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PubMed1988

Osteogenesis imperfecta.

Major advances have occurred in the classification of OI and in the definition of underlying molecular defects. A clearer understanding of the pathogenesis of OI and of the relationships between the phenotypes and genotypes should emerge. The study of induced mutations in selected regions of the collagen genes with expression in cultured cells or transgenic mice should hasten this process. These advances will also provide a basis for studies into the large number of other genetically determined connective tissue disorders that are grouped together as the skeletal dysplasias. The results of recent studies in OI are providing a unique insight into many aspects of collagen and connective tissue biochemistry, physiology and pathology.

Adolescent↗
PubMedDate not supplied

Generalization of a targeted library design protocol: application to 5-HT7 receptor ligands.

Herein a general concept for the design of targeted libraries for proteins with binding sites that are divided into subsites is laid out, including several practical aspects and their solutions. The design is based on a chemogenomic classification of the subsites followed by collection of bioactive molecular fragments and virtual library generation. The general process is outlined and applied to the assembly of a library of 500 molecules targeting the serotonin type 7 (5-HT7) receptor, a class A G-Protein Coupled Receptor (GPCR). Utilizing commercially available building blocks of similar size and composition, a reference library was created. Control sets of known ligands for the 5-HT7 receptor, other GPCRs, and nuclear receptors were collected from literature sources. Principal component analysis of molecular descriptors for the two libraries and the literature sets, displayed a focusing of the targeted library to the region in the chemical space defined by the literature actives, suggesting a denser coverage of the bioactive region than for the more diverse reference library. Additional computational validations, including PCA class predictions, 3D pharmacophore modeling, and docking calculations all indicated an enrichment factor of 5-HT7 ligand-like molecules in the range of 2-4 for the targeted library compared to the reference library.

Binding Sites↗
PubMed2005

Sensing the physicochemical nature of he and ne in micropores by adsorption measurements.

He and Ne in contact with molecular sieves in the form of crystalline A zeolites and amorphous carbon molecular sieves fibers (CMSF) were studied by adsorption measurements. Classification of the effective enclosure of zeolitic apertures and of graphitic constrictions, as determined by recent temperature-programmed desorption mass spectrometry (TPD-MS) studies of adsorption of He and Ne onto these materials, was utilized in making a prudent choice of samples and experimental conditions. In view of the former TPD information, the behaviors of adsorption and volumetric measurements reported herein are straightforwardly interpreted. The combined TPD, adsorption isotherms, and dead volume data deepen the understanding of the physicochemical nature of adsorbed gas, where gas adsorption in the vicinity of pore constrictions and/or apertures as well as on the inner surface areas of pores and/or cages could be resolved. Previous conclusions that the huge activation energies measured for Ne/CMSF at high temperatures are unlikely to characterize chemical desorption but reflect those required for overcoming the barrier of effectively constricted apertures were confirmed by the volumetric data presented here. At 77 K, considerable He adsorption was observed in the porous solids and found to be responsible for abnormal deduced values of dead volumes. The occurrence of significant adsorption of He onto A zeolites and CMSF at 77 K warrants the realization that in cases concerning porous materials, volumetrically deduced quantities should not be taken for granted, but should be carefully considered and uniquely interpreted in relation to the specific experimental conditions under which they are taken.

Journal Article↗
PubMed2007

Reduced genetic structure of north Ethiopian cattle revealed by Y-chromosome analysis.

