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Results for “recognition code”

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PubMed1990

Nucleotide sequence and transcriptional products of the csg locus of Myxococcus xanthus.

The csg locus of Myxococcus xanthus appears to control the production of an intercellular signal that is essential for development. The complete nucleotide sequence of a clone containing the csg locus was determined by the dideoxy-chain termination method. Pattern recognition analyses of the DNA sequence revealed the presence of two protein-coding regions that are convergently oriented and separated by only 8 nucleotides. Tn5 lac insertions into this clone detected two transcriptional units that are transcribed in a convergent fashion and whose expression increases during development. The two genes represented by these protein-coding regions and transcriptional units have been designated csgA and fprA. Northern (RNA) blot analyses detected an 800-nucleotide RNA specific to the csgA gene and a 900-nucleotide RNA specific to the fprA gene. Our results, along with mutational studies, identify csgA as the gene involved in cell communication. The function of the fprA gene is described in an accompanying paper (L. J. Shimkets, J. Bacteriol. 172:24-30, 1990).

Bacterial Proteins↗

PubMed1990

Human prolactin gene expression: positive correlation between site-specific methylation and gene activity in a set of human lymphoid cell lines.

From the human B-lymphoblastoid cell line IM-9-P, we derived the IM-9-P series of clonal sublines that differ from each other in the degree of human PRL (hPRL) production. To elucidate the mechanisms underlying the different levels of hPRL gene activity in these cell lines, we investigated the methylation status of the gene, since the methylation pattern of cytosine-residues in CpG dinucleotides has been implicated with the transcriptional activity of eukaryotic genes. Restriction enzyme analysis of the hPRL gene with methylation-sensitive endonucleases disclosed no correlation between the extent of methylation and gene activity for ThaI, AvaI, and HhaI recognition sequences. Hypermethylation of a MspI site (CCGG) in the second protein-coding exon, however, was found to coincide with hPRL gene activity. Exposure of the cells to the nucleoside 1-beta-D-arabinofuranosylcytosine, which has been reported to increase enzymatic DNA-methylation, led to an elevation of hPRL production that persisted after removal of the drug. However, treatment of PRL-positive cells with the demethylating cytidine analog, 5-azacytidine, caused a distinct and heritable reduction of hPRL secretion and hPRL mRNA abundance, concurrent with hypomethylation of the specific MspI site that is hypomethylated in PRL-negative cell lines of the IM-9-P family. Contrasting the generally favored inverse relationship between methylation and transcriptional activity of a gene we describe a system in which site-specific methylation is positively correlated with gene expression.

Azacitidine↗

PubMed2004

Spatial navigation and hippocampal place cell firing: the problem of goal encoding.

Place cells are hippocampal neurons whose discharge is strongly related to a rat's location in the environment. The existence of such cells, combined with the reliable impairments seen in spatial tasks after hippocampal damage, has led to the proposal that place cells form part of an integrated neural system dedicated to spatial navigation. This hypothesis is supported by the strong relationships between place cell activity and spatial problem solving, which indicate that the place cell representation must be both functional and in register with the surroundings for the animal to perform correctly in spatial tasks. The place cell system nevertheless requires other essential elements to be competent, such as a component that specifies the overall goal of the animal and computes the path required to take the rat from its current location to the goal. Here, we propose a model of the neural network responsible for spatial navigation that includes goal coding and path selection. In this model, the hippocampal formation allows for place recognition, and stores the set of places that can be accessed from each position in the environment. The prefrontal cortex is responsible for encoding goal location and for route planning. The nucleus accumbens translates paths in neural space into appropriate locomotor activity that moves the animal towards the goal in real space. The complete model assumes that the hippocampal output to nucleus accumbens and prefrontal cortex provides information for generating solutions to spatial problems. In support of this model, we finally present preliminary evidence that the goal representation necessary for path planning might be encoded in the prelimbic/infralimbic region of the medial prefrontal cortex.

