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At least 865 records · Page 48Linked to original sources
PubMed2006

Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication.

Gene duplication and loss are predicted to be at least of the order of the substitution rate and are key contributors to the development of novel gene function and overall genome evolution. Although it has been established that proteins evolve more rapidly after gene duplication, we were interested in testing to what extent this reflects causation or association. Therefore, we investigated the rate of evolution prior to gene duplication in chordates. Two patterns emerged; firstly, branches, which are both preceded by a duplication and followed by a duplication, display an elevated rate of amino acid replacement. This is reflected in the ratio of nonsynonymous to synonymous substitution (mean nonsynonymous to synonymous nucleotide substitution rate ratio [Ka:Ks]) of 0.44 compared with branches preceded by and followed by a speciation (mean Ka:Ks of 0.23). The observed patterns suggest that there can be simultaneous alteration in the selection pressures on both gene duplication and amino acid replacement, which may be consistent with co-occurring increases in positive selection, or alternatively with concurrent relaxation of purifying selection. The pattern is largely, but perhaps not completely, explained by the existence of certain families that have elevated rates of both gene duplication and amino acid replacement. Secondly, we observed accelerated amino acid replacement prior to duplication (mean Ka:Ks for postspeciation preduplication branches was 0.27). In some cases, this could reflect adaptive changes in protein function precipitating a gene duplication event. In conclusion, the circumstances surrounding the birth of new proteins may frequently involve a simultaneous change in selection pressures on both gene-copy number and amino acid replacement. More precise modeling of the relative importance of preduplication, postduplication, and simultaneous amino acid replacement will require larger and denser genomic data sets from multiple species, allowing simultaneous estimation of lineage-specific fluctuations in mutation rates and adaptive constraints.

Amino Acid Substitution↗
PubMed2001

Comparative biochemistry of disintegrins isolated from snake venom: consideration of the taxonomy and geographical distribution of snakes in the genus Echis.

Species in the genus Echis have been classified mainly based on their morphological appearance and the analytical patterns of their serum. However, re-classification of the genus Echis has recently been suggested by taxonomists, toxicologists, and clinicians, since there have been problems with the current classification, such as the efficacy of antivenoms used for treating bites and the broad geographical distribution of Echis snakes. In this study, we purified five novel disintegrins, the platelet aggregation inhibitors pyramidin A and B from the venom of Echis pyramidum, ocellatin from the venom of Echis ocellatus, and leucogastin A and B from the venom of Echis leucogaster, to compare their sequences and allow us to re-evaluate the classification of various species in the genus Echis. Comparison of the amino acid sequences of five new and four known isolated disintegrins from snake venoms of six Echis species and their distribution strongly support the recent re-classification of the genus Echis.

Africa↗
PubMed1997

Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution.

Various methods for detecting correlation between sites were evaluated by ascertaining their ability to discriminate positively correlated sites from background correlation at randomly evolved sites. A model for generating pairwise correlations of different degrees is also described. An assortment of physicochemical vectors and similarity and difference matrices were used to discriminate correlated change. There was little difference in effectiveness between the different matrices, but there were significant differences between the matrices and the physicochemical vectors. It is shown that all methods investigated exhibit significant inability to screen out background correlation, particularly in the presence of phylogenetic relatedness between the sequences. Methods using the matrices are unable to distinguish positively correlated from negatively correlated, or compensatory, replacements.

Amino Acid Sequence↗
PubMed2004

The analysis of placement values for evaluating discriminatory measures.