Ethiopia is considered to be a putative migratory corridor for both Near-East Bos taurine and Arabian and Indian B. indicus cattle into East Africa. African pastoralism, which is associated with adaptation to specific habitats and farming systems, has contributed to the composite constitution of Ethiopian cattle. We analyse, for the first time, five Y-chromosome microsatellite markers from seven north Ethiopian cattle populations, using a European Holstein-Friesian population as a reference, to assess the paternal gene pool and to explore the mechanisms behind the genetic structure. Our results reveal that the indicine alleles predominate in the present populations, with only one animal in the Arado carrying the taurine alleles. The north Ethiopian cattle populations with one exception (Abergelle) are characterized by a general low Y-chromosome haplotype diversity, as well as by a reduced interpopulation variance (Phi(ST)=4.0%), which can be a result of strong male-mediated selective sweeps. Population structure revealed by multidimensional-scaling analysis differentiates two populations (Arado and Abergelle) from the rest. Analysis of molecular variance does not lend support to the traditional classification for the populations, which is mainly based on physical characteristics. A network analysis indicates two closely related founding haplotypes accounting for a large proportion (50.0% in Abergelle and 85.0-94.7% in others) of north Ethiopian cattle Y-chromosomes. Our findings point to a common, but limited, paternal origin of the north Ethiopian cattle populations and strong male-mediated gene flow among them. The findings also provide insight into the historical immigration of cattle into East Africa.

Animals↗
PubMed2003

Computational analysis of flow-cytometry antigen expression profiles in childhood acute lymphoblastic leukemia: an MLL/AF4 identification.

Precursor B-acute lymphoblastic leukemia (pB-ALL) is a heterogeneous disease and multiparameter flow cytometry, molecular genetics, and cytogenetic studies have all contributed to classification of subgroups with prognostic significance. Recently, gene expression microarray technology has been used to investigate lymphoblastic leukemias, demonstrating that known and novel pB-ALL subclasses can be separated on the basis of gene expression profiles. The strength of microarray technique lays in part in the multivariate nature of the expression data. We propose a parallel multiparametric approach based on immunophenotypic flow-cytometry expression data for the analysis of leukemia patients. Specifically, we tested the potential of this approach on a data set of 145 samples of pediatric pB-ALL that included 46 samples positive for mixed lineage leukemia (MLL) translocations (MLL+) and 99 control pB-ALLs, negative for this translocation (MLL-). The expression levels of 16 marker proteins have been monitored by four-color flow cytometry using a standardized diagnostic panel of antibodies. The protein expression database has been then analyzed using those univariate and multivariate computational techniques normally applied to mine and model large microarray data sets. Marker protein expression profiling not only allowed separating pB-ALL cases with an MLL rearrangement from other ALLs, but also demonstrates that MLL+ leukemias constitute a heterogeneous group in which MLL/AF4 leukemias represent a homogenous subclass described by a specific expression fingerprint.

Adolescent↗
PubMed2001

The molecular biology of von Willebrand disease.

von Willebrand disease (VWD) is a common autosomally inherited bleeding disorder associated with mucosal or trauma-related bleeding in affected individuals. VWD results from either a quantitative or qualitative deficiency of von Willebrand factor (VWF)--a glycoprotein with essential roles in primary haemostasis and as a carrier of coagulation factor VIII (FVIII) in the circulation. In recent years the identification of mutations in the VWF gene in patients with VWD has improved our understanding of the structure and function of the VWF protein, and has illustrated the importance of specific regions of VWF for its interaction with other components of the vasculature. The underlying genetic lesions and associated molecular pathology have been identified in many cases of type 2A, type 2B, type 2M, type 2N and type 3 VWD. However in the most common variant, type 1 VWD, the causative molecular defect is unknown in the large majority of cases. In the absence of an understanding of the molecular pathology underlying type 1 VWD, precise diagnosis and classification of this common disorder remains problematic.

Family Health↗
PubMed2003

Immunohistochemistry in the diagnosis of soft tissue tumours.

Immunohistochemistry is particularly important in the field of soft tissue tumours because of their variety and the frequent difficulty of diagnosis. The first part of this paper discusses useful or new antibodies, together with others that are no longer of use. The second part is devoted to the role of immunohistochemistry in the diagnosis of soft tissue tumours: identification of some rare or atypical benign lesions, identification of non-mesenchymal malignant tumours, and classification of sarcomas. The respective roles of immunohistochemistry and molecular biology are underlined.

Antibodies↗
PubMed2004

Telangiectatic focal nodular hyperplasia: a variant of hepatocellular adenoma.

