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 1,405 records · Page 78Linked to original sources

PubMed1996

Association of the two lobes of ovotransferrin is a prerequisite for receptor recognition. Studies with recombinant ovotransferrins.

Different recombinant N-lobes of chicken ovotransferrin (oTF/2N) have been isolated from the tissue-culture medium of baby hamster kidney cells transfected with the plasmid pNUT containing the relevant DNA coding sequence. Levels of up to 40, 55 and 30 mg/1 oTF/2N were obtained for constructs defining residues 1-319, 1-332 and 1-337-(Ala)3 respectively. In addition, a full-length non-glycosylated oTF was expressed at a maximum of 80 mg/1 and a foreshortened oTF consisting of residues 1-682 was expressed at a level of 95 mg/l. These preparations were then used to produce, proteolytically, two different C-lobes (oTF/2C) comprising residues 342-686 and 342-682. The purified recombinant N-lobes (oTF/2N) are similar to the proteolytically derived half-molecule with regard to immunoreactivity and spectral properties; they show some interesting differences in thermal stability. A sequence analysis of the cDNA revealed six changes at the nucleotide level that led to six differences in the amino acid sequence compared with that reported by Jeltsch and Chambon [(1982) Eur. J. Biochem. 122, 291-295]. Electrospray mass spectrometry gives results consistent with these six changes. Interaction between the various N- and C-lobes was measured by titration calorimetry. Studies show that only those lobes that associate in solution are able to bind to the receptors on chick embryo red blood cells. These findings do not support a previous report by Oratore et al.

Animals↗

PubMed1980

Different pattern of codon recognition by mammalian mitochondrial tRNAs.

Analysis of an almost complete mammalian mitochondrial DNA sequence has identified 23 possible tRNA genes and we speculate here that these are sufficient to translate all the codons of the mitochondrial genetic code. This number is much smaller than the minimum of 31 required by the wobble hypothesis. For each of the eight genetic code boxes with four codons for one amino acid we find a single specific tRNA gene with T in the first (wobble) position of the anticodon. We suggest that these tRNAs with U in the wobble position can recognize all four codons in these genetic code boxes either by a "two out of three" base interaction or by U.N wobble.

Animals↗

PubMed2002

Multiple endocrine neoplasia type 1 (MEN1) in Austria.

Multiple endocrine neoplasia type 1 (MEN1) is a rare cancer predisposition syndrome. It results from the autosomal dominant inheritance of inactivating germ-line mutations of the MEN1 tumor suppressor gene. Mutation carriers are prone to develop tumors, preferentially, of the parathyroid and anterior pituitary glands as well as the enteropancreatic endocrine tissues. Because such tumors also occur without the MEN1 context, we have set up a molecular genetic screening program in Austria to discriminate between heritable and non-heritable tumor forms. Following the recognition of a MEN1-specific germ-line mutation in a tumor patient, we extend the screening to all first-degree relatives. To date, we have studied 42 individuals by sequencing the coding exons 2 to 10 of the MEN1 gene. A germ-line mutation was discovered in four of seven families suspected, clinically, to have MEN1, and in 3 of 22 (13.6%) patients with a presumed sporadic endocrine tumor. The respective mutations were also detected in three first-degree relatives of whom only one 6-year-old boy was asymptomatic at the time of investigation. The possibility to clearly discriminate between genetically predisposed and non-predisposed individuals has a significant impact on the diagnosis and clinical management of both patients and their relatives. Both symptomatic and asymptomatic mutation carriers can be closely monitored, thereby allowing early recognition and treatment of developing tumors. Non-affected relatives, on the other hand, do not require further controls. Finally, this approach also provides the information necessary for reliable genetic counseling.

Adolescent↗

PubMed2006

Genotyping of measles virus in clinical specimens on the basis of oligonucleotide microarray hybridization patterns.

