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Results for “alignment chaining method”

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PubMed2004

Molecular phylogeny of oribatid mites (Oribatida, Acari): evidence for multiple radiations of parthenogenetic lineages.

Nucleotide sequences of the D3 expansion segment and its flanking regions of the 28S rDNA gene were used to evaluate phylogenetic relationships among representative sexual and asexual oribatid mites (Oribatida, Acariformes). The aim of this study was to investigate the hypothesis that oribatid mites consist of species-rich clusters of asexual species that may have radiated while being parthenogenetic. Furthermore, the systematic position of the astigmate mites (Astigmata, Acariformes) which have been hypothesised to represent a paedomorphic lineage within the oribatid mites, is investigated. This is the first phylogenetic tree for oribatid mites s.l. (incl. Astigmata) based on nucleotide sequences. Intraspecific genetic variation in the D3 region was very low, confirming the hypothesis that this region is a good species marker. Results from neighbour joining (NJ) and maximum parsimony (MP) algorithms indicate that several species-rich parthenogenetic groups like Camisiidae, Nanhermanniidae and Malaconothridae are monophyletic, consistent with the hypothesis that some oribatid mite groups diversified despite being parthenogenetic. The MP and maximum likelihood (ML) method indicated that the D3 region is a good tool for elucidating the relationship of oribatid mite species on a small scale(genera, families) but is not reliable for large-scale taxonomy, because branches from the NJ algorithm collapsed in the MP and ML tree. In all trees calculated by different algorithms the Astigmata clustered within the oribatid mites, as proposed earlier.

Animals↗

PubMed2004

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data.

We describe a general likelihood-based 'mixture model' for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites in the alignment evolve in qualitatively distinct ways, but does not require prior knowledge of these patterns or partitioning of the data. We call this qualitative variability in the pattern of evolution across sites "pattern-heterogeneity" to distinguish it from both a homogenous process of evolution and from one characterized principally by differences in rates of evolution. We present studies to show that the model correctly retrieves the signals of pattern-heterogeneity from simulated gene-sequence data, and we apply the method to protein-coding genes and to a ribosomal 12S data set. The mixture model outperforms conventional partitioning in both these data sets. We implement the mixture model such that it can simultaneously detect rate- and pattern-heterogeneity. The model simplifies to a homogeneous model or a rate-variability model as special cases, and therefore always performs at least as well as these two approaches, and often considerably improves upon them. We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program.

Base Sequence↗

PubMed1994

Distribution of viral genotypes in Italy determined by hepatitis C virus typing by DNA immunoassay.

The distribution of hepatitis C virus (HCV) genotypes in Italy was investigated by PCR amplification of the E1 region and hybridization with type I- and type II-specific nonisotopic probes. Positive PCR results were obtained for 65 of 72 patients (90.3%). Type I was detected in 13 of 72 patients (18%), type II was detected in 39 patients (54.2%), and a mixed type I-type II infection was detected in 7 patients (9.7%). Six amplification products not classified by this method shared a low level of homology with HCV types I and II. HCV type I was significantly associated with human immunodeficiency virus, whereas HCV type II was detected in older subjects who were negative for human immunodeficiency virus markers. These results indicate different epidemiological distributions of HCV types I and II in Italy.

Adult↗

PubMed2004

Reverse transcription-polymerase chain reaction detection and nucleic acid sequence confirmation of reovirus infection in laboratory mice with discordant serologic indirect immunofluorescence assay and enzyme-linked immunosorbent assay results.

Reovirus infections are typically subclinical in weaned mice, and are best detected using serologic tests. After exposure to the soiled bedding of some mice obtained from various sources, numerous sentinel mice tested reovirus seropositive by use of indirect immunofluorescence assays (IIFA) in our institution. A major commercial rodent pathogen testing laboratory verified our IIFA results, but since the same samples were reovirus seronegative using their "more specific" enzyme-linked immunosorbent assay (ELISA), the IIFA results were reported as "false positives." As past in-house observations suggested transmission of the virus to sentinel and other animals, we sought to determine whether the IIFA results were always "false positives." An opportunity to test this notion arose after receipt of reovirus IIFA-positive transgenic mice from an academic source. Using reverse transcriptase-polymerase chain reaction (RT-PCR) assays, the presence of reovirus RNA was detected in fecal specimens taken from some sentinel animals that subsequently seroconverted from IIFA-negative to IIFA-positive for reovirus. The virus could not be isolated by use of tissue culturing methods. Nucleotide sequence analysis established the presence of unique reovirus sequences. These results indicate that contemporary reovirus infections may not be detected by use of some serologic tests, and that RT-PCR analysis may be useful for confirmation of active reovirus infection in certain situations.