BACKGROUND & AIMS: "Telangiectatic focal nodular hyperplasia" designate atypical lesions considered as variants of focal nodular hyperplasia (FNH). However, because "telangiectatic FNH" share several morphologic patterns with hepatocellular adenomas, classification of such lesions deserve further clarification. Therefore, the aim of the present study was to reconsider the classification of telangiectatic FNH with the help of a molecular approach. METHODS: Ten telangiectatic FNH, 6 typical FNH, and 6 hepatocellular adenomas were studied. DNA, RNA, and protein from each lesion were extracted. Clonality was assessed by the study of the X chromosome inactivation pattern (HUMARA assay). Angiopoietin (ANGPT-1 and ANGPT-2) mRNA, genes the expression of which is typically modified in FNH, were quantified by a real-time RT-PCR procedure. Protein profiles were analyzed by SELDI-TOF PROTEINCHIP (Cyphergen Biosystem, Inc., Fremont, CA) technology. RESULTS: Although all informative cases of FNH (5 of 6) and hepatocellular adenomas (6 of 6) were polyclonal and monoclonal, respectively, clonal analysis showed a nonrandom pattern of X chromosome inactivation consistent with a monoclonal lesion in 6 of 8 cases of telangiectatic FNH. The mean value of the ANGPT-1/ANGPT-2 mRNA ratio was 21.4 in FNH, 2.6 in adenomas, and 2.1 in telangiectatic FNH (P <or = 0.001 in telangiectatic FNH vs. FNH). SELDI-TOF PROTEINCHIP profiling and hierarchical clustering analysis showed that all except 1 telangiectatic FNH clustered within the group of hepatocellular adenomas. CONCLUSIONS: These results show that telangiectatic FNH display a molecular pattern closer to that of hepatocellular adenomas than to FNH and suggest that these lesions should instead be referred to as "telangiectatic hepatocellular adenomas."

Adenoma, Liver Cell↗
PubMed2001

MDM2+/CDK4+/p53+ oral liposarcoma: case report and review of the literature.

Although liposarcoma is one of the most common soft tissue sarcomas, its location in the oral cavity is very rare. To our knowledge, only 43 cases of liposarcoma originating in the oral tissues have been reported in the English-language literature. In this article, we report a case of well-differentiated liposarcoma affecting the cheek of a 28-year-old man and review the oral liposarcoma literature. Immunohistochemical analysis of the tumor revealed an MDM2+/CDK4+/p53+ immunophenotype that is consistent with the immunohistochemical profile of well-differentiated liposarcoma originating in other areas of the body. Quantitative polymerase chain reaction analysis of the DNA levels of the MDM2 (human homologue of the murine double-minute type 2), CDK4 (cyclin-dependent kinase 4), and SAS (sarcoma amplified sequence), genes was performed, revealing only SAS gene amplification. The possibility of misdiagnosis of oral liposarcoma because of its sometimes inconspicuous clinical and microscopic features is emphasized. Careful pathologic examination of liposarcoma is essential for discrimination from benign adipose tissue neoplasms and for precise histologic classification, both of major prognostic significance. Possible implications of molecular and cytogenetic analysis for unraveling the pathogenesis and determining the prognosis of liposarcoma are discussed.

Adult↗
PubMed2002

Automatic classification of protein structure by using Gauss integrals.

We introduce a method of looking at, analyzing, and comparing protein structures. The topology of a protein is captured by 30 numbers inspired by Vassiliev knot invariants. To illustrate the simplicity and power of this topological approach, we construct a measure (scaled Gauss metric, SGM) of similarity of protein shapes. Under this metric, protein chains naturally separate into fold clusters. We use SGM to construct an automatic classification procedure for the CATH2.4 database. The method is very fast because it requires neither alignment of the chains nor any chain-chain comparison. It also has only one adjustable parameter. We assign 95.51% of the chains into the proper C (class), A (architecture), T (topology), and H (homologous superfamily) fold, find all new folds, and detect no false geometric positives. Using the SGM, we display a "map" of the space of folds projected onto two dimensions, show the relative locations of the major structural classes, and "zoom into" the space of proteins to show architecture, topology, and fold clusters. The existence of a simple measure of a protein fold computed from the chain path will have a major impact on automatic fold classification.

