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PubMed1991

Characterization of the human MDR3 P-glycoprotein and its recognition by P-glycoprotein-specific monoclonal antibodies.

We have cloned a human MDR3 complementary DNA, coding for a P-glycoprotein, into a mammalian expression vector and cotransfected it with a selectable marker into drug-sensitive human BRO melanoma cells. With low frequency we obtained stable, MDR3-expressing clones. Immunocytochemical and immunoblotting analysis of these clones using the monoclonal antibody C219 indicated that human MDR3 P-glycoprotein, like human MDR1 P-glycoprotein, was mainly localized in the plasma membrane and probably glycosylated. Although a significant fraction of the cells (5-10%) in one of the MDR3-expressing clones expressed as much P-glycoprotein as a clearly drug-resistant MDR1-transfected clone, we found no resistance against a range of drugs affected by multidrug resistance. The drugs tested included vincristine, colchicine, VP16-213, daunorubicin, doxorubicin, actinomycin D, and gramicidin D. We did not detect enhanced daunorubicin efflux either in any of the MDR3-expressing cells by fluorescence microscopy. Direct selection with vincristine, actinomycin D, gramicidin D, or daunorubicin of BRO cells transfected with expression constructs containing the regular MDR3 complementary DNA, or a complementary DNA representing a major MDR3 splice variant (C(-141)), likewise failed to yield resistant clones. Thus, although human MDR3 P-glycoprotein is highly similar to human MDR1 P-glycoprotein, we found no indications that it can transport drugs. We investigated the cross-reactivity of the monoclonal antibodies C219, C494, JSB-1, HYB-241, and MRK16, recognizing human MDR1 P-glycoprotein, with human MDR3 P-glycoprotein using immunocytochemistry and immunoblotting. Apart from monoclonal antibody C219, none of the monoclonal antibodies showed detectable cross-reactivity with human MDR3 P-glycoprotein. In our hands, monoclonal antibodies MRK16 and HYB-241 were most suitable for sensitive and specific cytochemical detection of human MDR1 P-glycoprotein.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2001

Attractor networks for shape recognition.

We describe a system of thousands of binary perceptrons with coarse-oriented edges as input that is able to recognize shapes, even in a context with hundreds of classes. The perceptrons have randomized feedforward connections from the input layer and form a recurrent network among themselves. Each class is represented by a prelearned attractor (serving as an associative hook) in the recurrent net corresponding to a randomly selected subpopulation of the perceptrons. In training, first the attractor of the correct class is activated among the perceptrons; then the visual stimulus is presented at the input layer. The feedforward connections are modified using field-dependent Hebbian learning with positive synapses, which we show to be stable with respect to large variations in feature statistics and coding levels and allows the use of the same threshold on all perceptrons. Recognition is based on only the visual stimuli. These activate the recurrent network, which is then driven by the dynamics to a sustained attractor state, concentrated in the correct class subset and providing a form of working memory. We believe this architecture is more transparent than standard feedforward two-layer networks and has stronger biological analogies.

Animals↗

PubMed2002

Phoneme recognition and confusions with multichannel cochlear implants: consonants.

The aim of this study was to investigate how postlingually severely or profoundly hearing-impaired adults relearn to recognize consonants after receiving multichannel cochlear implants. Consonant recognition of 19 Finnish-speaking subjects was studied for a minimum of 6 months and a maximum of 24 months using an open-set nonsense-syllable test in a prospective repeated-measure design. Responses were coded for phoneme errors, and proportions of correct responses and 95% confidence intervals were calculated for recognition and confusions. Two years after the switch-on, the mean recognition of consonants was 71% (95% confidence interval = 68-73%). The manner of articulation was easier to classify than the place of articulation, and the consonants [s], [r], [k], [t], [p], [n], and [j] were easier to recognize than [h], [m], [l], and [v]. Adaptation to electrical hearing with a multichannel cochlear implant was successful, but consonants with alveolar, palatal, or velar transitions (high F2) were better recognized than consonants with labial transitions (low F2). The locus of the F2 transitions of the consonants with better recognition was at the frequencies 1.5-2 kHz, whereas the locus of the F2 transitions of the consonants with poorer recognition was at 1.2-1.4 kHz. A tendency to confuse consonants with the closest consonant with higher F2 transition was also noted.

Acoustic Stimulation↗

PubMed2001

Splicing of constitutive upstream introns is essential for the recognition of intra-exonic suboptimal splice sites in the thrombopoietin gene.