Amino Acid Sequence↗

PubMed1994

Molecular techniques for typing unrelated marrow donors: potential impact of molecular typing disparity on donor selection.

HLA matching between a bone marrow recipient and donor is one of the major factors influencing transplant success. However, it is not possible to locate an HLA-identical donor for about 70% of patients who might benefit from bone marrow transplantation (BMT). New molecular biological methods for detection of HLA polymorphism currently provide an opportunity to improve HLA matching of unrelated donors as well as a research tool to investigate the relationship between HLA disparity and transplant complications. These molecular HLA typing methods include sequence-specific amplification, hybridization with oligonucleotide probes, heteroduplex formation and direct nucleotide sequencing. Molecular HLA typing is being utilized to address questions regarding the extent of HLA disparity between two unrelated individuals and the effect of HLA disparity that is not detected using conventional HLA typing methods. Accumulating data suggest some HLA disparities may be tolerated while others are very immunogenic. Use of more precise HLA typing may contribute to the success of future transplants utilizing alternative donors. A better understanding of the relationship between HLA disparity and transplant complications may make it possible to relax the stringency of donor matching to make BMT available to larger numbers of patients.

Adult↗

PubMed2002

A genetic linkage map of the model legume Lotus japonicus and strategies for fast mapping of new loci.

A genetic map for the model legume Lotus japonicus has been developed. The F(2) mapping population was established from an interspecific cross between L. japonicus and L. filicaulis. A high level of DNA polymorphism between these parents was the source of markers for linkage analysis and the map is based on a framework of amplified fragment length polymorphism (AFLP) markers. Additional markers were generated by restriction fragment length polymorphism (RFLP) and sequence-specific PCR. A total of 524 AFLP markers, 3 RAPD markers, 39 gene-specific markers, 33 microsatellite markers, and six recessive symbiotic mutant loci were mapped. This genetic map consists of six linkage groups corresponding to the six chromosomes in L. japonicus. Fluorescent in situ hybridization (FISH) with selected markers aligned the linkage groups to chromosomes as described in the accompanying article by Pedrosa et al. 2002(this issue). The length of the linkage map is 367 cM and the average marker distance is 0.6 cM. Distorted segregation of markers was found in certain sections of the map and linkage group I could be assembled only by combining colormapping and cytogenetics (FISH). A fast method to position genetic loci employing three AFLP primer combinations yielding 89 markers was developed and evaluated by mapping three symbiotic loci, Ljsym1, Ljsym5, and Ljhar1-3.

Chromosome Mapping↗

PubMed2004

Yeast differentiation using histone promoter sequences.

AIMS: To evaluate a new platform for yeast differentiation based on histone promoter regions. METHODS AND RESULTS: The histone gene amino acid sequences of a wide phylogenetic range of organisms were aligned, and primers designed that were capable of amplifying the divergent promoters of the H3-H4 and H2a-H2b loci from yeast. Analysis indicated that the promoter regions were variable in length between species and represented rapidly changing sequences flanked by highly conserved sequences. CONCLUSIONS: The histone promoter regions in yeast provide an excellent locus for the rapid and accurate identification of yeast species. SIGNIFICANCE AND IMPACT OF THE STUDY: This study describes an alternative platform to the ribosomal internal transcribed spacer (ITS) sequences for the identification of yeast species.

Base Sequence↗

PubMed2004

The molecular diagnosis of Marteilia refringens and differentiation between Marteilia strains infecting oysters and mussels based on the rDNA IGS sequence.

Marteilia refringens is a paramyxean parasite which infects the flat oyster Ostrea edulis and mussels (Mytilus galloprovincialis), where it has been attributed to a separate species, Marteilia maurini, by several authors. Doubts persist though as to the existence or not of two species of Marteilia in Europe. We have devised a molecular method for the diagnosis of M. refringens based on 358 bp nested-PCR of the rDNA intergene spacer (rDNA IGS) which is capable of detecting 0.5 fg of M. refringens DNA. Molecular characterization of this spacer indicates that the Marteilia parasites which infect oysters and mussels are two different strains of the same species.

Animals↗

PubMed2003

Characterization of the carbohydrate moieties of the functional unit RvH1-a of Rapana venosa haemocyanin using HPLC/electrospray ionization MS and glycosidase digestion.