Action Potentials↗

PubMed1997

Sex differences in phonetic processing: speed of identification of alphabetical sequences.

Research on the sex difference in speed of matching strings of letters or digits has suggested that the difference is associated with the speed of the comparison and decision processes rather than with symbol recognition. In addition, the size of the difference is affected by whether the code used for the comparisons is figural or verbal. Given recent evidence on both the critical role of phonological processing in reading and sex differences in the lateralization of phonological processes in the brain, it was hypothesized that on a speeded task with high demands for phonological efficiency sex differences might be found even though no perceptual comparisons were required. In a study with 57 male and 60 female college students, the women were significantly faster in identifying alphabetical sequences and were more accurate than men. There were no significant sex differences on a perceptual matching condition. The results suggest that the verbal processes implicated in earlier work on sex differences in speed of symbol matching may be primarily due to sex differences in the efficiency of phonological processing.

Adult↗

PubMed2001

Preservation of enzyme activity and antigenicity after mutagenesis of the membrane anchoring domain of GAD65.

The smaller isoform of glutamic acid decarboxylase, GAD65, is an important autoantigen implicated in the pathogenesis of type 1 diabetes whereas the larger isoform, GAD67 appears to play no major role. The primary difference between the two isoforms resides in the N-terminal part of the molecule including the GAD65 membrane-anchoring domain. The aim of this study was to generate mutants of the membrane targeting domain spanning amino acids 24 to 31 of GAD65 to determine effects on enzyme activity and antibody recognition. Three GAD65 mutants were generated by substituting two, nine or eleven nucleotides coding for the membrane targeting with the corresponding bases of GAD67. SDS-PAGE and Western blotting wildtype (wt) and mutated GAD65 ascertained that they were of similar size and recognized GAD65-specific antibodies. No difference in enzymatic activity was found between the mutants and wt GAD65. GAD65 antibody positive sera from type 1 diabetes patients immunoprecipitated mutated GAD65 whether two, nine or eleven nucleotides were replaced. Mono-or polyclonal antibodies to the N-terminal region demonstrated that the mutated GAD65 with two or nine nucleotides replaced was immunoprecipitated markedly better than wt whereas no difference was detected using antibodies specific for the PLP-binding site in the middle part of GAD65 or the C-terminal region. Taken together, these data suggest that no major conformational changes have been introduced by mutating the membrane-anchoring domain of GAD65.

Autoimmunity↗

PubMed1996

Inhibition of naming by rhyming primes.

The priming effects of graphemically similar (e.g., HOSE) and graphemically dissimilar (e.g., ROWS) rhymes on the naming of target words (NOSE) were examined at prime-target stimulus onset asynchronies (SOA) of 36, 70, and 250 msec. A four-field presentation procedure was used of mask-prime-mask-target. The effects of rhyme primes were measured relative to those of nonrhyming control primes (CHEF, DISH) that matched the rhymes in frequency and length and shared no letters in the same positions. At SOAs of 36 and 70 msec, rhyme priming was inhibitory and equal for graphemically similar and graphemically dissimilar rhymes. At SOA = 250 msec, rhyme priming was insignificant with a tendency toward facilitation. The results are discussed in the context of (1) contrasting effects of complete versus partial phonological overlap within a prime-target pair, and (2) the hypothesis that phonological codes stabilize fastest and provide, therefore, the earliest and major constraint on word recognition.

Adult↗

PubMed1999

ATM is upregulated during the mitogenic response in peripheral blood mononuclear cells.

