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At least 667 records · Page 37Linked to original sources
PubMed1996

Influences of intentionality at encoding and retrieval on memory in adulthood and old age.

This research investigated whether different memory functions are differentially affected by the adult aging process. Four groups of normal adults (18-35, 60-68, 69-78, and 79-91 years of age) were presented with a set of pictures of faces with first names and surnames. Subjects were instructed to memorize the faces and the surnames for subsequent memory tests. Memory performance was assessed in four ways: stem completion of surnames; recognition of faces; recognition of surnames and recognition of first names. These memory tests varied in terms of intentionality at encoding and retrieval. The stem completion task involved intention at encoding, but not at retrieval, and thus served as a measure of implicit memory. With respect to the three explicit memory tasks, recognition of faces and surnames involved intention at both encoding and retrieval, whereas recognition of first names involved intention at retrieval, but not at encoding. Results indicated no age-related differences in implicit memory, as assessed by the stem completion test. In addition, there was an age-related deficit in recognition of faces and surnames, although there were no age-related differences in recognition of first names. The overall pattern of results suggests that age-related deficits in memory may be most likely to occur when there are demands of conscious mental activity at encoding and retrieval.

Adolescent↗
PubMed1997

The representational capacity of the distributed encoding of information provided by populations of neurons in primate temporal visual cortex.

It has been shown that it is possible to read, from the firing rates of just a small population of neurons, the code that is used in the macaque temporal lobe visual cortex to distinguish between different faces being looked at. To analyse the information provided by populations of single neurons in the primate temporal cortical visual areas, the responses of a population of 14 neurons to 20 visual stimuli were analysed in a macaque performing a visual fixation task. The population of neurons analysed responded primarily to faces, and the stimuli utilised were all human and monkey faces. Each neuron had its own response profile to the different members of the stimulus set. The mean response of each neuron to each stimulus in the set was calculated from a fraction of the ten trials of data available for every stimulus. From the remaining data, it was possible to calculate, for any population response vector, the relative likelihoods that it had been elicited by each of the stimuli in the set. By comparison with the stimuli actually shown, the mean percentage correct identification was computed and also the mean information about the stimuli, in bits, that the population of neurons carried on a single trial. When the decoding algorithm used for this calculation approximated an optimal, Bayesian estimate of the relative likelihoods, the percentage correct increased from 14% correct (chance was 5% correct) with one neuron to 67% with 14 neurons. The information conveyed by the population of neurons increased approximately linearly from 0.33 bits with one neuron to 2.77 bits with 14 neurons. This leads to the important conclusion that the number of stimuli that can be encoded by a population of neurons in this part of the visual system increases approximately exponentially as the number of cells in the sample increases (in that the log of the number of stimuli increases almost linearly). This is in contrast to a local encoding scheme (of "grandmother" cells), in which the number of stimuli encoded increases linearly with the number of cells in the sample. Thus one of the potentially important properties of distributed representations, an exponential increase in the number of stimuli that can be represented, has been demonstrated in the brain with this population of neurons. When the algorithm used for estimating stimulus likelihood was as simple as could be easily implemented by neurons receiving the population's output (based on just the dot product between the population response vector and each mean response vector), it was still found that the 14-neuron population produced 66% correct guesses and conveyed 2.30 bits of information, or 83% of the information that could be extracted with the nearly optimal procedure. It was also shown that, although there was some redundancy in the representation (with each neuron contributing to the information carried by the whole population 60% of the information it carried alone, rather than 100%), this is due to the fact that the number of stimuli in the set was limited (it was 20). The data are consistent with minimal redundancy for sufficiently large and diverse sets of stimuli. The implication for brain connectivity of the distributed encoding scheme, which was demonstrated here in the case of faces, is that a neuron can receive a great deal of information about what is encoded by a large population of neurons if it is able to receive its inputs from a random subset of these neurons, even of limited numbers (e.g. hundreds).

Algorithms↗
PubMed2000

CLN-encoded proteins do not interact with each other.

