SEARCH · PubMed Health

Results for “recognition code”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 739 records · Page 41Linked to original sources

PubMed1995

Building zinc fingers by selection: toward a therapeutic application.

A phage display approach was utilized to modify the specificity of each of the three fingers of the murine transcription factor Zif268. Selections were performed by using the consensus binding sequence of the natural protein and a conserved sequence in the genome of the type 1 human immunodeficiency virus. By using an extensive randomization strategy, the entire 3-bp specificity of a finger has been changed. Rapid analysis of selected zinc fingers was facilitated by the development of an immunoscreening assay for DNA binding and specificity. To investigate the mechanism of binding and specificity, the binding kinetics of Zif268 and 10 selected variants were determined in real time with an assay based on surface plasmon resonance. Differential mechanisms for sequence-specific recognition were observed. No evidence in support of a single general coding relationship between zinc finger and target DNA sequence was observed. The prospects for the development of this class of proteins in human therapy are considered.

Animals↗

PubMed1999

Molecular cloning of a novel human collectin from liver (CL-L1).

Collectins are a C-lectin family with collagen-like sequences and carbohydrate recognition domains. These proteins can bind to carbohydrate antigens of microorganisms and inhibit their infection by direct neutralization and agglutination, the activation of complement through the lectin pathway, and opsonization by collectin receptors. Here we report the cloning of a cDNA encoding human collectin from liver (CL-L1 (collectin liver 1)) that has typical collectin structural characteristics, consisting of an N-terminal cysteine-rich domain, a collagen-like domain, a neck domain, and a carbohydrate recognition domain. The cDNA has an insert of 831 base pairs coding for a protein of 277 amino acid residues. The deduced amino acid sequence shows that this collectin has a unique repeat of four lysine residues in its C-terminal area. Northern blot, Western blot, and reverse transcription-polymerase chain reaction analyses showed that CL-L1 is present mainly in liver as a cytosolic protein and at low levels in placenta. More sensitive analyses by reverse transcription-polymerase chain reactions showed that most tissues (except skeletal muscle) have CL-L1 mRNA. Zoo-blot analysis indicated that CL-L1 is limited to mammals and birds. A chromosomal localization study indicated that the CL-L1 gene localizes to chromosome 8q23-q24.1, different from chromosome 10 of other human collectin genes. Expression studies of fusion proteins lacking the collagen and N-terminal domains produced in Escherichia coli affirmed that CL-L1 binds mannose weakly. CL-L1 and recombinant CL-L1 fusion proteins do not bind to mannan columns. Analysis of the phylogenetic tree of CL-L1 and other collectins indicated that CL-L1 belongs to a fourth subfamily of collectins following the mannan-binding protein, surfactant protein A, and surfactant protein D subfamilies including bovine conglutinin and collectin-43 (CL-43). These findings indicate that CL-L1 may be involved in different biological functions.

Amino Acid Sequence↗

PubMed2000

Localisation of the DmCdc45 DNA replication factor in the mitotic cycle and during chorion gene amplification.

The cdc45 protein was originally identified in Saccharomyces cerevisiae and shown to be essential for initiation of eukaryotic DNA replication. Subsequent isolation and characterisation of the corresponding genes from fission yeast, Xenopus and mammals also support a replication role for the protein in these species. They further suggest that during the course of its function cdc45 interacts with a number of other replication proteins, including minichromosome maintenance proteins, the origin recognition complex and DNA polymerase alpha. We have cloned the gene coding for cdc45 protein from Drosophila melanogaster. We have analysed the expression pattern of the cdc45 protein throughout the cell cycle and the life cycle using a combination of indirect immunofluorescence and subcellular fractionation. Our data show that cellular localisation and developmental regulation of the protein is consistent with a role in DNA replication. DmCdc45 is predominantly expressed in proliferating cells. In addition, its subcellular location is nuclear during interphase and the protein shows association with chromatin. The chromatin-associated form of the protein shows a post-translational modification, which may be involved in control of the action of the protein. DmCdc45 shows interactions with mcm proteins, however, the interactions detected show some specificity, perhaps suggesting a preferential association with particular mcm proteins. In addition we show that a stoichiometric mcm interaction may not be obligatory for the function of cdc45 in follicle cell replication, because, unlike the mcm proteins, DmCdc45 localises to the chorion amplification foci in the follicle cells of the ovary.

