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Configurational pattern discrimination responsible for dishabituation in common toads Bufo bufo (L.): behavioral tests of the predictions of a neural model.

Recently, a neural model of visual pattern discrimination for stimulus-specific habituation was developed, based on previous behavioral studies which demonstrated that toads exhibit a dishabituation hierarchy for different worm-like stimuli. The model suggests that visual objects are represented by temporal coding and predicts that the dishabituation hierarchy changes when the stimulus/background contrast direction is reversed or the stimulus size is varied. The behavioral experiments reported in this paper were designed to test these predictions. (1) For a pair of stimuli from the contrast reversal prediction, the experimental results validated the theory. (2) For a pair of stimuli from the size reduction prediction, the experimental results failed to validate the theory. Further experiments concerning size effects suggest that configural visual pattern discrimination in toads exhibits size invariance. (3) Inspired by the Groves-Thompson account of habituation, we found that dishabituation by a second stimulus has a separate process from habituation to a first stimulus. This paper serves as an example of a fruitful dialogue between experimentation and modeling, crucial for understanding brain functions.

Animals

Computer prediction of the exon-intron structure of mammalian pre-mRNAs.

A novel approach to the problem of prediction of protein-coding regions is suggested. This approach combines the site prediction methods to predict splicing sites and the global coding region prediction methods to choose the best variant of spliced mRNA. One of the advantages of the suggested algorithm is that the resulting mRNA or protein sequence may then be immediately analyzed further. The true mRNA either coincides with the predicted one or ranks high in the list of variants. In the latter situation the predicted mRNA usually differs from the true one in only one or two of several exons. The combined approach allows the use of a priori information (e.g. the putative protein length or the number of exons). It is possible to use additional parameters not considered here, such as the preferred lengths of exons and introns, and particularly the preferred position of introns in the reading frame and the preferred codon position of exon termini.

Actins

Probability of coding of a DNA sequence: an algorithm to predict translated reading frames from their thermodynamic characteristics.

An algorithm to determine the probability that a reading frame codifies for a protein is presented. It is based on the results of our previous studies on the thermodynamic characteristics of a translated reading frame. We also develop a prediction procedure to distinguish between coding and non-coding reading frames. The procedure is based on the characteristics of the putative product of the DNA sequence and not on periodicity characteristics of the sequence, so the prediction is not biased by the presence of overlapping translated reading frames or by the presence of translated reading frames on the complementary DNA strand.

Amino Acid Sequence

The mas oncogene encodes an angiotensin receptor.

The class of receptors coupled to GTP-binding proteins share a conserved structural motif which is described as a 'seven-transmembrane segment' following the prediction that these hydrophobic segments form membrane-spanning alpha-helices. Identified examples include the mammalian opsins, alpha 1-, alpha 2-, beta 1- and beta 2-adrenergic receptors, the muscarinic receptor family, the 5-HT1C-receptor, and the substance-K receptor. In addition, two mammalian genes have been identified that code for predicted gene products with sequence similarity to these receptors, but whose ligand specificity is unknown namely, G21 and the mas oncogene. The mas oncogene shows the greatest sequence similarity to the substance-K receptor, and on this basis it was predicted that it would encode a peptide receptor with mitogenic activity which would act through the inositol lipid signalling pathways. The mas oncogene product was transiently expressed in Xenopus oocytes, and stably expressed in a transfected mammalian cell line. The results demonstrate that the mas gene product is a functional angiotensin receptor.

Angiotensins

Molecular and biological characterization of a herpes simplex virus type 1 (HSV-1) neuroinvasiveness gene.

