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PubMed1979

Configuration and position encoding in children.

2 experiments were carried out to clarify the process by which children encode briefly presented spatial positions. The task in both experiments was judging whether a test dot occupied the same position on a card as any 1 of a number of dots which had been presented tachistoscopically. Subjects were first, third, and fifth graders. In the first experiment, performance improved with grade level for stimulus arrays composed of more than 1 dot. The finding contrasts with an earlier report of only minimal developmental change in position encoding, but the procedures of the earlier study appear to have permitted a confounding of position and configural encoding. In the second experiment, position encoding was found to improve with increasing pattern goodness at all age levels. The finding attests to a powerful influence of pattern information on the perceptual system and further suggests that position information is encoded within configural information.

Age Factors↗
PubMed1984

Glucagon gene sequence. Four of six exons encode separate functional domains of rat pre-proglucagon.

Glucagon, a peptide of 29 amino acids that is produced and secreted by the pancreas, is a regulator of carbohydrate and protein metabolism. Recently, we determined the nucleotide sequence of a mRNA of 1300 nucleotides that encodes rat pre-proglucagon, a polyprotein precursor of glucagon. The polyprotein contains the sequences of glucagon and two glucagon-like peptides arranged in tandem and separated by intervening peptides. Now we report the structure of the gene encoding rat pre-proglucagon. The unique transcriptional unit of the gene spans 10 kilobase pairs and consists of six exons and five introns. Four of the six exons encode distinct functional domains of the pre-proglucagon. The signal sequence, glucagon, and two glucagon-like sequences arranged in tandem are each encoded by a separate exon. A promoter sequence TA-TAAA is located 26 base pairs upstream from the mRNA cap site, and two polyadenylation signals AA-TAAA are present in the 3' untranslated region of the encoded mRNA. The 3' flanking region of the gene contains repetitive sequence DNA.

Amino Acid Sequence↗
PubMed1983

Nucleotide sequences of two pea cDNA clones encoding the small subunit of ribulose 1,5-bisphosphate carboxylase and the major chlorophyll a/b-binding thylakoid polypeptide.

Two major chloroplast proteins are encoded by nuclear genes and synthesized on free cytoplasmic ribosomes: the small subunit of ribulose 1,5-bisphosphate carboxylase and the apoprotein components of the chlorophyll a/b light harvesting complex. We have recently reported the isolation of two cDNA clones from pea which encode both the small subunit of ribulose 1,5-bisphosphate carboxylase (pSS15) and the polypeptide 15 (pAB96), the major chlorophyll a/b binding protein (Broglie, R., Bellemare, G., Bartlett, S., Chua, N.-H., and Cashmore, A. R. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 7304-7308). To further characterize these clones, we determined their nucleotide sequence. Clone pSS15 contains a 691-base pair cDNA insert which encodes the entire 123 amino acids of the mature small subunit protein. In addition, this clone also encodes 33 amino acids of the NH2-terminal transit peptide extension and 148 nucleotides of the 3' noncoding region preceding the poly(A)tail. A second cDNA clone (pAB96) contains an 833-nucleotide insert which encodes most of polypeptide 15. The DNA sequence of this cloned cDNA was used to deduce the previously undetermined amino acid sequence of this integral thylakoid membrane protein. The nucleotide sequence of the cDNA clone, pSS15, should provide information concerning the role of the transit sequence in the transport of cytoplasmically synthesized chloroplast proteins. Similarly, the deduced amino acid sequence of polypeptide 15 will provide information for predicting its orientation in thylakoid membranes as well as its role in binding chlorophyll.

Amino Acid Sequence↗
PubMed1983

Effect of encoding instructions on children's spatial and color memory: is there evidence for automaticity?

