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PubMed1992

Phonology and orthography in visual word recognition: evidence from masked non-word priming.

Three lexical decision experiments in French investigated the effects of briefly presented forward-masked non-word primes on latencies to phonologically and/or orthographically related targets. At 64-msec prime presentation durations, primes that are pseudohomophones of the target produced facilitatory effects compared to orthographic controls, but these orthographically similar non-word primes did not facilitate target recognition compared to unrelated controls. These results were obtained independently of target word frequency and independently of the presence or absence of pseudohomophone targets in the experimental lists. With a 32-msec prime duration, on the other hand, pseudohomophone and orthographic primes had similar effects on target recognition, both producing facilitation relative to unrelated controls. The results are discussed in terms of the time course of phonological and orthographic code activation in the processing of pronounceable strings of letters.

Adult↗

PubMed1991

The protein structure code: what is its present status?

Current methods of prediction of protein conformation are reviewed and the algorithms on which they rely are presented. For non-homologous proteins and after cross-validation the reported methods exhibit a probability index, i.e. the per cent of correctly predicted residues per predicted residues, of 63-65% with a standard deviation of the order of 7% for three conformational states--helix, beta-strand and coil. This present limitation in the accuracy of predictions that use only the information of the local sequence can be related essentially to the effect of long-range interactions specific for each protein family. The methods based on sequence similarity can improve the accuracy of prediction by expressing explicitly the homology of the protein to be predicted with proteins in the database. In these circumstances the probability index can reach 87% with a standard deviation of 6.6%. This property can be used for modeling homologous proteins by aiding in amino acid sequence alignments. The prediction of the tertiary structure of a protein is still limited to the case of modeling a structure based on the known three-dimensional structure of a homologous protein.

Algorithms↗

PubMed1991

The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars.

No one questions the important practical contributions of computer sciences to molecular biology. It may well be that one day theoretical contributions also will become useful. One example of this type of interdisciplinary research is the attempt to construct a grammatical theory of the regulation of gene expression. In this paper, I demonstrate that context-free grammars are inadequate for the description of regulatory properties coded in the DNA. This result is supported by data available in the literature that show changes in the specificity of the recognition between regulatory proteins and their DNA targets. This result is an important limitation for the use of statistical approaches such as information theory as a source of inspiration for a theory of gene regulation. Additionally, such a demonstration gives formal justification to the search for more elaborate grammatical models in the study of gene regulation. Some basic proposals for such grammatical approach have been presented previously.

DNA↗

PubMed2001

An in vitro evolved precursor tRNA with aminoacylation activity.

A set of catalysts for aminoacyl-tRNA synthesis is an essential component for translation. The RNA world hypothesis postulates that RNA catalysts could have played this role. Here we show an in vitro evolved precursor tRNA consisting of two domains, a catalytic 5'-leader sequence and an aminoacyl-acceptor tRNA. The 5'-leader sequence domain selectively self-charges phenylalanine on the 3'-terminus of the tRNA domain. This cis-acting ribozyme is susceptible to RNase P RNA, generating the corresponding 5'-leader segment and the mature tRNA. Moreover, the 5'-leader segment is able to aminoacylate the mature tRNA in trans. Mutational studies have revealed that C(74) and C(75) at the tRNA aminoacyl-acceptor end form base pairs with G71 and G70 of the trans-acting ribozyme. Such Watson-Crick base pairing with tRNA has been observed in RNase P RNA and 23S rRNA, suggesting that all three ribozymes use a similar mechanism for the recognition of the aminoacyl-acceptor end. Our demonstrations indicate that catalytic precursor tRNAs could have provided the foundations for the genetic coding system in the proto-translation system.

Acylation↗

PubMed1994

Direct carrier testing of haemophilia B by SSCP.