Patients with the human genetic disorder ataxia-telangiectasia (A-T) are characterized by immunodeficiency and a predisposition to develop lymphoid malignancies. The gene mutated in A-T patients, ATM, codes for a high molecular weight protein that is implicated in DNA damage recognition and cell cycle control. The ATM protein does not change in amount or cellular distribution throughout the cell cycle or in response to DNA damaging agents. Because peripheral blood mononuclear cells (PBMCs) are largely in a state of quiescence and can be readily stimulated to enter a proliferative phase and because A-T cells exhibit growth abnormalities and senescence, indicative of a general intracellular defect in signalling, we chose PBMCs to examine the relationship of ATM to the proliferative status of the cell. We show here that ATM protein is present at low levels in freshly isolated PBMCs and increases approximately 6-fold to 10-fold in response to a mitogenic stimulus, reaching a maximum after 3 to 4 days. A similar, but delayed response, was evident in the presence of serum only. This increase in ATM protein was accompanied by an increase in ATM kinase activity. While expression of ATM protein increased during proliferation, ATM mRNA expression was unchanged in stimulated and unstimulated cells and there was no evidence for increased ATM protein stability in the phytohemagglutinin (PHA)-treated cells. In keeping with the reduced levels of ATM in quiescent cells, the extent of radiation-induction of the p53 pathway was significantly lower than in mitogen-stimulated cells. Basal levels of p21 were elevated in quiescent cells, and the response to radiation was negligible or reduced compared with proliferating cells over a 2-hour period. Overall, the data suggest that the increase in ATM protein in proliferating cells is due to posttranscriptional regulation and points to a role for ATM in more general signalling.

Ataxia Telangiectasia↗

PubMed1988

Abnormal recombination of Igh D and J gene segments in transformed pre-B cells of scid mice.

Studies of Ig and TCR genes in transformed lymphocytes of scid mice have revealed aberrant DNA rearrangements. Here we present a more detailed analysis of the Igh gene recombination in nine scid pre-B cell lines transformed by Abelson murine leukemia virus. We found 85% of the rearranged Igh alleles to contain abnormal Dh-Jh deletions of varying size. All of these deletions encompassed Jh elements and extended into the Igh enhancer region, occasionally involving the switch (S) region of the C mu gene. Some of these rearrangements removed most of the Dh elements, but none appeared to extend to the Vh genes. DNA sequence analysis of the two abnormally rearranged Igh alleles in one pre-B cell line showed that no Dh or Jh coding sequences were retained at the recombination sites though heptamer-like (CACTGTG) recognition signal sequences were present in the absence of nonamer (GGTTTTTGT) recognition signal sequences. These results imply that a deregulated recombinase activity may be responsible for the abnormal Dh-Jh deletions and the absence of Vh-Dh joining in established lines of Abelson murine leukemia virus-transformed scid pre-B cells.

Animals↗

PubMed1982

[Discovery of a unique strain-specific idiotypic antigenic determinant of mouse T-lymphocyte antigen-recognizing receptors].

The cellular radioimmunoassay using rabbit anti-CBA-anti-C57BL/6 antiidiotypic serum was performed to detect a private strain-specific antigenic idiotypic determinant (s) on activated CBA-anti-C57BL/6 T cells. This private idiotype was not expressed on other activated T cells under study: CBA-anti-BALB/C; C3H-anti-C57BL/6; AKR-anti-C57BL/6; A/Sn-anti-C57BL/6; BALB/C-anti-C57BL/6; DBA/2-anti-C57BL/6. It is suggested that gene (s) coding the private strain-specific idiotypic antigenic determinant of the antigen-recognition receptor of T cells is not localized on the H-2 complex of mice.

Animals↗

PubMedDate not supplied

Ménière's disease: effects of glycerol on tasks involving temporal processing.

The present study examined the effect of glycerol ingestion on aspects of auditory performance in subjects having Ménière's disease. It was hypothesized that Ménière's disease may be associated with abnormal firing in the auditory nerve and that this should result in a decreased ability to code the auditory temporal fine structure. Psychoacoustical measures of interaural time discrimination and quasi frequency modulation rate discrimination were used as measures of temporal coding, and performance on these tasks was examined both before and after glycerol ingestion. Pre- and postglycerol measures of speech recognition and audiometric thresholds were also obtained. In agreement with previous results, glycerol-related changes in audiometric thresholds were modest or absent, but improvements in speech recognition were relatively reliable. Improvements in interaural time discrimination and quasi frequency modulation rate discrimination were also observed. The results provide limited support for the hypothesis that Ménière's disease may be associated with a reduced ability to code the temporal fine structure of sound.