The human thrombopoietin (TPO) gene, which codes for the principal cytokine involved in platelet maturation, shows a peculiar alternative splicing of its last exon, where an intra-exonic 116 nt alternative intron is spliced out in a fraction of its mRNA. To characterize the molecular mechanism underlying this alternative splicing, minigenes of TPO genomic constructs with variable exon-intron configurations or carrying exclusively the TPO cDNA were generated and transiently transfected in the Hep3B cell line. We have found that the final rate of the alternative intron splicing is determined by three elements: the presence of upstream constitutive introns, the suboptimal splice sites of the alternative intron and the length of the alternative intron itself. Our results indicate that the recognition of suboptimal intra-exonic splice junctions in the TPO gene is influenced by the assembly of the spliceosome complex on constitutive introns and by a qualitative scanning of the sequence by the transcriptional/splicing machinery complex primed by upstream splicing signals.

Alternative Splicing↗

PubMed2000

Race as a visual feature: using visual search and perceptual discrimination tasks to understand face categories and the cross-race recognition deficit.

One of the most familiar empirical phenomena associated with face recognition is the cross-race (CR) recognition deficit whereby people have difficulty recognizing members of a race different from their own. Most researchers assume that the CR deficit is caused by failure to generalize perceptual encoding expertise from same-race (SR) faces to CR faces. However, this explanation ignores critical differences in the social cognitions and feature coding priorities associated with SR and CR faces. On the basis of data from visual search and perceptual discrimination tasks, it appears that the deficit occurs because people emphasize visual information specifying race at the expense of individuating information when recognizing CR faces. In particular, it is possible to observe a paradoxical improvement in both detection and perceptual discrimination accuracy for CR faces that is limited to those who recognize them poorly. These findings support a new explanation for the CR recognition deficit based on feature coding differences between CR and SR faces, and appear incompatible with similarity-based models of face categories.

Adult↗

PubMed1985

Recognition sequences of restriction endonucleases and methylases--a review.

The properties and sources of all known endonucleases and methylases acting site-specifically on DNA are listed. The enzymes are crossindexed (Table I), classified according to homologies within their recognition sequences (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the DNA of the bacteriophages lambda, phi X174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328 and the microorganisms from which they originate. Other tabulated properties of the restriction endonucleases include relaxed specificities (Table III), the structure of the restriction fragment ends (Table IV), and the sensitivity to different kinds of DNA methylation (Table V). Table VI classifies the methylases according to the nature of the methylated base(s) within their recognition sequences. This table also comprises those restriction endonucleases, which are known to be inhibited by the modified nucleotides. Furthermore, this review includes a restriction map of bacteriophage lambda DNA based on sequence data. Table VII lists the exact nucleotide positions of the cleavage sites, the length of the generated fragments ordered according to size, and the effects of the Escherichia coli dam- and dcmI-coded methylases M X Eco dam and M X Eco dcmI on the particular recognition sites.

Base Sequence↗

PubMed1983

Gödel's arithmetization procedure as the basis for a pattern recognition system: a nascent theory mapping pattern into number and number into phenomenal experience.

Prime numbers are used to code various dimensions of an input matrix (receptor surface), i.e., prime numbers code the position of each cell in the matrix, the position of each column and row constituted by the cells of the matrix, and the orientation of each such column or row. The coding permits any pattern or stimulus configuration to be changed into a single, unique number, viz., the serial product of the prime numbers which code the relevant dimensions of the pattern. Storage of a pattern is effected by storage of the serial product. By factoring the serial product, the pattern or stimulus configuration is analyzed into the dimensions (features) specified by the code. The factorization is also utilized in abstracting a schema, in approximating a feature count model, and in presenting a strategy for holistic vs sequential pattern processing. Finally, the relationship between the serial product representing a pattern and the phenomenal experience of a pattern is explored.

Computers↗

PubMed1992

Face recognition.

The study of face-selective neurons in the monkey temporal lobe, and face recognition deficits in humans after brain damage have both become very active fields of investigation. Face-selective neurons appear to be members of ensembles for coding faces rather than individual face detectors or grandmother cells. They reflect the more general role of temporal cortex in pattern recognition. In humans there are a variety of face-processing impairments that result from damage to different areas, and which reflect interference at different levels of processing of the facial image.

Animals↗

PubMed1993

Structure and metabolic control of the Yarrowia lipolytica peroxisomal 3-oxoacyl-CoA-thiolase gene.