Pathogenetic studies of herpes simplex virus type 1 (HSV-1) strains ANG and its mouse brain-passaged descendant ANG path revealed no difference in neurovirulence but a significant difference in neuroinvasiveness. Thus, both viruses induced a fatal encephalitis in mice after direct injection into the brain, but only ANG path induced lethal neurologic disease after inoculation on rear footpads. The difference in neuroinvasiveness is not related to the capacity to replicate in mouse neural tissues or mouse cells in general, but is specifically related to virus entry into the peripheral nervous system in the footpad. Marker rescue experiments in which ANG path genes were used to confer neuroinvasiveness on ANG indicated that the gene that codes for glycoprotein D (gD) is responsible for the phenotypic difference. Analyses of the gD genes by dideoxy-sequencing techniques identified a base difference in the coding sequences and predicted that the ANG gD gene codes for alanine (GCC codon) at amino acid position 84 in the open reading frame and the ANG path gD gene codes for glycine (GGC codon) at this site. Using these data, an oligonucleotide probe predicted to be specific for the ANG path gD gene was prepared, and in Southern blot analyses, this probe revealed that neuroinvasiveness-rescued agents had incorporated the base change seen in the ANG path gD gene. We conclude that HSV-1 glycoprotein D functions to effect neuroinvasiveness and we discuss potential mechanisms that may be involved.

Amino Acid Sequence

Characterization of the extracellular region of the human thyrotrophin receptor expressed as a recombinant protein.

DNA encoding the N-terminal 415 residues of the human thyrotrophin receptor (predicted to code for the large extracellular region) was introduced into Chinese hamster ovary (CHO) cells using the glutamine synthetase/cytomegalovirus amplifiable expression system, and into E. coli using the pGEX-3X expression vector. Substantial quantities of insoluble fusion protein product resulted from bacterial expression; by Western blot analysis, this was shown to be reactive with anti-receptor antibodies raised against a peptide corresponding to residues 313-330. Immunoreactivity was not retained by the solubilized protein. In eukaryotic expression, several successful CHO transfectants were observed and one (ExG2) was characterized thoroughly. Using agarose-bound Concanavalin A, a glycoprotein with an M(r) of approximately 60,000 was detected in a detergent extract of metabolically labelled ExG2 cells, agreeing with the predicted molecular size of 45,000, plus carbohydrate. The same protein could also be detected by immunoprecipitation using the experimental anti-peptide antisera and also sera from patients with Graves' disease. The protein was immunoreactive in Western blot analyses of ExG2 cells using the experimental antisera but not the pathological sera, supporting the view that linear sequences are not sufficient for autoantibody binding. These are the first studies in which visualization of eukaryotically expressed recombinant receptor by such immunological techniques has been possible, presumably because of the higher expression of the glutamine synthetase system. Surprisingly, the recombinant protein was retained within the cells rather than being secreted. The recombinant protein was very effective at absorbing the adenylate cyclase-stimulating activity of the sera from patients with Graves' disease, but not that of thyrotrophin. This suggests that the large N-terminal extracellular region contains epitopes for stimulatory autoantibodies, but that high affinity thyrotrophin binding requires additional components.

Adenylyl Cyclases

An unusual coding sequence from a Drosophila clock gene is conserved in vertebrates.

The per locus has a fundamental involvement in the expression of biological rhythms in Drosophila. Mutations at this locus can shorten, lengthen or eliminate a variety of rhythmic activities that range from circadian behaviours, exemplified by eclosion and locomotor activities, to short-period behaviour such as the 55-s rhythm of courtship song. DNA from the per locus has been cloned, and we have used P-element-mediated DNA transformation to establish that a 7.1-kilobase(kb) HindIII fragment contains a functional copy of the gene. This transforming DNA contains a single transcription unit which gives rise to a 4.5-kb poly(A)+ RNA. Here we report the results of a search for sequences homologous to the per locus DNA in the genomic DNA of several species of vertebrates. An unusual, tandemly repeated sequence forming a portion of the 4.5-kb per transcript is homologous to DNA in chicken, mouse and man. Cloned DNAs from the mouse and Drosophila are related by long, uninterrupted tandem repetitions of the sequence ACNGGN. At the per locus, these tandem repeats are predicted to code for poly(Thr-Gly) tracts up to 48 amino acids long. These repeated sequences are also transcribed in the mouse. Several long tracts of poly(Thr-Gly) appear to be encoded by DNA cloned from the mouse.

