Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “sequence types”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14Linked to original sources
PubMed1994

The existence of eukaryotic ribonucleoprotein consensus sequence-type RNA-binding proteins in a prokaryote, Synechococcus 6301.

A group of proteins containing a conserved ribonucleoprotein consensus sequence (RNP-CS)-type RNA-binding domain (CS-RBD) of approximately 80 amino acids is present in eukaryotic cells and binds specifically to a wide variety of RNA molecules. We have isolated 12 kDa single-stranded DNA binding proteins from the unicellular cyanobacterium Synechococcus 6301. The amino-terminal sequence was determined and two distinct genomic clones were isolated from a Synechococcus 6301 genomic library. Sequence analysis revealed that two closely related proteins contain a single CS-RBD of 82 amino acids and are named as 12RNP1 and 12RNP2. Both of the CS-RBDs share the highest amino acid identity with those of chloroplast ribonucleoproteins (40-51%). The 12RNP proteins were expressed in Escherichia coli bearing plasmids encoding glutathione S-transferase/12RNP fusion proteins and subjected to in vitro nucleic acid-binding assay. Both 12RNP1 and 12RNP2 bind to RNA homopolymers poly(U) and poly(G), indicating that they might be RNA-binding proteins. This is the first example of such proteins in prokaryotes. The 12RNP1 and 12RNP2 genes are transcribed as monocistronic mRNAs and the steady-state mRNA level of 12RNP1 is over 20-fold than that of 12RNP2. Due to the easiness of genetic manipulations the cyanobacterium will provide an excellent system to analyze the function of not only cyanobacterial but also plant RNA-binding proteins.

Base Sequence↗
PubMed2005

[Investigation of set-shifting ability in patients with Parkinson's disease: influence of task sequence type].

INTRODUCTION: The aim of the present study was to investigate the origin of set-shifting deficits observed in Parkinson's disease (PD). METHODS: Seventeen patients diagnosed as having idiopathic PD were compared with 15 control subjects. We used a task-switching paradigm, including two tasks (task A and task B) so that subjects were required to switch either immediately after a switch-trial (i.e. alternating switch or ABA task sequence) or following one or two non-switch trials (ABBA or ABBBA task sequences). RESULTS: In both groups, switch cost (SC) in ABA task sequence was larger than SC in ABBA task sequence (p<0.05) and SC was larger in ABBA than ABBBA task sequence (p<0.05). PD patients demonstrated an increased SC compared to controls for alternating switch trials (p<0.01). Alternatively, when required to switch to a task abandoned two or three trials earlier (i.e. ABBA and ABBBA tasks sequences), patients did not demonstrate increased SC compared to controls. DISCUSSION AND CONCLUSION: The fact that SC associated with alternating switch trials was exacerbated in PD patients may reflect difficulties for switching to a recently inhibited task-set. In conclusion, our results indicate that set-shifting deficits in PD patients may depend of the type of task sequence.

Cognition Disorders↗
PubMed1985

Structure of a murine alpha interferon pseudogene with a repetitive R-type sequence in the 3' flanking region.

A murine alpha interferon pseudogene was identified in a mouse genomic library. The nucleotide sequence revealed several in-phase termination codons within the gene and repetitive oligonucleotides in the flanking regions. The nucleotide sequences and the amino acids of the peptide signal sequences were compared with known human alpha interferon genes and the pseudogene.

Amino Acid Sequence↗
PubMed1993

Deletion of the mating-type sequences in Podospora anserina abolishes mating without affecting vegetative functions and sexual differentiation.

The mating-type locus of Podospora anserina controls fusion of sexual cells as well as subsequent stages of development of the fruiting bodies. The two alleles at the locus are defined by specific DNA regions comprising 3.8 kb for mat+ and 4.7 kb for mat-, which have identical flanking sequences. Here we present the characterization of several mutants that have lost mat(+)-specific sequences. One mutant was obtained fortuitously and the other two were constructed by gene replacement. The mutants are deficient in mating with strains of either mat genotype but are still able to differentiate sexual reproductive structures. The loss of the mating type does not lead to any discernible phenotype during vegetative growth: in particular it does not change the life span of the strain. The mutants can recover mating ability if they are transformed with DNA containing the complete mat+ or mat- information. The transformants behave in crosses as do the reference mat+ or mat- strains, thus indicating that the transgenic mat+ and mat- are fully functional even when they have integrated at ectopic sites.

