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PubMed2005

Analysis of prion strains by PrPSc profiling in sporadic Creutzfeldt-Jakob disease.

BACKGROUND: Prion diseases are a group of invariably fatal neurodegenerative disorders affecting humans and a wide range of mammals. An essential part of the infectious agent, termed the prion, is composed of an abnormal isoform (PrPSc) of a host-encoded normal cellular protein (PrPC). The conversion of PrPC to PrPSc is thought to play a crucial role in the development of prion diseases and leads to PrPSc deposition, mainly in the central nervous system. Sporadic Creutzfeldt-Jakob disease (sCJD), the most common form of human prion disease, presents with a marked clinical heterogeneity. This diversity is accompanied by a molecular signature which can be defined by histological, biochemical, and genetic means. The molecular classification of sCJD is an important tool to aid in the understanding of underlying disease mechanisms and the development of therapy protocols. Comparability of classifications is hampered by disparity of applied methods and inter-observer variability. METHODS AND FINDINGS: To overcome these difficulties, we developed a new quantification protocol for PrPSc by using internal standards on each Western blot, which allows for generation and direct comparison of individual PrPSc profiles. By studying PrPSc profiles and PrPSc type expression within nine defined central nervous system areas of 50 patients with sCJD, we were able to show distinct PrPSc distribution patterns in diverse subtypes of sCJD. Furthermore, we were able to demonstrate the co-existence of more than one PrPSc type in individuals with sCJD in about 20% of all patients and in more than 50% of patients heterozygous for a polymorphism on codon 129 of the gene encoding the prion protein (PRNP). CONCLUSION: PrPSc profiling represents a valuable tool for the molecular classification of human prion diseases and has important implications for their diagnosis by brain biopsy. Our results show that the co-existence of more than one PrPSc type might be influenced by genetic and brain region-specific determinants. These findings provide valuable insights into the generation of distinct PrPSc types.

Aged↗
PubMed2002

Two-dimensional mapping of three phenotype-associated isoforms of the prion protein in sporadic Creutzfeldt-Jakob disease.

Transmissible spongiform encephalopathies (TSE), or prion diseases, are mammalian neurodegenerative disorders characterized by a conformational modification of the host-encoded prion protein (PrP(C)) into an isoform which is detergent-insoluble and partially resistant to protease treatment (PrP(Sc)). Distinct types of PrP(Sc), differing in conformation and variation in the relative amount of their glycoforms, have been associated with different phenotypes of TSE. In sporadic Creutzfeldt-Jakob disease (sCJD), two major types of PrP(Sc), with proteinase K (PK)-resistant fragments of 21 and 19 kDa, have been described. No consensus exists, however, on the molecular classification of PrP(Sc) in sCJD, since further heterogeneity within PrPSc conformers has been reported. We studied 19 subjects with dementia or dementia/ataxia at onset and 12 subjects with ataxia at onset. Following two-dimensional gel electrophoresis, we characterized PrP(C) and PrP(Sc) species in normal and sCJD brains by immunoblotting with antibodies recognizing N-terminal and C-terminal PrP regions. Three types of PrP(Sc) were detected in detergent-insoluble fractions from sCJD brains, mainly consisting of full-length PrP(Sc) in subjects with rapidly progressive dementia, and two different sets of amino-truncated PrP(Sc) glycoforms in subjects with dementia/ataxia and ataxia at onset. Examination of the PrP(Sc) core fragment, following PK treatment and deglycosylation, confirmed the existence of three distinctive patterns. These findings have immediate implications for the molecular classification of sCJD.

Brain Chemistry↗
PubMed2005

Genotype-phenotype studies in bipolar disorder showing association between the DAOA/G30 locus and persecutory delusions: a first step toward a molecular genetic classification of psychiatric phenotypes.

