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PubMed1998

Identification of ligands for olfactory receptors by functional expression of a receptor library.

The recognition of odorants by olfactory receptors represents the first stage in odor discrimination. Here, we report the generation of an expression library containing a large and diverse repertoire of mouse olfactory receptor sequences in the transmembrane II-VII region. From this library, 80 chimeric receptors were tested against 26 odorants after transfection into HEK-293 cells. Three receptors were identified to respond to micromolecular concentrations of carvone, (-) citronellal, and limonene, respectively. We also found that the mouse I7 receptor, unlike the rat I7 receptor, prefers heptanal instead of octanal, as a result of a single valine-to-isoleucine substitution. This finding represents the beginning of a molecular understanding of odorant recognition. The identification, on a large scale, of cognate receptor-odorant interactions should provide insight into olfactory coding mechanisms.

Acetylcholine↗
PubMed2000

Fuzzy lattice neurocomputing (FLN) models.

In this work it is shown how fuzzy lattice neurocomputing (FLN) emerges as a connectionist paradigm in the framework of fuzzy lattices (FL-framework) whose advantages include the capacity to deal rigorously with: disparate types of data such as numeric and linguistic data, intervals of values, 'missing' and 'don't care' data. A novel notation for the FL-framework is introduced here in order to simplify mathematical expressions without losing content. Two concrete FLN models are presented, namely 'sigma-FLN' for competitive clustering, and 'FLN with tightest fits (FLNtf)' for supervised clustering. Learning by the sigma-FLN, is rapid as it requires a single pass through the data, whereas learning by the FLNtf, is incremental, data order independent, polynomial theta(n3), and it guarantees maximization of the degree of inclusion of an input in a learned class as explained in the text. Convenient geometric interpretations are provided. The sigma-FLN is presented here as fuzzy-ART's extension in the FL-framework such that sigma-FLN widens fuzzy-ART's domain of application to (mathematical) lattices by augmenting the scope of both of fuzzy-ART's choice (Weber) and match functions, and by enhancing fuzzy-ART's complement coding technique. The FLNtf neural model is applied to four benchmark data sets of various sizes for pattern recognition and rule extraction. The benchmark data sets in question involve jointly numeric and nominal data with 'missing' and/or 'don't care' attribute values, whereas the lattices involved include the unit-hypercube, a probability space, and a Boolean algebra. The potential of the FL-framework in computing is also delineated.

Fuzzy Logic↗
PubMed1997

From gene to screen with yeast.

With the complete sequence now available, the yeast genome project enters a post-sequencing phase that will concentrate on a comprehensive determination of gene function. Novel techniques have been developed to undertake genome-wide functional analysis at the levels of phenotype, transcript and protein. These include techniques for the efficient deletion of individual genes while tagging the deletants with specific oligonucleotide signatures, as well as strategies to quantify the physiological effects of such deletions by comparing growth rates and metabolite profiles under a range of conditions. Comprehensive approaches to the study of gene expression include hybridization array technology to identify and quantify transcripts, and the exploitation of mass spectometry to identify proteins resolved by two-dimensional gel electrophoresis. Yeast presents opportunities for the discovery of new human medicines both via the recognition of functional homologies between human and yeast genes and by the use of yeast to express human coding sequences specifying potential drug targets.

Fungal Proteins↗
PubMed2004

Structural basis of HP1/PXVXL motif peptide interactions and HP1 localisation to heterochromatin.

HP1 family proteins are adaptor molecules, containing two related chromo domains that are required for chromatin packaging and gene silencing. Here we present the structure of the chromo shadow domain from mouse HP1beta bound to a peptide containing a consensus PXVXL motif found in many HP1 binding partners. The shadow domain exhibits a novel mode of peptide recognition, where the peptide binds across the dimer interface, sandwiched in a beta-sheet between strands from each monomer. The structure allows us to predict which other shadow domains bind similar PXVXL motif-containing peptides and provides a framework for predicting the sequence specificity of the others. We show that targeting of HP1beta to heterochromatin requires shadow domain interactions with PXVXL-containing proteins in addition to chromo domain recognition of Lys-9-methylated histone H3. Interestingly, it also appears to require the simultaneous recognition of two Lys-9-methylated histone H3 molecules. This finding implies a further complexity to the histone code for regulation of chromatin structure and suggests how binding of HP1 family proteins may lead to its condensation.