Adult↗

PubMed2005

Identification of T cell epitopes by the use of rapidly generated mRNA fragments.

Although the number of defined T cell epitopes of clinically relevant antigens is constantly increasing, there is still an enormous need to identify further peptides, processed from new antigens or presented by rare HLA molecules, respectively. Here we introduce a novel two-step approach for the rapid identification of T cell epitopes. It was established in the CMV infection model. From the peripheral blood of healthy donors sharing HLA-A1 according to HLA serotyping we isolated CD8+ T lymphocytes and generated dendritic cells (DCs). DCs were electroporated with CMV pp65 mRNA and tested for recognition by autologous CD8+ T lymphocytes in IFN-gamma ELISPOT assays. In all 10 CMV-seropositive donors, CMV pp65-specific CD8+ T cells were readily detectable ex vivo. In 7 of them the response was at least in part restricted by HLA-A1.1 as verified in IFN-gamma ELISPOT assays with pp65 mRNA-electroporated K562 cells stably transfected with HLA-A*0101 (K562/A*0101). In a subsequent step various 3'-deleted pp65 RNA fragments were rapidly generated by in vitro transcription of plasmid DNA-templates linearized with restriction enzymes at different sites within the pp65-coding sequence. Polyadenylated mRNA fragments were then electroporated into K562/A*0101 cells and tested for recognition by ex vivo CD8+ T cells in IFN-gamma ELISPOT assays. We thereby identified a 76 bp-long sequence as target of the HLA-A*0101-associated pp65-specific T cell response. From this region, 10 peptides predicted by current algorithms were synthesized and tested for recognition. Peptide pp65 364-373 (previously identified by a reverse immunology approach by [Hebart, H., Daginik, S., Stevanovic, S., Grigoleit, U., Dobler, A., Baur, M., Rauser, G., Sinzger, C., Jahn, G., Loeffler, J., Kanz, L., Rammensee, H. G., Einsele, H., 2002. Sensitive detection of human cytomegalovirus peptide-specific cytotoxic T-lymphocyte responses by interferon-gamma-enzyme-linked immunospot assay and flow cytometry in healthy individuals and in patients after allogeneic stem cell transplantation, Blood 99, 3830.]) was positively tested and found to be the dominant target epitope of the HLA-A1-restricted anti pp65 T cell response in all donors. We conclude that (i) the use of HLA-transfected K562 cells allows to dissect antigen-specific T cell responses to partial responses associated with defined HLA class I alleles and (ii) transfection of in vitro transcribed RNA fragments allows to identify immunogenic regions of a given antigen. The latter technique bypasses the need of prior cloning and sequencing of cDNA fragments, reduces the number of synthetic peptides to be tested and thus saves both costs and time.

Antigen Presentation↗

PubMed1989

The human mannose-binding protein gene. Exon structure reveals its evolutionary relationship to a human pulmonary surfactant gene and localization to chromosome 10.

The human mannose-binding protein (MBP) plays a role in first line host defense against certain pathogens. It is an acute phase protein that exists in serum as a multimer of a 32-kD subunit. The NH2 terminus is rich in cysteines that mediate interchain disulphide bonds and stabilize the second collagen-like region. This is followed by a short intervening region, and the carbohydrate recognition domain is found in the COOH-terminal region. Analysis of the human MBP gene reveals that the coding region is interrupted by three introns, and all four exons appear to encode a distinct domain of the protein. It appears that the human MBP gene has evolved by recombination of an ancestral nonfibrillar collagen gene with a gene that encodes carbohydrate recognition, and is therefore similar to the human surfactant SP-A gene and the rat MBP gene. The gene for MBP is located on the long arm of chromosome 10 at 10q11.2-q21, a region that is included in the assignment for the gene for multiple endocrine neoplasia type 2A.

Acute-Phase Proteins↗

PubMed1981