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PubMedDate not supplied

Virtual screening of molecular databases using a support vector machine.

The Support Vector Machine (SVM) is an algorithm that derives a model used for the classification of data into two categories and which has good generalization properties. This study applies the SVM algorithm to the problem of virtual screening for molecules with a desired activity. In contrast to typical applications of the SVM, we emphasize not classification but enrichment of actives by using a modified version of the standard SVM function to rank molecules. The method employs a simple and novel criterion for picking molecular descriptors and uses cross-validation to select SVM parameters. The resulting method is more effective at enriching for active compounds with novel chemistries than binary fingerprint-based methods such as binary kernel discrimination.

Algorithms↗

PubMed1999

Toward more meaningful hierarchical classification of protein three-dimensional structures.

Recently, several hierarchical classifications of protein three-dimensional (3D) structures have been published. However, none of them provides any assessment of the validity of a hierarchical representation or test individual clusters contained within. In fact, testing here of published trees reveals that they vary in meaning. Protein structure similarity measures are then assessed in terms of the robustness of the resulting trees for 24 protein families. A meaningful tree is defined as one in which all the clusters are found to be reliable according to a jackknife test. With the use of this criterion, a previously published similarity measure described as a "better RMS" is shown in fact to be usually less suited to protein fold classification than normal RMS after superposition. Here the "best" protein structure similarity measure for hierarchical classification-in terms of that which after clustering produces the highest number of meaningful trees, 20, for the 24 families-is found to be a new one. This measure includes information on the relationship of a distance at a given aligned position in a pair to the rest of the unique distances at that position in a protein family. There are only 2 families of the 24 tested, the globins (3 trees) and Kazal-type serine proteinase inhibitors (21 trees), in which the topology (branching order) of the meaningful 3D structure-based trees is constant. Thus, a new view of protein family sequence-structure relationships is afforded by comparing meaningful trees for each family. More generally, there is a need for care in interpretation of the results of those molecular biology algorithms that force a tree structure on data without assessing its applicability. Proteins 1999;37:20-29.

Classification↗

PubMed2026

Exploratory proteomic and metabolomic profiling of pleural effusions identifies histone H4 and alanine as promising complementary markers for pleural tuberculosis.

The diagnosis of pleural tuberculosis (Pl-TB) remains challenging. Histopathological analysis and pathogen detection in pleural biopsies are informative but limited. We investigated differentially expressed proteins and metabolites in pleural effusions from patients with Pl-TB, malignancies, and other pathologies. A proteomic analysis of pooled pleural effusions identified 45 proteins exclusively detected or upregulated in Pl-TB samples, many linked to infectious processes. Conversely, 18 proteins were uniquely found or upregulated in malignant pleural effusions, mainly associated with detoxification and hemostasis. To validate these findings, we employed targeted proteomics in individual samples. Eight proteins were validated: S100-A9, histone H4, insulin-like growth factor-binding protein 2, fibrinogen beta chain, ficolin-3, immunoglobulin heavy constant alpha 1, sulfhydryl oxidase 1, and histidine-rich glycoprotein. Additionally, NMR-based metabolomics identified 13 metabolites with differential abundance between Pl-TB and non-TB samples. Notably, N-acetyl-glycoprotein and the branched-chain amino acids, alanine and lysine differed between groups. Proteomic and metabolomic analyses revealed distinct molecular profiles between Pl-TB and non-TB patients, despite intra-group variability. To address this, we applied classification models. Histone H4 and alanine consistently emerged as discriminative features. Overall, this study provides novel insights into the molecular landscape of Pl-TB. The combined quantification of proteins and metabolites may improve differential diagnosis, although should be further validated in larger, independent cohorts before clinical application.

Humans↗

PubMed2005

Clinicopathologic, immunophenotypic, and molecular cytogenetic fluorescence in situ hybridization analysis of primary and secondary cutaneous follicular lymphomas.