An oligonucleotide microarray hybridization method for identification of most known measles virus (MV) genotypes was developed. Like the conventional genotyping method, the microarray relied on detecting sequence differences in the 450-nucleotide region coding for the COOH-terminal 150 amino acids of the nucleoprotein (N). This region was amplified using PCR primers binding to all known MV genotypes. The microarray included 71 pairs of oligonucleotide probes (oligoprobes) immobilized on glass slides. Each pair consisted of a genotype-specific oligoprobe, which matched the sequence of only one target genotype, and a control oligoprobe, which contained mismatches at the nucleotide positions unique to this genotype. A pattern recognition algorithm based on cluster analysis of the ratios of hybridization signals from specific and control oligoprobes was used to identify the specific MV genotype. Following the initial validation, the method was used for rapid genotyping of two panels of coded samples. The results of this study showed good sensitivity (90.7%), specificity (100%), and genotype agreement (91.8%) for the new method compared to the results of genotyping conducted using phylogenetic analysis of viral sequences of the C terminus of the N gene. In addition, the microarray demonstrated the ability to identify potential new genotypes of MV based on the similarity of their hybridization patterns with those of known MV genotypes.

Genotype↗

PubMed1994

Nucleic acid sequence and DNase hypersensitive sites of the 5' region of the mouse progesterone receptor gene.

To allow study of the control of the promoter of the mouse progesterone receptor gene and its specific elements, we have isolated nine individual clones and selectively sequenced the 5' region, which includes 5' promoter sequence and the non-coding region. Sequence comparison was performed versus the progesterone receptor genes of other species. Moreover, potential estrogen response elements, progesterone response elements, and other transcription factor recognition sites were determined by sequence analysis. In addition, since it has been confirmed that chromatin structures are important for regulation of gene expression, we also examined them in different estrogen target organs using the DNase hypersensitivity assay. A different pattern of the DNase hypersensitivity sites was detected between uterus and mediobasal hypothalamus and these sites were close to specific recognition elements.

Animals↗

PubMed1998

Molecular systematics and biogeography of aridland gnatcatchers (genus Polioptila) and evidence supporting species status of the California gnatcatcher (Polioptila california).

Over 2000 basepairs of mitochondrial DNA (mtDNA) sequences were compared to (1) examine evolution in protein coding versus noncoding [control region (CR)] segments, and (2) test the species-level distinctiveness of the California gnatcatcher (Polioptila californica) and clarify its phylogenetic and biogeographic relationships to other arid-adapted gnatcatchers. Unlike some studies, CR region I (left domain) was not as variable as coding genes. As expected, the central domain of the CR varied little, whereas CR II (right domain) showed high levels of variation. CR sequences tended to be "phylogenetically noisy" as evidenced by lower rescaled consistency indices, relative to those for coding genes. The California gnatcatcher differs from its sister-species, the black-tailed gnatcatcher (P. melanura), by approximately 4.0%, which supports species-level recognition. Two other aridland gnatcatchers, the black-capped gnatcatcher. (P. nigriceps) and white-lored gnatcatcher (P. albiloris), are closely related to the previous two species, also at a level of about 4 to 4.5% sequence divergence. These species evolved over a relatively short time, but prior to the most recent Pleistocene glaciations.

Animals↗

PubMed1994

Truncated bovine herpesvirus-1 glycoprotein I (gpI) initiates a protective local immune response in its natural host.