Haemophilia B is due to multiple molecular defects in the factor IX gene. Most of them are single base substitutions, and can now be identified by direct sequencing of the coding sequence of the factor IX gene, preceded or not by a screening strategy. In some instances the mutation alters an enzyme recognition site and this allows rapid and accurate carrier testing and prenatal diagnosis in the affected pedigree. This was not the case for the previously described nt 31119 (G-->A) mutation that we found in an extended haemophilia B pedigree, during the search for mutations in the factor IX gene in patients from Southern France. We first detected this mutation by single stranded conformation polymorphism (SSCP) and then identified it by DNA sequencing. Carriership could be easily determined in the females of the pedigree by analysis of the SSCP patterns. Our results indicate that the SSCP analysis of amplified genomic DNA fragments can be successfully used as a diagnosis approach for direct carrier testing and prenatal diagnosis.

Base Sequence↗

PubMed1988

Expression of the gene encoding the 17-kilodalton antigen from Rickettsia rickettsii: transcription and posttranslational modification.

Recently, we reported the molecular cloning and nucleotide sequence analysis of a gene from Rickettsia rickettsii that codes for a 17-kilodalton antigen (17K antigen) and is preceded by sequences closely resembling the -10 and -35 consensus sequences for recognition by Escherichia coli RNA polymerase (Anderson et al., J. Bacteriol. 169:2385-2390, 1987). Experiments described in this report indicate that the start sites for initiating transcription of the 17K antigen gene are identical in the E. coli clone and in intact R. rickettsii. In each case, initiation was shown to begin 9 bases downstream of the presumed Pribnow box sequence (TATACT). A 169-base-pair fragment containing the promoter sequence initiated transcription in both directions when cloned into an E. coli promoter probe vector. The rickettsial fragment was found to contain sequences identical to the -10 region (but not the -35 region) of the E. coli promoter consensus sequence directed away from the 17K antigen gene. The amino-terminal portion (residues 17 to 20) of the deduced amino acid sequence for the 17K antigen contained the tetrapeptide Leu-Gln-Ala-Cys, a sequence that conforms favorably to those described for lipid modification and cleavage by lipoprotein signal peptidase II. The 17K antigen produced by the E. coli clone was shown to be labeled with [3H]palmitate and [3H]glycerol, indicative of lipid modification. In vitro mutagenesis designed to alter the cysteine at residue 20 to a glycine abolished incorporation of [3H]palmitate, suggesting that posttranslational modification occurs via a mechanism similar to that described for other gram-negative bacterial lipoproteins.

Amino Acid Sequence↗

PubMed2003

The cadherin superfamily in neural development: diversity, function and interaction with other molecules.

Cell-cell interactions are crucial steps for the development of the highly complex nervous system. A variety of cell-cell adhesion molecules of the cadherin superfamily have been found to be expressed in the developing nervous system. Recently it was proposed classic cadherins are involved in various aspects of neural development such as regionalization, brain nucleus formation, neurite outgrowth, target recognition and synaptogenesis. Classic cadherins preferentially bind to the same cadherin subtype ("homophilic adhesion"), and this binding specificity can provide an "adhesive code" that can account for various aspects of neural morphogenesis. In addition, novel members of the cadherin superfamily are also involved in various steps of neural development. The function of these cadherins molecules is orchestrated in the cellular context by a complex network of signaling pathways such as the small GTPase pathway. Here, we will review the molecular properties of the cadherin superfamily and their coordinated roles in the formation of the nervous system along with the accumulated knowledge in non-neuronal systems.

Animals↗

PubMed1985

Eukaryotic RNA polymerases.

This review will attempt to cover the present information on the multiple forms of eukaryotic DNA-dependent RNA polymerases, both at the structural and functional level. Nuclear RNA polymerases constitute a group of three large multimeric enzymes, each with a different and complex subunit structure and distinct specificity. The review will include a detailed description of their molecular structure. The current approaches to elucidate subunit function via chemical modification, phosphorylation, enzyme reconstitution, immunological studies, and mutant analysis will be described. In vitro reconstituted systems are available for the accurate transcription of cloned genes coding for rRNA, tRNA, 5 SRNA, and mRNA. These systems will be described with special attention to the cellular factors required for specific transcription. A section on future prospects will address questions concerning the significance of the complex subunit structure of the nuclear enzymes; the organization and regulation of the gene coding for RNA polymerase subunits; the obtention of mutants affected at the level of factors, or RNA polymerases; the mechanism of template recognition by factors and RNA polymerase.

