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PubMed2005

Molecular identification and phylogenetic analysis of baculoviruses from Lepidoptera.

PCR amplification of the highly conserved baculovirus genes late expression factor 8 (lef-8), late expression factor 9 (lef-9) and polyhedrin/granulin (polh/gran) combined with molecular phylogenetic analyses provide a powerful tool to identify lepidopteran-specific baculoviruses and to study their diversity. In the present investigation, we have improved the degenerate oligonucleotides and corroborated the approach that was recently described by Lange et al. (Lange, M., Wang, H., Zhihong, H., Jehle, J.A., 2004. Towards a molecular identification and classification system of lepidopteran-specific baculoviruses. Virology 325, 36-47.). Baculovirus DNA was isolated from 71 uncharacterized historic baculovirus samples, and partial gene sequences were amplified by using gene-specific degenerate PCR primers. The obtained PCR products were directly sequenced, and the deduced amino acid sequences were compiled and aligned with published sequences of these target genes. A phylogenetic tree of 117 baculoviruses was inferred using maximum parsimony and distance methods. Based on the comprehensive phylogenetic analysis of the partial lef-8, lef-9 and polh/gran genes, we propose a phylogenetic species criterion for lepidopteran-specific baculoviruses that uses the genetic distances of these genes for species demarcation.

Animals↗

PubMedDate not supplied

Design and evaluation of a molecular fingerprint involving the transformation of property descriptor values into a binary classification scheme.

A new fingerprint design concept is introduced that transforms molecular property descriptors into two-state descriptors and thus permits binary encoding. This transformation is based on the calculation of statistical medians of descriptor distributions in large compound collections and alleviates the need for value range encoding of these descriptors. For binary encoded property descriptors, bit positions that are set off capture as much information as bit positions that are set on, different from conventional fingerprint representations. Accordingly, a variant of the Tanimoto coefficient has been defined for comparison of these fingerprints. Following our design idea, a prototypic fingerprint termed MP-MFP was implemented by combining 61 binary encoded property descriptors with 110 structural fragment-type descriptors. The performance of this fingerprint was evaluated in systematic similarity search calculations in a database containing 549 molecules belonging to 38 different activity classes and 5000 background molecules. In these calculations, MP-MFP correctly recognized approximately 34% of all similarity relationships, with only 0.04% false positives, and performed better than previous designs and MACCS keys. The results suggest that combinations of simplified two-state property descriptors have predictive value in the analysis of molecular similarity.

Computing Methodologies↗

PubMed2005

Molecular phylogenetics of the Macaronesian-endemic genus Bystropogon (Lamiaceae): palaeo-islands, ecological shifts and interisland colonizations.

Abstract A molecular phylogenetic study of Bystropogon L'Her. (Lamiaceae) is presented. We performed a cladistic analysis of nucleotide sequences of the internal transcribed spacers (ITS), of the nuclear ribosomal DNA, and of the trnL gene and trnL-trnF intergenic spacer of the chloroplast DNA. Bystropogon odoratissimus is the only species endemic to the Canary Islands that occurs in the three palaeo-islands of Tenerife. This species is not part of an early diverging lineage of Bystropogon and we suggest that it has a recent origin. This phylogenetic pattern is followed by most of the species endemic to the palaeo-islands of Tenerife. The two sections currently recognized in Bystropogon form two monophyletic groups. Taxa belonging to the section Bystropogon clade show interisland colonization limited to the Canary Islands with ecological shifts among three ecological zones. Taxa from the section Canariense clade show interisland colonization both within the Canary Islands and between the Canary Islands and Madeira. Speciation events within this clade are mostly limited to the laurel forest. The genus has followed a colonization route from the Canaries towards Madeira. This route has also been followed by at least five other plant genera with species endemic to Macaronesia. Major incongruences were found between the current infrasectional classification and the molecular phylogeny, because the varieties of Bystropogon origanifolius and Bystropogon canariensis do not form two monophyletic groups. The widespread B. origanifolius appears as progenitor of the other species in section Bystropogon with a more restricted distribution.

