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At least 1,423 records · Page 79Linked to original sources
PubMed2006

Transcriptome profiling of human hepatocytes treated with Aroclor 1254 reveals transcription factor regulatory networks and clusters of regulated genes.

BACKGROUND: Aroclor 1254 is a well-known hepatotoxin and consists of a complex mixture of polychlorinated biphenyls (PCBs), some of which have the ability to activate the aryl hydrocarbon receptor (AhR) and other transcription factors (TFs). Altered transcription factor expression enables activation of promoters of many genes, thereby inducing a regulatory gene network. In the past, computational approaches were not applied to understand the combinatorial interplay of TFs acting in concert after treatment of human hepatocyte cultures with Aroclor 1254. We were particularly interested in interrogating promoters for transcription factor binding sites of regulated genes. RESULTS: Here, we present a framework for studying a gene regulatory network and the large-scale regulation of transcription on the level of chromatin structure. For that purpose, we employed cDNA and oligomicroarrays to investigate transcript signatures in human hepatocyte cultures treated with Aroclor 1254 and found 910 genes to be regulated, 52 of which code for TFs and 47 of which are involved in cell cycle and apoptosis. We identified regulatory elements proximal to AhR binding sites, and this included recognition sites for the transcription factors ETS, SP1, CREB, EGR, NF-kB, NKXH, and ZBP. Notably, ECAT and TBP binding sites were identified for Aroclor 1254-induced and E2F, MAZ, HOX, and WHZ for Aroclor 1254-repressed genes. We further examined the chromosomal distribution of regulated genes and observed a statistically significant high number of gene pairs within a distance of 200 kb. Genes regulated by Aroclor 1254, are much closer located to each other than genes distributed randomly all over the genome. 37 regulated gene pairs are even found to be directly neighbored. Within these directly neighbored gene pairs, not all genes were bona fide targets for AhR (primary effect). Upon further analyses many were targets for other transcription factors whose expression was regulated by Aroclor 1254 (secondary effect). CONCLUSION: We observed coordinate events in transcript regulation upon treatment of human hepatocytes with Aroclor 1254 and identified a regulatory gene network of different TFs acting in concert. We determined molecular rules for transcriptional regulation to explain, in part, the pleiotropic effect seen in animals and humans upon exposure to Aroclor 1254.

Apoptosis↗
PubMed2006

The orthology of HLA-E and H2-Qa1 is hidden by their concerted evolution with other MHC class I molecules.

BACKGROUND: Whether MHC molecules undergo concerted evolution or not has been the subject of a long-standing debate. RESULTS: By comparing sequences of eight functional homologues of HLA-E from primates and rodents with those of MHC class Ia molecules from the same eight species, we find that different portions of MHC class I molecules undergo different patterns of evolution. By focusing our analyses sequentially on these various portions, we have obtained clear evidence for concerted evolution of MHC class I molecules, suggesting the occurrence of extensive interallelic and intergenic exchanges. Intra-species homogenisation of sequences is particularly noticeable at the level of exon 4, which codes for the alpha3 domain, but our results suggest that homogenisation also concerns certain residues of the alpha1-alpha2 codomain that lie outside the antigen recognition site. CONCLUSION: A model is presented in which Darwinian selective pressures due to pathogens could, at the same time, favour diversification of MHC class Ia molecules and promote concerted evolution of separate loci by spreading advantageous motifs arising by mutations in individual MHC molecules to other alleles and to other loci of the MHC region. This would also allow MHC molecules to co-evolve with the proteins with which they interact to fulfil their functions of antigen presentation and regulation of NK cell activity. One of the raisons d'être of the MHC may therefore be to favour at the same time both diversification of MHC class Ia molecules and homogenisation of the whole pool of MHC class I molecules (Ia and Ib) involved in antigen presentation. REVIEWERS: This article was reviewed by Stephan Beck, Lutz Walter and Pierre Pontarotti.

Journal Article↗
PubMed2004

Hypoparathyroidism-retardation-Dysmorphism (HRD) syndrome--a review.

