screen 23 low molecular weight compounds of known classification for their allergenicity. Each laboratory was able to accurately detect the contact allergens, despite small variations in the protocols used. However, the classification of dermal irritants, which have often been falsely classified as allergens, varied between the two laboratories. Despite the current limitations of the HOSEC model, the accuracy of the predictions made (sensitiser or non-sensitiser) compare favourably with classifications obtained with commonly used animal models. The HOSEC model has the potential to be developed further as an in vitro alternative to animal models for screening for contact allergens.

Allergens↗
PubMedDate not supplied

Low incidence of hereditary nonpolyposis colorectal cancer syndrome in a selected area of the Lombardy Cancer Registry.

AIMS AND BACKGROUND: Epidemiological investigations on the frequency of hereditary nonpolyposis colorectal cancer (HNPCC) syndrome are few and have shown a variable worldwide incidence ranging from 1% to 7% of all colorectal cancers (CRCs). In Italy, relevant differences have been observed: 2.8-3% of all CRCs in northern regions and less than 1% in southern regions. The aim of the present study was to investigate the HNPCC incidence in a selected area of northern Italy belonging to the Lombardy Cancer Registry. METHODS AND STUDY DESIGN: We analyzed 197 consecutive patients with newly diagnosed CRCs, histologically verified, and resident in two areas of the Lombardy Cancer Registry. For each case, genetic counseling with at least three generations pedigree reconstruction, HNPCC classification according to Amsterdam criteria, molecular analysis for microsatellite instability and immunohistochemistry for hMLH1 and hMSH2 were performed. RESULTS: A very low frequency (0.5%) of HNPCC fulfilling the Amsterdam criteria was found in comparison to the other Italian areas. Such an incidence seems to be due to actual population differences and reflects a genetic heterogeneity. CONCLUSIONS: The data underline the importance of a precise knowledge of actual HNPCC incidence in different populations in order to optimize effectiveness and efficiency of screening programs for the disease.

Adult↗
PubMed2000

Non-Hodgkin's Lymphoma: Molecular Features of B Cell Lymphoma.

The rapid increase in the incidence of the B cell non-Hodgkin's lymphomas (NHL) and improved understanding of the mechanisms involved in their development renders timely a review of the theoretical and practical aspects of molecular abnormalities in B cell NHL. In Section I, Dr. Macintyre addresses the practical aspects of the use of molecular techniques for the diagnosis and therapeutic management of patients with B cell NHL. While detection of clonal Ig rearrangements is widely used to distinguish reactive from malignant lymphoproliferative disorders, molecular informativity is variable. The relative roles of cytogenetic, molecular and immunological techniques in the detection of genetic abnormalities and their protein products varies with the clinical situation. Consequently, the role of molecular analysis relative to morphological classification is evolving. Integrated diagnostic services are best equipped to cope with these changes. Recent evidence that large scale gene expression profiling allows improved prognostic stratification of diffuse large cell lymphoma suggests that the choice of diagnostic techniques will continue to change significantly and rapidly. In Section II, Dr. Willerford reviews current understanding of the mechanisms involved in immunoglobulin (Ig) gene rearrangement during B lymphoid development and the way in which these processes may contribute to Ig-locus chromosome translocations in lymphoma. Recent insights into the regulation of Ig gene diversification indicate that genetic plasticity in B lymphocytes is much greater than previously suspected. Physiological genomic instability, which may include isotype switching, recombination revision and somatic mutation, occurs in germinal centers in the context of immune responses and may explain longstanding clinical observations that link immunity and lymphoid neoplasia. Data from murine models and human disorders predisposing to NHL have been used to illustrate these issues. In Section III, Dr. Morris reviews the characteristics and consequences of deregulation of novel "proto-oncogenes" involved in B cell NHL, including PAX5 (chromosome 9p 13), BCL8 (15q11-q13), BCL9, MUC1, FcgammaRIIB and other 1q21-q22 genes and BCL10 (1p22). The AP12-MLT/MALT1 [t(11;18)(q21;q21)] fusion transcript is also described.