OBJECTIVE: The authors previously reported an association between the D-amino acid oxidase activator (DAOA)/G30 locus and both schizophrenia and bipolar affective disorder. Given the presumed role of DAOA/G30 in the neurochemistry of psychosis and its localization in a schizophrenia and bipolar affective disorder linkage region (13q34), it was hypothesized that the bipolar affective disorder finding would be mainly due to an association with psychotic features. METHOD: The marker/haplotype associations obtained in a subset of 173 bipolar affective disorder patients with psychotic features were similar to those in the overall patient group, suggesting that stratification on the basis of psychotic features in general might be too crude a procedure. The authors therefore tested whether confining caseness to specific psychotic features would improve detection of genotype-phenotype correlations. RESULTS: In a logistic regression, "persecutory delusions" were found to be the only significant explanatory variable for the DAOA/G30 risk genotype among 21 OPCRIT symptoms of psychosis. The authors therefore tested for association between DAOA/G30 and bipolar affective disorder in the 90 cases with a history of persecutory delusions. Whereas this subset showed strong association (odds ratio=1.83 for the best marker), the remaining larger sample of 165 patients with no such history did not differ from comparison subjects, suggesting that the association between DAOA/G30 and bipolar affective disorder is due to persecutory delusions. This was confirmed in an independent study of 294 bipolar affective disorder patients and 311 comparison subjects from Poland, in which an association between bipolar affective disorder and DAOA/G30 was only seen when case definition was restricted to cases with persecutory delusions. CONCLUSIONS: These data suggest that bipolar affective disorder with persecutory delusions constitutes a distinct subgroup of bipolar affective disorder that overlaps with schizophrenia.

Adult↗
PubMed2004

Incorporating pathologists' criteria of malignancy into the evolutionary model for cancer development.

A wide variety of alterations in cell and tissue structure still form the basis for cancer diagnosis by pathologists. Cancer development is recognized to be an evolutionary process [Foulds, 1954; Cairns, 1975; Nowell, 1976; Sager, 1982; Tomlinson et al., 1996; Cahill et al., 1999; Tomlinson and Bodmer, 1999], but the phenotypic changes diagnostic of cancer (pathologists' "criteria of malignancy") have not been integrated into the existing evolutionary framework. Since phenotypic changes bear an important relationship to the genetic and physiologic changes underlying Darwinian evolution, we propose that diagnostic structural alterations also bear an important and predictable relation to both the cancer genes and the functional alterations active at any particular step in the development of a cancer. Cancer genes are predicted to mediate the acquisition of cellular-level diagnostic criteria and the diagnostic cellular-level structural changes should reflect in a useful manner the altered cell physiology required for the cell to achieve increased "cellular fitness" at any particular step of colonal evolution. Tissue-level criteria of malignancy should relate less directly to specific cancer genes, but tissue-level criteria should still provide essential insight into the interplay of the altered cellular fitness with the constraints imposed by the cells' microenvironment. The evolutionary framework allows tissue-level criteria of malignancy to be expressed in terms of viable hypotheses for the mechanism of clonal expansion at any particular step in cancer development. This approach to conveying the tissue-level criteria of malignancy complements pattern recognition approaches to diagnosis, and establishes common ground between pathology and cell biology. When viewed from this perspective, the functions of cancer genes appear quite different from those predicted by the "Gatekeeper, Caretaker" or "Hallmarks of Cancer" models. Finally, a full evolutionary framework incorporating the criteria of malignancy restores congruity between the histogenetic classification and the emerging molecular classification of cancer.

Cell Transformation, Neoplastic↗
PubMed2002

Classification and molecular organization of satellites elucidated by phylogenetic network analysis - examples from Triturus salamanders and Palorus beetles.

A phylogenetic network of 244 satellite DNA sequences across five species of aquatic salamanders (genus Triturus) revealed four types of satellite DNAs in a 'p'-shaped 1-2*-3-4-2* arrangement. Analysis of dimer and trimer DNA sequences revealed a prevalence of homosequential (e.g. 1-1, 2-2) and particular (1-4 and 2-3) heterosequential repeat motifs. Genetic diversity across types and species phylogeny indicated that type 1 and type 4 are derived from types 2 and 3. Support was also found for alternating motifs in Palorus flour beetle tandem repeats. The results were statistically significant, whether or not the underlying satellite DNA phylogenies were robust under bootstrap analysis.

Animals↗
PubMed2004

Genotype classification and molecular evidence for the presence of mixed infections in Indian Citrus tristeza virus isolates.