Amino Acid Sequence

Nucleotide sequence of cloned cDNAs encoding chicken preproparathyroid hormone.

In order to characterize an avian parathyroid hormone gene, a lambda gt10 cDNA library constructed from chicken parathyroid gland mRNA was screened with a human preproparathyroid hormone (preproPTH) cDNA probe. Nucleotide sequence analysis of three independent clones confirmed that they encoded chicken preproPTH. This analysis, complemented by primer extension and Northern blot analysis of mRNA, demonstrated a 5'-untranslated region for chicken preproPTH of 127 nucleotides, a coding region of 357 nucleotides, and a 3'-untranslated region of approximately 2500 nucleotides. The coding sequence predicts a mature chicken PTH of 88 amino acids in contrast to the 84 amino acids of the mammalian hormones. Comparison of the avian and the mammalian hormones shows striking homology in the region of amino acids 1-32. The middle and carboxyl-terminal portions of chicken PTH, however, differ considerably from the mammalian hormones and include deletions of sequences conserved in mammalian PTH and insertions of novel peptide sequences. Comparison of the avian and mammalian structures suggests potential alterations of the mammalian sequences that may lead to altered bioactivity and/or hormone metabolism.

Amino Acid Sequence

The POL1 gene from the fission yeast, Schizosaccharomyces pombe, shows conserved amino acid blocks specific for eukaryotic DNA polymerases alpha.

The POL1 gene of the fission yeast, Schizosaccharomyces pombe, was isolated using a POL1 gene probe from the budding yeast Saccharomyces cerevisiae, cloned and sequenced. This gene is unique and located on chromosome II. It includes a single 91 bp intron and is transcribed into a mRNA of about 4500 nucleotides. The predicted protein coded for by the S. pombe POL1 gene is 1405 amino acid long and its calculated molecular weight is about 160,000 daltons. This peptide contains seven amino acid blocks conserved among several DNA polymerases from different organisms and shares overall 37% and 34% identity with DNA polymerases alpha from S. cerevisiae and human cells, respectively. These results indicate that this gene codes for the S. pombe catalytic subunit of DNA polymerase alpha. The comparisons with human DNA polymerase alpha and with the budding yeast DNA polymerases alpha, delta and epsilon reveal conserved blocks of amino acids which are structurally and/or functionally specific only for eukaryotic alpha-type DNA polymerases.

Amino Acid Sequence

Psychophysiological components of imagery.

McGuigan's neuromuscular model of information processing (1978a, 1978b, and 1989) was investigated by electrically recording eye movements (electro-oculograms), covert lip and preferred arm responses (electromyograms), and electroencephalograms. This model predicts that codes are generated as the lips are uniquely activated when processing words beginning with bilabial sounds like "p" or "b," as is the right arm to words like "pencil" that refer to its use. Twelve adult female participants selected for their high imagery ratings were asked to form images to three orally presented linguistic stimuli: the letter "p," the words "pencil" and "pasture," and to a control stimulus, the words "go blank." The following findings were significant beyond the 0.05 level: an increased covert lip response only to the letter "p," increased vertical eye activity to "p" and to the word "pencil," right arm response only to the word "pencil," and a decreased percentage of alpha waves from the right 02 lead only to the word "pasture." Since these covert responses uniquely occurred during specific imagery processes, it is inferred that they are components of neuromuscular circuits that function in accord with the model of information processing tested.

Adult

Codon usage in Plasmodium falciparum.

The codon frequencies used in 7874 codons from 17 sequences of Plasmodium falciparum have been examined. The frequency distribution is markedly biased. A and C occur with similar frequency in all positions but G is predominantly in the first base and T is predominantly in the last position. This information can be used to predict the coding strand and reading frame of P. falciparum genes.

Animals

Evidence for two forms of murine beta-1,4-galactosyltransferase based on cloning studies.