The lysosomal storage of lipofuscins is the common pathological feature that characterizes the infantile, late-infantile, juvenile (Batten's disease), and Finnish-variant neuronal ceroid lipofuscinosis (INCL, LINCL, JNCL and FNCL), which are due to mutations in the genes CLN1, CLN2, CLN3, and CLN5, respectively. The CLN1 and CLN2 genes encode lysosomal enzymes, but the CLN3 and CLN5 genes encode membrane-spanning proteins. Why deficiencies of lysosomal enzymes and membrane-spanning proteins produce similar clinical phenotypes and pathological changes is still unanswered. We hypothesize that CLN-encoded proteins may comprise a functional pathogenic pathway, in which protein associations may play important roles. To test this hypothesis, we studied protein-protein interactions among the CLN1-, CLN2-, and CLN3-encoded proteins using a yeast two-hybrid system. Our results provided no evidence that CLN-encoded proteins interact with each other. This suggests there may be unidentified components in NCL pathogenesis.

Chromosome Mapping↗
PubMed2006

Precuneus is involved in allocentric spatial location encoding and recognition.

Using a declarative memory paradigm, the anatomical correlates of spatial location encoding and retrieval in the healthy human brain as reflected by BOLD fMRI were investigated. During encoding, subjects were instructed to view and keep in mind different locations of an object on a platform seen from different viewpoints in virtual 3D. In retrieval trials, subjects had to recognize previously learned object locations. Comparing activation patterns associated with encoding and recognition on a voxel-by-voxel basis, we found regions in the precuneus bilaterally activated by both processes. To our knowledge, this is the first study that directly compared human brain activation patterns associated with allocentric encoding and retrieval of spatial locations in virtual 3D. Our results provide further information concerning the role of the precuneus in declarative memory processes, pointing to precuneus involvement in encoding and retrieval of spatial locations.

Adult↗
PubMed1999

Neuronal correlates of encoding and retrieval in episodic memory during a paired-word association learning task: a functional magnetic resonance imaging study.

The investigation of memory function using functional magnetic resonance imaging (fMRI) is an expanding field of research. The aim of this study was to demonstrate brain-activity patterns related to a word-pair association task employing a whole-brain EPI sequence. Six right-handed, healthy male volunteers (mean age: 27.5 years) took part in the study. fMRI was performed at a field strength of 1. 5 Tesla with 26-32 slices parallel to the AC-PC line, depending on individual brain size. Distributed brain regions were activated in episodic encoding and retrieval with similarities, but also (distinct) differences in activation patterns. Bilateral prefrontal cortical areas were involved when comparing encoding as well as retrieval to the reference condition (nonsense words). Furthermore, activation was observed in cerebellar areas during encoding, and activation in bilateral parietal areas (precuneus and inferior parietal cortex) was differentially more pronounced during retrieval. The activation of left dorsomedial thalamus during retrieval of high imagery-content word-pair associates may point to the role of this structure in episodic retrieval. The direct cognitive subtraction of encoding minus retrieval yielded a differentially larger left prefrontal activation. There was a differentially higher right prefrontal activation during retrieval than during encoding, underlining the proposed right/left asymmetry for episodic memory processes.

Adult↗
PubMed2001

Molecular chaperones encoded by a reduced nucleus: the cryptomonad nucleomorph.

Molecular chaperones mediate the correct folding of nascent or denatured proteins and are found in both the organelles and cytoplasm of eukaryotic cells. Cryptomonad algae are unusual in possessing an extra cytoplasmic compartment (the periplastid space), the result of having engulfed and retained a photosynthetic eukaryote. Within the periplastid space is a diminutive nucleus (the nucleomorph) that encodes mostly genes for its own expression as well as a few needed by the plastid. Two plastid-encoded chaperones (GroEL and DnaK) and a nucleomorph-encoded chaperone (Cpn60) have been reported from the cryptomonad, Guillardia theta. Here we analyse G. theta nucleomorph genes for members of the cytosolic HSP70 and HSP90 families of molecular chaperones, a heat shock transcription factor (HSF), and all eight subunits of the group II chaperonin, CCT. These are presumably all active in the periplastid space, assisting in the maturation of polypeptides required by the cell; we propose a central role for them also in the structure and assembly of a putative relict mitotic apparatus. Curiously, none of the genes for co-chaperones of HSP70, HSP90, or CCT have been detected in the nucleomorph genome; they are either not needed or are encoded in the host nuclear genome and targeted back into the periplastid space. Endoplasmic reticulum (ER) homologs of HSP70 and HSP90 are also not present. Striking differences in the degree of conservation of the various nucleomorph-encoded molecular chaperones were observed. While the G. theta HSP70 and HSP90 homologs are well conserved, each of the eight CCT subunits (alpha, beta, gamma, delta, epsilon, eta, theta, and zeta) is remarkably divergent. Such differences are likely evidence for reduced/different functional constraints on the various molecular chaperones functioning in the periplastid space.

