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PubMed2006

A study of relative-position priming with superset primes.

Four lexical decision experiments are reported that use the masked priming paradigm to study the role of letter position information in orthographic processing. In Experiments 1 and 2, superset primes, formed by repetition of 1 or 2 letters of the target (e.g., jusstice-JUSTICE) or by insertion of 1 or 2 unrelated letters (e.g., juastice-JUSTICE), generated significant priming compared with unrelated primes and did not differ significantly from an identity priming condition. In Experiment 3, identity primes generated significantly faster responses than subset primes formed by removal of 2 letters from the target (e.g., jutie-JUSTICE), and subset primes generated faster responses than substitution primes formed by substitution of 2 letters of the target with unrelated letters (e.g., jumlice-JUSTICE). In Experiment 4, insertion of 3 unrelated letters continued to generate facilitation relative to unrelated primes but significantly less so than the identity prime condition. The authors discuss the implications of these results for letter-position coding schemes.

Analysis of Variance↗
PubMed1983

Favored patterns in spike trains. II. Application.

In this paper we apply the two methods described in the companion paper (4) to experimentally recorded spike trains from two preparations, the crayfish claw and the cat striate cortex. Neurons in the crayfish claw control system produced favored patterns in 23 of 30 spike trains under a variety of experimental conditions. Favored patterns generally consisted of 3-7 spikes and were found to be in excess by both quantized and template methods. Spike trains from area 17 of the lightly anesthetized cat showed favored patterns in 16 of 27 cases (in quantized form). Some patterns were also found to be favored in template form; these were not as abundant in the cat data as in the crayfish data. Most firing of the cat neurons occurred at times near stimulation, and the observed patterns may represent stimulus information. Favored patterns generally contained up to 7 spikes. No obvious correlations between identified neurons or experimental conditions and the generation of favored patterns were apparent from these data in either preparation. This work adds to the existing evidence that pattern codes are available for use by the nervous system. The potential biological significance of pattern codes is discussed.

Action Potentials↗
PubMed1992

Effect of memory set-size upon event related potentials for concrete and abstract kanji stimuli.

Event related potentials (ERP) and reaction times (RT) were recorded during the performance of memory-retrieval tasks using the Japanese kanji characters. P300 latency and RT increased as the memory set-size increased. The slope differences between RT and P300 latency were larger for stimuli when concrete kanji were used than when abstract kanji were used. This suggests that, in memory search, the 20 subjects were likely to employ direct lexical access when processing concrete kanji and likely to use phonetic coding when processing abstract kanji.

Arousal↗
PubMed1999

Judgments of perceptual groups: reliability and sensitivity to stimulus transformation.

The reliability of subjects' judgments of the groups present in dot patterns and the sensitivity of those judgments to stimulus transformation were assessed. The subjects indicated the groups that they saw within random dot patterns, and each judgment was compared with those of other subjects and with their own judgments for related presentations. Within subjects, each pattern appeared in an initial presentation, an identical repetition, and a transformed state (a rotation or a change in scale). Within-subjects judgments were more reliable than between-subjects judgments. An interpretation of within-subjects results was made in relation to predictions made by a formal algorithm of grouping by proximity (the CODE algorithm), which assumes that grouping by proximity is invariant over transformations such as rotations or changes in scale. A slight cost to transforming the patterns was found. The implications for CODE and for using grouping judgments as data are discussed.

Humans↗
PubMed1989

Color correspondence in apparent motion.

To maintain figural identity during motion perception, the visual system must match images over space and time. Correct matching requires a metric for identifying "corresponding" images, those representing the same physical object. To test whether matching is based on achromatic (black/white) polarity and chromatic (red/green) color, observers viewed an ambiguous motion display and judged the path of apparent motion. Matching preserved black/white identity regardless of whether frames were viewed binocularly or dichoptically. Red/green identity was also preserved, but coherence of motion depended in part on the number of frames in the motion sequence and on the background luminance. These results suggest that correspondence is computed by a weighted metric containing terms for image features coded early in visual processing.

Color Perception↗
PubMed2002

The DBY gene codes for an HLA-DQ5-restricted human male-specific minor histocompatibility antigen involved in graft-versus-host disease.