Although primary cutaneous follicular lymphoma (FL) is considered a distinct variant of FL in the World Health Organization classification ("cutaneous follicle center lymphoma"), its biologic relationship to nodal FL remains controversial. The clinical, morphologic, immunophenotypic, and molecular cytogenetic features of 17 patients with primary cutaneous FL were studied and compared with 16 patients with secondary cutaneous FL. The head and neck region was the most frequent site at initial skin presentation in both the primary and secondary cases. Among the primary cases, 29% of the 31 biopsies were grade 1, 48% grade 2, 13% grade 3, and 10% grade 3 with diffuse large B-cell (DLBCL) areas. Among the secondary cases, 38% of the 29 skin biopsies were grade 1, 45% grade 2, 3% grade 3, and 7% grade 3 with DLBCL areas with two not evaluable. A floral-like pattern was observed in 32% of primary FL but only 5% of secondary cases. Histologic progression was found in 21% of patients. CD10 expression was demonstrated in 90% (27 of 30) of primary cases and 96% (22 of 23) of secondary cases. Bcl-6 was expressed in all cases tested. Bcl-2 expression was detected in 57% (17 of 30) of the primary cases (100% of grade 1, 43% of grade 2, 40% of grade 3), whereas all secondary cases were bcl-2 positive (P=0.0002). The t(14;18) translocation was identified by interphase fluorescence in situ hybridization (FISH) in biopsies from 31% (4 of 13) of the patients with primary FL compared with 77% (10 of 13) of those with secondary lymphoma (P <0.05). Seven of the 17 (41%) patients with primary disease had cutaneous relapse, including 1 who also developed nodal disease. Bcl-2 positivity was seen in 4 of these 7 patients. Eight of the 16 (50%) patients with secondary FL had cutaneous relapse. Primary and secondary cutaneous FL share many clinical and phenotypic features, but primary cases may have some distinctive morphologic features, more frequently lack bcl-2 protein, and often lack the t(14;18) translocation. These findings suggest that primary cutaneous FL are distinctive and often but not always have a pathogenesis different from most of nodal and secondary cutaneous FL.

Adult↗

PubMed1998

Technical note: chromosomal and mtDNA analysis of Oliver.

Oliver is an African ape whose species identity has been debated in the popular media and by various scientists since the early 1970s. Although decisive morphological data has never been adduced on Oliver, many reports indicated that Oliver was morphologically unusual for a chimpanzee, particularly in his habitual bipedal posture. In addition, his diploid chromosome number was reported to be inconsistent with either human or chimpanzee, but instead intermediate between those species. We performed standard chromosomal studies which demonstrated that Oliver had the diploid number expected for a chimpanzee (2N = 48) and that the banding patterns of his chromosomes were typical for a chimpanzee and different from both humans and bonobos. We also sequenced a 312 bp region of his mitochondrial DNA D-loop region. Results indicated a high sequence homology to the Central African variety of chimpanzee, Pan troglodytes troglodytes. The highest percent homology was observed with a previously characterized specimen from Gabon, strongly suggesting that Oliver originated from this region.

Animals↗

PubMed2026

Third Patient With Biallelic Variants in SMAD6 With an Overlapping Phenotype: Developmental Delays, Dysmorphic Features, and Cardiovascular Abnormalities.

SMAD6 encodes an inhibitory SMAD protein that modulates BMP and TGF-β signaling. Heterozygous pathogenic variants in SMAD6 have been primarily associated with aortic valve disease, radioulnar synostosis, and nonsyndromic sagittal and metopic synostosis. However, only two syndromic patients with biallelic variants have been reported in the literature. We report a 4-year-old girl with neurodevelopmental delays, dysmorphic features, complex congenital heart disease, renal asymmetry, and arterial tortuosity. Whole exome sequencing showed two homozygous SMAD6 variants of uncertain significance: c.161G>T (p.Gly54Val) and c.1A>G (p.Met1?). This is the third patient with biallelic SMAD6 variants associated with skeletal changes, more complex cardiovascular phenotype, facial dysmorphism, and novel arterial abnormalities. This suggests biallelic variants may cause a distinct and potentially more severe autosomal recessive syndrome. Functional investigation is needed to determine the molecular consequences of biallelic SMAD6 variants and to inform variant classification and mechanism. This report characterizes a potential unique genetic syndrome associated with biallelic SMAD6 variants, highlighting the importance of additional sequencing, vascular imaging, and multidisciplinary care coordination for these patients.