DNA, Chloroplast↗

PubMed2005

H5N2 avian influenza outbreak in Texas in 2004: the first highly pathogenic strain in the United States in 20 years?

In early 2004, an H5N2 avian influenza virus (AIV) that met the molecular criteria for classification as a highly pathogenic AIV was isolated from chickens in the state of Texas in the United States. However, clinical manifestations in the affected flock were consistent with avian influenza caused by a low-pathogenicity AIV and the representative virus (A/chicken/Texas/298313/04 [TX/04]) was not virulent for experimentally inoculated chickens. The hemagglutinin (HA) gene of the TX/04 isolate was similar in sequence to A/chicken/Texas/167280-4/02 (TX/02), a low-pathogenicity AIV isolate recovered from chickens in Texas in 2002. However, the TX/04 isolate had one additional basic amino acid at the HA cleavage site, which could be attributed to a single point mutation. The TX/04 isolate was similar in sequence to TX/02 isolate in several internal genes (NP, M, and NS), but some genes (PA, PB1, and PB2) had sequence of a clearly different origin. The TX/04 isolate also had a stalk deletion in the NA gene, characteristic of a chicken-adapted AIV. By analyzing viruses constructed by in vitro mutagenesis followed by reverse genetics, we found that the pathogenicity of the TX/04 virus could be increased in vitro and in vivo by the insertion of an additional basic amino acid at the HA cleavage site and not by the loss of a glycosylation site near the cleavage site. Our study provides the genetic and biologic characteristics of the TX/04 isolate, which highlight the complexity of the polygenic nature of the virulence of influenza viruses.

Animals↗

PubMed2004

Ectodermal dysplasias.

Ectodermal dysplasias are a large group of heritable conditions characterized by congenital defects of one or more ectodermal structures and their appendages: hair (hypotrichosis, partial, or total alopecia), nails (dystrophic, hypertrophic, abnormally keratinized), teeth (enamel defect or absent), and sweat glands (hypoplastic or aplastic). The ectodermal dysplasias, as a rule, are not pure "one-layer diseases." Mesodermal and, rarely, endodermal dysplasias coexist. Embryogenesis exhibits distinct tissue organizational fields and specific interactions among the germ layers that may lead to a wide range of ectodermal dysplasias when genes important for development are mutated or otherwise altered in expression. Of the approximately 200 different ectodermal dysplasias, about 30 have been studied at the molecular level with identification of the causative gene. Freire-Maia and Pinheiro used the clinical aspects for their classification, and Priolo integrated molecular genetic and clinical aspects for her scheme. Those two more historical classification schemes have the difficulty that, when applied strictly, several additional groups of diseases should be integrated within the term "ectodermal dysplasias," e.g. keratodermas with skin or hair alterations or the ichthyoses with associated features. Such consequent classification would lead to an endless list of diseases and would be useless for the practical work. Recent evidence implicates a genetic defect in different pathways orchestrating ectodermal organogenesis. Modern molecular genetics will increasingly elucidate the basic defects of the different syndromes and yield more insight into the regulatory mechanisms of embryology. In this way, a reclassification of ectodermal dysplasias will be possible according to the function of their involved mutated genes. Lamartine recently proposed a helpful classification according to the functions of the genes discovered in different types of ectodermal dysplasias. Accordingly, the present overview categorizes the various ectodermal dysplasias into four major functional subgroups: cell-cell communication and signaling, adhesion, transcription regulation, and development.

Cell Adhesion↗

PubMed1996

Monoblastic leukemia in an HIV-infected patient: absence of viral expression in RNA blasts.