Animals↗

PubMed1984

A system for the translation of receptor messenger-RNA and the study of the assembly of functional receptors.

The Xenopus oocyte translation system has been developed for the recognition of receptor messenger-RNA molecules. Observations with the nicotinic acetylcholine, GABA, glycine, glutamate and serotonin receptors show that the mRNAs coding for their subunits can be faithfully translated in the oocyte and the products processed, glycosylated, assembled to a receptor structure, inserted correctly in the cell membrane and organised to form the functional ion channel. The specific regulatory interactions between different sites on one receptor, as exemplified in the GABAA receptor, are established in this process. This system is of value for the detection of mRNAs for receptor gene cloning and for the study of receptor assembly and of the expression of multiple receptor genes. The receptor ion channels formed can also be studied in their own right in a highly accessible and controlled situation.

Acetylcholine↗

PubMed2000

Evaluation of SNOMED3.5 in representing concepts in chest radiology reports: integration of a SNOMED mapper with a radiology reporting workstation.

Standardized medical terminologies are gaining importance in the representation of medical data. In this paper, we present the evaluation of the SNOMED3.5 medical terminology to code concepts routinely used in chest radiology reports. Integration of this terminology mapper into a radiology reporting workstation that incorporates a speech recognition system and a natural language processor is also discussed. A total of 700 anatomical location terms (including synonyms) were tested and 72% of the terms had corresponding SNOMED terms. Of the 28% that did not result in a match, 16% were either morphological variants of SNOMED terms or could be found from a combination of terms from two or more SNOMED axes. Only 12% of the terms (primarily specialized radiology terms) were concepts not actually included in the SNOMED terminology.

Humans↗

PubMedDate not supplied

The living state of matter.

Progress in biology has been extremely fast in the second half of the twentieth century in terms of numbers and quality of data. However less attention has been paid to the revision of existing theories on living beings structure and dynamics in development and evolution. Within this frame, the discussion on the very definition of life is lagging in the sometimes ideological debate between mechanistic and holistic views often without serious trials to integrate the overwhelming amount of new data into the different theoretical frameworks. The aim of this short review is to try to define a series of parameters specific of the living state of matter on the basis of existing evidence. The analysis starts from mathematical, physical and experimental studies on DNA constraints in nucleotide distributions and the interactions with proteins in some basic processes of life. The data discussed seem to show that short and long range correlations in DNA, particularly significant in non coding regions and increasing during evolution may have been fixed because of the need of structural landscapes complementarity for DNA-protein recognition and complex dynamics. The need for highly efficient and frequent recognition between the molecules has been extended to gene expression, protein-protein, protein-ligand complex formation and to signal transduction pointing out to the relevance of plasticity on one hand, complementarity on the other. Compartmentalisation and individuality are then taken as critical conditions favouring such processes in the hierarchical networks of all levels, from the cell to organisms, populations, ecosystems, the biosphere. Finally the specific meaning in life of useful (correlated) and disruptive noise is discussed along with the dynamics of evolutionary change in terms of homeorrhetic, plastic maintenance of flexible equilibria continuously challenged by internal and external signals.

Biological Evolution↗

PubMed1994

Immunoglobulin and T-cell receptor gene rearrangement.

Gene rearrangement involves a complex process of DNA splicing and deletion that produces a unique genetic code in each B or T lymphocyte. These novel DNA sequences encode immunoglobulin or T-cell receptor proteins that function in recognition of foreign antigens. Recent advances in DNA technology permit laboratory detection of clonal gene rearrangements in lymphoid malignancies including lymphocytic leukemia, lymphoma, and myeloma. Practical applications of gene rearrangement testing include distinguishing reactive from malignant lymphoid proliferations, and assignment of B- or T-cell lineage to a neoplastic process. Active investigation is underway to devise practical strategies for detecting minimal residual disease based on tumor-specific gene rearrangements.