Amino Acid Motifs↗
PubMed1986

tRNA anticodon replacement experiments show that ribosomal frameshifting can be caused by doublet decoding.

The expression of certain normal genes requires a specific ribosomal frameshift event because the mRNA has the coding information for one protein in two different reading frames. One of several possible mechanisms for this involves recognition of a nontriplet codon by a noncognate tRNA. The AGUC-decoding Escherichia coli tRNASer3 reads a GCA alanine codon to cause a -1 frameshift. Replacement of the anticodon of tRNAPhe with the anticodon of tRNASer3 allows the constructed tRNA to cause this frameshifting. By altering the anticodon loop nucleotides at positions 33-36 in the constructed tRNAPhe molecules, the tRNA was found to recognize a 2-base codon. Instead of the usual anticodon, positions 34-36, the nucleotides in positions 34 and 35 form essential base pairs with the first two positions of the alanine codon. The uridine in position 36 is also required but not for base pairing.

Anticodon↗
PubMed1990

Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes.

Recognition of an AUG initiator codon in a suboptimal context improves when a modest amount of secondary structure is introduced near the beginning of the protein-coding sequence. This facilitating effect depends on the position of the downstream stem-loop (hairpin) structure. The strongest facilitation is seen when the hairpin is separated from the preceding AUG codon by 14 nucleotides. Because 14 nucleotides corresponds to the approximate distance between the leading edge of the ribosome and its AUG-recognition center as measured by ribonuclease protection experiments, a likely explanation for the enhancing effect of a downstream hairpin is that secondary structure slows scanning, thereby providing more time for recognition of the AUG codon, and the facilitation is greatest when the 40S ribosome stalls with its AUG-recognition center directly over the AUG. The variable ability of mammalian ribosomes to initiate at non-AUG codons in vitro is also explicable by the presence or absence of a stem-loop structure just downstream from the alternative initiator codon. This may be relevant to recent reports of adventitious upstream initiation events at non-AUG codons in some vertebrate mRNAs that have structure-prone, G + C-rich leader sequences.

Animals↗
PubMed1986

spoIID operon of Bacillus subtilis: cloning and sequence.

The locus spoIID, involved in the sporulation of Bacillus subtilis, was cloned into derivatives of the temperate phage phi 105. Two recombinant phages were obtained which contain chromosomal DNA covering 1.6 kbp. They are both able to complement mutations spo-68 and spo-298. These mutations, which were believed to be in different loci, spoIID and spoIIC respectively, were shown to be closely linked, and both map at the position assigned to spoIID on the genetic map of B. subtilis. The sequence of 1656 bp carrying the spoIID locus was determined. Only one open reading frame was found; this codes for a protein of 343 amino acids. It is preceded by a ribosome binding site and possible recognition sequences for sigma 32- and sigma 29-RNA polymerases. Studies of the locus by means of integrational plasmid vectors defined the outer limits of the transcriptional unit. These results are completely compatible with the sequence data. The combination of sequence and mapping and the information obtained by the use of integrational plasmids confirm that the spoIID locus functions as a monocistronic operon.

Bacillus subtilis↗
PubMed1998

Lectin ligands: new insights into their conformations and their dynamic behavior and the discovery of conformer selection by lectins.

The mysteries of the functions of complex glycoconjugates have enthralled scientists over decades. Theoretical considerations have ascribed an enormous capacity to store information to oligosaccharides. In the interplay with lectins sugar-code words of complex carbohydrate structures can be deciphered. To capitalize on knowledge about this type of molecular recognition for rational marker/drug design, the intimate details of the recognition process must be delineated. To this aim the required approach is garnered from several fields, profiting from advances primarily in X-ray crystallography, nuclear magnetic resonance spectroscopy and computational calculations encompassing molecular mechanics, molecular dynamics and homology modeling. Collectively considered, the results force us to jettison the preconception of a rigid ligand structure. On the contrary, a carbohydrate ligand may move rather freely between two or even more low-energy positions, affording the basis for conformer selection by a lectin. By an exemplary illustration of the interdisciplinary approach including up-to-date refinements in carbohydrate modeling it is underscored why this combination is considered to show promise of fostering innovative strategies in rational marker/drug design.