A small number of patients seropositive for the human immunodeficiency virus (HIV) have been reported as developing acute non-lymphoblastic leukemia (ANLL). In the cases previously published, the authors never reported a study of the link joining HIV infection and leukemia. We describe here the case of a 41-year-old HIV positive patient who developed ANLL (FAB classification M5). Using molecular techniques, we looked for a direct link between these two co-existing diseases. We showed the absence of HIV expression in the malignant clone, suggesting that the association of ANLL and Acquired Immune Deficiency Syndrome is not a direct consequence of the myeloid precursors infection. Nevertheless a relationship may exist through a disorganization of the bone marrow micro-environment.

Adult↗

PubMed1988

Peroxisomal disorders: clinical commentary and future prospects.

Recent progress in the classification, biochemistry, and molecular biology of peroxisomal disorders is reviewed from a clinical perspective. Diseases such as Zellweger syndrome, neonatal adrenoleukodystrophy, infantile Refsum disease, hyperpipecolic acidemia, chondrodysplasia punctata, and Leber amaurosis share a common phenotype and involve deficiency of multiple peroxisomal enzymes. These disorders are associated with diverse metabolic abnormalities which are useful in pre- or postnatal diagnosis and distinguish these disorders from others such as X-linked adrenoleukodystrophy, adult Refsum disease, hyperoxaluria type I, and acatalasemia. Peroxisome structure is difficult to quantify histologically, since recent studies emphasize its developmental variability and tissue heterogeneity. The ability to manipulate this structure by dietary or pharmaceutical means provides a novel approach to therapy. At the molecular level, deficiency of peroxisomal enzymes responsible for fatty acid beta-oxidation or ether lipid synthesis reflects enhanced protein degradation due to abnormal peroxisomes; messenger RNA for the beta-oxidation enzymes is transcribed normally in peroxisomal disorders and can be increased by peroxisome proliferators. At least one integral structural protein of the peroxisome is synthesized normally in Zellweger syndrome. Hypotheses for the basic defect include defective regulation, uptake, or coenzyme stimulation of imported proteins, as well as defective biosynthesis. One clue to this defect may be a similar evolutionary history of peroxisomes and mitochondria which would explain their common alteration in Zellweger syndrome.

Adrenoleukodystrophy↗

PubMed2006

Peripheral T-cell lymphoma gene expression profiles.

Expression profiling using DNA microarrays has been very helpful to improve our knowledge of the pathobiology of many tumour types, including lymphomas. Peripheral T-cell lymphomas (PTCL) constitute an heterogeneous group of tumours with different morphologic, immunophenotypic, and clinical characteristics. Their complexity and their low frequency in the western countries have made difficult the identification of molecular events responsible of the development of these tumours. The first studies on expression profiling of PTCL have also revealed heterogeneity at this level, mainly regarding the PTCL NOS subgroup. Different molecular subgroups within PTCL unspecified have been identified associated to different expression profiles. However, the clinical significance of this molecular sub-classification remains to be probed in studies involving larger number of samples. In addition, the expression level of NF-kB pathway genes allowed to differentiate two PTCL subgroups, and this difference could have clinical interest. In general, PTCL expression profiles are difficult to interpret due to the significant proportion of other infiltrating cells accompanying the tumour. However, microarrays are being a helpful tool in the initial task of dissecting the PTCL expression profile.

Cell Differentiation↗

PubMed1995

Facts, myths and legends on the prime industrial microorganism.

Archaic speculations and firmly established legends regarding the origin of the yeast Saccharomyces cerevisiae and related species are revisited in light of past and recent ecological evidence pointing to a strict association with artificial, man-made environments such as wineries and fermentation plants. The nomenclature within this industrially important group is also discussed in view of the modifications imposed from application of molecular techniques to classification.

Beer↗

PubMed2005

Delimitation of squamous cell cervical carcinoma using infrared microspectroscopic imaging.