Journal Article↗
PubMed2006

Microbial identification by mass cataloging.

BACKGROUND: The public availability of over 180,000 bacterial 16S ribosomal RNA (rRNA) sequences has facilitated microbial identification and classification using hybridization and other molecular approaches. In their usual format, such assays are based on the presence of unique subsequences in the target RNA and require a prior knowledge of what organisms are likely to be in a sample. They are thus limited in generality when analyzing an unknown sample.Herein, we demonstrate the utility of catalogs of masses to characterize the bacterial 16S rRNA(s) in any sample. Sample nucleic acids are digested with a nuclease of known specificity and the products characterized using mass spectrometry. The resulting catalogs of masses can subsequently be compared to the masses known to occur in previously-sequenced 16S rRNAs allowing organism identification. Alternatively, if the organism is not in the existing database, it will still be possible to determine its genetic affinity relative to the known organisms. RESULTS: Ribonuclease T1 and ribonuclease A digestion patterns were calculated for 1,921 complete 16S rRNAs. Oligoribonucleotides generated by RNase T1 of length 9 and longer produce sufficient diversity of masses to be informative. In addition, individual fragments or combinations thereof can be used to recognize the presence of specific organisms in a complex sample. In this regard, 140 strains out of 1,921 organisms (7.3%) could be identified by the presence of a unique RNase T1-generated oligoribonucleotide mass. Combinations of just two and three oligoribonucleotide masses allowed 54% and 72% of the specific strains to be identified, respectively. An initial algorithm for recovering likely organisms present in complex samples is also described. CONCLUSION: The use of catalogs of compositions (masses) of characteristic oligoribonucleotides for microbial identification appears extremely promising. RNase T1 is more useful than ribonuclease A in generating characteristic masses, though RNase A produces oligomers which are more readily distinguished due to the large mass difference between A and G. Identification of multiple species in mixtures is also feasible. Practical applicability of the method depends on high performance mass spectrometric determination, and/or use of methods that increase the one dalton (Da) mass difference between uracil and cytosine.

Algorithms↗
PubMed1992

Acute leukemias with the t(4;11)(q21;q23).

The t(4;11)(q21;q23) has been associated with marked lineage heterogeneity. Most of the reported cases were classified as acute lymphoblastic leukemia (ALL). The t(4;11) is one of the commonest specific chromosomal translocations in ALL, occurring in 2% of childhood and 5% of adult cases. In childhood ALL, this translocation is associated with female sex, age less than 1 year, hyperleukocytosis, CD10-/CD19+ B-precursor cell immunophenotype, and myeloid-associated antigen (CD15) expression. There also appears to be an age-related difference in treatment outcome. Adults had the worst prognosis, and children aged 1 to 9 years appeared to have a better outcome than infants or adolescents. Reported cases of acute myeloid leukemia (AML) or secondary leukemia with the t(4;11) have not been well characterized. It is intriguing that virtually all of the reported cases with secondary leukemia had received epipodophyllotoxins or doxorubicin, agents that affect topoisomerase II and are associated with secondary AML characterized by 11q23 abnormalities. Identification of the involved gene(s) in the t(4;11) will provide a molecular approach permitting more accurate classification of these cases.

Acute Disease↗
PubMed2002

DNA fingerprinting of jute germplasm by RAPD.

The genotype characteristic of cultivars was investigated, along with varieties of both of the jute species, Corchorus olitorius and Corchorus capsularis, in the germplasm collection at the Bangladesh Jute Research Institute (BJRI). DNA fingerprinting was generated for 9 different varieties and 12 accessions of jute cultivars by using random amplified polymorphic DNA (RAPD). A total of 29 arbitrary oligonucleotide primers were screened. Seven primers gave polymorphism within the varieties, and 6 primers detected polymorphism within the accessions that were tested. A dendrogram was engendered from these data, and this gave a distinct clustering of the cultivated species of jute. Therefore, we generated RAPD markers, which are species-specific. These primers can distinguish between C. olitorius and C. capsularis. From the dendrogram that we generated between the various members of these two species, we found the existing genetic classification that agrees with our molecular marking data. A different dendrogram showed that jute accessions could be clustered into three groups. These data will be invaluable in the conservation and utilization of the genetic pool in the germplasm collection.