Amino Acid Sequence↗

PubMed1980

On one system of methods of aphasics group rehabilitation.

One of the main and actual tasks of aphasic re-education is the development of group rehabilitation methods which contribute to the restoration of verbal communication and to the surmounting of personality problems in aphasics. In this paper, a new method for group lessons with aphasics is described. It is founded on theoretical conceptions concerning the relation between the word and its sensory basis and the problems of visual object images in aphasia. The group lesson is a system of methods including: (1) group discussion and classification of objects with a view to deblock verbal associations on the given theme; (2) drawing of objects or coding in drawing the meaning of utterances on this theme; (3) recognition of sensibilized pictures (patients' drawings). We have proposed two variants of the method: The first is to actualize the names for objects and the second one to increase the aphasics capacity for sentence making. This method was used in small therapeutic groups of aphasics and the influence of selected group factors on the patients' speech activity was studied. The described method ensures the system influence principle in the rehabilitation of aphasics.

Adult↗

PubMedDate not supplied

Electronic patient registration and tracking at mass vaccination clinics: a clinical study.

To protect the citizens of the United States from the use of dangerous biological agents, the Center for Disease Control and Prevention (CDC) has been actively preparing to deal with the consequences of such an attack. Their plans include the deployment of mass immunization clinics to handle postevent vaccinations. As part of the planning efforts by the Western New York Public Health Alliance, a Web-based electronic patient registration and tracking system was developed and tested at a recent trial smallpox vaccination clinic. Initial goals were to determine what the pitfalls and benefits of using such a system might be in comparison to other methods of data collection. This exercise proved that use of an electronic system capable of scanning two-dimensional bar codes was superior to both paper-based and optical character recognition (OCR) methods of data collection and management. Major improvements in speed and/or accuracy were evident in all areas of the clinic, especially in patient registration, vaccine tracking and postclinic data analysis.

Centers for Disease Control and Prevention, U.S.↗

PubMed1993

Osteogenesis imperfecta and type-I collagen mutations. A lethal variant caused by a Gly910-->Ala substitution in the alpha 1 (I) chain.

In this study we describe a new dominant point mutation in COL1A1 causing a lethal form of Osteogenesis imperfecta (type II B). Dermal cultured fibroblasts from the proband were shown to produce both normal and heavily overmodified type-I collagen. The mutation introduced a local conformational perturbation, which causes abnormal exposure of arginine residues; the triple helical domain was susceptible to trypsin digestion even at 30 degrees C. The chains bearing the point mutation were poorly secreted and short-term pulse experiments showed that the extensive intracellular retention of mutant trimers also impaired the secretion of normal chains. The molecular defect was localized in a COL1A1 allele by cloning and sequencing a cDNA region corresponding to the CB6 peptide. A G to C transversion which causes the substitution in the triple helical region of Gly910 with alanine was found. The mutation also causes the disappearance of a MspI-recognition site at nucleotide 3263 of the pro alpha 1 (I) coding sequence. Restriction analysis, along with the biochemical screening of collagens, allowed us to perform prenatal diagnosis on cells from chorionic-villus sampling and to exclude the recurrence of the mutation in the sibling.

Alanine↗

PubMed1981

Physical maps of Klebsiella aerogenes and Salmonella typhimurium hut genes.

The recognition sites for several restriction endonucleases were mapped within deoxyribonucleic acid coding for histidine utilization (hut) genes of Salmonella typhimurium and Klebsiella aerogenes. Deoxyribonucleic acid fragments containing the two hut promoters were identified by ribonucleic acid polymerase binding.