Using a Yarrowia lipolytica genomic library, several overlapping clones of the peroxisomal 3-oxoacyl-CoA-thiolase gene, POT1, were isolated. The library was prepared in the bacterial expression vector lambda gt11, thus allowing an immunological screening of recombinant bacteriophages with specific antibodies raised against purified peroxisomal thiolase. The isolated POT1 clones hybridized to a 1.4 kb RNA species, which was induced approximately 30-fold when oleate was the carbon source. A 3634-bp segment of the cloned DNA was sequenced. This segment contained, on both strands, three major overlapping open-reading frames of 678, 1122 and 1242 bp. Northern-hybridization analysis showed that only the largest of these reading frames was transcribed. It encodes a protein of 414 amino acids and molecular mass 43.059 kDa. Its deduced amino acid sequence has 30-60% identity and 50-70% sequence similarity when compared to other known thiolases. According to both the amount (68-71%) and location of conserved amino acids, the encoded protein belongs to the peroxisomal rather than the mitochondrial or cytoplasmic class of thiolases. Compared to bacterial and yeast cytosolic thiolases, the POT1 gene product contains a N-terminal extension of 25 amino acids which clearly differs from typical mitochondrial import signals. One of the isolated clones contained, in addition to the POT1 coding sequence, 784 bp of the corresponding 5' flanking region. Nevertheless, it was efficiently expressed in Escherichia coli suggesting the correct recognition of this fungal promoter by the prokaryotic transcriptional and translational machinery. The Y. lipolytica genomic POT1 gene was disrupted by replacing 120 bp of its coding sequence with 2.7 kbp of DNA including the Y. lipolytica LEU2 gene. The resulting delta pot1::LEU2 cells were free of immunologically cross-reacting thiolase. Western-blot analysis showed that the product of the non-disrupted gene had a molecular mass of approximately 42 kDa. This corresponds well to the molecular mass of purified Y. lipolytica peroxisomal thiolase. Disruption of POT1 abolished the ability of Y. lipolytica cells to grow on solid media with oleate as a carbon source. This inability to grow in the presence of oleate suggests both the catabolic function of POT1 and the absence of additional catabolic thiolases in Y. lipolytica. However, the delta pot1::LEU2 cells were unaffected in their ability to elongate externally added tridecanoic acid to its higher-chain-length homologues. Hence, another, POT1-independent and biosynthetic 3-oxoacyl-CoA thiolase must be responsible for this reaction in Y. lipolytica.

Acetyl-CoA C-Acyltransferase↗

PubMed1995

[Two types of facial impression judgments and recognition memory for faces].

The author investigated the semantic processing advantage effect on facial recognition memory using two types of personality traits and two types of recognition tests. In Experiment 1, based on the personality impression ratings for smiling and neutral faces made by 40 subjects, four expression-independent (i.e., intelligent, reliable, determined, and ambitious) and four expression-dependent (i.e. extroverted, friendly, affectionate, and likeable) personality trait words were selected. In Experiment 2, two groups of 22 subjects (expression-dependent trait group and expression-independent trait group) were asked to rate 32 faces in terms of physical features or personality traits. This was followed by an unexpected yes-no recognition test in which identical pictures of the target faces or the same person's expression-changed faces were randomly presented with distractor faces. In identical-picture recognition condition, the semantic processing advantage emerged in both expression-dependent and expression-independent trait groups, whereas in expression-changed recognition condition the advantage appeared only in expression-independent trait group. It was discussed that the semantic-codes explanation would be plausible to explain the results obtained.

Adult↗

PubMed1987

Alloreactivity of an OVA-specific T-cell clone. I. Stimulation by class II MHC and novel non-MHC B-cell determinants.

A T-cell clone (Ly1-03) derived from BALB/cBy mice, though highly specific for OVA/Ad, reacted to allogeneic spleen cells of 6 of 12 H-2 haplotypes tested. The reactivity to each particular H-2 haplotype required the expression of a non-major histocompatibility complex (MHC) gene product present on the B cells of certain strains of mice. All the alloreactive responses were MHC restricted and were inhibited by class II-specific and L3T4-specific monoclonal antibodies. The non-MHC gene product, X, is a new lymphocyte-stimulating determinant that is not expressed in mice with the xid defect. We favor a model that proposes two independent sites (or receptors) for X and the class II molecule. Contrary to previous models for alloreactivity, the anti-MHC site is not directed to a polymorphic receptor for self-class II epitope on the foreign class II molecule, but rather to a conserved determinant present on both self- and allo-class II molecules. If there is only one antigen receptor on the T-cell clone Ly1-03, then anti-X receptor must bind to a cross-reactive determinant found on immunogenic OVA and the non-MHC coded gene product expressed on the cell surface membrane. We further postulate that class II plus "X" recognition may be a general rule for alloreactive as well as autoreactive responses. Thus, both allo-class II and allo-class I reactive T cells are similar in that both bind a non-MHC coded gene product prior to activation.