Hypoparathyroidism, retardation, and dysmorphism (HRD) is a newly recognized genetic syndrome, described in patients of Arab origin. The syndrome consists of permanent congenital hypoparathyroidism, severe prenatal and postnatal growth retardation, and profound global developmental delay. The patients are susceptible to severe infections including life-threatening pneumococcal infections especially during infancy. The main dysmorphic features are microcephaly, deep-set eyes or microphthalmia, ear abnormalities, depressed nasal bridge, thin upper lip, hooked small nose, micrognathia, and small hands and feet. A single 12-bp deletion (del52-55) in the second coding exon of the tubulin cofactor E (TCFE) gene, located on the long arm of chromosome 1, is the cause of HRD among Arab patients. Early recognition and therapy of hypocalcemia is important as is daily antibiotic prophylaxis against pneumococcal infections.

Abnormalities, Multiple↗
PubMed1993

[Consonant sounds processing in 22 channel cochlear implant device and consonant recognition of patients].

This report describes studies on electrode selection of the speech processor of a 22 channel cochlear implant device for 14 Japanese consonants, and on consonant recognition of 23 cochlear implant patients as they relate to electrode selection. The means of electrode selection was studied using a special device capable of detecting code signals delivered from the speech processor for electrode selection. Young male voices consisting of/a/+consonant+/a/ were presented as sound stimuli, and the electrode numbers selected were recorded for each consonant. The recorded numbers were grossly divided into two groups; a higher frequency range of about 500Hz to 4,000Hz and a lower range of 0Hz to about 1,100Hz. They showed characteristic patterns for each consonant, and these electrode number patterns were compared with patterns estimated from a sonogram. Although there were some differences between these two patterns in unvoiced stop consonants, they were roughly parallel to each other in other consonants. The information transfer ratio was calculated based on confusion matrices obtained from test results on 23 patients for 14 consonants. The ratio was high in voicing and semivowels, whereas it was relatively lower in plosives. This seems reasonable on the basis of patterns of electrode number transitions. Nasals and fricatives, however, showed lower information transfer ratios despite adequate electrode selection, and this may due to poorer information transition or the high frequency components of these consonants.

Cochlear Implants↗
PubMed1991

Extrathymic positive selection of gamma delta T cells. V gamma 4J gamma 1 rearrangements with "GxYS" junctions.

Neither function nor Ag recognition properties of gamma delta T cells are well understood yet. A TCR gamma-chain family, characterized by distinct N region sequences that converge in coding for a "GxYS" VJ junctional sequence, appears late in ontogeny among highly diversified V gamma 4J gamma 1C gamma 1 chains of C57BL/6 and BALB/c mice. The glycine and serine codons are of germline V gamma 4 and J gamma 1 origin, respectively, whereas the N region consists of a variable amino acid residue x, followed by an invariant tyrosine Y. The high expression of V gamma 4 xYJ gamma 1C gamma 1 in the lung of BALB/c mice compared to that of C57BL/6 is apparently due to a novel pattern of strain-dependent positive selection which, unlike for alpha beta TCR, operates extrathymically. This type of selection seems to be determined by strain specific polymorphic ligands encoded outside of the classical H-2 region.

Amino Acid Sequence↗
PubMed1990

Expression and assembly of mature apotransacylase (E2b) of bovine branched-chain alpha-keto acid dehydrogenase complex in Escherichia coli. Demonstration of transacylase activity and modification by lipoylation.

A cDNA clone encoding the entire transacylase (E2b) precursor of the bovine branched-chain alpha-keto acid dehydrogenase complex (Griffin, T. A., Lau, K. S., and Chuang, D. T. (1988) J. Biol. Chem. 263, 14008-14014) was used to construct a prokaryotic expression vector for recombinant mature E2b. The overexpression in Escherichia coli correlates with the presence near the 5'-terminus of the mature E2b coding region (nucleotides 20 to 28) of the sequence 5'-TCAAACT-CT-3'. It has been proposed that this sequence is involved in secondary mRNA recognition through interaction with the 5'-terminus of the bacterial 16 S rRNA. The mature E2b protein has transacylase activity when assayed with exogenous dihydrolipoamide and [1-14C] isovaleryl-CoA as substrates. However, the recombinant protein has no attached lipoic acid. This was established by the absence of radiolabel incorporation when transformed E. coli cells were grown in a medium containing DL-[2-3H]lipoic acid. The recombinant mature E2b protein was purified to greater than 95% purity in one step using Sepharose 4B column chromatography. The purified recombinant protein was shown to have a cubic 24-mer structure by electron microscopy and to possess a specific activity similar to that of the purified natural bovine E2b. The purified recombinant mature E2b was lipoylated in vitro in the presence of 2 mM ATP using a mitochondrial extract prepared from bovine liver. The above results provide the first evidence that the proper folding and assembly of mature bovine E2b is independent of the attachment of lipoyl moieties and that mammalian lipoylation activity is present in mitochondria.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗
PubMed1990

Interpretation of short ECGs with a personal computer: the Porto program.