Amino Acid Motifs↗
PubMed2006

Plasmid DNA vaccine encoding prostatic acid phosphatase is effective in eliciting autologous antigen-specific CD8+ T cells.

Prostatic acid phosphatase (PAP) is a prostate cancer tumor antigen and a prostate-specific protein shared by rats and humans. Previous studies indicated that Copenhagen rats immunized with a recombinant vaccinia virus expressing human PAP (hPAP) developed PAP-specific cytotoxic T cells (CTL) with cross reactivity to rat PAP (rPAP) and evidence of prostate inflammation. Viral delivery of vaccine antigens is an active area of clinical investigation. However, a potential difficulty with viral-based immunizations is that immune responses elicited to the viral vector might limit the possibility of multiple immunizations. In this paper, we investigate the ability of another genetic immunization method, a DNA vaccine encoding PAP, to elicit antigen-specific CD8+ T cell immune responses. Specifically, Lewis rats were immunized with either a plasmid DNA-based (pTVG-HP) or vaccinia-based (VV-HP) vaccine each encoding hPAP. We determined that rats immunized with a DNA vaccine encoding hPAP developed a Th1-biased immune response as indicated by proliferating PAP-specific CD4+ and CD8+ cells and IFNgamma production. Rats immunized with vaccinia virus encoding PAP did not develop a PAP-specific response unless boosted with a heterologous vaccination scheme. Most importantly, multiple immunizations with a DNA vaccine encoding the rat PAP homologue (pTVG-RP) could overcome peripheral self-tolerance against rPAP and generate a Th1-biased antigen-specific CD4+ and CD8+ T cell response. Overall, DNA vaccines provide a safe and effective method of generating prostate antigen-specific T cell responses. These findings support the investigation of PAP-specific DNA vaccines in human clinical trials.

Acid Phosphatase↗
PubMed1997

Molecular characterization of the clusters of genes encoding the botulinum neurotoxin complex in clostridium botulinum (Clostridium argentinense) type G and nonproteolytic Clostridium botulinum type B.

The cluster of genes encoding components of the progenitor botulinum neurotoxin complex has been mapped and cloned in Clostridium botulinum type G strain ATCC 27322. Determination of the nucleotide sequence of the region has revealed open reading frames encoding nontoxic components of the complex, upstream of the gene encoding BoNT/G (botG). The arrangement of these genes differs from that in strains of other antigenic toxin types. Immediately upstream of botG lies a gene encoding a protein of 1198 amino acids, which shows homology with the nontoxic-nonhemagglutinin (NTNH) component of the progenitor complex. Further upstream there are genes encoding proteins with homology to hemagglutinin components (HA-17, HA-70) and a putative positive regulator of gene expression (P-21). Sequence comparison has shown that BoNT/G has highest homology with BoNT/B. The sequence of the BoNT-cluster of genes in non-proteolytic C. botulinum type B strain Eklund 17B has been extended to include the complete NTNH and HA-17, and partial HA-70 gene sequences. Comparison of NTNH/G with other NTNHs reveals that it shows highest homology with NTNH/B consistent with the genealogical affinity shown between BoNT/G and BoNT/B genes.

Amino Acid Sequence↗
PubMed1998

Characterization of the genes encoding the botulinum neurotoxin complex in a strain of Clostridium botulinum producing type B and F neurotoxins.