The idea of using measurements such as biomarkers, clinical data, or molecular biology assays for classification and prediction is popular in modern medicine. The scientific evaluation of such measures includes assessing the accuracy with which they predict the outcome of interest. Receiver operating characteristic curves are commonly used for evaluating the accuracy of diagnostic tests. They can be applied more broadly, indeed to any problem involving classification to two states or populations (D= 0 or 1). We show that the ROC curve can be interpreted as a cumulative distribution function for the discriminatory measure Y in the affected population (D= 1) after Y has been standardized to the distribution in the reference population (D= 0). The standardized values are called placement values. If the placement values have a uniform(0, 1) distribution, then Y is not discriminatory, because its distribution in the affected population is the same as that in the reference population. The degree to which the distribution of the standardized measure differs from uniform(0, 1) is a natural way to characterize the discriminatory capacity of Y and provides a nontraditional interpretation for the ROC curve. Statistical methods for making inference about distribution functions therefore motivate new approaches to making inference about ROC curves. We demonstrate this by considering the ROC-GLM regression model and observing that it is equivalent to a regression model for the distribution of placement values. The likelihood of the placement values provides a new approach to ROC parameter estimation that appears to be more efficient than previously proposed methods. The method is applied to evaluate a pulmonary function measure in cystic fibrosis patients as a predictor of future occurrence of severe acute pulmonary infection requiring hospitalization. Finally, we note the relationship between regression models for the mean placement value and recently proposed models for the area under the ROC curve which is the classic summary index of discrimination.

Biometry↗
PubMed2006

Prevalence of vaccine-derived polioviruses in stools of immunodeficient children in South Africa.

AIMS: The aim of the study was to determine the prevalence of vaccine-derived polioviruses (VDPVs) in stool specimens of immunodeficient patients such as HIV-positive children (including those with an AIDS indicator condition, according to the Centres for Disease Control and Prevention classification) by applying various molecular techniques. METHODS AND RESULTS: A total of 164 stool samples from HIV-positive children and 23 stool samples from healthy immunocompetent children (the control group) were analysed during 2003 and 2004. By applying a reverse transcription polymerase chain reaction (RT-PCR) in combination with a nested PCR, a total of 54 enteroviruses were detected in the stool specimens of the immunodeficient children. The use of restriction enzymes and a Sabin specific RT-triplex PCR confirmed the presence of 13 polioviruses (PVs), such as seven Sabin PV type 1, four Sabin PV type 3 and two Sabin PV type 2 isolates. The 5'untranslated region and the VP1 capsid-encoding protein of the 13 PVs and the three PVs from the stools of the immunocompetent children were partially sequenced and their genetic relatedness was deduced from the constructed phylogenetic trees. The majority of the PVs isolated from the stools of the immunodeficient children (10 of 13 isolates) were classified as 'oral poliovirus vaccine (OPV)-like viruses', as these isolates had close sequence relationships (>99% in VP1 nucleotide sequences) to the original Sabin PV vaccine strains. Three PVs showed < or =99% VP1 sequence identity to the Sabin PV vaccine strains and were classified as 'suspected' immunodeficient VDPVs (iVDPVs). All of the OPV-like isolates and the 'suspected' iVDPVs carried mutations at specific positions in their partially sequenced regions, which have been associated with reversion of the attenuated Sabin PV vaccine strains to increased neurovirulence. CONCLUSIONS: Thus, this study adds further evidence to the observation that immunodeficient individuals may excrete OPV strains with potential neurovirulent phenotypes. SIGNIFICANCE AND IMPACT OF THE STUDY: Prolonged excretion of PVs by immunodeficient individuals is of major concern, because continued replication of PVs in the human gut could result in the reversion of these viruses to greater neurovirulence. When exposed to OPV, immunodeficient patients may become chronically infected, spreading potentially neurovirulent VDPVs for many months or years to close contacts and children who are no longer being vaccinated after termination of OPV vaccination in the near future.

5' Untranslated Regions↗
PubMedDate not supplied

Phylogenetic analysis of the small subunit ribosomal RNA of Marteilia refringens validates the existence of phylum Paramyxea (Desportes and Perkins, 1990).