SMAD6↗

PubMed2005

Cytologic diagnosis of Burkitt lymphoma.

BACKGROUND: The diagnosis and classification of lymphoma require correlation of morphologic, immunophenotypic, and molecular-cytogenetic studies. Fine-needle aspiration biopsy (FNAB) is a valuable diagnostic technique that allows material to be collected for these ancillary studies, and for morphologic evaluation. METHODS: The authors report a series of seven cases clinically or morphologically suspicious for Burkitt lymphoma. Fluorescence in situ hybridization studies (FISH) for c-myc were performed on FNAB material and correlated with cytologic and immunophenotypic data. RESULTS: Six of seven specimens were positive for c-myc rearrangement by FISH. However, only three of these cases represented Burkitt lymphoma, with one additional case of atypical Burkitt lymphoma. The other cases included diffuse large B-cell lymphoma, monomorphic posttransplant B-cell lymphoma, and an aggressive B-cell lymphoma, with the latter case negative for c-myc rearrangement by FISH. Of 2 non-Burkitt lymphoma specimens tested, 1 was positive for the immunoglobulin H/bcl-2 rearrangement, in addition to the c-myc rearrangement, suggesting transformation from a lower grade lymphoma. CONCLUSIONS: These cases illustrated the value of FNAB in the diagnosis of Burkitt lymphoma, as well as the importance of obtaining material for, and integrating results of, ancillary studies for the final diagnosis.

Adult↗

PubMed2004

New developments in the symmetry-adapted algorithm of the Polarizable Continuum Model.

We present recent developments in the symmetry implementation of the Polarizable Continuum Model (PCM). The structure of the matrix, which defines the PCM solvent response, is examined, and we demonstrate how this matrix can be transformed to a block diagonal form where each block belongs to different irreducible representations of the molecular point group. This development is especially important at the Multi-configurational Self-Consistent Field (MCSCF) level where symmetry is needed to avoid problems with symmetry breaking in the wave function and facilitate the optimization of electronic excited states. Moreover, although only the totally symmetric part of the solvent interaction is needed for energy calculations, in response or perturbation theory calculations of molecular properties, other irreps play an important role and the classification of solvent interaction terms by irrep is, therefore, desirable. In addition, the use of symmetry reduces the computational cost. The implementation presented here is illustrated with a series of calculations of absorption and emission processes in solution on the diazines pyrazine, pyrimidine, and pyridazine. These calculations allow us to illustrate both formal aspects of the implementation such as the choice of active spaces based on orbital symmetry as well as practical aspects such as the speed-up of the calculation.

Journal Article↗

PubMed2004

Pathology of melanocytic lesions: new, controversial, and clinically important issues.

Patients with primary cutaneous melanocytic lesions rely not only on the knowledge, skills, and experience of their treating clinician but also on the fundamentally important input of their pathologist for accurate diagnosis and appropriate management. Free and precise communication between pathologists and surgeons is important and undoubtedly improves patient care, particularly when managing difficult or complicated cases. To provide both patient and surgeon with the necessary information they require to make the most appropriate decisions, the pathology report should include all pathologic factors that are important in determining the patient's prognosis and management. Use of a synoptic format for pathology reporting of melanomas can facilitate this. Recent studies have established that the dermal mitotic rate of a primary cutaneous melanoma is a major prognostic determinant, and have shown that its assessment and that of other important histopathologic prognostic variables are reproducible between pathologists. Sentinel node (SN) biopsy has provided a minimally invasive procedure that can accurately predict the regional node status of melanoma patients. It is well demonstrated that the use of immunohistochemical stains assists in the detection of melanoma micrometastases in SNs, although it remains unclear which is the optimal pathologic protocol for SN evaluation and whether there is a role for reverse transcriptase polymerase chain reaction (RT-PCR) in SN assessment. False negative SN biopsies may occur as a result of errors in lymphatic mapping or sentinel lymphadenectomy, or because of a deficiency in the process of histopathologic evaluation. Recent studies have shown that the likelihood of non-SN involvement when the SN is positive correlates mostly with the extent of SN involvement, in particular the tumor penetrative depth (defined as the maximum distance of melanoma cells from the inner margin of the SN capsule). It appears that assessment of the micromorphometric features of positive SNs may be useful in predicting which patients have a low probability of having metastatic tumor in non-SNs, and therefore in selecting patients who potentially may be spared a completion lymph node dissection. It is likely that future advances in our understanding of the molecular biology of melanoma will provide new insights into tumor classification, improve diagnostic accuracy and prognostic ability, and lead to the development of more precisely targeted therapies.