Graft rejection or graft-versus-host (GVH) disease after HLA-identical stem cell transplantation is the result of recognition of minor histocompatibility antigens (mHags) by immunocompetent T lymphocytes from recipient or donor origin, respectively. Cytolytic T lymphocyte (CTL) clones can be isolated during graft rejection and GVH disease to identify mHags and their corresponding genes. Thus far, all human mHags identified appeared to be HLA class I-restricted. Here, we report the characterization of the first human HLA class II-restricted sex-linked mHag involved in GVH disease. Previously, we isolated an HLA-DQ5-restricted CD4(+) CTL clone from a male patient with chronic myeloid leukemia who developed acute GVH disease grade III-IV after transplantation of HLA genotypically identical female stem cells. Using a panel of female HLA-DQ5(+) EBV cells that we stably transfected with Y chromosome-specific genes, we determined that the HLA class II male-specific mHag (H-Y) was encoded by the Y chromosome-specific gene DBY. The H-Y epitope was localized in the DBY protein using female HLA-DQ5(+) peripheral blood mononuclear cells loaded with DBY protein fragments. The minimal peptide sequence leading to maximal recognition by the specific HLA-DQ5-restricted CTL clone was characterized as the 12-amino acid sequence HIENFSDIDMGE. Although the epitope differed by 3 amino acids from its X-homolog DBX, only 2 polymorphisms were shown to be essential for recognition by the CTL clone.

Amino Acid Sequence↗
PubMed2004

MISAE: a new approach for regulatory motif extraction.

The recognition of regulatory motifs of co-regulated genes is essential for understanding the regulatory mechanisms. However, the automatic extraction of regulatory motifs from a given data set of the upstream non-coding DNA sequences of a family of co-regulated genes is difficult because regulatory motifs are often subtle and inexact. This problem is further complicated by the corruption of the data sets. In this paper, a new approach called Mismatch-allowed Probabilistic Suffix Tree Motif Extraction (MISAE) is proposed. It combines the mismatch-allowed probabilistic suffix tree that is a probabilistic model and local prediction for the extraction of regulatory motifs. The proposed approach is tested on 15 co-regulated gene families and compares favorably with other state-of-the-art approaches. Moreover, MISAE performs well on "corrupted" data sets. It is able to extract the motif from a "corrupted" data set with less than one fourth of the sequences containing the real motif.

Algorithms↗
PubMed1994

A V beta 8.2-specific superantigen from exogenous mouse mammary tumor virus carried by FM mice.

A number of endogenous mouse mammary tumor virus (MMTV) proviruses encode superantigen that have the ability to stimulate T cells with a certain T cell receptor (TCR) beta-chain variable region (V beta) and to mediate the V beta-specific clonal deletion. The tumorigenic milk-borne MMTV carried by C3H and GR mice also have superantigenic properties in vivo. In the present study we identified and characterized a novel V beta 8.2-specific superantigen of exogenous MMTV carried by FM mice. The open reading frame (ORF) in the 3' long terminal repeat of the MMTV was cloned by polymerase chain reaction with primers corresponding to conserved regions spanning the ORF coding region. Sequence analysis of the ORF revealed that there is no sequence identical to those in other known MMTV in the carboxy terminus implicated in TCR V beta recognition. Subcutaneous injection of the virus into adult BALB/c mice induced an approximately three- to fourfold enlargement of draining lymph nodes and a substantial increase of V beta 8.2+ CD4+ T cells in the lymph nodes within 6 days. The exposure of newborn BALB/c mice to the virus by foster nursing resulted in a marked deletion of V beta 8.2+ cells both in CD4+ and CD8+ T cells. Thus, a novel milk-borne MMTV in FM mice expresses strong superantigenic properties capable of stimulating V beta 8.2+ T cells. V beta 8.2+ T cells have been demonstrated to be frequently involved in recognition of conventional antigens and responsible for autoimmune diseases such as experimental allergic encephalomyelitis. Therefore, the MMTV (FM) may provide a new mouse model system for inducing immunodeficiency or autoimmune disease by retroviral infection.

Amino Acid Sequence↗
PubMed1992

Allele-specific expression of the cytoplasmic exon of HLA-DQB1 gene.