The organization of the clusters of genes encoding proteins of the botulinum neurotoxin (BoNT) progenitor complex was elucidated in a strain of Clostridium botulinum producing type B and F neurotoxins. With PCR and sequencing strategies, the type B BoNT-gene cluster was found to be composed of genes encoding BoNT/B, nontoxic nonhemagglutinin component (NTNH), P-21, and the hemagglutinins HA-33, HA-17, and HA-70, whereas the type F BoNT-gene cluster has genes encoding BoNT/F, NTNH, P-47, and P-21. Comparative sequence analysis showed that BoNT/F in type BF strain 3281 shares highest homology with BoNT/F of non-proteolytic (group II) C. botulinum whereas NTNH and P-21 in the type F cluster of strain 3281 are more similar to the corresponding proteins in proteolytic (group I) type F C. botulinum. These findings indicate diverse evolutionary origins for genes encoding BoNT/F and its associated non-toxic proteins, although the genes are contiguous. By contrast, sequence comparisons indicate that genes encoding BoNT/B and associated non-toxic proteins in strain 3281 possess a similar evolutionary origin. It was demonstrated that the genes present in the BoNT/B gene cluster of this type BF strain show exceptionally high homology with the equivalent genes in the silent BoNT/B gene cluster of C. botulinum type A(B), possibly indicating their common ancestry.

Base Sequence↗
PubMed2004

A mitochondrial plasmid and plasmid-like RNA and DNA polymerases encoded within the mitochondrial genome of carrot (Daucus carota L.).

The mitochondrial genome of mitochondrial type (mitotype) SW3 of carrot (Daucus carota L.) encodes intact reading frames for a RNA polymerase (Rpo) and a DNA polymerase (Dpo) similar to those encoded by linear mitochondrial plasmids from plants. A BLAST search of translated nucleotide sequences in GenBank revealed previously unreported plasmid-like Rpo or Dpo sequence fragments in many plant mitochondrial DNAs. Phylogenetic analyses of the relationships between mitochondrial (mt)DNA-encoded and plasmid-encoded Rpos and Dpos from plants suggest that the mitochondrial sequences were derived from integrated plant plasmid sequences. A linear mitochondrial plasmid was detected in a different mitotype (FG21) of carrot by Southern hybridization of the Rpo and Dpo to undigested mtDNAs. Transcripts of the mtDNA-encoded Rpo and Dpo in mitotype SW3 were detected by RT-PCR.

Amino Acid Sequence↗
PubMed1996

Occurrence of nuclear-encoded tRNAIle in mitochondria of the liverwort Marchantia polymorpha.

Although 29 tRNA genes have been deduced from the complete nucleotide sequence of the mitochondrial genome from the liverwort Marchantia polymorpha, a tRNAIle gene decoding AUU and AUC codons is conspicuously absent. In order to address the question of the possible involvement of nuclear-encoded tRNA, we isolated and identified three variant copies of the nuclear-encoded tRNAIle(AAU) gene from the liverwort. Northern analysis showed the presence of nuclear-encoded tRNAIle both in the mitochondrion and the cytosol, while both chloroplast DNA-encoded tRNAIle and nuclear-encoded tRNATyr were absent in liverwort mitochondria. These results unequivocally establish that import of nuclear tRNAIle into mitochondria indeed occurs in one of the most primitive plants, M. polymorpha.

Base Sequence↗
PubMed2000

Mater encodes a maternal protein in mice with a leucine-rich repeat domain homologous to porcine ribonuclease inhibitor.

MATER (Maternal Antigen That Embryos Require) is an ooplasm-specific protein first identified as an antigen (OP1) associated with ovarian autoimmunity in mice. Its primary structure has been deduced from full-length cDNA that encodes a 125-kDa protein required for progression of the mouse embryo beyond two cells. Expression of the gene encoding MATER is restricted to the oocyte, which makes it one of a growing, but still limited, number of maternal-effect genes in mammals. To further investigate the function of MATER during oogenesis and early development, we have characterized the gene and resultant protein. Mater is a single-copy gene in the genome of 129/Sv mice and is located at the proximal end of Chromosome (Chr) 7. The gene, spanning approximately 32 kbp, contains 15 exons ranging in size from 48 to 1576 bp, which together encode the 111 amino acid MATER protein. The first five exons encode 26-27 amino acid hydrophilic repeats and exons 8-14 encode 14 leucine-rich repeats. The three-dimensional structure of the latter domain can be closely modeled on the previously determined X-ray crystallographic coordinates of porcine ribonuclease inhibitor. These characterizations of the gene and protein provide the basis for genetic investigations of MATER function in early mammalian development.