Crystallography↗
PubMed1977

Teaching psychotherapy by use of brief typescripts.

A typescript of a 10-minute segment of a taped therapeutic interview, coded by using a modification of the Gottshalk scales, quite clearly demonstrates the patient's current focal conflict. Recognition of the current focal conflict is thus taught, and this is used as an organizing principle in supervision of psychotherapy.

Conflict, Psychological↗
PubMed2002

Olfactory fingerprints for major histocompatibility complex-determined body odors II: relationship among odor maps, genetics, odor composition, and behavior.

The olfactory system detects small differences in the composition of natural odorants, made up of hundreds of molecules. Odorous quality is hypothetically represented by a combinatorial code: activation of distinct but overlapping subsets of olfactory receptors resulting in activation of a distinct subset of glomeruli in the main olfactory bulb (MOB). Here we show that modification of a single gene (the K gene of the major histocompatibility locus), which results in a subtle change in the odiferous quality of urine, causes a small but significant change in the composition of urine volatiles and consequently the evoked glomerular activation pattern in the MOB. The magnitude of disparity between urine-evoked glomerular activation patterns is predictive of the extent of (1) the genetic difference among the urine donors, (2) the difference in the chemical composition of urine, and (3) the odor detector's ability to discriminate. These data on natural odors are consistent with the combinatorial code hypothesis and identify subsets of glomeruli that are apt to play a significant role in mediating individual recognition.

Animals↗
PubMed2004

Intraspecific nucleotide variation in Anopheles gambiae: new insights into the biology of malaria vectors.

The Anopheles gambiae genome sequence, together with the recent development of molecular tools for genome-wide analysis, promises new insights into the biology of the malaria vector. These insights should help define the best possible breakdown point for interrupting transmission in the mosquito vector. A survey of the intraspecific nucleotide diversity in coding regions of three different mosquito strains showed an average of one single nucleotide polymorphism (SNP) every 125 coding base pairs. High levels of nucleotide polymorphism were observed in mosquito immune-related genes and pathogen recognition receptors harbored higher replacement substitutions. Genotyping at SNP loci in natural populations of An. gambiae from three malaria foci showed contrasting patterns. The distribution of mutation Y443H in the thioester-containing protein 3 (TEP3) gene suggested this mutational event has occurred under selective constraints. Our results show that SNP-based studies will be valuable in identifying the sequence variation associated with phenotypic traits shaping vector competence.

Animals↗
PubMed1987

From Jenner to genes--the next generation of virus vaccines.

Vaccination has played a major role in the control of many virus diseases affecting man and animals. Two kinds of vaccines are in use: (i) attenuated vaccines, which infect the host without causing disease and (ii) killed vaccines, which consist of large amounts of virus particles that have been inactivated by either physical or chemical agents under conditions that ensure retention of their antigenic properties. Despite the success of vaccination there is still a need for products that are safer and more effective. Even more important, there are diseases for which 'conventional' vaccines are not available. New approaches that will ultimately solve these problems have been provided by the detailed analysis of viruses at the molecular level. Thus we are now beginning to understand virulence in molecular terms and particularly rapid advances have been made with poliovirus, holding out the promise of a completely avirulent attenuated vaccine. With killed vaccines, the major advance has come from the recognition that the immune response to most viruses is determined by a single protein. By identifying the genes coding for these proteins it has become possible to express them in large quantities not only in a variety of cells, but also in virus vectors that can be grown in vitro and in vivo. Moreover, in some instances, fragments of immunogenic proteins, small enough to be synthesized chemically, have been shown to be protective. The rapid pace of these conceptual and technological advances leads the author to the expectation that viruses and antigens that are defined in precise chemical terms will form the basis of the vaccines of the future.

Animals↗
PubMed1979

A code for reporting and comparing results in phage typing.