The primary structures of two biantennary N -glycans of the glycoprotein Rapana venosa (marine snail) haemocyanin were determined. Two different structural subunits have been found in R. venosa haemocyanin: RvH1 and RvH2. The carbohydrate content of the N-terminal functional unit RvH1-a of RvH1 was studied and compared with the N-terminal functional unit RvH2-a of RvH2. Oligosaccharide fragments were released from the glycoprotein by Smith degradation of a haemocyanin pronase digest and separated on a Superdex 300 column. The glycopeptide fragments, giving a positive reaction for the orcinol/H2SO4 method, were separated by HPLC. In order to determine the linked sugar chains to the hinge glycopeptides isolated from the functional unit RvH1-a, several techniques were applied, including capillary electrophoresis, matrix-assisted laser desorption ionization-MS and electrospray ionization-MS in combination with glycosidase digestion. On the basis of these results and amino acid sequence analysis, we concluded that the functional unit RvH1-a contains 7% oligosaccharides N-glycosidically attached to Asn262 and Asn401, and the following structures were suggested:[structure: see text]

Amino Acid Sequence↗

PubMed2006

A simple DNA stretching method for fluorescence imaging of single DNA molecules.

Stretching or aligning DNA molecules onto a surface by means of molecular combing techniques is one of the critical steps in single DNA molecule analysis. However, many of the current studies have focused on lambda-DNA, or other large DNA molecules. There are very few studies on stretching methodologies for DNA molecules generated via PCR (typically smaller than 20 kb). Here we describe a simple method of stretching DNA molecules up to 18 kb in size on a modified glass surface. The very low background fluorescence allows efficient detection of single fluorescent dye labels incorporated into the stretched DNA molecules.

DNA↗

PubMed1996

Anonymous nuclear DNA markers in the American oyster and their implications for the heterozygote deficiency phenomenon in marine bivalves.

A puzzling population-genetic phenomenon widely reported in allozyme surveys of marine bivalves is the occurrence of heterozygote deficits relative to Hardy-Weinberg expectations. Possible explanations for this pattern are categorized with respect to whether the effects should be confined to protein-level assays or are genomically pervasive and expected to be registered in both protein- and DNA-level assays. Anonymous nuclear DNA markers from the American oyster were employed to reexamine the phenomenon. In assays based on the polymerase chain reaction (PCR), two DNA-level processes were encountered that can lead to artifactual genotypic scorings: (a) differential amplification of alleles at a target locus and (b) amplification from multiple paralogous loci. We describe symptoms of these complications and prescribe methods that should generally help to ameliorate them. When artifactual scorings at two anonymous DNA loci in the American oyster were corrected, Hardy-Weinberg deviations registered in preliminary population assays decreased to nonsignificant values. Implications of these findings for the heterozygote-deficit phenomenon in marine bivalves, and for the general development and use of PCR-based assays, are discussed.

Alleles↗

PubMed1999

[Sequencing of cytochrome C oxidase 1 gene of Ancylostoma duodenale and Necator americanus].

AIM: To identify the genetic diversity between Ancylostoma duodenale and Necator americanus. METHODS: Mitochondrial cytochrome C oxidase subunit 1 (CO1) gene was amplified from genomic DNA of human hookworms collected from infected patients in Hejiang County, Sichuan Province, and the purified PCR products were directly sequenced by using Licor auto-sequencer. RESULTS: The PCR products were about 700 bp. Alignment of CO1 gene fragment sequences showed 89.7% similarity between Ancylostoma duodenale and Necator americanus, but still certain nucleotide variations (10.3%) existed. CONCLUSION: CO1 gene sequence can be used as a marker to identify the two species of human hookworms.

Amino Acid Sequence↗

PubMed2001

Intracoronary infusion of skeletal myoblasts improves cardiac function in doxorubicin-induced heart failure.