Marteilia refringens is recognized as one of the most significant pathogens of bivalve molluscs. The nucleotide sequence of the small subunit ribosomal RNA gene of Marteilia refringens is used to elucidate the phylogenetic position of the phylum Paramyxea. Genomic DNA was extracted from sporangia of Marteilia, purified from infected blue mussels, Mytilus edulis, and flat oysters, Ostrea edulis. The sequences obtained from Marteilia species purified from both oysters and mussels were identical. The sequence identity was confirmed by in situ hybridization using a DNA probe targeted to a variable region of the ribosomal DNA. The small subunit ribosomal RNA gene sequence of M. refringens is very different from all known sequences of eukaryotic organisms, including those of myxosporeans and haplosporeans. Therefore, the phylum Paramyxea should continue to be recognized as an independent eukaryotic phylum.

Animals↗
PubMed2006

The late Miocene radiation of modern Felidae: a genetic assessment.

Modern felid species descend from relatively recent (<11 million years ago) divergence and speciation events that produced successful predatory carnivores worldwide but that have confounded taxonomic classifications. A highly resolved molecular phylogeny with divergence dates for all living cat species, derived from autosomal, X-linked, Y-linked, and mitochondrial gene segments (22,789 base pairs) and 16 fossil calibrations define eight principal lineages produced through at least 10 intercontinental migrations facilitated by sea-level fluctuations. A ghost lineage analysis indicates that available felid fossils underestimate (i.e., unrepresented basal branch length) first occurrence by an average of 76%, revealing a low representation of felid lineages in paleontological remains. The phylogenetic performance of distinct gene classes showed that Y-chromosome segments are appreciably more informative than mitochondrial DNA, X-linked, or autosomal genes in resolving the rapid Felidae species radiation.

Africa↗
PubMed2001

Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiological research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made.

Bacteria↗
PubMed1997

Streptothricin biosynthesis is catalyzed by enzymes related to nonribosomal peptide bond formation.

In a search for strains producing biocides with a wide spectrum of activity, a new strain was isolated. This strain was taxonomically characterized as Streptomyces rochei F20, and the chemical structure of the bioactive product extracted from its fermentation broth was determined to be a mixture of streptothricins. From a genomic library of the producer strain prepared in the heterologous host Streptomyces lividans, a 7.2-kb DNA fragment which conferred resistance to the antibiotic was isolated. DNA sequencing of 5.2 kb from the cloned fragment revealed five open reading frames (ORFs) such that ORF1, -2, -3, and -4 were transcribed in the same direction while ORF5 was convergently arranged. The deduced product of ORF1 strongly resembled those of genes involved in peptide formation by a nonribosomal mechanism; the ORF2 product strongly resembled that of mphA and mphB isolated from Escherichia coli, which determines resistance to several macrolides by a macrolide 2'-phosphotransferase activity; the ORF3 product had similarities with several hydrolases; and the ORF5 product strongly resembled streptothricin acetyltransferases from different gram-positive and gram-negative bacteria. ORF5 was shown to be responsible for acetyl coenzyme A-dependent streptothricin acetylation. No similarities in the databases for the ORF4 product were found. Unlike other peptide synthases, that for streptothricin biosynthesis was arranged as a multienzymatic system rather than a multifunctional protein. Insertional inactivation of ORF1 and ORF2 (and to a lesser degree, of ORF3) abolishes antibiotic biosynthesis, suggesting their involvement in the streptothricin biosynthetic pathway.

Acetyl Coenzyme A↗
PubMed2002

The Phage Proteomic Tree: a genome-based taxonomy for phage.

There are approximately 10(31) phage in the biosphere, making them the most abundant biological entities on the planet. Despite their great numbers and ubiquitous presence, very little is known about phage biodiversity, biogeography, or phylogeny. Information is limited, in part, because the current ICTV taxonomical system is based on culturing phage and measuring physical parameters of the free virion. No sequence-based taxonomic systems have previously been established for phage. We present here the "Phage Proteomic Tree," which is based on the overall similarity of 105 completely sequenced phage genomes. The Phage Proteomic Tree places phage relative to both their near neighbors and all other phage included in the analysis. This method groups phage into taxa that predicts several aspects of phage biology and highlights genetic markers that can be used for monitoring phage biodiversity. We propose that the Phage Proteomic Tree be used as the basis of a genome-based taxonomical system for phage.