Antibodies↗

PubMed1993

Genomic organization of human surfactant protein D (SP-D). SP-D is encoded on chromosome 10q22.2-23.1.

Surfactant protein D (SP-D) is a member of the family of mammalian C-type lectins. SP-D is secreted into the pulmonary airspaces by lung epithelial cells and is believed to contribute to the lung's defense against inhaled microorganisms. We have previously characterized cDNAs specific for human SP-D (hSP-D). We now describe the partial characterization of genomic clones for hSP-D and present evidence for an SP-D gene with coding sequences spanning > 11 kilobases on the long arm of chromosome 10. Genomic sequencing demonstrated that the signal peptide/amino-terminal domain, the carbohydrate recognition domain, and the linking sequence between the collagen domain, and carbohydrate recognition domain are each encoded by a single exon, as for surfactant protein A and the mannose-binding protein C. However, sequencing also demonstrated a unique intron-exon structure for the collagen domain which is encoded on five exons, including four tandem exons of 117 bp. The latter exons show marked conservation in the predicted distribution of hydrophilic amino acids, consistent with tandem replication of this collagen gene sequence during evolution. Segregation analysis of HindIII digests of genomic DNA using specific cDNA probes demonstrated selective hybridization of radiolabeled hSP-D cDNA to chromosome 10- and 10q-containing human/hamster somatic hybrids. The presence of SP-D gene sequences was confirmed by DNA amplification using oligomers specific for sequences within the collagen domain of the hSP-D gene. Fluorescence in situ hybridization of metaphase chromosomes using genomic probes gave selective labeling of 10q22.2-23.1. We speculate that SP-D is encoded at a locus on 10q that includes the genes for surfactant protein A.

Amino Acid Sequence↗

PubMed1999

Calcium-dependent immunoglobulin E recognition of the apo- and calcium-bound form of a cross-reactive two EF-hand timothy grass pollen allergen, Phl p 7.

Type I allergy, an immunodisorder that affects almost 20% of the population worldwide, is based on the immunoglobulin E (IgE) recognition of per se innocuous antigens (allergens). Pollen from wind-pollinated plants belong to the most potent allergen sources. We report the isolation of a cDNA coding for a 8.6 kDa two EF-hand calcium binding allergen, Phl p 7, from a timothy grass (Phleum pratense) pollen expression cDNA library, using serum IgE from a grass pollen allergic patient. Sequence analysis identified Phl p 7 as a member of a recently discovered subfamily of pollen-specific calcium binding proteins. Recombinant Phl p 7 was expressed in Escherichia coli and purified to homogeneity as determined by mass spectroscopy. Approximately 10% of pollen allergic patients displayed IgE reactivity to rPhl p 7 and Phl p 7-homologous allergens present in pollens of monocotyledonic and dicotyledonic plants. Circular dichroism analysis of the calcium-bound and apo-rPhl p 7 indicated that differences in IgE recognition may be due to calcium-induced changes in the protein conformation. The fact that patients mount IgE antibodies against different protein conformations is interpreted as a footprint of a preferential sensitization against either form. The biological activity of rPhl p 7 was demonstrated by its ability to induce basophil histamine release and immediate type skin reactions in sensitized individuals. In conclusion, IgE binding to Phl p 7 represents an example for the conformation-dependent IgE recognition of an allergen. Recombinant Phl p 7 may be used for diagnosis and perhaps treatment of a group of patients who suffer from allergy to pollens of many unrelated plant species.

Allergens↗

PubMed2003

Optimized delivery radiological reports: applying Six Sigma methodology to a radiology department.