DNA Restriction Enzymes↗

PubMed1994

A new gene of bacteriophage P4 that controls DNA replication.

Bacteriophage P4 replication may result in either a lytic cycle or plasmid maintenance, depending on the presence or absence, respectively, of helper phase P2 genome. Bacteriophage P4 DNA replication depends on the product of gene alpha, which has origin recognition, primase, and helicase activities. An open reading frame with the coding capacity for a protein of 106 amino acids (orf106) is located upstream of the alpha gene. Genes orf106 and alpha are transcriptionally coregulated. Three amber mutations and an internal deletion (del51) were introduced into orf106. All of the amber mutations exhibited a polar effect on transcription of the downstream alpha gene. The P4 del51 mutant was slightly defective in lytic growth and could not be propagated in the plasmid state. In this latter condition, P4 DNA overreplication was observed. Overexpression of Orf106 severely inhibited P4 DNA replication, preventing P4 lytic growth and plasmid maintenance. The inhibitory effect of Orf106 on P4 replication was not observed when both orf106 and alpha were overexpressed. We suggest that orf106 is involved in P4 replication and that a balanced expression of orf106 relative to alpha may be necessary for proper P4 DNA replication. In particular, orf106 appears to be essential for the control of P4 genome replication in the plasmid state. We propose that orf106 be named cnr, for copy number regulation.

Amino Acid Sequence↗

PubMed1991

Two distinct mutations at a single BamHI site in phenylketonuria.

Classical phenylketonuria is an autosomal recessive disease caused by a deficiency of hepatic phenylalanine hydroxylase (PAH). The abolition of an invariant BamHI site located in the coding sequence of the PAH gene (exon 7) led to the recognition of two new point mutations at codon 272 and 273 (272gly----stop and 273ser----phe, respectively). Both mutations were detected in north eastern France or Belgium and occurred on the background of RFLP haplotype 7 alleles. The present study supports the view that the clinical heterogeneity in PKU is accounted for by the large variety of mutant genotypes associated with PAH deficiencies.

Base Sequence↗

PubMed1984

[Chemico-enzymatic synthesis of an oligonucleotide template for an analog of ACTH (4-10) fragment].

Six oligodeoxyribonucleotides ranging from 9-mer to 13-mer were synthesized in solution by the phosphotriester approach and enzymatically joined by T4 DNA ligase. The obtained double-stranded DNA (32 b.p.) with protruding 5'-ends corresponding to the recognition sites for restrictases EcoRI and BamHI represents an oligonucleotide template coding for the modified amino acid sequence 4-10 of the adrenocorticotropic hormone, [Pro8,Gly9,Pro10]ACTH-(4-10).

Adrenocorticotropic Hormone↗

PubMed1972

Coding properties of reticulocyte lysine transfer RNA's in hemoglobin synthesis.

Two isoacceptor transfer RNA's for lysine were found in rabbit reticulocytes. The codon recognition properties of these isoacceptors were studied in hemoglobin synthesis in a cell-free systemn. The two isoacceptors transferred lysine into different sites in hemoglobin, but showed no preference for one chain over the other. Codon cross recognition was less than 4 percent.

Adenosine↗

PubMed2005

Effects of identical context on visual pattern recognition by pigeons.

The effects of identical context on pattern recognition by pigeons for outline drawings of faces were investigated by training pigeons to identify (Experiment 1) and categorize (Experiment 2) these stimuli according to the orientation of the mouth-an upright U shape representing a smiling mouth or an inverted U shape representing a sad mouth. These target stimuli were presented alone (Pair 1), with three dots in a triangular orientation to represent a nose and eyes (Pair 2), and with the face pattern surrounded by an oval (Pair 3). In Experiment 1, the pigeons trained with Pair 1 were most accurate, those trained with Pair 2 were less so, and those trained with Pair 3 failed to acquire the discrimination within eighty 100-trial sessions. The same ordering was found in Experiment 2 for pigeons trained on the three pairs simultaneously. The authors suggest that a contrasting finding in humans, the face superiority effect, might be due to a gain in discriminability resulting from recognition of the pattern as a face. An exemplar model of information processing that excludes linguistic coding accounts for the present results.