Biopsy, Fine-Needle↗

PubMed2006

Overview on chronic viral cardiomyopathy/chronic myocarditis.

Myocarditis is most often induced by cardiotropic viruses and often resolves with minimal cardiac remodelling and without discernable prognostic impact. Acute myocarditis has a highly diverse clinical presentation (asymptomatic, infarct-like presentation, atrioventricular (AV)-block, atrial fibrillation, sudden death due to ventricular tachycardia, fulminant myocarditis with severely depressed contractility). Progression of myocarditis to its sequela, dilated cardiomyopathy (DCM), has been documented in 20% of cases and is pathogenically linked to chronic inflammation and viral persistence. Persistence of cardiotropic viruses (enterovirus, adenovirus) constitutes one of the predominant aetiological factors in DCM. Additionally, circulating autoantibodies to distinct cardiac autoantigens have been described in patients with DCM, providing evidence for autoimmune involvement. Since clinical complaints of myocarditis and DCM are unspecific, a positive effect of any specific therapy depends on an accurate biopsy-based diagnosis and characterization of the patients with histological, immunohistological and molecular biological methods (PCR), which have developed into sensitive tools for the detection of different viruses, active viral replication, and myocardial inflammation. The immunohistochemical characterization of infiltrates has supported a new era in the diagnosis of myocardial inflammation compared with the Dallas criteria, which has led to a new entity of secondary cardiomyopathies acknowledged by the WHO, the inflammatory cardiomyopathies (DCMi). Immunohistochemically quantified lymphocytes significantly better reflect troponin levels and correlate with findings by anti-myosin scintigraphy compared with the histological analysis. Furthermore, the orchestrated induction of endothelial cell adhesion molecules (CAMs) in 65% of DCM patients has confirmed that CAM induction is a prerequisite for lymphocytic infiltration in DCMi. The combination of these immunohistological with molecular biological diagnostic techniques of virus analysis allows a further classification of dilated cardiomyopathy by differentiating the disease entity in subgroups of virus-positive and virus-negative patients with or without cardiac inflammation. Further analysis of the predominant Th1-/Th2-immune response may provide additional prognostic information on the natural course of the disease. This differential analysis improves the clinical management of patients and is an indispensable prerequisite for the development of specific antiviral or immunomodulatory treatment strategies.

Cardiomyopathies↗

PubMed1989

Pneumocystis carinii: taxing taxonomy.

The detailed taxonomy of Pneumocystis carinii has not been decided. Most experts agree that it is either a fungus or a protozoan. In favor of a fungal designation are the recent reports that 16s and 18s rRNA sequences of P. carinii have greater homology to Saccharomyces cerevisiae and Neurospora crassa than to selected protozoa. Other studies show that sequences of the 18s and 26s rRNA, microtubular ultrastructure, membrane fusion potential and DNA content per cell resemble protozoa more than fungi. Therapeutic responsiveness to drugs effective against protozoa, namely pentamidine (Trypanosoma, Leishmania, sp), trimethoprim-sulfamethoxazole (Isospora sp), pyrimethamine-sulfadiazine (Toxoplasma, Plasmodium sp) and nonresponsiveness to antifungal drugs such as amphotericin B and ketoconazole indicate characteristics similar to protozoa. Taxonomic placement is based upon multifactional determinants, not a single attribute. Data are not yet available to make such a determination for P. carinii. Furthermore, detailed rules on qualifying criteria for both protozoan and fungal classifications are lacking, especially in the utilization of methods in molecular genetics for this purpose.

Animals↗

PubMed2004

New methods for detecting positive selection at single amino acid sites.