The beta chain of the HLA-DQ molecule is shorter by eight amino acid residues than other major histocompatibility complex class II beta chains due to elimination of the fifth exon coding for part of the cytoplasmic domain. This elimination is caused by one base substitution in the splice acceptor site of the exon. We found that two HLA-DQB1 alleles, DQB1*0503 and DQB1*0601, did not have this substitution, and the exon was utilized in these two alleles. However, two forms of HLA-DQB mRNA, with or without exon 5, were generated in Epstein-Barr virus-transformed cell lines homozygous for DQB1*0503 or DQB1*0601, indicating alternative mRNA splicing. The alternative splicing of DQB1*0601 mRNA was also found in peripheral blood lymphocytes and L cell transfectants. To investigate the functional relevance of the allele-specific long cytoplasmic tail of HLA-DQ beta chain, we developed three types of L cell transfectants expressing exclusively the HLA-DQw6 molecules with short cytoplasmic tail, long cytoplasmic tail, or both forms of the beta chain, and used them as antigen presenting cells for streptococcal cell wall antigen-specific T cell lines. These three types of transfectants could function almost equally well as antigen presenting cells. It was thus demonstrated that both forms of HLA-DQ beta chain, with or without eight amino acid residues coded for by the exon 5, can be associated with the HLA-DQ alpha chain, be expressed on the cell surface, and function as restriction molecules in antigen recognition by the CD4+ T cells.

Alleles↗
PubMed1992

An accurate method for determining the helical repeat of DNA in solution reveals differences to the crystal structures of two B-DNA decamers.

Many DNA sequences have been studied by X-ray crystallography with the goal of deciphering a sequence-structure code. We have determined the helical repeats of two B-type DNA decamers in solution employing an electrophoretic method based on phasing of bent segments. The decamers contain recognition sites for the dcm methyltransferase and for the restriction nuclease NarI with a mutational hotspot. Their helical repeats are 10.59(+/- 0.05) bp and 10.52(+/- 0.03) bp, respectively, whereas crystallographic analysis yielded 10.0 bp in the solid state. This difference is greater than that for the transition between B- and A-type DNA in solution. Thus, reliable information about the polymorphism of DNA in solution must be based on both X-ray and solution data. We describe a generally applicable approach to accurately determine helical repeats of small DNA duplexes in solution.

Base Sequence↗
PubMed2005

Genetic and functional subdivision of the Drosophila antennal lobe.

Olfactory systems confer the recognition and discrimination of a large number of structurally distinct odor molecules. Recent molecular analysis of odorant receptor (OR) genes and circuits has led to a model of odor coding in which a population of olfactory sensory neurons (OSNs) expressing a single OR converges upon a unique olfactory glomerulus. Activation of the OR can thus be read out by the activation of its cognate glomerulus. Drosophila is a powerful system in which to test this model because the entire repertoire of 62 ORs can be manipulated genetically. However, a complete understanding of how fly olfactory circuits are organized is lacking. Here, we present a nearly complete map of OR projections from OSNs to the antennal lobe (AL) in the fly brain. Four populations of OSNs coexpress two ORs along with Or83b, and a fifth expresses one OR and one gustatory receptor (GR) along with Or83b. One glomerulus receives coconvergent input from two separate populations of OSNs. Three ORs label sexually dimorphic glomeruli implicated in sexual courtship and are thus candidate Drosophila pheromone receptors. This olfactory sensory map provides an experimental framework for relating ORs to glomeruli and ultimately behavior.

Animals↗
PubMed2006

A novel method to detect functional microRNA targets.

MicroRNA (miRNA) molecules are non-coding RNAs, 19 to 24 nt in length that have been identified recently as important regulators of gene expression. Several computational methods have been developed to describe the target recognition mechanism by miRNA. We propose here a novel method to detect miRNA-mRNA complexes in eukaryotic cells. As a first step, we synthesize cDNA on an mRNA template using miRNAs as the endogenous cytoplasmic primer. This step extends miRNA and overcomes the problem of low complementary binding of miRNAs to their targets. Purified hybrid 3'-cDNA-miRNA-5' molecules are used in a second round of reverse transcription to anneal to target mRNA in a highly gene-specific manner. The 5'-end analysis of these cDNA molecules demonstrated that primers for cDNAs were "signatures" of miRNA molecules, and over-expression of their full-length mature miRNAs resulted in functional inhibition of target protein expression.

Base Sequence↗
PubMed1998

Molecular cloning of a bombinin gene from Bombina orientalis: detection of NF-kappaB and NF-IL6 binding sites in its promoter.

