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Results for “alignment chaining method”

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PubMed1999

Using protein structural information in evolutionary inference: transmembrane proteins.

We present a model of amino acid sequence evolution based on a hidden Markov model that extends to transmembrane proteins previous methods that incorporate protein structural information into phylogenetics. Our model aims to give a better understanding of processes of molecular evolution and to extract structural information from multiple alignments of transmembrane sequences and use such information to improve phylogenetic analyses. This should be of value in phylogenetic studies of transmembrane proteins: for example, mitochondrial proteins have acquired a special importance in phylogenetics and are mostly transmembrane proteins. The improvement in fit to example data sets of our new model relative to less complex models of amino acid sequence evolution is statistically tested. To further illustrate the potential utility of our method, phylogeny estimation is performed on primate CCR5 receptor sequences, sequences of l and m subunits of the light reaction center in purple bacteria, guinea pig sequences with respect to lagomorph and rodent sequences of calcitonin receptor and K-substance receptor, and cetacean sequences of cytochrome b.

Animals↗

PubMed1995

Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase.

BACKGROUND: Tryptophanyl-tRNA synthetase (TrpRS) catalyzes activation of tryptophan by ATP and transfer to tRNA(Trp), ensuring translation of the genetic code for tryptophan. Interest focuses on mechanisms for specific recognition of both amino acid and tRNA substrates. RESULTS: Maximum-entropy methods enabled us to solve the TrpRS structure. Its three parts, a canonical dinucleotide-binding fold, a dimer interface, and a helical domain, have enough structural homology to tyrosyl-tRNA synthetase (TyrRS) that the two enzymes can be described as conformational isomers. Structure-based sequence alignment shows statistically significant genetic homology. Structural elements interacting with the activated amino acid, tryptophanyl-5'AMP, are almost exactly as seen in the TyrRS:tyrosyl-5'AMP complex. Unexpectedly, side chains that recognize indole are also highly conserved, and require reorientation of a 'specificity-determining' helix containing a conserved aspartate to assure selection of tryptophan versus tyrosine. The carboxy terminus, which is disordered and therefore not seen in TyrRS, forms part of the dimer interface in TrpRS. CONCLUSIONS: For the first time, the Bayesian statistical paradigm of entropy maximization and likelihood scoring has played a critical role in an X-ray structure solution. Sequence relatedness of structurally superimposable residues throughout TrpRS and TyrRS implies that they diverged more recently than most aminoacyl-tRNA synthetases. Subtle, tertiary structure changes are crucial for specific recognition of the two different amino acids. The conformational isomerism suggests that movement of the KMSKS loop, known to occur in the TyrRS transition state for amino acid activation, may provide a basis for conformational coupling during catalysis.

Amino Acid Sequence↗

PubMedDate not supplied

Single mutations of the PTEN gene in recurrent ovarian carcinomas.

OBJECTIVE: To establish the role of phosphate and tensin homologue on chromosome 10 (PTEN) mutations in tumorigenesis of the ovary, we determined the mutational spectrum of the PTENgene in surgical specimens of ovarian carcinomas. METHODS: The study group consisted of 86 ovarian cancer specimens (18 fluids, 68 solid specimens), including 30 primary ovarian cancer specimens and 56 of relapsed ovarian cancer from women with a median age of 57.9 years and a range of 27-85 years. Each of the nine exons of the PTEN gene was amplified separately by polymerase chain reaction (PCR). Both strands of the PCR products were sequenced directly by standard cycle sequencing procedures and subsequent computer-aided alignments with the wild-type sequence. RESULTS: In ascitic fluids of two women with recurrence of cancer, we observed mutations: one seven-base-pair insertion at codon 52 (GATGATG) and the other a base-pair substitution resulting in an amino acid change (T131I). We found no mutation in the primary ovarian cancers. CONCLUSIONS: Our data indicate that PTEN mutations have a subordinate role in tumorigenesis of the ovary.

Adult↗

PubMed1999

Cryptosporidium is more closely related to the gregarines than to coccidia as shown by phylogenetic analysis of apicomplexan parasites inferred using small-subunit ribosomal RNA gene sequences.