Inferring positive selection at single amino acid sites is of particular importance for studying evolutionary mechanisms of a protein. For this purpose, Suzuki and Gojobori (1999) developed a method (SG method) for comparing the rates of synonymous and nonsynonymous substitutions at each codon site in a protein-coding nucleotide sequence, using ancestral codons at interior nodes of the phylogenetic tree as inferred by the maximum parsimony method. In the SG method, however, selective neutrality of nucleotide substitutions cannot be tested at codon sites, where only termination codons are inferred at any interior node or the number of equally parsimonious inferences of ancestral codons at all interior nodes exceeds 10,000. Here I present a modified SG method which is free from these problems. Specifically, I use the distance-based Bayesian method for inferring the single most likely ancestral codon from 61 sense codons at each interior node. In the computer simulation and real data analysis, the modified SG method showed a higher overall efficiency of detecting positive selection than the original SG method, particularly at highly polymorphic codon sites. These results indicate that the modified SG method is useful for inferring positive selection at codon sites where neutrality cannot be tested by the original SG method. I also discuss that the p-distance is preferable to the number of synonymous substitutions for inferring the phylogenetic tree in the SG method, and present a maximum likelihood method for detecting positive selection at single amino acid sites, which produced reasonable results in the real data analysis.

Amino Acids↗

PubMed2001

Fish retroposons related to the Penelope element of Drosophila virilis define a new group of retrotransposable elements.

Poseidon and Neptune are two ancient lineages of retroposons related to the Penelope element from Drosophila virilis. They have been identified in various teleost fish species, including the medakafish (Oryzias latipes), and the pufferfishes Fugu rubripes and Tetraodon nigroviridis, whose genomes are currently being sequenced. Some of these elements are highly reiterated in fish genomes. Penelope-related elements were also identified in blood fluke, shrimp, sea urchin, cichlid fish and frog, showing that they are widespread in animals. Penelope-related retroposons were not detected among sequences from the Drosophila melanogaster and human genome projects, suggesting that they have been lost from certain animal lineages. A sequence encoding a putative Uri (also called GIY-YIG) endonuclease domain was detected downstream from the gene for reverse transcriptase. To the best of our knowledge, this type of endonuclease sequence has previously been identified in group I introns and in genes for prokaryotic excinucleases but not in retrotransposable elements. Penelope-related elements are frequently truncated at their 5' ends and can also be flanked by long terminal repeat-like structures. Phylogenetic analysis of the reverse transcriptase domain failed to assign Penelope-related retroposons to one of the major groups of retroelements. Overall, therefore, the evidence strongly suggests that these sequences represent a new group of retrotransposable elements.

Amino Acid Sequence↗

PubMed2006

Molecular biology in acute leukemia.

Acute leukemia is a clonal expansion of tumoral cells in bone marrow, blood or other tissues. The acute leukemias are classified as myeloid or lymphoid based on the lineage of the blast cells. Over the past three decades, remarkable advances have been made in the classification and treatment of acute leukemias. In the last years, the research into the molecular pathogenesis of acute leukemia has progressed. The knowledge of chromosomal translocations breakpoints and possible candidate oncogenes and tumor suppressor genes has allowed the integration of all these events into multistep cascades that impact specific signal transduction pathways and lead to leukemic transformation.

Acute Disease↗

PubMed1989

The analysis of five carbenicillin-hydrolysing enzymes by electrophoretic methods.

Five carbenicillin-hydrolysing enzymes (carbenicillinases, or CARB), PSE-4 (CARB-1), PSE-1 (CARB-2), CARB-3, CARB-4 and CARB-5, and the beta-lactamase PSE-2 were compared by analysing their isoelectric points (pI), electrophoretic mobilities (mR) and titration curves (pH gradient electrophoresis). The pI determined by isoelectric focusing were 4.3 (CARB-4), 5.3 (PSE-4/CARB-1), 5.7 (PSE-1/CARB-2), 5.75 (CARB-3), 6.1 (PSE-2) and 6.35 (CARB-5). Their mR were estimated by zone electrophoresis as congruent to 26 for PSE-1 (CARB-2), CARB-3 and CARB-5, congruent to 30 for PSE-2, congruent to 33 for PSE-4 (CARB-1) and congruent to 61 for CARB-4. Titration curve analyses indicated that (1) PSE-4 (CARB-1), PSE-1 (CARB-2), CARB-3 and CARB-5 are closely related variants differing by a few amino acid substitutions; (2) the qualitative titration curve of CARB-4 is different from those of PSE-4 (CARB-1), PSE-1 (CARB-2), CARB-3 and CARB-5, although their patterns are somewhat similar; and (3) PSE-2 has no structural relationship with any of the other carbenicillin-hydrolysing enzymes or carbenicillinases (CARB) studied. Electrophoretic methods, and in particular titration curve determination combined with other physicochemical and enzymatic data, allowed a rapid comparison of the molecular structures of the beta-lactamases, and hence their classification.