This code, like the others proposed, involves the definition of a characteristic reaction for each system. Each reaction must be positive or negative. As regards the interpretation of results, it is worth noting that if the bacteriophage typing system uses not less than 5 phages, there is no problem for interpreting the results of small series of 10 to 20 strains, whatever the code used. But should the system use more than 5 phages, the advantage offered by the octal code becomes obvious because, without computer, the manual coding for comparing the results of various series is always possible. Beyond 6 phages, the binary pattern reporting, unintelligible without correction, is possible with an octal number not exceeding 7 digits for a pattern corresponding to a 21-phage set. When very large series of strains are considered, the coding can be completely done and printed out by any computer through a very simple program. This proposed code is not only rational but also a useful method even if the number of phages used is larger than 20 or 30, but after a computer becomes necessary however the coding system used.

Bacteriophage Typing↗
PubMed1982

Two distinct allotypic determinants on the antigen-specific suppressor and enhancing T cell factors that are encoded by genes linked to the immunoglobulin heavy chain locus.

The alloantiserum was raised in BALB/c (H-2d, Igh-1a) mice hyperimmunized with spleen cells of Igh allotype congenic mice, CB-20 (H-2d, Igh-1b). It was found to define the new allotypic determinants (distinct from B cell Igh constant region determinants: Igh allotype) expressed only on a small population of T cells belonging to the Thy-1 dull-stained Lyt-2- or Lyt-2+ population of Igh-1b mice. Genes coding for the determinants were shown to be accommodated somewhere in the right side of the Igh variable region gene (Igh-V) cluster, as the antibody activity was completely absorbed with BAB-14 thymocytes. It was also demonstrated that the products detected by the antiserum represent the allotypic determinants (probably constant region determinants) on the antigen-binding moiety of the antigen-specific augmenting (TaF) and suppressor (TsF) T cell factors. Moreover, determinants on TsF were found to be distinct from those on TaF. Therefore, it can be suggested that the two genes coding for the T cell allodeterminants (distinct from those of the B cell Igh) are located in the right side of the B cell Igh-V on the 12th chromosome, and that both encode the antigen-recognition units of the functionally distinct T cell factors.

Animals↗
PubMed1999

[Cloning and expression of tyrosinase gene from Pseudomonas maltophilia in E. coli].

The enzyme tyrosinase, encoded by tyrosinase gene (mel), is responsible for melanin formation. In a shotgun cloning experiment, a SalI-digested DNA fragment coding for tyrosinase was cloned from Pseudomonas maltophilia DNA into plasmid vector (pUC18) to generate the hybrid plasmid (pWSY). The recombinant plasmid imparted the ability of melanin synthesis to an E. coli host (HB101). The foreign DNA fragment (0.7 kb) possessed no recognition sites for BamHI, HindIII, EcoRI or BclI. Hybridization studies confirmed that the small fragment cloned in pWSY was from P. maltophilia DNA. Nucleotide sequence analysis identified an ORF of 504 nt coding tyrosinase. SDS-PAGE analysis also revealed an additional protein of 18 kDa, which was equal to the putative tyrosinase according to the size of mel fragment, was expressed in the E. coli recombinant carrying the plasmid pWSY.

Amino Acid Sequence↗
PubMed1999

Speed of face recognition in humans: an event-related potentials study.

Event-related potentials (ERPs) were measured while subjects passively looked at a line drawing of a normal face or a line drawing in which parts of the face were scattered so as not to be recognized as a face (scattered face) in order to estimate the speed of face recognition in humans. Because the spatial frequencies of these two types of line drawings were very similar, one could minimize the potentials due to the structure coding stage of the face processing. In addition, passive viewing of these stimuli eliminates the contribution of other processing such as discrimination or memory retrieval. Comparing these two conditions, statistically significant positive potentials were observed in frontal areas from 135ms after stimulus onset for the normal face. These early positive differences were probably due to the face processing per se in human visual recognition. Although statistically significant differences were observed in frontal areas, these are probably related to fusiform or inferior temporal area activation that is often reported using neuro-imaging technologies such as PET or fMRI.

Adult↗