The phylogenetic placement of gregarine parasites (Apicomplexa: Gregarinasina) within the Apicomplexa was derived by comparison of small-subunit ribosomal RNA gene sequences. Gregarine sequences were obtained from Gregarina niphandrodes Clopton, Percival, and Janovy, 1991, and Monocystis agilis Stein, 1848 (Eugregarinorida Léger 1900), as well as from Ophriocystis elektroscirrha McLaughlin and Myers, 1970 (Neogregarinorida Grassé 1953). The sequences were aligned with several other gregarine and apicomplexan sequences from GenBank and the resulting data matrix analyzed by parsimony and maximum-likelihood methods. The gregarines form a monophyletic clade that is a sister group to Cryptosporidium spp. The gregarine/ Cryptosporidium clade is separate from the other major apicomplexan clade containing the coccidia, adeleids, piroplasms, and haemosporinids. The trees indicate that the genus Cryptosporidium has a closer phylogenetic affinity with the gregarines than with the coccidia. These results do not support the present classification of the Cryptosporidiidae in the suborder Eimerioirina Léger, 1911.

Animals↗

PubMed2000

HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.

We describe a hidden Markov model, HMMSTR, for general protein sequence based on the I-sites library of sequence-structure motifs. Unlike the linear hidden Markov models used to model individual protein families, HMMSTR has a highly branched topology and captures recurrent local features of protein sequences and structures that transcend protein family boundaries. The model extends the I-sites library by describing the adjacencies of different sequence-structure motifs as observed in the protein database and, by representing overlapping motifs in a much more compact form, achieves a great reduction in parameters. The HMM attributes a considerably higher probability to coding sequence than does an equivalent dipeptide model, predicts secondary structure with an accuracy of 74.3 %, backbone torsion angles better than any previously reported method and the structural context of beta strands and turns with an accuracy that should be useful for tertiary structure prediction.

Amino Acid Motifs↗

PubMed1994

A rapid method for the analysis of influenza virus genes: application to the reassortment of equine influenza virus genes.

We describe a rapid method for genetic characterisation of influenza virus genes using reverse transcription and amplification by polymerase chain reaction (RT/PCR) of all virus segments simultaneously (multiplex RT/PCR) using primers based on the conserved terminal sequences. The product has been shown to be suitable for determination of partial nucleotide sequences which can be used to search nucleotide sequence databases and rapidly map the genetic origin of each segment. We illustrate the use of the method by analysing genetic reassortment in H7N7 equine influenza viruses.

Base Sequence↗

PubMed2005

A PCR based assay for detection and differentiation of African trypanosome species in blood.

Direct PCR analysis of trypanosome infected blood samples in the quantities required for large scale epidemiological study has always been problematic. Current methods for identifying and differentiating trypanosomes typically require several species-specific reactions, many of which rely on mouse passaged samples to obtain quality concentrated genomic DNA. As a consequence important epidemiological information may be lost during the sample preparation stage. Here, we report a PCR methodology that reduces processing and improves on the sensitivity of present screening methods. The PCR technique targets the gene encoding the small ribosomal subunit in order to identify and differentiate all clinically important African trypanosome species and some subspecies. The method is more economical, simple, and sensitive than current screening methods, and yields more detailed information, thereby making it a viable tool for large-scale epidemiological studies.

Animals↗

PubMed2004

Generic detection and differentiation of tobamoviruses by a spot nested RT-PCR-RFLP using dI-containing primers along with homologous dG-containing primers.

A spot nested RT-PCR-RFLP method to detect and identify all members of the Tobamovirus genus is described. It involves a one-step RT-PCR, in which the combination of degenerate deoxyinosine (dI)-substituted primers amplified part of the polymerase region of tobamoviruses, followed by a nested PCR amplification that increased specificity and sensitivity of detection. Virus species differentiation was achieved by subsequent restriction enzyme analysis. The sensitivity of the method was increased further when along with one primer containing many dIs, another homologous primer in which dIs were substituted by dGs was used. The homologous primer was shorter than the dI-containing primer and with lower degeneracy, resulting in higher overall amplification efficiency due to the increased stability of the primer-target duplex. With this strategy, highly degenerate primers containing many dIs can be used effectively to improve detection sensitivity, alleviating problems of primer-target duplex destabilisation that can occur due to many dI substitutions. This method can be useful on the diagnosis, epidemiological investigation, and characterisation of known and unidentified Tobamovirus species.

Amino Acid Sequence↗

PubMed2006

PCR-RFLP method for the identification of four members of the Anopheles annularis group of mosquitoes (Diptera: Culicidae).

The Anopheles annularis group of mosquitoes is widely distributed in Southeast Asia and may be locally important as malaria vectors. Members of this group are morphologically very similar and often difficult to distinguish, particularly A. nivipes and A. philippinensis. We report the sequence analysis of the rDNA internal transcribed spacer 2 (ITS2) and Domain-3 (D3) regions of the four members of the A. annularis group -A. nivipes, A. philippinensis, A. annularis and A. pallidus - and a method for their molecular identification. No intraspecies sequence variation was detected among the specimens, while interspecific sequence differences were greater for ITS2 than the D3 regions. Comparison of the D3 sequences of the four species revealed two SmaI restriction sites in A. nivipes, but only one site in A. philippinensis, A. annularis and A. pallidus. The ApaI site was present in both A. philippinensis and A. pallidus, while an NcoI site was present in A. pallidus only. Restriction digestion of the PCR products of D3 fragment individually with SmaI, ApaI and NcoI produced a distinctive pattern for all the four species. We present, for the first time, a PCR-RFLP method to distinguish the four members of the A. annularis group of mosquitoes.