A computer program for ECG analysis and interpretation developed at the University of Porto, Portugal is presented. The program runs on a microcomputer and employs the three-lead Frank VCG. The signals are sampled at 250 Hz with 8-bit precision during 5.5 s. Details on signal conditioning and wave recognition and measurement techniques are given. The diagnostic part of the program uses decision-tree logic. The decision rules are mainly derived from the Washington Code. The diagnostic accuracy of four classes (normal, left and right ventricular hypertrophies and myocardial infarction), evaluated in a sample of 1,075 pediatric and adult patients and classified by ECG-independent means was 76%. The program is currently being evaluated on the CSE database.

Adolescent↗
PubMed1995

Plant transcription factors.

Transcriptional regulation of gene expression relies on the recognition of promoter elements by transcription factors. In the past several years, a considerable number of (putative) transcription factors have been identified in plants. Some genes coding for these factors were isolated by south-western screening with oligonucleotides as a probe or by homology-based screening, and others were initially isolated by genetic means and subsequently identified as the genes for transcription factors. These transcription factors often form families of structurally related proteins with similar DNA-binding specificities and in addition, they are sometimes involved in related phenomena. Some groups of factors homo- and/or heterodimerize to increase the length and variability of the target sequences. Transcriptional activators, in general, comprise a modular activation domain. The activities of the transcription factors are controlled by post-translational modification, like phosphorylation and glycosylation, as well as at the levels of nuclear transport, oligomerization, etc. In this review, we will summarize the current knowledge of plant transcription factors to help understand the mechanistic aspects of the transcriptional regulation of genes.

Amino Acid Sequence↗
PubMed2003

Context in verbal short-term memory.

We tested the hypothesis that stimulus-related contextual information that is incidental to task demands-an episodic code-is automatically, obligatorily encoded and stored as a part of short-term memory (STM) representations. Four experiments employed a running span task to investigate the effects of manipulating two types of contextual information: stimulus grouping and color. Three experiments established that grouping context effects are sensitive neither to volitional control nor to task difficulty and that they generalize across testing procedures (yes/no recognition and immediate serial recall). A fourth experiment demonstrated an effect of manipulating the congruity of the color of stimuli between study and test. These demonstrations of the robustness and generality of context effects in STM are consistent with the predictions of the episodic coding model of STM.

Adolescent↗
PubMed2004

Letter binding and invariant recognition of masked words: behavioral and neuroimaging evidence.

Fluent readers recognize visual words across changes in case and retinal location, while maintaining a high sensitivity to the arrangement of letters. To evaluate the automaticity and functional anatomy of invariant word recognition, we measured brain activity during subliminal masked priming. By preceding target words with an unrelated prime, a repeated prime, or an anagram made of the same letters, we separated letter-level and whole-word codes. By changing the case and the retinal location of primes and targets, we evaluated the invariance of those codes. Our results indicate that an invariant binding of letters into words is achieved unconsciously through a series of increasingly invariant stages in the left occipito-temporal pathway.

Adult↗
PubMed1989

Strand specificity of the topoisomerase II mediated double-stranded DNA cleavage reaction.

The strand specificity of topoisomerase II mediated DNA cleavage was analyzed at the nucleotide level by characterizing the enzyme's interaction with a strong DNA recognition site. This site was isolated from the promoter region of the extrachromosomal rRNA genes of Tetrahymena thermophila and was recognized by type II topoisomerases from a variety of phylogenetically diverse eukaryotic organisms, including Drosophila, Tetrahymena, and calf thymus. When incubated with this site, topoisomerase II was found to introduce single-stranded breaks (i.e., nicks) in addition to double-stranded breaks in the nucleic acid backbone. Although the nucleotide position of cleavage on both the noncoding and coding strands of the rDNA remained unchanged, the relative ratios of single- and double-stranded DNA breaks could be varied by altering reaction conditions. Under all conditions which promoted topoisomerase II mediated DNA nicking, the enzyme displayed a 3-10-fold specificity for cleavage at the noncoding strand of its recognition site. To determine whether this specificity of topoisomerase II was due to a faster forward rate of cleavage of the noncoding strand or a slower rate of its religation, a DNA religation assay was performed. Results indicated that both the noncoding and coding strands were religated by the enzyme at approximately the same rate. Therefore, the DNA strand preference of topoisomerase II appears to be embodied in the enzyme's forward cleavage reaction.