Alleles↗
PubMed2000

MR imaging in the presence of vascular stents: A systematic assessment of artifacts for various stent orientations, sequence types, and field strengths.

A systematic evaluation of the potential quality of magnetic resonance images recorded in the presence of metallic stents was performed on a low-field open imager operating at 0.2 T and on a high-field closed unit operating at 1.0 T. Eight different stent types were examined by two-dimensional gradient-echo sequences with echo times of 4 and 10 msec and by a fast spin-echo technique. In addition, a three-dimensional gradient-echo sequence was applied with an echo time of 2.4 msec. A set of sequence and slice parameters was used on both scanners. Thus, artifacts due to susceptibility effects depending on the magnetic field strength could be distinguished from radiofrequency shielding effects in the lumen of the stents (independent of the field strength). Nine different orthogonal orientations of the stent axis and the image (in terms of slice, read, and phase-encoding direction) were tested, and the artifacts (extension of signal void and visibility of the lumen) were compared. The optimal strategy for visualization of vascular and perivascular regions outside the stents was fast spin-echo imaging with the stent axis and read direction parallel to the static field. Susceptibility-induced signal void in gradient-echo images was minimal using the three-dimensional approach. Increased transmitter amplitudes above usual values provided clearly improved insight in the lumen using gradient-echo sequences.

Alloys↗
PubMed2004

Multilocus sequence typing of Listeria monocytogenes by use of hypervariable genes reveals clonal and recombination histories of three lineages.

In an attempt to develop a method to discriminate among isolates of Listeria monocytogenes, the sequences of all of the annotated genes from the fully sequenced strain L. monocytogenes EGD-e (serotype 1/2a) were compared by BLASTn to a file of the unfinished genomic sequence of L. monocytogenes ATCC 19115 (serotype 4b). Approximately 7% of the matching genes demonstrated 90% or lower identity between the two strains, and the lowest observed identity was 80%. Nine genes (hisJ, cbiE, truB, ribC, comEA, purM, aroE, hisC, and addB) in the 80 to 90% identity group and two genes (gyrB and rnhB) with approximately 97% identity were selected for multilocus sequence analysis in two sets of L. monocytogenes isolates (a 15-strain diversity set and a set of 19 isolates from a single food-processing plant). Based on concatenated sequences, a total of 33 allotypes were differentiated among the 34 isolates tested. Population genetics analyses revealed three lineages of L. monocytogenes that differed in their history of apparent recombination. Lineage I appeared to be completely clonal, whereas representatives of the other lineages demonstrated evidence of horizontal gene transfer and recombination. Although most of the gene sequences for lineage II strains were distinct from those of lineage I, a few strains with the majority of genes characteristic of lineage II had some that were characteristic of lineage I. Genes from lineage III organisms were mostly similar to lineage I genes, with instances of genes appearing to be mosaics with lineage II genes. Even though lineage I and lineage II generally demonstrated very distinct sequences, the sequences for the 11 selected genes demonstrated little discriminatory power within each lineage. In the L. monocytogenes isolate set obtained from one food-processing plant, lineage I and lineage II were found to be almost equally prevalent. While it appears that different lineages of L. monocytogenes can share habitats, they appear to differ in their histories of horizontal gene transfer.

Animals↗
PubMed2002

Browsing gene banks for Fe2S2 ferredoxins and structural modeling of 88 plant-type sequences: an analysis of fold and function.

One-hundred-and-seventy-nine sequences of Fe2S2 ferredoxins and ferredoxin precursors were identified in and retrieved from currently available protein and cDNA databases. On the basis of their cluster-binding patterns, these sequences were divided into three groups: those containing the CX4CX2CXnC pattern (plant-type ferredoxins), those with the CX5CX2CXnC pattern (adrenodoxins), and those with a different pattern. These three groups contain, respectively, 139, 36, and 4 sequences. After excluding ferredoxin precursors in the first group, two subgroups were identified, again based on their cluster-binding patterns: 88 sequences had the CX4CX2CX29C pattern, and 29 had the CX4CX2CXmC (m not equal 29) pattern. The structures of the 88 ferredoxins with the CX4CX2CX29C pattern were modeled based on the available experimental structures of nine proteins within this same group. The modeling procedure was tested by building structural models for the ferredoxins with known structures. The models resulted, on average, in being within 1 A of the backbone root-mean-square deviation from the corresponding experimental structures. In addition, these structural models were shown to be of high quality by using assessment procedures based on energetic and stereochemical parameters. Thus, these models formed a reliable structural database for this group of ferredoxins, which is meaningful within the framework of current structural genomics efforts. From the analysis of the structural database generated it was observed that the secondary structural elements and the overall three-dimensional structures are maintained throughout the superfamily. In particular, the residues in the hydrophobic core of the protein were found to be either absolutely conserved or conservatively substituted. In addition, certain solvent-accessible charged groups, as well as hydrophobic groups, were found to be conserved to the same degree as the core residues. The patterns of conservation of exposed residues identified the regions of the protein that are critical for its function in electron transfer. An extensive analysis of protein-protein interactions is now possible. Some conserved interactions between residues have been identified and related to structural and/or functional features. All this information could not be obtained from the analyses of the primary sequences alone. Finally, the analysis of the sequences of the related subgroup featuring the CX4CX2CXmC (m not equal 29) cluster-binding pattern in the light of the structural and functional insights provided by the inspection of the mentioned structural database affords some hints on the functional features of ferredoxins belonging to this subgroup.