Base Sequence↗
PubMed2000

Multifaceted approach to the diagnosis and classification of acute leukemias.

Until recently, the diagnosis and classification of acute myeloid (AML) and acute lymphoblastic (ALL) leukemias was based almost exclusively on well-defined morphologic criteria and cytochemical stains. Although most cases can be diagnosed by these methods, there is only modest correlation between morphologic categories and treatment responsiveness and prognosis. The expansion of therapeutic options and improvement in remission induction and disease-free survival for both AML and ALL have stimulated emphasis on defining good and poor treatment response groups. This is most effectively accomplished by a multifaceted approach to diagnosis and classification using immunophenotyping, cytogenetics, and molecular analysis in addition to the traditional methods. Immunophenotyping is important in characterizing morphologically poorly differentiated acute leukemias and in defining prognostic categories of ALL. Cytogenetic and molecular studies provide important prognostic information and are becoming vitally important in determining the appropriate treatment protocol. With optimal application of these techniques in the diagnosis of acute leukemias, treatment strategies can be more specifically directed and new therapeutic approaches can be evaluated more effectively.

Acute Disease↗
PubMed2001

Pituitary adenomas.

Human pituitary adenomas are benign neoplasms composed of hormonal adenohypophyseal cells. They arise in the sella turcica, and are characterized by a wide range of biological behavioral related not only to hormonal but also to proliferative activities. In the past, pituitary adenoma studies have mainly been devoted to histological and ultrastructural classification improved by immunohistochemical techniques. Molecular biology, cytogenetic studies, associated to experimental animal models, transgenic and knockout mice technologies, have allowed new approaches, especially concerning pathogenesis and progression. It became obvious that tumorigenesis has to be considered as a multistep event, inasmuch as different factors share numerous homologies. On the other hand, it could be supposed that the knowledge of the biological aggressiveness could led to an appropriate follow-up as well as specific therapy.

Adenoma↗
PubMed2003

[The application of RAPD technology in genetic diversity detection of Jute].

The fingerprints of 10 species including 27 accessions in genus Corchorus were investigated with the technique of RAPD. Twenty-five primers were screened from 119 random primers, and a total of 329 DNA fragments were amplified ranging from 0.3-3.0 kb, 253 (87.78%), which were polymorphic. The average number of DNA band produced by each primer was 13.16. UPGMA cluster analysis and Nei's similarity coefficients were carried out and a dendrogram was constructed using software Biol D++. The results showed as follows: (1) There were abundant genetic diversities among 15 wild species and 12 cultivated species in Corchorus with genetic similarity coefficients ranging from 0.49-0.98. (2) The accessions could be clustered into three groups at cultivated species, and their close wild species were obviously different from wild species genetically. (3) At the level of D = 0.850, 27 accessions of Jute could be classified into ten groups, including C. sestuans, C. tridens, C. fascicularis, C. psendo-olitorius, C. psendo-capsularis, C. tilacutaris, Tian Jute (untitled), C. capsularis, C. olitorius and C. uriticifolius. Among which C. capsularis presented closer relationship with C. olitorius and further relationship with C. uriticifolius. The results matched well with that of the morphologic classification. (4) According to the molecular cluster tree, C. uritifolius, Chinese Tina Jute (untitled) and C. aestuans were at the basic level, revealing that these three species could be the primary wild species of Jute. (5) The tree also showed that C. tilacularis 21C from Africa could be a ecological subspecies of C. tilacularis, whilst niannian cai, ma cai and zhu cai collected different ecological types of C. aestuans, C. capsularis from Hainan was a close wild species of round fruit Jute cultivated species, and three species of C. olitorius collected from zhangpu, Henan and Mali were close wild species of long fruit Jute cultivated species. (6) within two cultivated species, the genetic similarity coefficients in round fruit cultivated species was higher than that of in long fruit cultivated species.

Corchorus↗