Animals↗

PubMed1997

A method of independent time and frequency decomposition of bioacoustic signals: inter-individual recognition in four species of penguins.

The aim of this paper is to introduce a method for analyzing acoustic signals capable of assessing the potential for individual coding information. Signals are analysed both in the time domain (rhythm of emission of the song independent of its frequency content) and in the spectral domain (spectral content of the song independent of the rhythm of emission). The method is then applied to a comparative study of four penguin species, where the problem posed by inter-individual recognition differs from species to species. A direct relationship was shown between the potential of individual coding and the difficulty in partner identification.

Acoustic Stimulation↗

PubMed1987

In vivo identification of multiple promoter domains of adenovirus EIIA-late promoter.

The transcriptional control elements of the Adenovirus (Ad) type 5 EIIA-late (L) promoter were analyzed in the context of the viral chromosome. Promoter mutants constructed in vitro [deletion and linker-scanning (LS)] were re-introduced into the non-essential EIII region of an Ad5 variant which lacked the EIA gene. They were then analyzed in human 293 cells for EIA-dependent and in HeLa cells for EIA-independent transcription. These studies revealed that a minimum of approximately 157 bp upstream from the Cap site are sufficient for the efficient transcription of this promoter in the presence or absence of the EIA gene products. Within the 157-bp sequence, multiple control elements can be identified. These are (i) a sequence block between -55 and -21 which contained a sequence resembling the TATA box and an Sp1 recognition site 5'-TGGGCGTGGT-3', (ii) a sequence block between -84 and -67 which contained a second Sp1 recognition sequence, 5'-CGGGCGGGAT-3' and a 5'-CCAAT-3' box in the non-coding strand and (iii) a 56-bp sequence block between -157 and -101 which contained a 5'-CCAAT-3' sequence in the non-coding strand. The transcriptional pattern of the LS mutants in 293 cells was very similar to that of HeLa cells suggesting that neither of the EIA gene products interact with EIIA-L promoter directly to modulate transcription. A purified Sp1 protein protected DNA sequences from -56 to -33 which includes the Sp1 recognition sequence closer to the cap site whereas the distal Sp1 recognition sequence showed a very weak affinity for the Sp1 factor.(ABSTRACT TRUNCATED AT 250 WORDS)

Adenovirus Early Proteins↗

PubMed1997

Species-specific tRNA recognition in relation to tRNA synthetase contact residues.

In spite of variations in the sequences of tRNAs, the genetic code (anticodon trinucleotides) is conserved in evolution. However, non-anticodon nucleotides which are species specific are known to prevent a given tRNA from functioning in all organisms. Conversely, species-specific tRNA contact residues in synthetases should also prevent cross-species acylation in a predictable way. To address this question, we investigated the relatively small tyrosine tRNA synthetase where contacts of Escherichia coli tRNA(Tyr) with the alpha2 dimeric protein have been localized by others to four specific sequence clusters on the three-dimensional structure of the Bacillus stearothermophilus enzyme. We used specific functional tests with a previously not-sequenced and not-characterized Mycobacterium tuberculosis enzyme and showed that it demonstrates species-specific aminoacylation in vivo and in vitro. The specificity observed fits exactly with the presence of the clusters characteristic of those established as important for recognition of E. coli tRNA. Conversely, we noted that a recent analysis of the tyrosine enzyme from the eukaryote pathogen Pneumocystis carinii showed just the opposite species specificity of tRNA recognition. According to our alignments, the sequences of the clusters diverge substantially from those seen with the M. tuberculosis, B. stearothermophilus and other enzymes. Thus, the presence or absence of species-specific residues in tRNA synthetases correlates in both directions with cross-species aminoacylation phenotypes, without reference to the associated tRNA sequences. We suggest that this kind of analysis can identify those synthetase-tRNA covariations which are needed to preserve the genetic code. These co-variations might be exploited to develop novel antibiotics against pathogens such as M. tuberculosis and P. carinii.

Acylation↗

PubMed1992

Cognitive ergonomics of a mail order filling company: Part 2--influence of shelf coding and address information on acquisition time.

This is the second part of a study on a mail order picking task. In the first part of the study, recognition time was addressed by varying colour, position and highlighting cues in a computer-simulated version of the picking task. This study addresses the product acquisition time. Shelf coding and continuous presentation of the address information were varied in a factorial experiment in which 14 subjects (seven experts and seven novices) had participated. Experts were slower but more accurate than the novices. Continuous display of address information appears to be a good training aid for implementing new shelf coding systems, and for new operators. Shelf coding effect appears to disappear with practice. A summary of the recommendations is given.