BACKGROUND: Skeletal myoblast transplantation is promising for the treatment of end-stage heart failure. Direct intramyocardial injection is useful for local cell delivery but may not be effective in global dissemination of cells into the heart, which would be advantageous in treating generalized cardiac dysfunction as in dilated cardiomyopathy. We hypothesized that intracoronary infusion of myoblasts would disseminate cells more effectively, leading to functional improvement in global heart failure. METHODS AND RESULTS: Heart failure was induced by the intraperitoneal administration of doxorubicin (total dose 15 mg/kg) in rat. One million primary skeletal myoblasts were then infused via the coronary arteries of an excised, failing doxorubicin-treated heart. After incubation under increased intracoronary pressure, the hearts were subsequently transplanted into syngeneic recipients. For the control group, doxorubicin-treated hearts were infused with medium only and transplanted. Four weeks after transplantation, Langendorff perfusion demonstrated that both maximum dP/dt (2797.6+/-103.3 versus 2326.9+/-133.1 mm Hg/s, P=0.01) and minimum dP/dt (-2067.4+/-88.1 versus -1718.8+/-91.3 mm Hg/s, P=0.02) were improved in myoblast-transplanted hearts compared with medium-infused hearts. This was associated with a sharper slope of the left ventricular developed pressure-volume curve and a reduced slope of the end-diastolic pressure-volume relation in the myoblast-transplanted hearts. Immunohistochemistry for skeletal myosin heavy chain showed that globally disseminated myoblasts had survived and differentiated into multinucleated myotubes that had aligned with the cardiac fiber axis within host myocardium. No significant myocardial infarction was observed. CONCLUSIONS: We demonstrated the feasibility and efficiency of skeletal myoblast transplantation via the intracoronary route as a promising strategy for improving cardiac function in global heart failure.

Animals↗

PubMed1996

A dynamic bundle of four adjacent hydrophobic segments in the denatured state of staphylococcal nuclease.

In an earlier study of the denatured state of staphylococcal nuclease (Wang Y, Shortle D, 1995, Biochemistry 34:15895-15905), we reported evidence of a three-strand antiparallel beta sheet that persists at high urea concentrations and is stabilized by a local "non-native" interaction with four large hydrophobic residues. Because the amide proton resonances for all of the involved residues are severely broadened, this unusual structure is not amenable to conventional NMR analysis and must be studied by indirect methods. In this report, we present data that confirm the important role of interactions involving four hydrophobic residues (Leu 36, Leu 37, Leu 38, and Val 39) in stabilizing the structure formed by the chain segments corresponding to beta 1-beta 2-beta 3-h, interactions that are not present in the native state. Glycine substitutions for each of these large hydrophobic residues destabilizes or disrupts this beta structure, as assessed by HN line sharpening and changes in the CD spectrum. The 13C resonances of the carbonyl carbon for several of the residues in this structure indicate conformational dynamics that respond in a complex way to addition of urea or changes in sequence. Studies of hydrogen exchange kinetics in a closely related variant of staphylococcal nuclease demonstrate the absence of the stable hydrogen bonding between the strands expected for a native-like three-strand beta sheet. Instead, the data are more consistent with the three beta strand segments plus the four adjacent hydrophobic residues forming a dynamic, aligned array or bundle held together by hydrophobic interactions.

Carbon Isotopes↗

PubMed2004

The effects of cholesterol on magnetically aligned phospholipid bilayers: a solid-state NMR and EPR spectroscopy study.

This paper presents the first time that both solid-state NMR spectroscopy and EPR spectroscopy are used to study the effects of cholesterol on magnetically aligned phospholipid bilayers (bicelles). Solid-state deuterium NMR spectroscopy was carried out using both chain perdeuterated 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC-d(54)) and a partially deuterated beta-[2,2,3,4,4,6-(2)H(6)]cholesterol (cholesterol-d(6)). Also, EPR spectroscopy was carried out utilizing a 3 beta-doxyl-5 alpha-cholestane (cholestane) spin probe incorporated into magnetically aligned bilayers to provide a more complete picture about the ordering and dynamics of the phospholipid and cholesterol molecules in the bicelle membrane system. The results demonstrate that cholesterol was successfully incorporated into the phospholipid bilayers. The molecular order parameters extracted directly from the (2)H NMR spectra of both DMPC-d(54) and cholesterol-d(6) were compared to that from the EPR study of cholestane. The order parameters indicate that the sterol was motionally restricted, and that the DMPC had high order and low motion for the hydrocarbon segments close to the head groups of the phospholipids and less order and more rapid motion toward the terminal methyl groups. Both methods clearly indicate an overall increase in the degree of ordering of the molecules in the presence of cholesterol and a decrease in the degree of ordering at higher temperatures. However, EPR spectroscopy and (2)H NMR spectroscopy exhibit different degrees of sensitivity in detecting the phospholipid molecular motions in the membrane. Finally, cholesterol increases the minimum alignment temperature necessary to magnetically align the phospholipid bilayers.

Dimyristoylphosphatidylcholine↗

PubMed1999

Phylogenetic analysis based on full-length large subunit ribosomal RNA gene sequence comparison reveals that Neospora caninum is more closely related to Hammondia heydorni than to Toxoplasma gondii.