The sequence of a gene from Bombina orientalis was determined which codes for antibacterial peptides. The gene comprises two exons separated by a large intron. Exon 1 codes for the signal peptide, while exon 2 contains the genetic information for two identical bombinins and one bombinin H. The promoter region of the bombinin gene contains putative recognition sites for nuclear factors, such as NFkappaB and NF-IL6. In vivo experiments on B. orientalis have shown that a short contact with bacteria is sufficient to induce a marked increase in the amount of antibacterial peptides in the skin secretion of frogs. This increase was suppressed by pretreatment with glucocorticoids. In the latter case, a significant increase of I kappaB alpha in the secretion is also detectable.

Aeromonas↗
PubMed2000

Sequence of a gene from Bombina orientalis coding for the antimicrobial peptide BLP-7.

The structure of a gene coding for bombinin-like peptides (BLP) in Bombina orientalis was determined. It comprises two exons separated by a 1337 bp intron. Exon 1 codes for the signal peptide, while exon 2 contains the genetic information for BLP-7 and a bombinin H-type peptide (GH-2). The promoter region contains putative recognition sites for nuclear factors, such as NF-IL6 and NF-kappaB. The analysis of the structure of this gene, compared with that of the previously reported BLP-3 gene sequence, suggests the occurrence of a gene duplication event, rather than an alternative splicing mechanism, which leads to the generation of both inter- and intra-families variability in this class of cytolytic peptides. Furthermore, chromosome walking analysis indicates that this gene family is not densely clustered.

Amino Acid Sequence↗
PubMed2003

Efficient inhibition of beta-secretase gene expression in HEK293 cells by tRNAVal-driven and CTE-helicase associated hammerhead ribozymes.

The beta-amyloid peptide (Abeta) is a major component of toxic amyloid plaques found in the brains of patients with Alzheimer's disease. Abeta is liberated by sequential cleavage of amyloid precursor protein (APP) by beta- and gamma-secretases. The level of Abeta depends directly on the hydrolytic activity of beta-secretase. Therefore, beta-secretase is an excellent target for drug design. An approach based on RNA-cleaving ribozymes was developed to control expression of beta-secretase. Two sites of mRNA coding beta-site APP cleaving enzyme were chosen as target sequences for endogenously delivered ribozymes. The ribozyme cassette was designed to constitute a catalytic hammerhead core and substrate recognition arms, flanked at the 5'-terminus by tRNAVal and at the 3'-terminus by constitutive transport element sequences. Ribozyme cassettes were cloned into a pUC19 plasmid and used for transient transfection of HEK293 cells. We demonstrate that such ribozymes efficiently inhibit beta-secretase gene expression at both the mRNA (up to 95%) and the protein (up to 90%) levels. Inhibition of beta-site APP cleaving enzyme activity directly influences the intra- and extracellular population of Abeta peptide. Therefore, such ribozymes may be considered as molecular tools for silencing the beta-secretase activity, and further, as therapeutic agents for anti-amyloid treatment.

Amyloid beta-Peptides↗
PubMed2001

Regulation of c-maf gene expression by Pax6 in cultured cells.

c-Maf is a bZip transcription factor expressed in developmental and cellular differentiation processes. Recently, a c-maf knockout mouse model, showing abnormal lens development, has been reported. In order to study the regulation mechanisms of c-maf gene expression during the differentiation process we have cloned and functionally characterized the rat c-maf (maf-2) gene. The rat c-maf gene is an intronless gene, covering a length of 3.5 kb. Transient transfection analysis of the 5'-flanking region of the c-maf gene using luciferase as the reporter gene shows that Pax6, a master transcription factor for lens development, strongly activates the c-maf promoter construct. Endogenous c-maf is also activated by the Pax6 expression vector. Electrophoresis mobility shift assay and DNase I footprinting analysis show that at least three Pax6-binding sites are located in the 5'-flanking and 5'-non-coding regions of the rat c-maf gene. The c-maf gene was also markedly activated by its own product, c-Maf, through the MARE (Maf recognition element), suggesting that a positive autoregulatory mechanism controls this gene. In situ hybridization histochemical detection of Pax6 and c-Maf in the E14 lens showed that both mRNAs are expressed in the lens equator where lens epithelial cells are differentiating to lens fiber cells. These results suggest that a Pax6/c-Maf transcription factor cascade is working in lens development.

Animals↗