Citrus tristeza virus (CTV) is usually present in field trees as a mixture or complex of isolates. Different biological types of CTV exist in India and this affects disease incidence and yield in the various citrus growing areas. Genotypic profiles were determined for 21 Indian CTV isolates. Of the 21 isolates, 15 contained only the VT genotype. The other isolates contained mixtures of either T30 or T3 with VT or T30, T3 and VT genotypes. One exception was isolate BAN-1, which contained a mixture of T36, T30 and T3 genotypes. Sequence diversity of Indian CTV isolates was determined by characterization in the k17 region of ORF 1a and the overlapping region of RdRp, gene p33, and sequence differences were utilized to identify group-specific genome features. A phylogenetic analysis of these regions divided the isolates into five distinct groups. There was a general trend for severe isolates to cluster into one of four groups and mild isolates into the fifth group. All the sequences from the two different regions of the CTV genome showed nucleotide identity to either VT, T30 or T36 isolates and confirmed the mixed infection of mild isolates with severe CTV isolates from three distinct geographical citrus growing regions in India.

Amino Acid Sequence↗
PubMed2004

Toward a molecular genetic classification of familial hemiplegic migraine.

The genetics of migraine is a fascinating and rapidly moving research area. Familial hemiplegic migraine, a rare subtype of migraine with a Mendelian pattern of inheritance, is caused by mutations in the chromosome 19 CACNA1A gene or in the chromosome 1 ATP1A2 gene. Familial migraine variants are classified on the basis of clinical, descriptive criteria, but this is insufficient. In the future, a diagnostic classification based on mutation-analysis is needed.

Humans↗
PubMed1991

Outliers: their origin and use in the classification of molecular mechanisms of toxicity.

Quantitative structure-activity relationships (QSARs) provide a useful tool for defining a mathematical relationship between chemical structure and toxicity, and for applying such statistically derived models for predicting the toxicity of untested chemicals. Outlier chemicals can be encountered both in the derivation of QSAR models as well as in their application. Information regarding the relationship between molecular descriptors and molecular mechanism of toxicity can provide insight into the origin of outlier behavior as well as guidance regarding the predictive limitations of such models. Comparison of measured toxicity data for fish and rats with baseline QSAR prediction provides a means of identifying outliers and for categorizing more specific molecular mechanisms.

Alcohol Dehydrogenase↗
PubMed2006

Classification of chronic myeloid disorders: from Dameshek towards a semi-molecular system.

Hematological malignancies are phenotypically organized into lymphoid and myeloid disorders, although such a distinction might not be precise from the standpoint of lineage clonality. In turn, myeloid malignancies are broadly categorized into either acute myeloid leukemia (AML) or chronic myeloid disorder (CMD), depending on the presence or absence, respectively, of AML-defining cytomorphologic and cytogenetic features. The CMD are traditionally classified by their morphologic appearances into discrete clinicopathologic entities based primarily on subjective technologies. It has now become evident that most CMD represent clonal stem cell processes where the primary oncogenic event has been characterized in certain instances; Bcr/Abl in chronic myeloid leukemia, FIP1L1-PDGFRA or c-kit(D816V) in systemic mastocytosis, rearrangements of PDGFRB in chronic eosinophilic leukemia, and rearrangements of FGFR1 in stem cell leukemia/lymphoma syndrome. In addition, Bcr/Abl-negative classic myeloproliferative disorders are characterized by recurrent JAK2(V617F) mutations, whereas other mutations affecting the RAS signaling pathway molecules have been associated with juvenile myelomonocytic leukemia. Such progress is paving the way for a transition from a histologic to a semi-molecular classification system that preserves conventional terminology, while incorporating new information on molecular pathogenesis.

Fusion Proteins, bcr-abl↗
PubMed2003

Classification and molecular biology of polycythemias (erythrocytoses) and thrombocytosis.

In this article, polycythemic disorders are classified based on the current understanding of biology of erythropoieses and divided into primary and secondary polycythemias. Special emphasis is given to recently uncovered molecular bases of newly described congenital polycythemic disorders. This clarification of the pathophysiology of some of the congenital polycythemic states has obvious utility for more accurate diagnosis and rational prognostic determination. The molecular basis of congenital thrombocytoses is only beginning to be uncovered. In contrast, the molecular bases of polycythemia vera and essential thrombocythemia remain unknown, thus their diagnostic criteria are imprecise and their treatment remains largely empirical. The central premise of this article is that deciphering the molecular basis of human diseases leads to improved understanding of hematopoiesis, precise diagnosis, and the potential for development of a specific therapy.