Current modified live and killed BHV-1 vaccines have not reduced the incidence of bovine herpesvirus-1 (BHV-1), the principal viral agent in bovine respiratory disease complex. The requirement for production of viral proteins for immune study has resulted in the establishment of a cell line which constitutively expresses BHV-1 gpI. A truncated BHV-1 envelope gpI protein was secreted into the culture supernatant of D17 cells transfected with the gpI gene lacking the coding sequence for the transmembrane region (TMR). The transmembrane domain is essential for gpI stability in the envelope, virus infectivity and, most probably, natural killer cell recognition; however, we have tested the possibility that this domain is not required for inducing an adaptive, protective immune response. Immunization of calves with this truncated gpI protein induced gpI-specific nasal IgA, IgG1, serum neutralizing antibodies and gpI-specific peripheral lymphocyte proliferation. All immunized calves were protected from clinical disease after BHV-1 challenge. Further, nine of ten immunized calves had no intranasal viral shedding. One animal shed a minimal amount of virus following challenge, but produced no antibodies to other viral proteins as evidenced by immunoprecipitation of 35S-labelled viral proteins by sera from virus-challenged animals. This study represents the first evidence that a recombinant truncated gpI subunit vaccine can confer local mucosal immunity and establish a strong protective barrier against disease caused by BHV-1 in the natural host. Also, these data demonstrate the feasibility of preventing initial viral replication in the host and distinguishing vaccinated from wild-type virus-infected animals.

Animals↗

PubMed2006

Hin4II, a new prototype restriction endonuclease from Haemophilus influenzae RFL4: discovery, cloning and expression in Escherichia coli.

The genes encoding restriction-modification system of unknown specificity Hin4II from Haemophilus influenzae RFL4 were cloned in Escherichia coli and sequenced. The Hin4II system comprises three tandemly arranged genes coding for m6A DNA methyltransferase, m5C DNA methyltransferase and restriction endonuclease, respectively. Restriction endonuclease was expressed in E. coli and purified to apparent homogeneity. The DNA recognition sequence and cleavage positions were determined. R.Hin4II recognizes the novel non-palindromic sequence 5'-CCTTC-3' and cleaves the DNA 6 and 5 nt downstream in the top and bottom strand, respectively. The new prototype restriction endonuclease Hin4II was classified as a potential candidate of HNH nuclease family after comparison against SMART database. An amino acid sequence motif 297H-X14-N-X8-H of Hin4II was proposed as forming a putative catalytic center.

Amino Acid Sequence↗

PubMed2005

Computational searches for splicing signals.

The removal of introns from pre-mRNA requires as an initial event the accurate molecular recognition of the proper exon-intron borders. It is now evident that RNA sequence elements in addition to the consensus splice site sequences themselves are required for this recognition. Genomic analyses have contributed to the definition of these elements as exonic and intronic splicing enhancers and silencers, comprising what has been called the "splicing code." Many computational methods have been brought to bear in such studies. We describe here some of the methods we have used to discover functional splicing signals. What these methods have in common is a comparison of sequences in and around exons to sequences found elsewhere in the genome. We have especially made use of comparisons to "pseudo exons," intronic sequences resembling exons by virtue of being bounded by sequences indistinguishable from splice sites. Two computational strategies are emphasized: (1) the use of a machine learning technique in which a computational algorithm, a support vector machine, is first trained on known examples and then used to predict sequences associated with splicing; and (2) straight statistical analysis of differences between regions associated with exons and other regions in the genome. In most cases, the predictions made using these methods have been validated by subsequent empirical tests. An attempt has been made to make this description understandable by researchers unfamiliar with computational practice and to include practical references to specific databases and programs.

Alternative Splicing↗

PubMed1996

Characterization of Campylobacter upsaliensis fur and its localization in a highly conserved region of the Campylobacter genome.