Journal Article↗

PubMed1992

Structure of a gene encoding heat-shock protein HSP70 from the unicellular alga Chlamydomonas reinhardtii.

The structure of a gene encoding a 70-kDa heat-shock protein (HSP70) from the unicellular alga, Chlamydomonas reinhardtii, is described. This gene shows a remarkable expression pattern, because it is inducible by light as well as by elevated temperature [von Gromoff et al., Mol. Cell. Biol. 9 (1989) 3911-3918]. As a first step in the investigation of trans-acting factors involved in environmentally controlled expression of this hsp70 gene, the nucleotide sequence of the entire gene, including its 5'- and 3'-flanking regions was determined. Although the deduced amino acid sequence exhibits a high degree of conservation to the HSP70 from higher plants, the C. reinhardtii gene has a unique structure among the members of the hsp70 gene family. While most hsp70 genes have only one or no intron, the coding region of the C. reinhardtii gene is interrupted by six introns. Besides putative TATA and CCAAT boxes, two heat-shock elements (HSE) were found in the promoter region, and a third HSE motif was located within the fourth intron. A computer search for regulatory cis-acting elements revealed a noted similarity of a 5'-upstream sequence motif to the G-box motif conserved in higher plants. A polyadenylation recognition sequence canonical for nuclear genes of C. reinhardtii is located downstream from the coding sequence.

Amino Acid Sequence↗

PubMed2000

Penguins use the two-voice system to recognize each other.

The sound-producing structure in birds is the syrinx, which is usually a two-part organ located at the junction of the bronchi. As each branch of the syrinx produces sound independently, many birds have two acoustic sources. Thirty years ago, we had anatomical, physiological and acoustical evidence of this two-voice phenomenon but no function was known. In songbirds, often these two voices with their respective harmonics are not activated simultaneously but they are obvious in large penguins and generate a beat pattern which varies between individuals. The emperor penguin breeds during the Antarctic winter, incubating and carrying its egg on its feet. Without the topographical cue of a nest, birds identify each other only by vocal means when switching duties during incubation or chick rearing. To test whether the two-voice system contains the identity code, we played back the modified call of their mate to both adults and also the modified call of their parents to chicks. Both the adults and the chicks replied to controls (two voices) but not to modified signals (one voice being experimentally suppressed). Our experiments demonstrate that the beat generated by the interaction of these two fundamental frequencies conveys information about individual identity and also propagates well through obstacles, being robust to sound degradation through the medium of bodies in a penguin colony. The two-voice structure is also clear in the call of other birds such as the king penguin, another non-nesting species, but not in the 14 other nesting penguins. We concluded that the two-voice phenomenon functions as an individual recognition system in species using few if any landmarks to meet. In penguins, this coding process, increasing the call complexity and resisting sound degradation, has evolved in parallel with the loss of territoriality.

Animals↗

PubMed1997

A strategy of tRNA recognition that includes determinants of RNA structure.

Recognition of tRNAs by aminoacyl tRNA synthetases establishes the connection between amino acids and anticodon triplets of the genetic code. Although anticodons and nucleotides adjacent to the amino acid attachment site are generally important, the tertiary structural framework of tRNAs has recently been implicated to have a role in tRNA recognition. A G15:G48 tertiary hydrogen base pair of E. coli tRNA(Cys) is important for recognition of the tRNA by cysteine tRNA synthetase. This base pair is proposed to consist of N2:N3, rather than N1:O6, hydrogen bonds. The reproduction of the hydrogen pairing scheme of tRNA(Gly). This reproduction required an A13:A22 mismatch in the dihyrouridine stem. To determine if A13:A22 is a determinant of the structural features of G15:G48, we investigated the A15:U48 and A15:A48 variants of tRNA(Gly) which harbored specific substitutions of A13:A22. We show here that introduction of A13:A22 to both tRNA frameworks confers structural features similar to those of G15:G48 in E. coli tRNA(Cys). These structural features are accompanied by efficient recognition of both tRNAs by cysteine tRNA synthetase. Substitution of A13:A22 with U13:A22 alters the structural features at 15:48 and impairs tRNA recognition. The dependence on A13:22 for tRNA recognition has a distinct similarity to that of E. coli tRNA(Cys) and to that of the G15:G48 variant of tRNA(Gly). The results have implications for the design and manipulation of RNA structural elements as the basis for tRNA recognition.

Acetylation↗