Humans↗
PubMed2005

Advances in overgrowth syndromes: clinical classification to molecular delineation in Sotos syndrome and Beckwith-Wiedemann syndrome.

PURPOSE OF REVIEW: The clinical importance of overgrowth syndromes in the pediatric patient population has been increasingly recognized during the past decade, but clinical overlap among overgrowth syndromes often makes diagnostic categorization difficult. Advances in the molecular delineation of overgrowth syndromes in recent years have furthered our knowledge of the phenotypic spectrum of this group of conditions. This review focuses on developments in our understanding of the molecular mechanisms and phenotype-genotype correlations in the two most common overgrowth syndromes, Beckwith-Wiedemann syndrome and Sotos syndrome. The implications of these findings with respect to clinical diagnosis, medical management, and genetic counseling are discussed. RECENT FINDINGS: Recent reports have redefined the cardinal clinical features of Sotos syndrome, and the identification of two distinct types of molecular alterations in patients with this syndrome has enabled assessment of phenotype-genotype correlations. Recent studies in patients with Beckwith-Wiedemann syndrome have further expanded our understanding of the causative molecular mechanisms of this condition and provide evidence for specific genotype-phenotype correlations, most notably with respect to tumor risk. SUMMARY: Recognition of childhood overgrowth and investigation of diagnostic causes is important in anticipating appropriate medical management and facilitating the provision of genetic counseling. New developments in our understanding of the molecular basis and phenotypic expression of overgrowth syndromes provide additional tools in this often challenging process.

Beckwith-Wiedemann Syndrome↗
PubMed1993

Isolation, classification and molecular characterization of bacteriophages for Enterobacter species.

Out of 22 Enterobacter phages investigated, nine were found to be suitable for phage typing based on their different lytic spectra on 398 strains of Enterobacter spp. isolated from milk powder and other foods. These phages were compared on the basis of morphology, protein composition, restriction endonuclease patterns and DNA-DNA hybridization. Two phages (WS-EP19, WS-EP13) belonged to the Podoviridae family (morphotype C1), and three (WS-EP20, WS-EP26, WS-EP28) were classified as Siphoviridae (morphotype B1). The other four phages were Myoviridae of the morphological groups A1 (WS-EP57) and A2 (WS-EP32, WS-EP94, WS-EP96). SDS-PAGE revealed individual protein profiles for each phage, which corresponded to different restriction enzyme fragment patterns. DNA-DNA hybridization demonstrated the close relationship of phages WS-EP20 and WS-EP26, and of WS-EP94 and WS-EP96. In general, a good correlation was found between groupings obtained with the various methods. The nine phages could be attributed to existing enterobacterial phage species although some differences to the described type phages were observed.

Bacteriophage Typing↗
PubMed1991

Epidemiology of progressive muscular dystrophy in Okinawa, Japan. Classification with molecular biological techniques.

We studied the prevalence of various types of progressive muscular dystrophy (PMD) in Okinawa, Japan on December 31, 1989 and the incidence of Duchenne muscular dystrophy (DMD) in 5-year periods from 1957 to 1985. We classified patients with PMD clinically, electrophysiologically, molecular biologically and immunohistochemically with antidystrophin antibody, especially for sporadic cases of DMD, Becker muscular dystrophy (BMD) and limb-girdle muscular dystrophy (LG). The prevalence for all PMD in Okinawa was 7.13 X 10(-5) for DMD, 1.82 X 10(-5) for BMD in the male population, 1.55 X 10(-5) for LG, 1.14 X 10(-5) for congenital muscular dystrophy, 2.03 X 10(-5) for facioscapulohumeral muscular dystrophy (FSH), and 9.13 X 10(-5) for myotonic dystrophy (MD) in the total population. The incidence of DMD in the period 1957-1985 was 15.41 X 10(-5) live-born males (LBM) and 3.21 X 10(-5) LBM for BMD. The incidence has apparently declined in Okinawa since 1975. The prevalence of BMD, FSH and MD was rather high in Okinawa compared with previous reports. Molecular biological techniques for classifying patients were indispensable for the epidemiological study of PMD.

Cross-Cultural Comparison↗