Bacteriophages↗
PubMed1991

Temporal synthesis of proteins and RNAs during human astrovirus infection of cultured cells.

Astroviruses are nonenveloped particles with a distinctive star-shaped surface structure that have been detected by electron microscopy in stool samples from humans and animals with gastroenteritis. We examined the patterns of macromolecular synthesis in astrovirus-infected cells with a goal of establishing a molecular basis for taxonomic classification. Trypsin is required for continuous replication of astrovirus in cultured cells; however, during a single cycle of infection, astrovirus antigen was synthesized earlier and at higher levels when serum, rather than trypsin, was included in the growth medium. This enhanced production of antigen, as measured by enzyme immunoassay, was accompanied by the appearance of aggregates of virus particles in the cytoplasm of infected cells. During astrovirus replication in cells cultured in the presence of serum, we detected a single infection-specific protein (90 kDa) beginning at 12 h postinfection. This protein was recognized by antiastrovirus rabbit serum and was sensitive to trypsin digestion in vitro, with the concomitant appearance of three smaller immunoreactive proteins (31, 29, and 20 kDa). We also detected two dactinomycin-resistant RNAs (7.2 and 2.8 kb), both of which were polyadenylated, in the cytoplasm of astrovirus-infected cells. The larger of these two RNAs is presumably the viral genome, whereas the smaller species may be a subgenomic messenger. Comparison of the proteins and RNAs synthesized in astrovirus-infected cells with those of the recognized families of nonenveloped single-stranded RNA animal viruses suggests that astroviruses should not be classified as members of either Caliciviridae or Picornaviridae.

Antigens, Viral↗
PubMed2002

Ascertaining maternal and paternal lineage within Musa by chloroplast and mitochondrial DNA RFLP analyses.

In banana, the maternal transmission of chloroplast DNA and paternal transmission of the mitochondrial DNA provides an exceptional opportunity for studying the maternal and paternal lineage of clones. In the present study, RFLP combined with hybridization of heterologous mitochondrial and chloroplastic probes have been used to characterize 71 wild accessions and 131 diploid and 103 triploid cultivated clones. In additon to Musa acuminata and Musa balbisiana, other species from the four Musa sections were studied to investigate their contribution to the origin of cultivated bananas. These molecular analyses enable the classification of the Musa complex to be discussed. Results ascertain relationships among and between the wild accessions and the mono- and interspecific diploid and triploid bananas, particularly for the acuminata genome. Parthenocarpic varieties are shown to be linked to M. acuminata banksii and M. acuminata errans, thus suggesting that the first center of domestication was in the Philippines - New Guinea area.

DNA Probes↗
PubMed2007

Keys and the crisis in taxonomy: extinction or reinvention?

Dichotomous keys that follow a single pathway of character state choices to an end point have been the primary tools for the identification of unknown organisms for more than two centuries. However, a revolution in computer diagnostics is now under way that may result in the replacement of traditional keys by matrix-based computer interactive keys that have many paths to a correct identification and make extensive use of hypertext to link to images, glossaries, and other support material. Progress is also being made on replacing keys entirely by optical matching of specimens to digital databases and DNA sequences. These new tools may go some way toward alleviating the taxonomic impediment to biodiversity studies and other ecological and evolutionary research, especially with better coordination between those who produce keys and those who use them and by integrating interactive keys into larger biological Web sites.

Animals↗
PubMed2026

DEK::AFF2 Fusion-Associated Sinonasal Carcinoma With Intracranial and Orbital Involvement.