Despite increasing recognition of the importance of Campylobacter upsaliensis in human disease little is known about either the virulence properties or genetics of this enteric pathogen. The complete coding sequence of a C. upsaliensis gene has yet to be published. We have cloned and sequenced the complete iron-uptake regulatory (fur) gene from the type strain of this species. The C. upsaliensis fur homolog was isolated from a genomic library of C. upsaliensis ATCC 43954 constructed in phage lambdaGEM-11. The open reading frame identified encodes a polypeptide consisting of 156 amino acids. The 5'-flanking region of the C. upsaliensis fur gene contains 3 putative Fur-binding sequences and two catabolite activator-binding sequences indicating the potential for autogenous and cAMP-mediated regulation, respectively. Primer extension analysis identified a single transcription start site 262 nt upstream from the AUG initiation codon. Sequence analysis indicates that the Fur protein of C. upsaliensis is highly homologous (87% amino acid identity) to Campylobacter jejuni Fur. Furthermore, the arrangement of the lysS and glyA genes downstream of fur is precisely conserved in both C. upsaliensis ATCC 43954 and C. jejuni TGH9011. Using the polymerase chain reaction close linkage of fur with lysS and glyA was also observed among multiple isolates of C. upsaliensis, C. jejuni and C. coli suggesting a possible functional relevance for this conserved genetic arrangement in campylobacteria.

Amino Acid Sequence↗

PubMed1993

A distinct intron-DNA structure in simian virus 40 T-antigen and adenovirus 2 E1A genes.

Distinct structures delineating the introns of simian virus 40 T-antigen and adenovirus 2 E1A genes have been discovered. The structures, which are centered around the branch points of the genes inserted in supercoiled double-stranded plasmids, are specifically targeted through photoactivated strand cleavage by the metal complex tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III). The DNA sites that are recognized lack sequence homology but are similar in demarcating functionally important sites on the RNA level. The single-stranded DNA fragment corresponding to the coding strand of the E1A gene was also found to fold into a structure apparently identical to that in the supercoiled E1A gene based on the recognition by the metal complex. Further investigation of different single-stranded DNA fragments showed that the structure requires the sequences at both ends of the intron plus the flanking sequences but not the middle of the intron. These results provide direct evidence that the positions of these introns are structurally encoded on the DNA level.

Adenovirus E1A Proteins↗

PubMed2006

Sulfation patterns of glycosaminoglycans encode molecular recognition and activity.

Although glycosaminoglycans contribute to diverse physiological processes, an understanding of their molecular mechanisms has been hampered by the inability to access homogeneous glycosaminoglycan structures. Here, we assembled well-defined chondroitin sulfate oligosaccharides using a convergent, synthetic approach that permits installation of sulfate groups at precise positions along the carbohydrate backbone. Using these defined structures, we demonstrate that specific sulfation motifs function as molecular recognition elements for growth factors and modulate neuronal growth. These results provide both fundamental insights into the role of sulfation and direct evidence for a 'sulfation code' whereby glycosaminoglycans encode functional information in a sequence-specific manner analogous to that of DNA, RNA and proteins.

Animals↗

PubMed1990

DNA recombination and natural selection pressure sustain genetic sequence diversity of the feline MHC class I genes.

Sequence comparisons of seven distinct MHC class I cDNA clones revealed that feline class I molecules have a remarkable similarity to human HLA genes in their organization of functional domains as well as in the nonrandom partitioning of genetic variability according to the functional constraints ascribed to different regions of the MHC molecule. The distribution of the pattern of sequence polymorphism in the cat as compared with genetic diversity of human and mouse class I genes provides evidence for four coordinate factors that contribute to the origin and sustenance of abundant allele diversity that characterizes the MHC in the species. These include: (a) a gradual accumulation of spontaneous mutational substitution over evolutionary time; (b) selection against mutational divergence in regions of the class I molecule involved in T cell receptor interaction and also in certain regions that interact with common features of antigens; (c) positive selection pressure in favor of persistence of polymorphism and heterozygosity at 57 nucleotide residues that comprise the antigen recognition site; and (d) periodic intragenic (interallelic) and intergenic recombination within the class I genes. We describe a highly conserved 23-bp nucleotide sequence within the coding region of the first alpha-helix that separates two relatively polymorphic segments located in the alpha 1 domain that may act as a template or "hot spot" for homologous recombination between class I alleles.

Amino Acid Sequence↗

PubMed2007

Dignity and the challenge of dying in nursing homes: the residents' view.