Amino Acid Sequence↗
PubMed1989

Chloroplast ribosomal protein gene rps12 of Chlamydomonas reinhardtii. Wild-type sequence, mutation to streptomycin resistance and dependence, and function in Escherichia coli.

The chloroplast rps12 gene encoding ribosomal protein S12 from wild-type as well as from streptomycin-resistant and -dependent mutants of Chlamydomonas reinhardtii was cloned and sequenced. At least six mRNA transcripts ranging in size from 800 to 4800 nucleotides were found to contain the rps12 coding sequence. As in Escherichia coli and Euglena, the C. reinhardtii rps12 gene is continuous, in contrast to its trans-spliced structure in higher plants. However, rps12 of C. reinhardtii is no longer immediately adjacent to the rps7 gene encoding ribosomal protein S7 as it is in other organisms. The deduced amino acid sequence of C. reinhardtii S12 protein shows strong homologies (48-79% identity) to S12 protein sequences of other organisms, but it has extra amino acid residues at its C terminus. Single base pair changes at different sites result in streptomycin-resistant or -dependent mutants with amino acid changes identical to comparable mutations in the E. coli S12 protein. The chloroplast rps12 gene is also expressed under the control of its own promoter in E. coli cells, and the C. reinhardtii S12 protein produced assembles into the E. coli ribosomes where it appears to function efficiently.

Amino Acid Sequence↗
PubMed1994

Insertion sequence typing of Mycobacterium tuberculosis: characterization of a widespread subtype with a single copy of IS6110.

DNA fingerprinting with the insertion sequence IS6110 (also known as IS986) has become established as a major tool for investigating the spread of tuberculosis. Most strains of Mycobacterium tuberculosis have multiple copies of IS6110, but a small minority carry a single copy only. We have examined selected strains from Malaysia, Tanzania and Oman, in comparison with M. bovis isolates and BCG strains carrying one or two copies of IS6110. The insertion sequence appears to be present in the same position in all these strains, which suggests that in these organisms the element is defective in transposition and that the loss of transposability may have occurred at an early stage in the evolution of the M. tuberculosis complex.

Base Sequence↗
PubMed2001

Effector-dependent acquisition of novel typing sequences.

In an earlier report we found that when pairs of letters were physically transposed on the keyboard and typists were required to type letters in their new location, the disruptions in typing were reduced when the transpositions involved mirror movements of homologous fingers of the two hands compared with transpositions involving the same hand. We hypothesized that acquisition may be facilitated when a new movement mirrors a previously learned movement. In order to test this hypothesis, in the present study we transposed various pairs of letters between the two hands. Experienced typists (n = 6) typed phrases in which a key was physically transposed with another key on the keyboard and subjects typed the letters in their new location (for 200 trials). The pairs of transpositions involved: (1) similar movements of homologous fingers; (2) different movements of homologous fingers; (3) similar movements of non-homologous fingers; and (4) different movements of non-homologous fingers. After the transposition of keys, there were non-uniform prolongations in the typing intervals of words containing transposed keys, with the largest delay occurring directly before the transposition. Practice had a differential effect on these intervals; some key press intervals achieved control levels, while others did not improve at all. The disruptions in typing were dependent on the specific keys transposed. Transpositions involving non-homologous digits of the two hands were less disruptive than transpositions involving homologous digits. The results do not support our earlier hypothesis that acquisition may be facilitated when a new movement mirrors a previously learned one. These results provide some possible insights into how distinct levels of movement organization develop in typing as a result of practice. Furthermore, the non-uniformity of the typing intervals in the words containing transposed keys supports the notion that typing is organized at multiple levels, including the individual key press and word level.