Sinonasal carcinomas encompass a molecularly heterogeneous group of malignancies. DEK::AFF2 fusion-associated carcinoma is a recently recognized subtype of nonkeratinizing squamous cell carcinoma characterized by deceptively bland morphology yet clinically aggressive behavior. We report the case of a 67-year-old woman who presented with a rapidly enlarging sinonasal mass with extensive local invasion involving both the intracranial compartment and orbit. Histologically, the tumor was composed of cytologically bland cells with monotonous nuclei and exhibited a combination of exophytic and endophytic growth patterns that closely mimicked a sinonasal papilloma. Although the tumor shows predominantly squamous differentiation, focal extracellular mucin was also present. The brain-invasive foci demonstrated tumor cells in sheets and nests floating within pools of mucin, a pattern focally reminiscent of mucinous adenocarcinoma. RNA sequencing identified a DEK::AFF2 fusion with breakpoints at DEK exon 7 and AFF2 exon 6, confirming the diagnosis. The tumor demonstrated positive PD-L1 expression with a combined positive score (CPS) of 40 and a low tumor mutational burden (TMB) of 0.5 mutations/Mb. This case highlights the diagnostic challenges posed by DEK::AFF2 fusion-associated carcinoma, underscores the importance of molecular profiling for accurate classification, and demonstrates the aggressive clinical behavior of this rare entity.

Journal Article↗
PubMed2004

[Distinguishing pleural transudates and exudates through the quantification of biochemical parameters].

OBJECTIVES: 1) to evaluate the possibility of distinguishing pleural transudates and exudates through the joint determination of 26 biochemical parameters in pleural effusion and in plasma (including the determination of high molecular weight proteins, acute phase reactants, and proinflammatory citokines), and 2) to formulate a logistic regression equation for optimizing the classification efficiency, comparing the equation obtained with Light's criteria. PATIENTS AND METHODS: All diagnostic thoracocentesis carried out in La Rioja Autonomous Community during a 22-month period were evaluated. The 245 clinical records were evaluated periodically along a minimum of 2 years, after the discharge of the patients. In pleural effusion and in plasma the following were quantified: total proteins, LDH, glucose, amylase, cholesterol, albumin, cholinesterase, phosphatase alkaline, urea, beta2-microglobulin, IgG, IgM, alpha2-macroglobulin, C reactive protein, transferrin, alpha1-antitrypsin, serum amyloid A protein, interleukin 1-beta, interleukin 6, tumoral necrosis factor-alpha, and lysozyme. In addition, the cellularity, polymorphonuclear elastase and adenosine deaminase were evaluated in pleural fluid. RESULTS: The LDH pleural effusion/plasma ratio was the individual parameter that showed higher area under the receiver operating characteristic curve for the separation of pleural transudates and exudates. Interleukin 6 and tumoral necrosis factor-alpha showed pleural effusion/plasma ratios higher than the unit, which suggests an in situ citokines production. An predictive logistic regression equation was obtained that incorporates only LDH and cholesterol ratios, including the diuretic treatment of the patient at the time of thoracocentesis, which did not modify the protein concentrations in pleural effusion. Except for LDH ratio, the logistic regression equation showed an area under the receiver operating characteristic curve higher than that of all the evaluated individual parameters, with a sensitivity of 95% and a specificity of 85% (70% for the Light's criteria). CONCLUSIONS: LDH ratio is the best individual parameter for distinguishing pleural transudates and exudates. The additional evaluation of cholesterol ratio and of the diuretic state of the patient make possible to improve the clinical efficiency of this classification. The quantification of high molecular weight proteins, acute phase reactants and citokines does not contribute additional significant information.

Adult↗
PubMed2004

Sinonasal malignancy: what's new?

Tumors of the nasal cavity are located at a complex anatomic site and show a huge histological diversity. Although dealing with a rare malignancy, the last decade has brought--besides new histological and clinical classifications--a variety of new insights into etiological agents, tumor biology and therapeutic concepts as well as valuable overviews of rare histological subtypes. This review tries to disentangle the different medical and scientific aspects of the most frequently encountered histological types of tumors in the nasal cavity and the paranasal sinuses. We concentrate on epidemiology, classification, etiology, cytogenetics and molecular genetics, outcome and prognosis as well as treatment modalities, as far as the past few years have brought considerable new insights. Our principal aim is to provide the clinician with important data from publications of the last decade.

Humans↗