We have isolated overlapping cDNA clones representing the full-length transcript (4038 base pairs) for murine beta-1,4-galactosyltransferase. The coding sequence predicts a membrane-bound glycoprotein with 3 distinct structural features: 1) a large, potentially glycosylated COOH-terminal domain (355 amino acids) which is positioned within the Golgi lumen and contains both the catalytic and alpha-lactalbumin binding site; 2) a single transmembrane domain (20 amino acids); and 3) a short NH2-terminal domain containing 2 Met residues, separated by 12 amino acids. The gene for murine beta-1,4-galactosyltransferase is unusual in that it specifies 2 mRNA transcripts which differ in length by about 200 base pairs. The longer transcript contains both Met residues found in the NH2-terminal domain; the shorter transcript contains only the downstream Met. These results predict that 2 related forms of beta-1,4-galactosyltransferase of 399 and 386 amino acids are synthesized as a consequence of alternative translation initiation. Both forms of the enzyme are identical in primary structure with the exception that the long form has an NH2-terminal extension of 13 amino acids which, in part, potentially encodes a cleavable signal sequence. The structural implications, topological distribution and potential biological significance of the 2 forms of the enzyme are discussed.

Amino Acid Sequence

Internal Bayesian precision modulates the neural representation of social attention: Disentangling implicit and explicit components via model-informed multivariate EEG analysis.

Social attention integrates sensory cues with high-level cognitive expectations, yet the generative mechanisms through which implicit orienting and explicit belief-driven modulation interact remain poorly understood. This ambiguity complicates the distinction between specialized social modules and domain-general attentional processes. We combined a dynamic cueing task with hierarchical Bayesian modeling and model-informed multivariate EEG decoding to address this. Behavioral results revealed a computational double dissociation: symbolic arrow cues elicited heterogeneous strategies, whereas averted gaze recruited a consistent, surprise-driven computational phenotype. At the neural level, time-resolved decoding and temporal generalization revealed a critical representational shift starting approximately 400 ms post-cue. Initial activity related to physical cue features was rapidly replaced by stable neural templates of predicted spatial intent. Crucially, topographical activation patterns showed that this intentional template, characterized by a lateralized temporo-occipital distribution, emerged exclusively under high internal certainty. Furthermore, partial representational similarity analysis demonstrated that late-stage neural manifolds were overwhelmingly organized around integrated spatial goals rather than isolated sensory or motivational signals. These findings suggest that social attention is a specialized generative process, where internal certainty modulates the transformation of social perceptions into actionable top-down intentions.

Bayesian computational modeling

cDNA cloning and sequencing of a new gene intensely expressed in early differentiation stages of embryonal carcinoma cells and in mid-gestation period of mouse embryogenesis.

By the differential hybridization technique, we isolated a cDNA clone, MK1, whose RNA level increased in early stages of retinoic acid-induced differentiation of embryonal carcinoma cells. The amount of MK1 RNA progressively decreased in the later stages of the differentiation. In mouse embryos, MK1 RNA was abundant in mid-gestation stages (Day 8 to Day 11) and decreased thereafter. The corresponding RNA was 1.0 killobase in size. From the nucleotide sequence, MK1 gene was predicted to code a polypeptide of molecular weight 9,971, which was rich in basic amino acids.

Animals

Phase variation in Bordetella pertussis by frameshift mutation in a gene for a novel two-component system.

Bordetella pertussis, the aetiological agent of whooping cough, coordinately regulates the expression of many virulence-associated determinants, including filamentous haemagglutinin, pertussis toxin, adenylyl cyclase toxin, dermonecrotic toxin and haemolysin. The coordinate regulation is apparent in the repression of synthesis of these determinants in response to environmental stimuli; a phenomenon known as antigenic or phenotypic modulation. B. pertussis also varies between metastable genetic states, or phases. There is a virulent phase in which virulence-associated determinants are synthesized, and an avirulent phase in which they are not. Previous studies have shown that a genetic locus, vir, is required for expression from many virulence-associated loci, and that replacing the cloned vir locus in trans can restore the virulent phase phenotype to spontaneously occurring avirulent phase strains. Here, we show that phase variation in one series of strains is due to a frameshift mutation within an open reading frame that is predicted to code for a Vir protein product. The deduced protein sequence is similar to both components of the 'two-component' regulatory system which control gene expression in response to environmental stimuli in a range of bacterial species.