BACKGROUND: human dignity is discussed in almost all public debates on the care of the dying, as well as in international policies for health and social care of older people. Because nursing homes are gaining importance as places where residents live out their lives in modern western societies and since there is evidence that end-of-life care in nursing homes lacks quality, there is a growing discussion on introducing improved end-of-life care in these institutions. In order to accomplish this, the view of those who are most affected is of utmost importance. OBJECTIVE: to explore the meaning of dignity with regard to end-of-life issues from the perspective of older nursing home residents in western Germany. METHODS: this qualitative study is based on the Grounded Theory Approach, and the design included three steps of data generation; narrative interviews with residents of nursing homes constitute the main data pool (n = 20) of the results presented in this paper. Theoretical sampling was aimed at maximising the variety of organisational as well as residents' characteristics. Analysis of the transcripts was supported by Atlas/ti program and followed several different coding procedures and aimed at generating a concept of dignity. RESULTS: dignity was differentiated into intrapersonal dignity and relational dignity, socially constructed by the act of recognition. Social relations and encounters are a prerequisite for relational dignity, which underlines the vulnerability of nursing home residents' who increasingly lack social networks. A broad spectrum of attitudes and behaviour, which aimed at recognising dignity, was bundled under the category 'not being a burden'. In this light, dignity was challenged most by the threat of illness and having care needs. This was fostered by the perception of insufficient care in the nursing homes. In the light of this concept, death with dignity meant 'death at the right time', though the residents in the sample did not want to comment on the time of death, other than aspects like (i) being active to the very last, (ii) respecting one's will and being allowed to die, (iii) not being in pain, (iv) being amongst persons close to one (valediction and showing respect). CONCLUSION: the study emphasizes the high vulnerability of nursing home residents with regard to dignity. They place their dignity under the constraints of the need for help and care into question. This appears alarming, if one does not manage to, with the help of different ethics, obtain a new perspective on these phases of life. It is evident that the understanding of dignity is not solely individualistic and personal, but rather has a close relationship to social ideas of value, which ultimately influence the basic requirements of institutions in which 'frail old people' live.

Aged↗

PubMed1979

I-region-coded products expressed on both macrophages and thymus epithelium influence T-cell activities.

I-region-coded products expressed on the surface of both macrophages (Mph) and thymus epithelium were shown to restrict T-cell activities at the level of antigen recognition and determination of the T-cell repertoire. Thus keyhole limpet haemocyanin (KLH) -pulsed Mph could elicit a delayed-type hypersensitivity response in a KLH-sensitized mouse only when the Mph and the sensitized mouse were compatible at the I-A region of the major histocompatibility complex. Also, experiments with thymus-grafted chimaeras showed that I-region compatibility between the thymus of the cell donor and the reticuloendothelial system of the recipient was essential for successful transfer of the DTH reaction. Thus, F1 T cells derived from stem cells differentiating in a P1 thymus graft, where F1 parents (P1 and P2) differed only at defined regions of the H-2 complex, could always transfer sensitivity to P1 mice. However, successful transfer to P2 mice was possible only if P1 and P2 were H-21-compatible.

Animals↗

PubMed1992

Type II DNA restriction-modification system and an endonuclease from the ruminal bacterium Fibrobacter succinogenes S85.