This experiment is concerned with assessing whether there is evidence for the automatic processing of spatial and color information by children and with the development of control of encoding operations. First, third, and fifth graders viewed pictures of simple objects that varied in color (red or green) and spatial location (left or right). Subjects were instructed to encode (a) only the item, (b) the item and its color, (c) the item and its position, (d) the item, its color, and its position. The data yielded evidence for nonchance incidental memory of spatial, but not color, information. The data also suggested that children at all age levels were able to control their encoding operations similarly, as there was no evidence for an interaction of development with encoding instructions. These findings are discussed with respect to a model for automatic encoding processes and work on memory for central and incidental information.

Child↗
PubMed1980

Encoding and cuing sounds and senses.

These experiments address the issue of how retrieval cues operate, and they focus on two problems of cuing research. The first concerns attempts to determine the useful limits of information residing in the cues themselves. Retrieval cues may be effective only because they provide direct information about the encoded trace or, alternatively, because they can be used to reconstruct encoded information outside of their immediate domains. The second problem concerns the nature of contextual cues appearing on the study trial and their relationship to what is encoded of spreading activation occurring on this trial. In these experiments, semantic and sensory set sizes of the target words were varied with recall cued by either the endings of the targets or by associatively related words. The targets were encoded without specific contextual cues, in the presence of associatively related context cues, or, finally, in the presence of rhyme-related context cues. The results suggest that retrieved information extends beyond the domain of features inherent in the test cue and that what is encoded in the study-trial activation is dependent on the nature of the context.

Association Learning↗
PubMed1993

Identification of an mRNA species which encodes a voltage-operated Ca2+ channel in rat liver mRNA.

cDNA which encodes part of the alpha 1-subunit of the rabbit skeletal muscle L-type voltage-operated Ca2+ channel (VOCC cDNA) was employed to search for the presence in whole liver and hepatocytes of poly (A+) RNA homologous to mRNA which encodes VOCCs. Such homologous mRNA would be a candidate for mRNA which encodes the putative hepatocyte receptor-activated Ca2+ inflow system (RACIS). Northern blot analysis showed that poly (A+) RNA prepared from intact liver tissue, but not hepatocytes, contained a poly (A+) RNA species comparable in size to that which encodes the alpha 1-subunit of the L-type VOCC. It is concluded (a) that hepatocytes do not possess VOCCs or that the levels of VOCC poly(A+) RNA in hepatocytes are too low to be detected by Northern analysis and (b) that another cell type present in liver tissue does possess a VOCC. In a low stringency screen of a rat liver cDNA library employing VOCC cDNA as a probe, seven positive cDNA clones were obtained. While regions of the 2.3 kb cDNA insert from one of these clones showed sequence similarities with regions of VOCC cDNA, the 2.3 kb sequence did not appear to encode a Ca2+ channel. The present results suggest that the approach of low stringency cDNA library screening is unlikely to allow isolation of RACIS cDNA.

Animals↗
PubMed1995

Identification of a stable RNA encoded by the H-strand of the mouse mitochondrial D-loop region and a conserved sequence motif immediately upstream of its polyadenylation site.

By using a combination of Northern blot hybridization with strand-specific DNA probes, S1 nuclease protection, and sequencing of oligo-dT-primed cDNA clones, we have identified a 0.8 kb poly(A)-containing RNA encoded by the H-strand of the mouse mitochondrial D-loop region. The 5' end of the RNA maps to nucleotide 15417, a region complementary to the start of tRNA(Pro) gene and the 3' polyadenylated end maps to nucleotide 16295 of the genome, immediately upstream of tRNA(Phe) gene. The H-strand D-loop region encoded transcripts of similar size are also detected in other vertebrate systems. In the mouse, rat, and human systems, the 3' ends of the D-loop encoded RNA are preceded by conserved sequences AAUAAA, AAUUAA, or AACUAA, that resemble the polyadenylation signal. The steady-state level of the RNA is generally low in dividing or in vitro cultured cells, and markedly higher in differentiated tissues like liver, kidney, heart, and brain. Furthermore, an over 10-fold increase in the level of this RNA is observed during the induced differentiation of C2C12 mouse myoblast cells into myotubes. These results suggest that the D-loop H-strand encoded RNA may have yet unknown biological functions. A 20 base pair DNA sequence from the 3' terminal region containing the conserved sequence motif binds to a protein from the mitochondrial extracts in a sequence-specific manner. The binding specificity of this protein is distinctly different from the previously characterized H-strand DNA termination sequence in the D-loop or the H-strand transcription terminator immediately downstream of the 16S rRNA gene. Thus, we have characterized a novel poly(A)-containing RNA encoded by the H-strand of the mitochondrial D-loop region and also identified the putative ultimate termination site for the H-strand transcription.