Animals↗

PubMed2001

Color and form as support for picture recognition in old age.

This study examined the effect of color and form as support for picture recognition measured immediately and after a period of 20 minutes in two groups: a random sample of 80-year-old men and women, with a Mini-Mental-State-Examination (MMSE) score of >26 points (N=142), and individuals with confirmed diagnosis of Alzheimer's disease (AD) with a MMSE score ranging from 7-26 points (N=50). The result showed that individuals with AD could make use of spatial support for recognition at a significantly lower level than among the cognitively intact 80-year olds, but most interestingly with a similar pattern. Chromatic pictures had an advantage over achromatic ones on immediate recognition measured as less time consumption and a higher number of correct answers in both groups. However, after 20 minutes' retention time, achromatic pictures were better recognized than chromatic ones by both the 80-year olds and the individuals with AD. It is suggested that immediate recognition had most support from self-generated cues concerning color, in contrast to retained recognition where instead cues concerning form had the strongest impact. Gender and age had no influence on recognition. Visual function and abstract vs concrete objects showed a slight impact on the result. Factors of intelligence and memory in the group of 80-year olds only had a minor influence on recognition, contrary to dementia which had a profound impact. It is concluded that spatial support as to color and form could be used for recognition in old age groups. The result will encourage further experimental research in using coding and cueing strategies for future implications in clinical practice.

Aged↗

PubMed1980

Complex molecular structure of the gene coding for rat ceruloplasmin.

The distribution of ceruloplasmin-coding sequences among the fragments of rat nuclear DNA obtained after the complete digestion with seven restriction endonucleases (EcoRI, BamHI, BspI, HindIII, KpnI, BglII and XhoI) was studied using highly specific cDNA probes. Although only a single copy of this gene per rat haploid genome was detected in DNA-cDNA hybridization in solution, the number of restriction fragments carrying the sequences of ceruloplasmin (CP) gene varied from two to five, depending upon the enzyme used, and their total length was several times higher than the minimal length of CP-coding gene, as deduced from the size of mRNA (2.3 Md for double-stranded DNA). The partial double stranded DNA transcript of ceruloplasmin mRNA coding for about 70% of its length (from 3'-end) does not contain recognition sites for some restriction endonucleases generating multiple fragments of CP gene in cellular DNA. These data are consistent with a split pattern of CP gene which seems to consist of several exons and introns. The partial protection from S1 nuclease of discrete fragments of full-length cDNA after annealing with high molecular weight nuclear RNA is consistent with this assumption and seems to be an indication that exons and introns are joined into a functional unit coding for high mol wt. CP pre-mRNA.

Animals↗

PubMed1995

Cloning and expression of the gene coding for IL-2(60)-PE40, a molecular targeted protein.

It has recently been shown that chimeric toxin composed of IL2 fused tp PE40, a mutant form of Pseudomonas Exotoxin A devoid of its native cell recognition and binding domain was cytotoxic to IL2 receptor bearing cells. We here amplified the gene IL-2 (60), which codes for the N-terminal 1-60 amino acids of human IL-2 by PCR. After that, we fused it to PE40 and the new chimeric protein IL-2(60)-PE40 was expressed in E. coli. SDS-PAGE revealed that IL-2(60)-PE40 chimeric protein accounts for more than 18% of total cell proteins. As the region IL-2 binds with its receptor was defined in the N-terminal residues 8-54 of IL-2, such fusion proteins will have the same activity with IL-2-PE40. Following primary purification, IL-2(60)-PE40 was shown to be very toxic to IL-2 receptor-positive cells but non measurable effect on the cells lacking IL-2 receptors. Such a structure has not been reported by now. The fusion protein is useful for suppressing the immune response in cases of rejection of allografts and organ transplants and as therapeutic agents for the treatment of IL-2 receptor related diseases such as autoimmune disease, ATL (adult T-cell leukemia), et al.