Since its first description in the late 1980s, Neospora caninum has been recognised as a prominent tissue cyst-forming parasite due to its ability to induce congenital disease and abortion in animals, especially cattle. It is found worldwide and is a cause of significant economic losses for the livestock industry. However, its place within the family Sarcocystidae, like that of several other taxa, remains unresolved. Neospora caninum shares several morphological and life cycle characters with Hammondia heydorni, although it is most commonly thought of as being a close relative of Toxoplasma gondii. This study presents information regarding the phylogenetic relationship of N. caninum to species currently classified into the genus Hammondia, as well as to two strains (RH and ME49) of T. gondii based on the full-length large subunit ribosomal RNA gene. Phylogenetic analyses using two alignment strategies and three different tree-building methods showed that the two species in the genus Hammondia are paraphyletic. Neospora caninum was shown to form a monophyletic clade with H. heydorni instead of T. gondii, which in turn was shown to be most closely related to H. hammondi. The finding that N. caninum and H. heydorni are closely related phylogenetically may aid the elucidation of currently unknown aspects of their biology and epidemiology, and suggests that H. heydorni should be considered in the differential diagnosis of N. caninum from other apicomplexan parasites.

Animals↗

PubMed1990

Purification of human smooth muscle filamin and characterization of structural domains and functional sites.

A method was developed to purify human smooth muscle filamin in high yield and structural domains were defined by using mild proteolysis to dissect the molecule into intermediate-sized peptides. Unique domains were defined and aligned by using high-resolution peptide mapping of iodinated peptides on cellulose plates. The amino- and carboxyl-terminal orientation of these domains within the molecule was determined by amino acid sequence analysis of several aligned peptides. In addition to the three unique domains which were identified, a number of smaller and larger fragments were also characterized and aligned within the intact molecule. These structural domains and related peptides provide a useful set of defined fragments for further elucidation of structure-function relationships. The two known functionally important binding sites of filamin, the self-association site and the actin-binding site, have been localized. Self-association of two monomers in a tail-to-tail orientation involves a small protease-sensitive region near the carboxyl terminal of the intact polypeptide chain. Sedimentation assays indicate that an actin-binding site is located near the blocked amino terminal of the filamin molecule. Sequences derived from large peptides mapping near the amino terminal show homology to the amino-terminal actin-binding site of alpha-actinin (chicken fibroblast and Dictyostelium), Dictyostelium 120-kDa actin gelation factor, beta-spectrin (human red cell and Drosophila), and human dystrophin. This homology is particularly interesting for two reasons. The functional form of filamin is single stranded, in contrast to alpha-actinin and spectrin which are antiparallel double-stranded actin cross-linkers. Also, no homology to the spectrin-like segments which comprise most of the mass of spectrin, alpha-actinin, and dystrophin was found. Instead, the sequence of a domain located near the center of the filamin molecule (tryptic 100-kDa peptide, T100) shows homology to the published internal repeats of the Dictyostelium 120-kDa actin gelation factor. On the basis of these results, a model of human smooth muscle filamin substructure is presented. Also, comparisons of human smooth muscle filamin, avian smooth muscle filamin, and human platelet filamin are reported.

Amino Acid Sequence↗

PubMed2004

DNA-based identification of the eastern subterranean termite, Reticulitermes flavipes (Isoptera: Rhinotermitidae).

A DNA-based system for the identification of Reticulitermes flavipes (Koller) was established based on the following criteria: adequate molecular variation, comprehensive specimen sampling, explicit morphological species identification, and cladistic analysis. Termite soldiers were identified by labral shape, and these specimens and associated pseudergates were used in subsequent molecular analyses. Mitochondrial DNA from the AT-rich region was sequenced for 173 R. flavipes, Reticulitermes hageni Banks and Reticulitermes virginicus (Banks) soldiers and pseudergates collected from several widely dispersed Texan localities. Cladistic analysis was performed after exploration of an optimal sequence alignment inclusive of DNA sequences from Texas and published sequences from Georgia and Canada. Among the Texan individuals, 29, 5, and 1 mitochondrial DNA haplotypes were identified respectively with R. flavipes, R. hageni, and R. virginicus. One haplotype from El Paso likely represented a different Reticulitermes species. Species were monophyletic; however, individual relationships were unresolved in a strict consensus of 700 most parsimonious trees. Texas haplotypes were isolated by distance, and a correlation between genetic and geographic distance was observed among the Texas, Georgia, and Canada haplotypes. These results suggest that the methods outlined in this study will allow for the identification of R. flavipes from localities between Texas and Canada.

Animals↗