Adenine↗
PubMed1995

Autoantibody germ-line gene segment encodes VH and VL regions of a human anti-streptococcal monoclonal antibody recognizing streptococcal M protein and human cardiac myosin epitopes.

Cross-reactivity of anti-streptococcal Abs with human cardiac myosin may result in sequelae following group A streptococcal infections. Molecular mimicry between group A streptococcal M protein and cardiac myosin may be the basis for the immunologic cross-reactivity. In this study, a cross-reactive human anti-streptococcal/anti-myosin mAb (10.2.3) was characterized, and the myosin epitopes were recognized by the Ab identified. mAb 10.2.3 reacted with four peptides from the light meromyosin (LMM) tail fragment of human cardiac myosin, including LMM-10 (1411-1428), LMM-23 (1580-1597), LMM-27 (1632-1649), and LMM-30 (1671-1687). Only LMM-30 inhibited binding of mAb 10.2.3 to streptococcal M protein and human cardiac myosin. Human mAb 10.2.3 labeled cytoskeletal structures within rat heart cells in indirect immunofluorescence, and reacted with group A streptococci expressing various M protein serotypes, PepM5, and recombinant M protein. The nucleotide sequence of gene segments encoding the Ig heavy and light chain V region of mAb 10.2.3 was determined. The light chain V segment was encoded by a V kappa 1 gene segment that was 98.5% identical with germ-line gene humig kappa Vi5. The V segment of the heavy chain was encoded by a VH3a gene segment that differed from the VH26 germ-line gene by a single base change. VH26 is expressed preferentially in early development and encodes autoantibodies with anti-DNA and rheumatoid factor specificities. Anti-streptococcal mAb 10.2.3 is an autoantibody encoded by VH and VL genes, with little or no somatic mutation.

Amino Acid Sequence↗
PubMed1994

Comparison of three Knowledge Representation formalisms for encoding the NCEP Cholesterol Guidelines.

Although many Knowledge Representation (KR) formalisms have been used to encode care guidelines, there are few direct comparisons among different formalisms. In order to compare their suitability for encoding care guidelines, three different KR formalisms were used to encode the National Cholesterol Education Panel (NCEP) guideline. PROLOG, a First Order Logic system, CLASSIC, a frame-based representation system, and CLIPS, a production rule system, were used in the comparison. All three representations allowed accurate encoding of the guideline. PROLOG produced the most compact representation, but proved the most difficult to debug. The lack of arbitrary disjunction in CLASSIC greatly increased the complexity of the encoding. Overall, the CLIPS representation was the most intuitive and easiest to use.

Artificial Intelligence↗
PubMed1994

Identification of the cis-acting DNA sequence elements regulating the transcription of the Saccharomyces cerevisiae gene encoding TBP, the TATA box binding protein.