Animals↗
PubMedDate not supplied

Aging and the locus of the global precedence effect: a short review and new empirical data.

Precedence of the global over the local level in visual perception is well established by the use of compound, or hierarchical, stimuli. However, (a) virtually nothing is known concerning the fate of global precedence with normal aging, and (b) there is still a debate about the early versus late perceptual locus of the effect. The present study was planned to investigate both topics. Two experiments are reported where young adult and elderly subjects were enrolled for the recognition of compound letters either at the global or at the local level. In order to recruit late perceptual processes, the case of the letters varied in such a way that subjects had to activate graphemic codes to take their decision. It appeared that the global precedence effect was preserved. This observation shows an early perceptual source of the global precedence effect, which is then transferred to later stages of information processing. Age did not affect the global precedence phenomenon.

Adult↗
PubMed1995

Cloning of the cDNA for a brain glycine-, glutamate- and thienylcyclohexylpiperidine-binding protein.

Polyclonal antibodies (Ab's) were raised against a 43-kDa component of a protein complex that has ligand recognition sites similar to those of brain N-methyl-D-aspartate (NMDA) receptors. The Ab's were used to immunopurify from brain synaptic membranes a 60-kDa glycine (Gly), glutamate (Glu) and thienylcyclohexylpiperidine (TCP)-binding protein and to screen a rat hippocampal cDNA expression library. A 1.85-kb clone, pGlyBP, coding for a protein of 470 amino acids (52.7 kDa) was identified. Northern blot analyses performed on poly(A+) RNA from brain revealed hybridization of the labeled cDNA probes to transcripts of 1.9 kb. E. coli transformed with the pGyBP expressed a protein that was recognized by the anti-43 kDa Ab's and had recognition sites for Gly, Glu and TCP. The cloned protein has 2 glycosylation sites, 3 hydrophobic domains, 4 cysteine-rich motifs (C-X2-C-X16-20-C-X5-11), and 2 regions homologous to the NR1 receptor protein.

Amino Acid Sequence↗
PubMed1999

Cloning and characterization of the rat Crisp-1 gene.

Rat androgen-regulated acidic epididymal glycoprotein (AEG), also known as Protein DE, is a product of the Crisp-1 gene. Protein DE is secreted into the epididymal lumen and binds to sperm heads during their transit through the epididymis. In experiments reported here, the rat Crisp-1 gene has been cloned and its structure determined. The rat Crisp-1 gene spans 38kb and contains nine exons encoding an 1120bp epididymal Protein DE mRNA. The boundaries of the protein-coding exons are structurally organized similar to the mouse Crisp-1 gene, except for the 5' untranslated sequence, which is encoded by one exon in the mouse Crisp-1 gene and two exons in the rat gene. All the introns are flanked by AG/GT consensus splice sequences. Crisp-1 is a single-copy gene as shown by the presence of single bands by Southern blot analysis and PCR using rat genomic DNA as template. Recognition sites for steroid hormone receptors are present in the 5' flanking region and in intron 1, consistent with the known regulation of Protein DE expression by androgens. RT-PCR experiments demonstrate three splice variant mRNAs involving the non-coding exon 2. The Crisp-1 gene also produces an mRNA without an exon 1 sequence by utilizing a transcription start site in intron 1, 5' of the start of exon 2. All forms of the Crisp-1 mRNA are predicted to encode Protein DE.

Alternative Splicing↗
PubMed1993

Attachment factors of Bordetella pertussis: mimicry of eukaryotic cell recognition molecules.

Bacteria localize to specific target organs during infection by recognizing eukaryotic cell surface addresses. This address system exists to facilitate normal trafficking of host cells such as leukocytes. The mechanisms by which bacteria subvert host targeting codes provide a unique link between microbial pathogenesis and eukaryotic cell trafficking, and can point to a new array of antibodies and peptides of potential therapeutic value.

Amino Acid Sequence↗