Infrared (IR) spectroscopic imaging coupled with microscopy has been used to investigate thin sections of cervix uteri encompassing normal tissue, precancerous structures, and squamous cell carcinoma. Methods for unsupervised distinction of tissue types based on IR spectroscopy were developed. One-hundred and twenty-two images of cervical tissue were recorded by an FTIR spectrometer with a 64x64 focal plane array detector. The 499,712 IR spectra obtained were grouped by an approach which used fuzzy C-means clustering followed by hierarchical cluster analysis. The resulting false color maps were correlated with the morphological characteristics of an adjacent section of hematoxylin and eosin-stained tissue. In the first step, cervical stroma, epithelium, inflammation, blood vessels, and mucus could be distinguished in IR images by analysis of the spectral fingerprint region (950-1480 cm(-1)). In the second step, analysis in the spectral window 1420-1480 cm(-1) enables, for the first time, IR spectroscopic distinction between the basal layer, dysplastic lesions and squamous cell carcinoma within a particular sample. The joint application of IR microspectroscopic imaging and multivariate spectral processing combines diffraction-limited lateral optical resolution on the single cell level with highly specific and sensitive spectral classification on the molecular level. Compared with previous reports our approach constitutes a significant progress in the development of optical molecular spectroscopic techniques toward an additional diagnostic tool for the early histopathological characterization of cervical cancer.

Carcinoma, Squamous Cell↗

PubMed2003

Evolution of the AMP-forming acetyl-CoA synthetase gene in the Drosophilidae family.

Analysis of the AMP-forming ACS gene was performed in 12 species of the Drosophilidae family. Systematically four introns, aligned at the same positions, were detected, but none of them showed a position similar to those known for species outside the Drosophilidae family. The average length of introns varied from 63 to 75 bp but in two species Drosophila takahashii and D. kikkawai the length of the second intron was 343 and 210 bp, respectively. In coding regions, about 80% of the third codon positions were substituted while first and second positions showed, respectively, 14% and 6% substitutions. Interestingly, the divergence observed at the protein level between species was very low. The phylogenetic tree based on the DNA sequences of the exons was mainly in agreement with taxonomic classification and previous molecular phylogenies except for D. ananassae, which appeared more closely related to D. subobscura and D. funebris than to the species of the melanogaster group.

Acetate-CoA Ligase↗

PubMed2004

Recent progress in predictive biomarkers for metastatic recurrence of human hepatocellular carcinoma: a review of the literature.

Molecular markers (biomarkers) for hepatocellular carcinoma (HCC) metastasis and recurrence could provide additional information to that gained from traditional histopathological features. A large number of biomarkers have been shown to have potential predictive significance. One important aspect of this is to detect the transcripts of tumor-associated antigens (such as AFP, MAGEs, and CK19), which are proposed as predictive markers of HCC cells disseminated into the circulation and for metastatic recurrence. Another important aspect is to analyze the molecular markers for cellular malignancy phenotype, including DNA ploidy, cellular proliferation index, cell cycle regulators, oncogenes, and tumor suppressors (especially p53 gene), as well as telomerase activity. Molecular factors involved in the process of HCC invasion and metastasis, including adhesion molecules (E-cadherin, catenins, ICAM-1, laminin-5, CD44 variants, osteopontin), proteinases responsible for the degradation of extracellular matrix (MMPs, uPA system), as well as angiogenesis regulators (such as VEGF, intratumor MVD), have also been shown to be potential predictors for HCC metastatic recurrence and clinical outcomes. One important new trend is to widely delineate biomarkers with genomic and proteomic expression with reference to predicting metastatic recurrence, molecular diagnosis, and classification, which has been drawing more attention recently. Body fluid (particularly blood and urine) testing for biomarkers is easily accessible and more useful in clinical patients. The prognostic significance of circulating DNA in plasma or serum and its genetic alterations is another important direction. More attention should be paid to these areas in the future. As understanding of tumor biology deepens, more and more new biomarkers with high sensitivity and specificity for HCC metastatic recurrence could be found and routinely used in clinical assays. However, the combination of the pathological features and some of the biomarkers mentioned above seems to be more practical up to now.