Models, Molecular↗
PubMed2003

Etiologic diagnosis of infective endocarditis by broad-range polymerase chain reaction: a 3-year experience.

We analyzed surgically resected endocardial specimens from 49 patients by broad-range PCR. PCR results were compared with (1) results of previous blood cultures, (2) results of culture and Gram staining of resected specimens, and (3) clinical data (Duke criteria). Molecular analyses of resected specimens and previous blood cultures showed good overall agreement. However, in 18% of patients with sterile blood cultures, bacterial DNA was found in the resected materials. When data from patients with definite or rejected cases of infective endocarditis (IE) were included, the sensitivity, specificity, and positive and negative predictive values of broad-range PCR were 82.6%, 100%, 100%, and 76.5%, respectively, overall, and 94.1%, 100%, 100%, and 90%, for cases of native valve endocarditis. The sensitivity, specificity, and positive and negative predictive values of culture of resected specimens from patients with native valve endocarditis were 17.6%, 88.9%, 75%, and 36.4%. We recommend broad-range PCR of surgically resected endocardial material in cases of possible IE, in cases of suspected IE in which blood cultures are sterile, and in cases in which organisms grow in blood cultures but only Duke minor criteria are met. We propose to add molecular techniques to the pathologic criteria of the Duke classification scheme.

Adolescent↗
PubMed2003

Probabilistic disease classification of expression-dependent proteomic data from mass spectrometry of human serum.

We have developed an algorithm called Q5 for probabilistic classification of healthy versus disease whole serum samples using mass spectrometry. The algorithm employs principal components analysis (PCA) followed by linear discriminant analysis (LDA) on whole spectrum surface-enhanced laser desorption/ionization time of flight (SELDI-TOF) mass spectrometry (MS) data and is demonstrated on four real datasets from complete, complex SELDI spectra of human blood serum. Q5 is a closed-form, exact solution to the problem of classification of complete mass spectra of a complex protein mixture. Q5 employs a probabilistic classification algorithm built upon a dimension-reduced linear discriminant analysis. Our solution is computationally efficient; it is noniterative and computes the optimal linear discriminant using closed-form equations. The optimal discriminant is computed and verified for datasets of complete, complex SELDI spectra of human blood serum. Replicate experiments of different training/testing splits of each dataset are employed to verify robustness of the algorithm. The probabilistic classification method achieves excellent performance. We achieve sensitivity, specificity, and positive predictive values above 97% on three ovarian cancer datasets and one prostate cancer dataset. The Q5 method outperforms previous full-spectrum complex sample spectral classification techniques and can provide clues as to the molecular identities of differentially expressed proteins and peptides.

Algorithms↗
PubMed1999

Mutations in the SLC3A1 gene in cystinuric patients: frequencies and identification of a novel mutation.

Cystinuria is a frequent autosomal recessive transport disorder characterized by defective renal resorption of cystine and other dibasic amino acids. Biochemically, three types of cystinuria can be defined. Here we present our results of screening for mutations in the SLC3A1 gene, which codes for a dibasic amino acid transporter protein and appears to be involved in the pathogenesis of cystinuria type I. Our study population consists of 5 Italian cystinuria type I patients and 10 cystinuric patients as yet unclassified as to clinical type. The latter were of different ethnic origin. In total, we found 13 point mutations and 8 genomic rearrangements in 15 cystinuric patients, i.e., our detection rate was 70% (23/30 chromosomes). Remarkably, in patients known to be suffering from cystinuria type I, the mutation detection rate was only 50%, whereas in patients unselected as to cystinuria type, we found 80% of mutations. Additionally, our results, as with those published in the literature, indicate a possible population specific distribution of mutations: Each of the 4 Greek patients analyzed here showed homozygosity for mutation T216M in exon 3. Analysis of a Yugoslavian patient showed homozygosity for a novel mutation, R365L, in exon 6 (nt1094G > T). Findings from molecular genetic studies, as well as physiological investigations, suggest that there are further genes that play a role in the etiology of cystinuria. Nevertheless, our results show that screening for mutations in the SLC3A1 gene can be a meaningful step toward molecular genetic diagnosis of cystinuria in patients without biochemical classification. As with cystic fibrosis, the finding of specific mutations in particular ethnic populations, suggest that the diagnostic approach should take into consideration a patient's ethnic origins.