Animals↗

PubMed1990

Performance of cochlear implant patients as a function of time.

The speech perception abilities of 15 patients were measured preoperatively using hearing aids and postoperatively using the Nucleus 22-channel cochlear implant over a period of 1, 2, or 3 years. Analysis of mean data revealed that, although the greatest amount of improvement in speech perception scores occurred between the preoperative and 3-month poststimulation evaluation, there was also significant improvement in perception of segmental features and open-set speech recognition over the 3-year time period. When individual patient data were examined, however, it was clear that these improvements were due, in large part, to the performance of a subset of patients who had measurable open-set speech recognition abilities at the time of their 3-month, poststimulation evaluation. Subjects who used the processing scheme that included coding of F1 showed significantly more improvement over time than subjects who used the original F0F2 processing scheme exclusively. It was concluded that open-set speech recognition ability at 3 months is an important prognostic indicator of continued improvement in speech perception abilities over time.

Adult↗

PubMed2005

Interferon-gamma renders tumors that express low levels of Her-2/neu sensitive to cytotoxic T cells.

Her-2/neu is a tumor-associated antigen that has been targeted with both antibodies and cytotoxic T lymphocytes (CTL). Despite the isolation of Her-2/neu-reactive CTL in vaccinated patients, their therapeutic use has been limited by the observation that they often do not robustly recognize Her-2/neu(+) tumors. We sought to determine the mechanism for this escape using Ag201P and Ag201M cells, which are murine osteosarcoma tumor lines that express a functional HLA-A2/K(b) molecule. We now demonstrate that Ag201P and Ag201M express low levels of murine Her-2/neu, and that Ag201M was modestly and inconsistently recognized by an HLA-A2-restricted, Her-2/neu-reactive human CTL clone. In order to determine whether inefficient antigen processing might account for the weak recognition, COS-A2 cells were transfected with a short Her-2/neu minigene coding for the immunodominant Her-2/neu:369 epitope that did not require antigen processing or a long Her-2/neu minigene that did require antigen processing. Her-2/neu-reactive CTL clones only recognized COS-A2 cells transfected with the short minigene, indicating that lack of proper antigen processing could be responsible for the poor recognition of target cells. To confirm these results, it was demonstrated that following treatment with interferon-gamma, both Ag201P and Ag201M robustly and consistently stimulated the CTL clones. Furthermore, CTL clone recognition was enhanced following interferon-gamma treatment using another murine tumor line that expressed low levels of Her-2/neu (B16-A2/K(b)). The enhanced recognition of Ag201P and Ag201M in the presence of interferon-gamma was not due to an upregulation of Her-2/neu protein expression. Collectively, these results suggest that inefficient antigen processing of Her-2/neu can contribute to the lack of tumor recognition by CTL. These results also suggest that even tissues that express low levels of Her-2/neu might become CTL targets under conditions in which antigen processing is enhanced.

Animals↗

PubMed1995

Switching recognition of two tRNA synthetases with an amino acid swap in a designed peptide.

The genetic code is based on specific interactions between transfer RNA (tRNA) synthetases and their cognate tRNAs. The anticodons for methionine and isoleucine tRNAs differ by a single nucleotide, and changing this nucleotide in an isoleucine tRNA is sufficient to change aminoacylation specificity to methionine. Results of combinatorial mutagenesis of an anticodon-binding-helix loop peptide were used to design a hybrid sequence composed of amino acid residues from methionyl- and isoleucyl-tRNA synthetases. When the hybrid sequence was transplanted into isoleucyl-tRNA synthetase, active enzyme was generated in vivo and in vitro. The transplanted peptide did not confer function to methionyl-tRNA synthetase, but the substitution of a single amino acid within the transplanted peptide conferred methionylation and prevented isoleucylation. Thus, the swap of a single amino acid in the transplanted peptide switches specificity between anticodons that differ by one nucleotide.

Amino Acid Sequence↗