PURPOSE: To optimise the process of reporting and delivering radiological examinations with a view to achieving 100% service delivery within 72 hours to outpatients and 36 hours to inpatients. To this end, we used the Six Sigma method which adopts a systematic approach and rigorous statistical analysis to analyse and improve processes, by reducing variability and minimising errors. More specifically, our study focused on the process of radiological report creation, from the end of the examination to the time when the report is made available to the patient, to examine the bottlenecks and identify the measures to be taken to improve the process. MATERIALS AND METHODS: Six Sigma uses a five-step problem-solving process called DMAIC, an acronym for Define, Measure, Analyze, Improve and Control. The first step is to define the problem and the elements crucial to quality, in terms of Total Quality Control. Next, the situation is analysed to identify the root causes of the problem and determine which of these is most influential. The situation is then improved by implementing change. Finally, to make sure that the change is long-lasting, measures are taken to sustain the improvements and obtain long-term control. In our case we analysed all of the phases the report passes through before reaching the user, and studied the impact of voice-recognition reporting on the speed of the report creation process. RESULTS: Analysis of the information collected showed that the tools available for report creation (dictaphone, voice-recognition system) and the transport of films and reports were the two critical elements on which to focus our efforts. Of all the phases making up the process, reporting (from end of examination to end of reporting) and distribution (from the report available to administrative staff to report available to the patient) account for 90% of process variability (73% and 17%, respectively). We further found that the reports dictated into a voice-recognition reporting system are delivered in 45 hours (median), whereas those dictated using a dictaphone take 96 hours: voice-recognition reporting systems therefore improve performance by 50 hours. Unfortunately, 38% of our reports are delivered within longer timeframes than the 72h for outpatients and 36h for inpatients agreed with the service users. Reports for inpatients have much faster delivery times and lower variability, as 95% of these examinations are reported using voice-recognition reporting (as a result of the greater sensitivity of physicians to the problem of inpatient waiting times). For conventional radiology examinations, numerically greater than CT or MRI, there is a stronger tendency to use the dictaphone which allows for faster dictation as it is unburdened by administrative tasks such as entering examination codes, correcting errors, etc. Freelance status has no impact on report delivery times, service delivery being the same as in the institutional setting. The subprocess of reporting is strongly affected by the choice of reporting method (voice-recognition system or dictaphone), whereas report delivery is affected by the individual's behaviour patterns and ultimately by habits generated by the lack of a clearly charted process (lack of synchronisation among the various phases), and therefore potentially avoidable. DISCUSSION: The analytical study of the various phases of examination reporting, from writing to delivery, allowed us to identify the process bottlenecks and take corrective measures. Regardless of imaging modality and individual physician, examination reporting consistently takes longer when a dictaphone is used instead of a voice-recognition reporting system, as this makes the process more complex. To improve the two critical subprocesses whilst maintaining constant resources, a first step is to abandon the dictaphone in favour of the voice-recognition system. In addition, we are experimenting other measures to improve the collection and sorting of examinations and the delivery of reports: the technical staff take the films from the examination rooms to the reporting rooms three times a day; the radiologists collect their examinations and prepare the reports, possibly on the same day; the radiologists leave their signed reports on the table in the central reporting room; the administrative staff collect the signed reports three times a day in the morning and afternoon to be able to deliver them on the same day. CONCLUSIONS: This project has allowed us to become familiar with the principles of total quality, to better understand our internal processes and to take effective measures to optimise them. This has resulted in enhanced satisfaction of all the department staff and has laid the grounds for further measures in the future.

Humans↗

PubMed1992

T cell recognition of Epstein-Barr virus associated lymphomas.

Epstein-Barr virus, a lymphotropic herpesvirus of humans, has potent B cell growth transforming activity yet persists in the lymphoid tissues of most individuals as a lifelong asymptomatic infection. Virus induced B cell growth transformation in vitro is associated with the expression of a limited set of viral genes encoding six nuclear antigens (EBNA 1, 2, 3A, 3B, 3C and LP) and two latent membrane proteins (LMP 1, 2). Healthy virus carriers possess strong EBV specific CTL memory that can be reactivated in vitro. Here, we summarize experiments in which the antigenic specificities of these HLA class I restricted memory CTL responses have been mapped in a range of individuals with different HLA backgrounds. Of the known EBV latent proteins, EBNA 3A, 3B and 3C are frequently the dominant targets for such responses, but examples of responses directed against epitopes of EBNA 2, EBNA-LP or the LMP have been identified; by contrast, CTL responses against epitopes of EBNA 1 have not been observed. Epstein-Barr virus is associated with at least three malignancies of lymphoid origin--immunoblastic lymphomas of the immunosuppressed, endemic Burkitt's lymphoma and a subset of Hodgkin's disease. The immunoblastic lymphomas express the complete spectrum of EBV coded latent proteins and a cellular phenotype similar to that of in vitro transformed B lymphoblastoid cell lines; accordingly, they remain sensitive to EBV specific CTL recognition. Endemic BL cells are not recognized by such CTL, and at least three consistent features of this tumour could contribute to immune escape: (a) allele specific downregulation of HLA class I antigen expression, (b) absence/low expression of cellular adhesion molecules and (c) restriction of EBV latent protein expression to EBNA 1 only. The relative importance of these three features of the BL cell phenotype with regard to sensitivity to CTL recognition is re-interpreted in the light of recent results. Finally, the pattern of virus latent protein expression in EBV positive Hodgkin's disease is described, and the possibility of EBV specific CTL control against this tumour is discussed.