Amino Acid Transport Systems, Basic↗
PubMed2000

Cowden disease and Lhermitte-Duclos disease: characterization of a new phakomatosis.

OBJECTIVE: Lhermitte-Duclos disease, or dysplastic gangliocytoma of the cerebellum, is an unusual hamartomatous lesion that can cause progressive mass effects in the posterior fossa. Cowden disease, or multiple hamartoma-neoplasia syndrome, is a rare autosomal dominant disorder characterized by mucocutaneous hamartomas and high incidences of systemic malignancies. We recently treated a patient with manifestations of both Lhermitte-Duclos disease and Cowden disease, and we were intrigued by the occurrence of these two rare disorders in the same patient. The purpose of the present study was to examine the nature of the association between Lhermitte-Duclos disease and Cowden disease. METHODS: The records for all patients who had been diagnosed at our institution as having Lhermitte-Duclos disease were reviewed, to determine whether these patients also exhibited manifestations of Cowden disease. Data were obtained from multiple sources, including patient interviews, correspondence with treating physicians, and chart reviews. RESULTS: During the past 40 years, five patients were diagnosed at Case Western Reserve University as having Lhermitte-Duclos disease. All five patients exhibited manifestations of Cowden disease. Before this review, Cowden disease had not been diagnosed for three of the patients. In our most recent case, the diagnoses of both disorders were established preoperatively. That patient was observed to have a deletion in the critical portion of Exon 5 of the PTEN gene, the gene associated with Cowden disease. CONCLUSION: Inclusion of Lhermitte-Duclos disease in the Cowden disease spectrum suggests that Cowden disease is a true phakomatosis, with hamartomas arising from cutaneous and neural ectoderm. Recent advances in molecular genetics may help to refine the current descriptive classification of the phakomatoses. The association between Lhermitte-Duclos disease and Cowden disease has been under-recognized and under-reported. Recognition of this association has direct clinical relevance, because diligent long-term follow-up monitoring of individuals with Lhermitte-Duclos disease and Cowden disease may lead to the early detection of malignancy.

Adolescent↗
PubMed2005

The spectrum of cutaneous T-cell lymphomas: new insights into biology and therapy.

PURPOSE OF REVIEW: Cutaneous T-cell lymphomas represent clinically and biologically a heterogeneous group of non-Hodgkin lymphomas according to the new revised European Organization for Research and Treatment of Cancer and World Health Organization consensus classification for cutaneous lymphomas. Recent progress in immune and molecular biology and novel therapeutic targets have increased our understanding of these diseases and have led to novel treatment approaches. This review outlines the most recent advances. RECENT FINDINGS: New immunologic and molecular findings may influence tumor phenotype and growth and provide a biologic basis for novel treatment approaches. Several reports have focused on new prognostic markers. Among the novel therapies for cutaneous T-cell lymphoma, interleukin-2 fusion toxins, monoclonal antibodies, histone deacetylase inhibitors, and immunomodulatory cytosine-phosphorothiolated guanine oligomers have shown promising results and are under further investigation. SUMMARY: This review provides an update of recent findings of immunologic, molecular, and cytogenetic features and treatment approaches for patients with cutaneous T-cell lymphoma with special emphasis on mycosis fungoides and Sezary syndrome.

Anticarcinogenic Agents↗
PubMed1994

Nucleotide sequence of the original Brazilian isolate of coleus yellow viroid from Solenostemon scutellarioides and infectivity of its complementary DNA.