Animals↗

PubMed2004

Development of a polymerase chain reaction for the detection of Mycoplasma felis in domestic cats.

Mycoplasma felis is associated with conjunctivitis and respiratory disease in domestic cats. Currently no rapid diagnostic test is available for the detection of M. felis in clinical samples that does not rely on prior cultivation of the organism. The objective of this study was to determine whether a polymerase chain reaction (PCR) based upon the 16S/23S rRNA intergenic spacer sequence is suitable for the identification of M. felis directly in feline clinical samples. The high conservation between the 16S/23S rRNA intergenic spacers (IGS) of differing isolates of M. felis was established by sequence analysis and a PCR was developed to this region by comparison to IGS of other mycoplasmas. The PCR was found to be highly specific for M. felis and further PCR analysis on clinical samples showed the PCR to be highly sensitive and more rapid than the other methods of identification currently available.

Animals↗

PubMed2003

Cloning, expression, and tissue distribution of bovine interleukin-21.

Bovine interleukin-21 (IL-21) cDNA was cloned and sequenced from bovine peripheral blood lymphocytes (PBLs) stimulated with 10 microg/ml concanavalin A (ConA), 10 microg/ml phytohemagglutinin (PHA), and 50 ng/ml phorbol 12-myristate 13-acetate (PMA) for 48 h. The open reading frame of the bovine IL-21 cDNA is 459 bp in length and encodes 152 amino acids. The predicted amino acid sequence is 78.2 and 58.5% homologous to the human and murine IL-21 amino acid sequences, respectively. Recombinant bovine IL-21 was expressed by a baculovirus expression system. The bovine IL-21 was processed to the mature form in insect cells and secreted to the supernatant confirmed by N-terminal amino acid sequencing. The recombinant bovine mature IL-21 induced the proliferation of human IL-2-dependent cells, ILT-MAT. The mRNA expression for bovine IL-21 was observed in the spleen, but not in the brain, heart, lung, liver, and kidney. The bovine IL-21 identified in this study may provide new methods for the enhancement of innate immunity in cows.

Amino Acid Sequence↗

PubMed2003

Historical demography and genetic structure of sister species: deermice (Peromyscus) in the North American temperate rain forest.

To investigate the evolutionary and biogeographical history of Peromyscus keeni and P. maniculatus within the coastal forest ecosystem of the Pacific Northwest of North America, we sampled 128 individuals from 43 localities from southeastern Alaska through Oregon. We analysed mitochondrial DNA variation using DNA sequence data from the mitochondrial cytochrome-b (cyt-b) gene and control region, and we found two distinct clades consistent with the morphological designation of the two species. The sequence divergence between the two clades was 0.0484 substitutions per site for cyt-b and 0.0396 for the control region, suggesting that divergence of the two clades occurred during the middle to late Pleistocene. We also examined the historical demography of the two clades using stepwise and exponential expansion models, both of which indicated recent rapid population growth. Furthermore, using the program migrate we found evidence of migration from populations north of the Fraser River (British Columbia) to the south in both clades. This study demonstrates the utility of these model-based demographic methods in illuminating the evolutionary and biogegographic history of natural systems.

Animals↗

PubMed1997

Specific and sensitive detection of Trichomonas tenax by the polymerase chain reaction.

A polymerase chain reaction (PCR) protocol was developed for specific detection of Trichomonas tenax by using a pair of primers designed for its 18S rRNA gene. The detection was specific for T. tenax, since no amplification was detected with DNAs from Trichomonas vaginalis, which belongs to the same genus as T. tenax, in addition to various species of oral protists, fungi and bacteria, and human leukocytes. This method had a detection limit of 100 fg for T. tenax genomic DNA and could detect T. tenax cells in dental plaque at a concentration of as low as 5 cells per PCR mixture. Direct detection from clinical dental plaque samples was also possible; therefore, the present PCR procedure could provide a simple and rapid detection method of T. tenax in dental plaque.

Animals↗

PubMed2004

Fold-specific substitution matrices for protein classification.