Adult↗
PubMed1996

The utility of optical waveguide DNA array hybridization and melting for rapid resolution of mismatches, and for detection of minor mutant components in the presence of a majority of wild type sequence: Statistical model and supporting data.

We have derived a statistical model to determine binding and dissociation kinetics of oligonucleotide-antibody-microparticle complexes to oligonucleotides on a surface illuminated by the evanescent wave. The model supports the extremely rapid binding kinetics previously observed and predicts very rapid thermal dissociation kinetics. Experimental results confirmed the model and showed that the most rapid heating available achieved meltoff in 8 s with discrimination of single base differences. Similarly, a model of particulate labels with multiple points of interaction predicted that the system would be very sensitive to a minority of matched interactions in the presence of a majority of mismatched interactions. Conversely, the system would be relatively insensitive to the presence of a higher proportion of matched species. These predictions are born out by experiment. A 1:10 mixture of matched:mismatched gave a melting curve which was approximately the sum of melting curves of the two species alone, and a 50:50 mixture gave a melting curve almost indistinguishable from the highest melting component. Thus, the system will be amenable to detection of infrequent mutations in the presence of an excess of the wild type allele provided the mutant sequence is present on the chip. Further, it lends itself to high throughput automation due to the rapidity with which the thermal melt can be achieved.

DNA↗
PubMed2005

Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data.

The inference of population recombination (rho), population mutation (Theta), and adaptive selection is of great interest in microbial population genetics. These parameters can be efficiently estimated using explicit statistical frameworks (evolutionary models) that describe their effect on gene sequences. Within this framework, we estimated rho and Theta using a coalescent approach, and adaptive (or destabilizing) selection under heterogeneous codon-based and amino acid property models in microbial sequences from MLST databases. We analyzed a total of 91 different housekeeping gene regions (loci) corresponding to one fungal and sixteen bacterial pathogens. Our results show that these three population parameters vary extensively across species and loci, but they do not seem to be correlated. For the most part, estimated recombination rates among species agree well with previous studies. Over all taxa, the rho/Theta ratio suggests that each factor contributes similarly to the emergence of variant alleles. Comparisons of Theta estimated under finite- and infinite-site models indicate that recurrent mutation (i.e., multiple mutations at some sites) can increase Theta by up to 39%. Significant evidence of molecular adaptation was detected in 28 loci from 13 pathogens. Three of these loci showed concordant patterns of adaptive selection in two to four different species.

Alleles↗
PubMed2003

LR-CAHSQC: an application of a Carr-Purcell-Meiboom-Gill-type sequence to heteronuclear multiple bond correlation spectroscopy.

A new pulse sequence, long-range CPMG-adjusted heteronuclear single quantum coherence (LR-CAHSQC), is proposed for the determination of long-range JCH coupling constants from a long-range 1H-13C correlation experiment. The long-range heteronuclear coupling constants can be directly extracted from COSY-type antiphase peak patterns. The current approach utilizes CPMG-sequences for polarization transfer, and thus avoids the evolution of homonuclear JHH couplings, which normally may introduce abnormalities into the cross peak pattern. The differences between LR-CAHSQC and normal LR-HSQC are discussed.

Algorithms↗
PubMed2001

Sequence type analysis and recombinational tests (START).

UNLABELLED: The 32-bit Windows application START is implemented using Visual Basic and C(++) and performs analyses to aid in the investigation of bacterial population structure using multilocus sequence data. These analyses include data summary, lineage assignment, and tests for recombination and selection. AVAILABILITY: START is available at http://outbreak.ceid.ox.ac.uk/software.htm. CONTACT: keith.jolley@ceid.ox.ac.uk

Databases, Nucleic Acid↗
PubMed2004

[Multilocus sequence typing: the molecular marker of the Internet era].

Global or longer term epidemiology track the spread of clonal lineages, associated with hipervirulence or resistance or multi-resistance to antimicrobial agents. Therefore, the application of a molecular typing system for this purpose should produce data easily shared by different and geographically distant laboratories, as well as distinguish those clonal lineages even with low levels of variability accumulated in the genome.A marker based on the DNA sequence will produce objective results easily organized in data bases accessible by Internet. The application of a similar strategy that was used in the analysis of isoenzymes, by sequencing variable fragments of selected housekeeping genes, will allow obtaining a general view of the distribution of the clonal lineages and tracking their spread.