TBP, the TATA-box binding protein, plays a key role in eukaryotic gene transcription since it is required for transcription initiation by all three eukaryotic nuclear DNA-dependent RNA polymerases. In order to gain insight into the mechanisms of regulation of this key basal transcription factor, we undertook a mutational analysis of the sequences involved in directing transcription of the gene encoding TBP in Saccharomyces cerevisiae. An extensive family of mutations in the promoter of the gene encoding TBP were fused to the Escherichia coli reporter gene lacZ, transferred back into yeast, and assayed for their ability to direct expression of beta-galactosidase. Levels of beta-galactosidase activity measured from yeast transformed with this family of constructs indicate that both positive- and negative-acting cis-elements located within 400 nucleotides of the transcription start site are involved in regulating transcription of the TBP-encoding gene. Analyses of RNA prepared from these same cells showed that specific transcription initiation is maintained in the mutant reporter constructs and that RNA levels mirror beta-galactosidase levels. In order to corroborate the results of these mutational analyses of the TBP-encoding gene, in vivo cis-element occupancy was examined using several different footprinting reagents. The patterns of protection observed demonstrated that the sequence elements implicated in the control of TBP gene transcription by reporter gene analyses appear to be bound by protein(s) in vivo. Interesting sequence similarities were noted between two TBP-gene regulatory elements and 5'-flanking sequences of genes encoding several other basal transcription factors.

Base Sequence↗
PubMed1994

Characterization of the human gene encoding LBR, an integral protein of the nuclear envelope inner membrane.

We have characterized the human gene encoding LBR, an integral protein of the nuclear envelope inner membrane. Restriction mapping shows that the transcription unit spans approximately 35 kilobases. A transcription start site is located approximately 4 kilobases 5' to the translation initiation codon, and an RNA splice of 3863 bases occurs in the 5'-untranslated region to generate mature HeLa cell mRNA. 5' to the identified transcription start site are two CCAAT sequences and potential recognition sites for several transcription factors including Sp1, AP-1, AP-2, and NF-kB. There are 13 protein coding exons in the LBR gene. LBR's nucleoplasmic domain is encoded by exons 1-4, and its hydrophobic domain, with eight putative transmembrane segments, is encoded by exons 5-13. The hydrophobic domain is homologous to three yeast polypeptides, suggesting that this higher eukaryotic gene could have evolved from recombination between a gene that encoded a soluble nuclear protein and a membrane protein gene similar to those in yeast. These results are the first to demonstrate the structural organization of a vertebrate gene encoding an integral membrane protein of the nuclear envelope that may be a member of a family of polypeptides conserved in evolution.

Amino Acid Sequence↗
PubMed1993

DNA polymerase III accessory proteins. III. holC and holD encoding chi and psi.

Genes encoding the chi and psi accessory proteins of the DNA polymerase III holoenzyme replicase of Escherichia coli have been identified, sequenced, and used to express and purify both chi and psi in quantity. The holC gene encoding chi is located between the xerB and valS genes at 96.5 min on the chromosome; it encodes a 147-amino acid protein of 16.6 kDa. holD encoding psi lies upstream of rimI at 99.3 min and encodes a 137-amino acid protein of 15.2 kDa. The genes have been cloned into expression vectors, and both chi and psi have been purified in quantity. The accompanying report characterizes the function and physical interactions of chi and psi with other holenzyme subunits (Xiao, H., Dong, Z., and O'Donnell, M. (1993) J. Biol. Chem. 268, 11779-11784).

Amino Acid Sequence↗
PubMed1996

Staphylococcal protein A simultaneously interacts with framework region 1, complementarity-determining region 2, and framework region 3 on human VH3-encoded Igs.

Staphylococcal protein A (SPA) is a B cell superantigen that binds to human VH3-encoded Igs independently of the D- and JH-encoded regions and light chain sequences. The SPA-binding structure formed by VH3-encoded Igs remains controversial. We localized the regions in a VH3-encoded Ab required for SPA binding by producing mutant Abs in the baculovirus expression system in which regions of a human-derived Ab known to bind SPA were exchanged with those from a mouse Ab of the J558 family, a family not associated with SPA binding. The pattern of SPA binding indicates not only that residues in FR1, CDR2, and FR3 are involved but also that the three regions are required to interact simultaneously with SPA for binding to occur. When any one of the three regions was replaced with the corresponding region from the nonbinding Ab, SPA binding was severely disrupted. These data indicate that SPA requires simultaneous interaction with three distinct regions of a VH3 structure, which together in three-dimensional space form an extended solvent-exposed surface. These studies more precisely define the genetic requirements for VH3-encoded Ig binding to SPA.