Amino Acid Sequence↗
PubMed2002

Free recall and organization as a function of varying relational encoding in action memory.

A new approach was taken to study the question whether the free recall advantage of enacting actions (SPT), over only listening to their verbal descriptions (VT), is due to better relational encoding of SPTs than of VTs. The approach consisted of studying related lists and manipulating the degree of relational encoding by repeated list presentation in Experiment 1 and by presenting the list items at random or blocked in Experiment 2. In both experiments, free recall and adjusted ratio of clustering (ARC) scores increased as to be expected with repeated list presentation and blocking. However, these effects proved to be independent of the type of encoding. There was a clear SPT effect in free recall, but in contrast a slight though nonsignificant advantage of VTs over SPTs in ARC scores. Altogether, the experiments show that the SPT effect in free recall is not due to better relational encoding in SPTs than in VTs, in line with the assumption that this effect is due to good item-specific encoding.

Adult↗
PubMed2005

Characterisation of the Aspergillus niger dapB gene, which encodes a novel fungal type IV dipeptidyl aminopeptidase.

We have cloned the Aspergillus niger dapB gene. Analysis of its nucleotide sequence and the corresponding protein sequence indicates that the gene encodes a type IV dipeptidyl aminopeptidase (DPP IV). Based upon its deduced sequence we predict the presence of a transmembrane domain in the protein. Furthermore, dapB-overexpressing transformants display an increase in intracellular DPP IV activity. This is the first reported characterisation of a dipeptidyl aminopeptidase with a transmembrane domain from a filamentous fungus. Using the dapB sequence as a query, we were able to identify 14 DPP IV-encoding genes, and 12 additional DPPIV proteases in public genomic databases. Phylogenetic analysis reveals that in yeasts there are two clades of genes that encode DPP IV proteases with a transmembrane domain. In this study we demonstrate that, as in yeasts, two classes of DPP IV-encoding genes exist in filamentous fungi. However, only one of these codes for DPP IV proteases with a transmembrane domain. The second type present in filamentous fungi encodes extracellular DPP IV proteases. The dapB gene belongs to the first cluster. We propose that DapB plays a role in the proteolytic maturation of enzymes produced by A. niger.

Aspergillus niger↗
PubMed1997

Southern analysis of BT-R1, the Manduca sexta gene encoding the receptor for the Cry1Ab toxin of Bacillus thuringiensis.

Various subspecies of the gram-positive bacterium Bacillus thuringiensis are known to produce a wide array of insecticidal crystal proteins (ICPs) upon sporulation. These ICPs act primarily on the brush border of midgut epithelial cells of susceptible larvae. Recently, a protein of 210 kDa, isolated from the midgut of Manduca sexta, has been demonstrated to bind the Cry1Ab toxin produced by B. thuringiensis subsp, berliner and is therefore postulated to be involved in mediating the toxicity of Cry1Ab. The cDNA encoding the 210 kDa protein, termed BT-R1 (Bacillus thuringiensis receptor-1), was recently cloned, and shows limited homology to the cadherin superfamily of proteins. Quite naturally, there is a great deal of interest in the characterization of BT-R1, the gene encoding the 210 kDa Cry1Ab binding protein. The studies presented here involve the use of various restriction fragments prepared from the cDNA encoding BT-R1 as probes of Southern blots bearing M. sexta genomic DNA cleaved with a variety of restriction endonucleases. These Southern blot data reveal that there are two discrete regions within the M. sexta genome which encode sequences homologous to BT-R1. On the basis of the signal intensities seen on Southern blots, it appears that only one of these genes encodes BT-R1, whereas the other is a closely related homologue.