The complete nucleotide (nt) sequence of the original coleus yellow viroid (CYVd) from Solenostemon scutellarioides, 'Golden Bedder', has been determined. The covalently closed single-stranded CYVd RNA molecule consists of 248 nt residues which assumes a rod-like secondary structure when folded in the model of lowest free energy. The sequence was determined by direct sequencing of RNA and from three overlapping cDNA clones. Comparison of the CYVd sequence with that of Coleus blumei viroid 1 (CbVd 1) from Germany demonstrated that they are closely related. The differences observed in the genome organization of CYVd relative to CbVd 1 were at three sites: position 25 (one U deletion), position 26 (a U was replaced by an A) and position 241 (one A insertion). The first two mutations were detected in one A-rich segment of eight nt (between positions 25 and 34). Northern blot hybridization of partially purified nucleic acids from the leaf tissue of S. scutellarioides 'Frilled Fantasy', inoculated with double-stranded cDNA, demonstrated that this fragment was infectious. These data enable CYVd to be assigned to the viroid class of plant pathogens, based on its biological properties and molecular structure. This work also gives additional support to the present classification system, in which the viroids isolated from S. scutellarioides form a distinct subgroup.

Base Sequence↗
PubMed2005

Serous borderline tumours of the ovary.

Serous borderline tumours of the ovaryIn this Expert Opinion we have invited articles from two leading groups, to discuss serous borderline tumours (serous tumours of low malignant potential) of the ovary from their own perspectives. Controversy remains over heterogeneity within this group of tumours and their relationship to ovarian cancer. Our authors discuss the histopathological classification of these tumours in relation to morphological appearances, molecular and clinical data. The significance of a micropapillary pattern is discussed, and issues related to extra-ovarian implants.

Cystadenoma, Serous↗
PubMed2002

International Union of Pharmacology. XXIX. Update on endothelin receptor nomenclature.

In mammals, the endothelin (ET) family comprises three endogenous isoforms, ET-1, ET-2, and ET-3. ET-1 is the principal isoform in the human cardiovascular system and remains the most potent and long-lasting constrictor of human vessels discovered. In humans, endothelins mediate their actions via only two receptor types that have been cloned and classified as the ET(A) and ET(B) receptors in the first NC-IUPHAR (International Union of Pharmacology Committee on Receptor Nomenclature and Drug Classification) report on nomenclature in 1994. This report was compiled before the discovery of the majority of endothelin receptor antagonists (particularly nonpeptides) currently used in the characterization of receptors and now updated in the present review. Endothelin receptors continue to be classified according to their rank order of potency for the three endogenous isoforms of endothelin. A selective ET(A) receptor agonist has not been discovered, but highly selective antagonists include peptides (BQ123, cyclo-[D-Asp-L-Pro-D-Val-L-Leu-D-Trp-]; FR139317, N- [(hexahydro-1-azepinyl)carbonyl]L-Leu(1-Me)D-Trp-3 (2-pyridyl)-D-Ala) and the generally more potent nonpeptides, such as PD156707, SB234551, L754142, A127722, and TBC11251. Sarafotoxin S6c, BQ3020 ([Ala(11,15)]Ac-ET-1((6-21))), and IRL1620 [Suc-(Glu(9), Ala(11,15))-ET-1((8-21))] are widely used synthetic ET(B) receptor agonists. A limited number of peptide (BQ788) and nonpeptide (A192621) ET(B) antagonists have also been developed. They are generally less potent than ET(A) antagonists and display lower selectivity (usually only 1 to 2 orders of magnitude) for the ET(B) receptor. Radioligands highly selective for either ET(A) ((125)I-PD151242, (125)I-PD164333, and (3)H-BQ123) or ET(B) receptors ((125)I-BQ3020 and (125)I-IRL1620) have further consolidated classification into only these two types, with no strong molecular or pharmacological evidence to support the existence of further receptors in mammals.

Amino Acid Sequence↗