Fibrobacter succinogenes is an important cellulolytic bacterium found in the rumen and cecum of herbivores. Numerous attempts to introduce foreign DNA into F. succinogenes S85 have failed, suggesting the presence of genetic barriers in this organism. Results from this study clearly demonstrate that F. succinogenes S85 possesses a type II restriction endonuclease, FsuI, which recognizes the sequence 5'-GG(A/T)CC-3'. Analysis of the restriction products on sequencing gels showed that FsuI cleaves between the two deoxyguanosine residues, yielding a 3-base 5' protruding end. These data demonstrate that FsuI is an isoschizomer of AvaII. A methyltransferase activity has been identified in the cell extract of F. succinogenes S85. This activity modified DNA in vitro and protected the DNA from the restriction by FsuI and AvaII. DNA modified in vivo by a cloned methylase gene, which codes for M.Eco47II, also protected the DNA from restriction by FsuI, suggesting that FsuI is inhibited by methylation at one or both deoxycytosine residues of the recognition sequence. The methyltransferase activity in F. succinogenes S85 is likely modifying the same deoxycytosine residues, but the exact site(s) is unknown. A highly active DNase (DNase A) was also isolated from the cell extract of this organism. DNase A is an endonuclease which showed high activity on all forms of DNA (single stranded, double-stranded, linear, and circular) but no activity on RNA. In vitro, the DNase A hydrolyzed F. succinogenes S85 DNA extensively, indicating the lack of protection against hydrolysis by this enzyme. In the presence of Mg2+, DNA was hydrolyzed to fragments of 8 to 10 nucleotides in length. The presence of DNase A and the type II restriction-modification system of F. succinogenes S85 may be the barriers preventing the introduction of foreign DNA into this bacterium.

Base Sequence↗

PubMed1993

Restoration of pathogenicity of avirulent Xanthomonas oryzae pv. oryzae and X. campestris pathovars by reciprocal complementation with the hrpXo and hrpXc genes and identification of HrpX function by sequence analyses.

The molecular basis of pathogenesis by Xanthomonas oryzae pv. oryzae has been partly elucidated by the identification of a gene, hrpXo, required for bacterial blight on rice. A mutation in hrpXo results in the loss of pathogenicity on rice and the loss of hypersensitivity on nonhosts such as Datura stramonium and radishes. Pathogenicity and its ability to cause the hypersensitive reaction is restored by complementing the mutant with the heterologous hrpXc gene derived from X. campestris pv. campestris. Conversely, hrpXo complements nonpathogenic mutants of X. campestris pv. campestris and X. campetstris pv, armoraciae. Mutants bearing the heterologous hrpX gene are restored in their abilities to cause diseases typical of their chromosomal background and not the hypersensitive reaction on their respective hosts. The hrpXo and hrpXc genes are therefore functionally equivalent, and this functional equivalence extends into X. campestris pv. armoraciae and possibly into other X. campestris pathovars, since this gene is highly conserved among eight other pathovars tested. Sequence analyses of hrpXo revealed an open reading frame of 1,452 bp with a coding capacity for a protein of 52.3 kDa. The protein contains a consensus domain for possible protein myristoylation whose consequence may result in a loss of recognition by host defense and surveillance systems.

Amino Acid Sequence↗

PubMed1998

Homology-dependent maternal inhibition of developmental excision of internal eliminated sequences in Paramecium tetraurelia.

Thousands of single-copy internal eliminated sequences (IESs) are excised from the germ line genome of ciliates during development of the polygenomic somatic macronucleus, following sexual events. Paramecium IESs are short, noncoding elements that frequently interrupt coding sequences. No absolutely conserved sequence element, other than flanking 5'-TA-3' direct repeats, has been identified among sequenced IESs; the mechanisms of their specific recognition and precise elimination are unknown. Previous work has revealed the existence of an epigenetic control of excision. It was shown that the presence of one IES in the vegetative macronucleus results in a specific inhibition of the excision of the same element during the development of a new macronucleus, in the following sexual generation. We have assessed the generality and sequence specificity of this transnuclear maternal control by studying the effects of macronuclear transformation with 13 different IESs. We show that at least five of them can be maintained in the new macronuclear genome; sequence specificity is complete both between genes and between different IESs in the same gene. In all cases, the degree of excision inhibition correlates with the copy number of the maternal IES, but each IES shows a characteristic inhibition efficiency. Short internal IES-like segments were found to be excised from two of the IESs when excision between normal boundaries was inhibited. Available data suggest that the sequence specificity of these maternal effects is mediated by pairing interactions between homologous nucleic acids.

Animals↗