Animals↗
PubMed2001

The Aspergillus niger cypA gene encodes a cyclophilin that mediates sensitivity to the immunosuppressant cyclosporin A.

Here we report the cloning and characterization of a gene, cypA, from Aspergillus niger that encodes a peptidyl prolyl cis-trans isomerase (PPIase) belonging to the cyclophilin family. Sequencing of both genomic and cDNA clones revealed two ORFs in cypA, one encoding a 19-kDa protein of 174 amino acid residues and the other a 24-kDa protein of 219 amino acid residues, with overall identities of 27-77% to the homologous cyclophilins from prokaryotic and eukaryotic organisms. Expression of the 19-kDa CYPA-(His)(6) in E. coli shows that the purified protein has PPIase activity which is inhibited by cyclosporin A. Northern analysis shows two specific cypA transcripts, the smaller transcript encodes the cytosolic 19-kDa CYPA protein, the larger transcript encodes the putative mitochondrial 24 kDa CYPA protein. The transcript for the cytosolic CYPA is expressed at a higher basal level than that for the mitochondrial protein. The presence of tunicamycin, DTT or cyclosporin A in the medium does not affect the expression level of cypA. Its expression is however slightly induced by heat shock. Growing A. niger mycelium in the presence of cyclosporin A leads to an increase in hyphal branching prior to growth arrest. Overexpression of cypA under the control of its own promoter in A. niger results in increased sensitivity to cyclosporin A, suggesting that cypA encodes the cellular target for cyclosporin A in A. niger.

Amino Acid Sequence↗
PubMed2000

Identification of a novel 23kDa protein encoded by putative open reading frame 2 of TT virus (TTV) genotype 1 different from the other genotypes.

We report the entire open reading frames (ORFs) sequences of four TT virus (TTV) isolates, one genotype 2 (G2) and three G4 isolates. Despite a DNA virus, TTV possesses high rate of amino acid (aa) substitution: the aa sequence homology of ORF1 and 2 is lower than the nucleotide homology. The partial 'N22' region of ORF1 is suitable for genotyping of 'prototype TTV' isolates, because the phylogenetic tree from partial 'N22' sequence is consistent with that from the entire ORF1. Based on our sequence data, ORF2 from most isolates excluding G1 encode truncated 49 aa (pORF2a) because of an in-frame stop codon, although ORF2s from most G1 isolates encode 202 aa (pORF2ab). Just downstream the stop codon, another ORF encoding a protein of approximately 150 aa (pORF2b) is found, whose homology is quite low among these genotypes. Our in vitro transcription/translation study supports that all G1a and a part of G b without an in-frame stop codon dominantly encode pORF2ab, a novel 23 kDa protein, whereas the other genotypes with an in-frame stop codon encode pORF2b (17 kDa). Our data indicate TTV G1a and a part of G1b should have different characteristics from the other genotypes.

Amino Acid Sequence↗
PubMed2003

Stimulus-dependent translocation of egg-laying hormone encoding mRNA into the axonal compartment of the neuroendocrine caudodorsal cells.

To get insight into the stimulus-dependent translocation of mRNA encoding neuropeptides to the axonal compartment of neurons, we investigated this process in the egg-laying hormone producing caudodorsal cells of the mollusk Lymnaea stagnalis. The axonal compartment including the nerve terminals of these neurons harbors high amounts of mRNA encoding the egg-laying hormone precursor. We determined how a sensory stimulus, that results in egg-laying, affected the amount of egg-laying hormone encoding transcripts in the axon endings. Four hours after stimulation high amounts of transcripts were detected in the axonal compartment and maximum values were reached after 8 h. Transcript levels in the somata were affected in a similar fashion, although the increase was not as pronounced as in the axons. Next, we investigated the ultrastructural localization of egg-laying hormone encoding transcripts in axons and axon terminals by means of electron microscopic in situ hybridization and showed that transcripts were localized in the axoplasm. By means of conventional electron microscopy we showed that axon terminals of egg-laying hormone producing neurons contained large amounts of polyribosomes. Together, these data support the notion that egg-laying hormone encoding transcripts are translated in the axonal compartment.

Animals↗