Bacterial Infections↗
PubMed1984

Hybrid character of a large neurofilament protein (NF-M): intermediate filament type sequence followed by a long and acidic carboxy-terminal extension.

The sequence of the amino-terminal 436 residues of porcine neurofilament component NF-M (apparent mol. wt. in gel electrophoresis 160 kd), one of the two high mol. wt. components of mammalian neurofilaments, reveals the typical structural organization of an intermediate filament (IF) protein of the non-epithelial type. A non-alpha-helical arginine-rich headpiece with multiple beta-turns (residues 1-98) precedes a highly alpha-helical rod domain able to form double-stranded coiled-coils (residues 99-412) and a non-alpha-helical tailpiece array starting at residue 413. All extra mass of NF-M forms, as a carboxy-terminal tailpiece extension of approximately 500 residues, an autonomous domain of unique composition. Limited sequence data in the amino-terminal region of this domain document a lysine- and particularly glutamic acid-rich array somewhat reminiscent of the much shorter tailpiece extension of NF-L (apparent mol. wt. 68 kd), the major neurofilament protein. NF-M is therefore a true intermediate filament protein co-polymerized with NF-L via presumptive coiled-coil type interactions and not a peripherally bound associated protein of a filament backbone built exclusively from NF-L. Along the structurally conserved coiled-coil domains the two neurofilament proteins show only approximately 65% sequence identity, a value similar to that seen when NF-L and NF-M are compared with mesenchymal vimentin. The highly charged and acidic tailpiece extensions of all triplet proteins particularly rich in glutamic acid seem unique to the neurofilament type of IFs. They could form extra-filamentous scaffolds suitable for interactions with other neuronal components.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1976

Serum glycoprotein-type sequence of monosaccharides in membrane glycoproteins of Semliki Forest virus.

Semliki Forest virus was grown in BHK-21 cells and labelled in vivo with radioactive monosaccharides. The virus was disrupted with sodium dodecyl sulphate and the polypeptides were hydrolyzed with pronase. A mixture of type A glycopeptides (for nomenclature, see Johnson and Clamp (1971) Biochem. J. 123, 739-745) of the membrane glycoproteins E1 and E3 was isolated by gel filtration and subjected to sequential degradation with exo-glycosidases. The reduction in the apparent molecular weight and the cleavage of radioactive monosaccharides were monitored with gel filtration. The results suggest that the type A oligosaccharides have similar average structures and contain at the non-reducing terminus 3.4 mol of alpha-D-sialic acid and 0.7 mol of alpha-L-focose, folloled by 3.1 mol of beta-D-galactose, 4.2 mol of N-acetyl-beta-D-glucosamine, 0.7-1.5 mol of alpha-D-mannose, 0.5 mol of beta-D-mannose and 0.6-2.2 mol of N-acetyl-beta-D-glucosamine attached to 1.0 mol of N-acetylglucosamine resistant to N-acetyl-beta-D-glucosaminidase. This innermost monosaccharide unit, therefore, appears to be attached to the peptide. The peptides attached to this N-acetyl-glucosamine had an apparent molecular weight of 720+/-100. We propose the following average structure, compatible with most of our data, for the type A glycopeptides of Semliki Forest virus:.

Animals↗
PubMed2001

Extension of the Lancefield classification for group A streptococci by addition of 22 new M protein gene sequence types from clinical isolates: emm103 to emm124.

Classic M protein serotyping has been invaluable during the past 60 years for the determination of relationships between different group A streptococci (GAS) strains and the varied clinical manifestations inflicted by these organisms worldwide. Nonetheless, during the past 20 years, the difficulties of continued expansion of the serology-based Lancefield classification scheme for GAS have become increasingly apparent. By use of a less demanding sequence-based methodology that closely adheres to previously established strain criteria while being predictive of known M protein serotypes, we recently added types emm94-emm102 to the Lancefield scheme. Continued expansion by the addition of types emm103 to emm124 are now proposed. As with types emm94-emm102, each of these new emm types was represented by multiple independent isolates recovered from serious disease manifestations, each was M protein nontypeable with all typing sera stocks available to international GAS reference laboratories, and each demonstrated antiphagocytic properties in vitro by multiplying in normal human blood.

Antigens, Bacterial↗