Animals↗
PubMed1997

Characterization of two cDNAs encoding cysteine proteinases from the soybean cyst nematode Heterodera glycines.

Two cDNAs encoding cysteine proteinases were isolated from a cDNA library constructed from feeding females of Heterodera glycines. The library was screened with a cysteine proteinase gene fragment originally amplified from cDNA of H. glycines. Database searches predict that 1 cDNA (hgcp-I) encodes a cathepsin L-like proteinase, while the second (hgcp-II) encodes a cathepsin S-like enzyme. Both predicted proteins contain a short secretion signal sequence, a long propeptide and a mature protein of 219 amino acids. Southern blot analysis suggests that the cathepsin S-like enzyme, HGCP-II, is encoded by a single-copy gene in contrast to the cathepsin L-like proteinase, HGCP-I which may have 2 homologues. The regions encoding the mature proteinases were cloned into an expression vector and recombinant protein produced in E. coli. HGCP-I was shown, after refolding, to cleave the synthetic peptide Z-Phe-Arg-AMC, and this activity could be inhibited by the engineered rice cystatin Oc-I delta D86. HGCP-II showed no activity against the synthetic substrates tested. The knowledge gained from these studies will improve our understanding of plant nematode proteinases and aid the development of a rational proteinase inhibitor-based approach to plant nematode resistance.

Amino Acid Sequence↗
PubMed1998

Genomic alterations of the p19ARF encoding exons in T-cell acute lymphoblastic leukemia.

We have previously shown that the disruption/deletion of the MTS(MTS1-MTS2) locus due to illegitimate V(D)J recombinase activity is a genetic event characteristic of T-cell acute lymphoblastic leukemia (T-ALL). Inactivation of the p16INK4a tumor suppressor protein, encoded by MTS1, is thought to be the major functional consequence of these chromosomal rearrangements. The two other cell cycle inhibitors encoded by genes identified in the locus (p19ARF by MTS1 and p15INK4b by MTS2), also represent possible candidates for inactivating events. By analyzing p16INK4a expression in three cases in which an identical 36-kb deletion had deleted MTS2 and disrupted the p19ARF, but spared the p16INK4a MTS1 encoding exons, we have excluded p16INK4a and pinpointed p19ARF and/or p15INK4b as the functional target(s) of this rearrangement. Moreover, by the study of the MTS genomic configuration of 149 rearranged alleles from a large series of T-ALL cases, we have shown that p19ARF encoding exons were always disrupted or deleted, whereas p16INK4a and p15INK4b encoding exons were spared in four and 21 cases, respectively. These results suggest that p19ARF may be targeted by the genetic events that occur in the MTS locus in the majority of T-ALLs.

Adolescent↗
PubMed1997

Deoxyribonucleic acid vaccines encoding antigens with rapid proteasome-dependent degradation are highly efficient inducers of cytolytic T lymphocytes.

We generated plasmid expression vectors encoding ubiquitin and beta-galactosidase (beta-gal) with different intervening amino acids, allowing for the production of processed protein products that have either stabilizing or destabilizing residues at their N-termini. P815 cells transfected with plasmids encoding beta-gal with a destabilizing N-terminus did not have detectable expression beta-gal unless they were treated with inhibitors specific for the proteasome. Inhibitors of other proteolysis pathways had no such effect. Nevertheless, transfectants expressing beta-gal with different amino acid residues were equally sensitive to cytolysis by a CTL clone specific for a beta-gal peptide presented in the context of H-2Ld. In contrast to vectors encoding native beta-gal, plasmid vectors encoding beta-gal with a destabilizing residue did not induce detectable anti-beta-gal Abs when injected into skeletal muscle of BALB/c mice. However, such vectors were significantly more effective than vectors encoding native beta-gal or beta-gal with a stabilizing residue in stimulating CTL specific for P13.2, a lacZ transfectant of P815. We conclude that incorporation of strategies that enhance proteasome-dependent degradation may generate DNA vaccines that are more effective in inducing cellular immunity against targeted Ags.