Base Sequence

Chromosome-level genome assembly and annotation of the porcupine fish (Diodon hystrix).

The porcupinefish (Diodon hystrix), a coral reef teleost, is widely distributed in tropical/subtropical waters of the Pacific, Atlantic, Indian Oceans, and Mediterranean Sea. It shares easily recognizable features with pufferfish, such as body inflation and spines. Additionally, its culinary value makes D. hystrix a highly desirable species in many tropical coastal regions, with considerable market potential. However, lack of a high-quality genome hindered further studies on its reproduction, molecular biology, and genomic improvement. Here, we assembled the chromosome-scale genome using PacBio HiFi, ultra-long reads, and Hi-C. Of the 713.62 Mb genome, 98.63% anchored to 23 chromosomes (scaffold N50: 31.52 Mb) with 39.82% repetitive sequences. The assembled genome achieved a BUSCO completeness score of 97.7%, with 23,171 protein-coding genes predicted, 22,221 of which were functionally annotated. Phylogenetic analysis identified D. hystrix's evolutionary relationships with other species in the Tetraodontiformes. In summary, the high-quality genome of D. hystrix sheds light on valuable insights into genome size evolution, and provides a valuable resource for exploiting genomic study and breeding applications in this species.

Animals

Human somatostatin I: sequence of the cDNA.

RNA has been isolated from a human pancreatic somatostatinoma and used to prepare a cDNA library. After prescreening, clones containing somatostatin I sequences were identified by hybridization with an anglerfish somatostatin I-cloned cDNA probe. From the nucleotide sequence of two of these clones, we have deduced an essentially full-length mRNA sequence, including the preprosomatostatin coding region, 105 nucleotides from the 5' untranslated region and the complete 150-nucleotide 3' untranslated region. The coding region predicts a 116-amino acid precursor protein (Mr, 12.727) that contains somatostatin-14 and -28 at its COOH terminus. The predicted amino acid sequence of human somatostatin-28 is identical to that of somatostatin-28 isolated from the porcine and ovine species. A comparison of the amino acid sequences of human and anglerfish preprosomatostatin I indicated that the COOH-terminal region encoding somatostatin-14 and the adjacent 6 amino acids are highly conserved, whereas the remainder of the molecule, including the signal peptide region, is more divergent. However, many of the amino acid differences found in the pro region of the human and anglerfish proteins are conservative changes. This suggests that the propeptides have a similar secondary structure, which in turn may imply a biological function for this region of the molecule.

Amino Acid Sequence

Cystic fibrosis gene expression is not correlated with rectifying Cl- channels.

Cystic fibrosis (CF) involves a profound reduction of Cl- permeability in several exocrine tissues. A distinctive, outwardly rectifying, depolarization-induced Cl- channel (ORDIC channel) has been proposed to account for the Cl- conductance that is defective in CF. The recently identified CF gene is predicted to code for a 1480-amino acid integral membrane protein termed the CF transmembrane conductance regulator (CFTR). The CFTR shares sequence similarity with a superfamily of ATP-binding membrane transport proteins such as P-glycoprotein and STE6, but it also has features consistent with an ion channel function. It has been proposed that the CFTR might be an ORDIC channel. To determine if CFTR and ORDIC channel expression are correlated, we surveyed various cell lines for natural variation in CFTR and ORDIC channel expression. In four human epithelial cell lines (T84, CaCo2, PANC-1, and 9HTEo-/S) that encompass the full observed range of CFTR mRNA levels and ORDIC channel density we found no correlation.

Base Sequence