Acinetobacter↗

PubMed2006

Functional aquaporin diversity in plants.

Due to the fact that most plants are immobile, a rapid response of physiological processes to changing environmental conditions is essential for their survival. Thus, in comparison to many other organisms, plants might need a more sophisticated tuning of water balance. Among others, this is reflected by the comparable large amount of aquaporin genes in plant genomes. So far, aquaporins were shown to be involved in many physiological processes like root water uptake, reproduction or photosynthesis. Their classification as simple water pores has changed according to their molecular function into channels permeable for water, small solutes and/or gases. An adjustment of the corresponding physiological process could be achieved by regulation mechanisms. Concerning aquaporins these range from posttranslational modification, molecular trafficking to heteromerization of aquaporin isoforms. The aim of this review is to underline the function of the four plant aquaporin family subclasses with regard to the substrate specificity, regulation and physiological relevance.

Aquaporins↗

PubMed2006

A molecular phylogeny of New Zealand's Petroica (Aves: Petroicidae) species based on mitochondrial DNA sequences.

The New Zealand robin (Petroica australis), tomtit (P. macrocephala), and Chatham Island black robin (P. traversi) are members of the Petroicidae family of Australo-Papuan robins, found throughout Australasia and the western Pacific. In the nearly 200 years since the New Zealand members of Petroicidae were first described, the division of species, subspecies, and even genera has undergone many changes. In this study, we investigate whether molecular phylogenies based on mitochondrial DNA sequences support current taxonomic classifications based on morphology. Petroica traversi, P. australis, and P. macrocephala form distinct clades in phylogenetic trees constructed from Cytochrome b and control region sequences, however the position of the black robin is at odds with the morphological and behavioral data. The black robin does not appear to be a derivative of the New Zealand robin, instead it groups strongly with the tomtit, indicating that lineage sorting and/or introgressive hybridization may have occurred. There is some evidence to support the hypothesis that two invasions of Petroica from Australia have occurred, however additional data from Australian Petroica taxa are required to confirm this. Control region sequences confirm a deep split between the North and South Island P. australis lineages, but suggest a recent radiation of P. macrocephala.

Animals↗

PubMed2003

Apoptotic detection methods--from morphology to gene.

To date, many terms have been given for cell death and forgotten before they became widely accepted. Most researchers studying cell death use some terms for cell death that have survived over centuries and regard apoptosis and programmed cell death (PCD), and necrosis and oncosis as synonymous. The different terminologies used for cell death depending on the preference of researchers sometimes cause confusion in the study of apoptosis. The study of apoptosis was first based on cell morphology using transmission electron microscopy (TEM): chromatin condensation, cellular shrinkage, budding and apoptotic body formation. Recently, marked progress in biochemistry, molecular biology and genetics provided researchers of apoptosis various tools for apoptosis detection, such as the terminal deoxynucleotidyl transferase (TdT)-mediated dUTP-biotin nick end-labeling (TUNEL) method, agarose gel electrophoresis using extracted DNA, staining methods using fluorescence dyes, and flow cytometry. This review focuses on the following topics: history of the study of cell death and its classification, apoptosis-related proteins and their signal pathways, morphological, biochemical and molecular biological methods of apoptosis detection, and the transcriptional regulation of bcl-2 using the real-time Southwestern method and cancer gene therapy. In addition, the merits and demerits of the above-mentioned apoptosis detection methods are discussed.

Animals↗