Angiogenesis Inducing Agents↗

PubMed1998

Novel and recurrent COMP (cartilage oligomeric matrix protein) mutations in pseudoachondroplasia and multiple epiphyseal dysplasia.

Pseudoachondroplasia (PSACH) and multiple epiphyseal dysplasia (MED) are common skeletal dysplasias with impaired enchondral ossification and premature degenerative joint disease. The two disorders were in the past considered to be distinct clinical entities; however, recent studies have proven that both diseases can result from mutations of the gene encoding cartilage oligomeric matrix protein (COMP). To characterize further COMP mutations and investigate phenotype-genotype relationships, we screened this gene in 15 patients with PSACH or MED by directly sequencing polymerase chain reaction products from genomic DNA. We identified ten mutations involving conserved residues among the eight calmodulin-like repeats of the gene product: seven were novel missense mutations in exons 9, 10, 11, 13 or 14, and the other three resulted from deletion of one of the five GAC repeats in exon 13. We have found that the GAC repeats in the 7th calmodulin-like repeat in exon 13 represent a hot-spot for mutation, and that mutations in the 7th calmodulin-like repeat produce severe PSACH phenotypes while mutations elsewhere in the gene exhibit mild PSACH or MED phenotypes. These genotype-phenotype correlations may facilitate molecular diagnosis and classification of PSACH and MED, and provide insight into the relationship between structure and function of the COMP gene product.

Achondroplasia↗

PubMed2006

Proposal of a scoring scale as a survival predictor in intracranial oligodendrogliomas.

INTRODUCTION: Histological, clinical and radiological features, and molecular genetic analysis are among the factors that have been considered in defining the prognosis of oligodendrogliomas (OD), but they have yielded conflicting results. The purpose of this study was to test out a scoring scale based on clinical, radiological, pathological and molecular features. MATERIAL AND METHOD: To identify factors with prognostic significance, we analyzed 87 treated patients with a histological diagnosis of OD. Of the parameters analyzed, age, onset, clinical status, radiological enhancement, histological necrosis, mitosis and chromosomal anomalies emerged as significant prognosis factors using univariate analysis. Multivariate analysis revealed age and chromosomal anomalies as independent factors of survival. RESULTS: The factors with a significant prognostic value were combined to determine which grouping factors best predict outcome. The proposed score is a pure number resulting from a combination of: 2 major factors: age and chromosomal anomalies (scored 3-0); 5 minor factors: onset, clinical examination, necrosis, mitoses (scored 1-0), and radiological enhancement (scored 2-0). According to our scale, 10 survival curves were produced for overall survival. Recursive partitioning of patients with the nearest score and outcome produced four groups with a significant difference in survival (p=10(-5)). The power of both the scale and the partitioned groups for predicting outcome was more accurate than the WHO and St Anne grading systems, and the molecular sub-classification. CONCLUSIONS: Our scale is a plausible way of classifying patients harboring intracranial OD according to expected survival.

Adolescent↗

PubMed2025

Quantifying evidence for phenotypic specificity (PP4) for syndromic phenotypes: Large-scale integration of rare germline FH variants from diagnostic laboratory testing for HLRCC and renal cancer.