MOTIVATION: Methods that focus on secondary structures, such as Position Specific Scoring Matrices and Hidden Markov Models, have proved useful for assigning proteins to families. However, for assigning proteins to an attribute class within a family these methods may introduce more free parameters than are needed. There are fewer members and there is less variability among sequences within a family. We describe a method for organizing proteins in a family that exhibits up to an order of magnitude reduction in the number of parameters. The basis is the log odds ratio commonly used to measure similarity. We adapt this to characterize the sequence dissimilarities that give rise to attribute differentiation. This leads to the definition of Class Attribute Substitution Matrices (CLASSUM), a dual of the BLOSUM. RESULTS: The method was applied to classify sequences hierarchically in the lambda and kappa subgroups of the immunoglobulin superfamily. Positions conferring class were identified based on the degree of amino acid variability at a position. The CLASSUM computed for these positions classified better than 90% of test data correctly compared with 35-50% for BLOSUM-62. The expected value for a random matrix is 14%. The results suggest that family-specific data-derived substitution matrices can improve the resolution of automated methods that use generic substitution matrices for searching for and classifying proteins.

Algorithms↗

PubMed1999

New method for automatic identification identification and typing of single and multiple superimposed human papillomavirus sequences.

This study of specimens of human papillomaviruses (HPV) through HPV-specific polymerase chain reaction (PCR), followed by direct sequencing, resulted in 11% (38/354) superimposed HPV sequences, signifying coinfection with more than one HPV type. To address the diagnostic problem that these superimposed ("degenerated," overlapping) sequences pose, the authors created a papillomavirus database in Microsoft Excel (Microsoft Corporation, Redmond, WA, U.S.A.) and Corel Quattro Pro 9 (Corel Corporation, Ottawa, Ontario, Canada) formats, retrievable from http://www2.crosswinds.net/ -crosswindswatson/index.html. This sequence database is simultaneously a search and comparison tool for quick (several seconds) typing of HPV from regular and "degenerated" sequencing results. Some of the advantages of the method are as follows: (1) superimposed HPV sequences that differ in length could be readily identified from a single input; (2) the search is restricted to the currently known 127 PV types, which speeds up the typing; (3) the most common HPV sequencing artifacts are included for quick detection; (4) there is no proprietary code and the database could be easily improved; (5) HPV sequence identification does not require internet connection; and (6) new HPV types could be easily detected. This method allowed resolution of all but 1 of 354 HPV-positive specimens. From 38 superimposed HPV sequences, this method identified one known HPV type (3 specimens), two HPV types (30 specimens) and three HPV types (4 specimens).

DNA Primers↗

PubMed2002

Nucleotide sequence and expression of the feline vascular endothelial growth factor.

Vascular endothelial growth factor (VEGF) is an angiogenic factor which targets vascular endothelial cells. In this study, cDNA encoding a feline VEGF (fVEGF) isoform was cloned from a feline lymphoid tumor cell line and sequenced. The fVEGF cDNA contained an open reading frame of 567 nucleotides coding for a polypeptide of 163 amino acids with a putative signal peptide of 26 amino acids. The predicted fVEGF amino acid sequence shared 98.4, 94.2 and 94.2% homology with the sequences of canine, bovine and human VEGF, respectively. Though predicted fVEGF polypeptide was two amino acid residues shorter than human VEGF165, a potential glycosylation site and regions critical for receptor binding were conserved in all the species examined. Transient expression of fVEGF in mammalian cells resulted in secretion of VEGF which could be detected by antibodies against human VEGF165. Furthermore, wide expression of fVEGF mRNA was observed in various feline tissues using RT-PCR methods.

Amino Acid Sequence↗

PubMed1998

Partial amplification of the measles virus nucleocapsid gene from stored sera and cerebrospinal fluids for molecular epidemiological studies.

The analysis of stored sera for retrospective molecular epidemiological studies provides a powerful tool to investigate strain variation in measles viruses that had circulated up to 20 years ago. For this purpose, a rapid and simple method for extraction of RNA from stored sera and cerebrospinal fluids (CSF) was developed. When used on sera and CSFs that have been frozen for as long as 20 years, this method proved to be more efficient than established techniques. The extracted RNA was reverse transcribed into cDNA by using random hexamer primers. The PCR amplification of the 3' terminus of the nucleocapsid gene (N) was divided into two overlapping fragments of 375 and 384 bp length, covering the entire region of interest. This region is thought to have the highest variability within the MV genome and has previously been shown to be suitable for strain characterization. The resulting PCR fragments were sequenced manually by using standard methods without the need of further clean-up steps.

Amino Acid Sequence↗

PubMed2006

Relaxed phylogenetics and dating with confidence.

In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of "relaxed phylogenetics." Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.

Animals↗