Antigens, Viral↗

PubMed1990

Primary sequence of the EcoRII endonuclease and properties of its fusions with beta-galactosidase.

The EcoRII endonuclease cleaves DNA containing the sequence CC(A/T)GG before the first cytosine. The methylation of the second cytosine in the sequence by either the EcoRII methylase or Dcm, a chromosomally coded protein in Escherichia coli, inhibits the cleavage. The gene for the EcoRII endonuclease was mapped by analysis of derivatives containing linker insertions, transposon insertions, and restriction fragment deletions. Surprisingly, plasmids carrying the wild-type endonuclease gene and the EcoRII methylase gene interrupted by transposon insertions appeared to be lethal to dcm+ strains of E. coli. We conclude that not all the EcoRII/Dcm recognition sites in the cellular DNA are methylated in dcm+ strains. The DNA sequence of a 1650-base pair fragment containing the endonuclease gene was determined. It revealed an open reading frame that could code for a 45.6-kDa protein. This predicted size is consistent with the known size of the endonuclease monomer (44 kDa). The endonuclease and methylase genes appear to be transcribed convergently from separate promoters. The reading frame of the endonuclease gene was confirmed at three points by generating random protein fusions between the endonuclease and beta-galactosidase, followed by an analysis of the sequence at the junctions. One of these fusions is missing 18 COOH-terminal amino acids of the endonuclease but still displays significant ability to restrict incoming phage in addition to beta-galactosidase activity. No striking similarity between the sequence of the endonuclease and any other protein in the PIR data base was found. The knowledge of the primary sequence of the endonuclease and the availability of the various constructs involving its gene should be helpful in the study of the interaction of the enzyme with its substrate DNA.

Amino Acid Sequence↗

PubMed1987

Recognition of translational termination signals.

Ribosomes can specifically shift at certain codons so that the mRNA is read in two different reading frames. To determine if frameshifting occurs at the level of termination, polymers of defined sequence containing AUG, a coding sequence and an in- or out-of-phase nonsense codon were used to bind a termination substrate or to program synthesis and release of dipeptides in a highly purified in vitro translation system. fMet-tRNA bound to ribosomes with AUGUAA, AUGUAAn, AUGUUU, AUGUUA or AUGUAn was not a substrate for release factor RF-1. In contrast, AUGU1UAA, AUGU3UAAn, AUGU4UAAn, AUGU5UAAn effected RF-1-dependent release of fMet from ribosomes. This suggests that nonsense codons can stimulate release whether they occur in- or out-of-phase. Addition of exogenous UAA and RF-1 stimulated release with all oligonucleotides tested. Propagation restricted the RF-1-dependent recognition of out-of-phase nonsense codons but did not restrict recognition of in-phase UAA in AUGU3UAAn. Release of dipeptides from ribosomes programmed with AUGU4UAAn occurred without EF-G and with a mutant lacking EF-G activity, suggesting that out-of-phase termination can occur prior to translocation outside the ribosomal A-site. We propose that the ribosome X RF complex is required to complete proteins, but is also able to frameshift at a nonsense codon resulting in occasional out-of-phase termination of protein synthesis.

Codon↗