PURPOSE: Hereditary leiomyomatosis and renal cell cancer (HLRCC) is a rare cancer susceptibility syndrome exclusively attributable to pathogenic variants in FH (HGNC:3700). This article quantitatively weights the phenotypic context (PP4/PS4) of such very rare variants in FH. METHODS: We collated clinical diagnostic testing data on germline FH variants from 387 individuals with HLRCC and 1780 individuals with renal cancer and compared the frequency of "very-rare" variants in each phenotypic cohort with 562,295 population controls. We generated pan-gene very rare variant likelihood ratios (PG-VRV-LRs), domain-specific likelihood ratios for missense variants (DS-VRMV-LR) using spatial clustering analysis, and log2.08 likelihood ratios (LLRs) as applicable within the updated American College of Medical Genetics and Genomics/Association for Molecular Pathology variant classification framework. RESULTS: For HLRCC, the PG-VRV-LR was estimated to be 2669.4 (95% CI 1843.4-3881.2, LLR 10.77) for truncating variants and 214.7 (95% CI 185.0-246.9, LLR 7.33) for missense variants. For renal cancer, the PG-VRV-LR was 95.5 (95% CI 48.9-183.0, LLR 6.23) for truncating variants and 5.8 (95% CI 3.5-9.3, LLR 2.39) for missense variants. Clustering analysis in HLRCC cases revealed 3 "hotspot" regions wherein the DS-VRMV-LR increased to 1226.9. CONCLUSION: These data provide quantitative measures for very rare missense and truncating variants in FH, which reflect the differing phenotypic specificity of HLRCC and renal cancer and may be applicable in clinical variant classification.

Humans↗

PubMed2004

Whole genome amplification of DNA from laser capture-microdissected tissue for high-throughput single nucleotide polymorphism and short tandem repeat genotyping.

Genome-wide screening of genetic alterations between normal and cancer cells, as well as among subgroups of tumors, is important for establishing molecular mechanism and classification of cancer. Gene silencing through loss of heterozygosity is widely observed in cancer cells and detectable by analyzing allelic loss of single nucleotide polymorphism and/or short tandem repeat markers. To use minute quantities of DNA that are available through laser capture microdissection (LCM) of cancer cells, a whole genome amplification method that maintains locus and allele balance is essential. We have successfully used a ø29 polymerase-based isothermal whole genome amplification method to amplify LCM DNA using a proteinase K lysis procedure coupled with a pooling strategy. Through single nucleotide polymorphism and short tandem repeat genotype analysis we demonstrate that using pooled DNA from two or three separate amplification reactions significantly reduces any allele bias introduced during amplification. This strategy is especially effective when using small quantities of source DNA. Although a convenient alkaline lysis DNA extraction procedure provided satisfactory results from using 1500 to 3000 LCM cells, proteinase K digestion was superior for lower cell numbers. Accurate genotyping is achieved with as few as 100 cells when both proteinase K extraction and pooling are applied.

Female↗

PubMed2005

[Electrophysiological signs of muscle channelopathies by causal mutation].

Nondystrophic myotonias and familial periodic paralyses are disorders of muscle excitability caused by mutations in genes coding for voltage-gated ion channels. Electromyographic (EMG) diagnosis of these diseases is based on needle searching of myotonic discharges and on several exercise tests, performed by surface recording of compound muscle action potential (CMAP) before and after voluntary contractions of various durations. After a short exercise test (10 seconds contraction), three abnormal changes of CMAP have been defined in muscle channelopathies: 1) appearance of repetitive discharges (post-exercise myotonic potentials, PEMP), 2) transient or long-lasting amplitude reduction, 3) long-lasting amplitude increase. These abnormalities become more marked or decline with exercise repetition (repeated brief exercise test), depending on the causal mutation. After long exercise test (5 minutes contraction), three other abnormalities of CMAP amplitude have been described: 1) immediate increase, 2) immediate decrease, 3) progressive or delayed decrease. Combining the responses to the different tests has disclosed five main EMG types of muscle channelopathies (I to V), that correlated with different pathophysiological mechanisms and with subgroups of mutations. This classification may guide molecular diagnosis in clinical practice.

Action Potentials↗

PubMed2000

Ectodermal dysplasias: not only 'skin' deep.

The ectodermal dysplasias (EDs) are a large and complex nosologic group of diseases; more than 170 different pathologic clinical conditions have been identified. Despite the great number of EDs described so far, few causative genes have been identified. We review EDs in the light of the most recent molecular findings and propose a new classification of EDs integrating both molecular-genetic data and corresponding clinical findings of related diseases.

Animals↗