Animals↗
PubMed1998

Associative encoding of pictures activates the medial temporal lobes.

It remains unresolved whether the medial temporal lobe activations found in recent neuroimaging studies are mediated by novelty detection alone, by specific kinds of encoding or consolidation operations, or both. This study attempted to see whether associative encoding or consolidation is sufficient to cause such activation by matching for novelty across conditions. Using single-photon emission computer tomography (SPECT) (with TC99mHMPAO), we compared the activation patterns produced by the associative encoding and the perceptual matching of novel complex scenes in 10 normal subjects using both statistical parametric mapping (SPM) and a regions-of-interest (ROI) approach. During the encoding condition, significant activations were detected in the left hippocampal/parahippocampal region, the left cingulate cortex, and the right prefrontal cortex, using both statistical techniques. Additionally, activation was found in the right cingulate cortex, and a trend towards activation was found in the right hippocampal/parahippocampal region using the ROI approach. In contrast, no medial temporal activations were found during the matching condition, which produced bilateral occipito-parietal and right posterior inferior parietal (supramarginal gyrus) activations. These results no only confirm that the associative encoding and/or consolidation of complex scenes is partially mediated by medial temporal lobe structures, but also demonstrate, for the first time, that associative encoding/consolidation is sufficient to produce such an activation. The implications of the high degree of consistency revealed by the results of the SPM and ROI comparison are discussed.

Adult↗
PubMed1998

Overproduction of SM28GST in a baculovirus expression vector and its use to evaluate the in vivo immune responses of mice vaccinated against Schistosoma mansoni with naked DNA encoding the SM28GST gene.

To evaluate the immune responses of mice vaccinated intramuscularly with naked DNA encoding a single parasite-derived gene, sufficient quantities of protein are necessary for use in the immunological assays. A plasmid carrying the cDNA encoding the entire sequence for the 28-kDa Schistosoma mansoni glutathione S-transferase (Sm28GST) was used as a source of naked DNA to vaccinate mice. Using polymerase chain reaction employing custom primers to add Eco RI and Hind III restriction sites at the 5' and 3' ends, respectively, a 651-bp fragment was amplified from the vaccine plasmid. This product was isolated, ligated into the pFastBac HTb donor plasmid containing a 6X histidine (6X-his) tag, and transposed into the baculovirus expression vector system. Following blue white selection screening, high molecular weight DNA was isolated and transfected in Sf21 insect ovary cells using a liposomal preparation. Culture medium containing infective virus particles was used to infect a series of Sf21 cultures and the cells were lysed after 3-5 days. The lysates were subjected to immobilized metal (Ni-NTA) affinity chromatography from which the 6X-his-tagged recombinant Sm28GST was eluted in 250 mM imidazole. The eluted protein was probed with a polyclonal rabbit antibody specific for the Sm28GST and subsequently recognized using a monoclonal antibody specific for the 6X-his tag following concentration of the pooled fractions. Mice were vaccinated intramuscularly with purified plasmid DNA encoding either the Sm28GST or firefly luciferase. Skin tests performed using recombinant Sm28GST were positive in only those mice vaccinated with naked DNA encoding the Sm28GST gene. In a different group of experimental mice, only sera from mice vaccinated with naked DNA encoding Sm28GST contained IgG-specific anti-Sm28GST antibodies at 14 days postvaccination, and at 42 days the levels were suggestive of an anamnestic response. These results suggest that naked DNA vaccination of mice is capable of inducing both antigen-specific cell-mediated and humoral immune responses against Sm28GST and further strengthen the case for this antigen being a vaccine candidate.

Animals↗