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PubMed2006

Biases in judgments of separation and orientation of elements belonging to different clusters.

If two demarcated dots are embedded in separate clusters of similar dots in off centre positions, their perceived separation is biased towards the separation between the centres of the clusters (Morgan, Hole, & Glennerster, 1990). We replicated these results and went on to determine whether a similar bias is present for orientation judgments, using a staircase method and a range of cluster orientations and separations. A complex pattern of biases was found including biases for targets at centroids. Orientation attraction towards tangents to the clusters seemed to be involved. We conclude that orientation is subject to different contextual constraints from separation, and that bias towards the edges of clusters needs to be included in models of position coding.

Adult↗

PubMed1998

On the independence of modality effects and end-term and distance effects in episodic comparative judgement: dissociations of errors and reaction times.

The experiments reported in this paper explore the effect of modality variations on end-term and distance effects in an episodic comparative judgement task. In each experiment, subjects were to store serial orders of objects on a size dimension. Memory was tested after a brief retention interval by a comparative judgement task, in which subjects were presented with two elements of an order and had to point to the formerly larger one. Regarding the response times, we hypothesized that modality variations affect speed of stimulus identification and code access processes. We further hypothesized that distance variations and end-term variations affect processing components that are independent of the component affected by the modality variation. Finally, we assumed that end-term and distance effects interact in a predictable way, because they mirror competing response selection strategies. The latency data clearly support these hypotheses. As regards the accuracy data, we argued that modality and end-term effects, if they show up within the accuracy data, very likely have a different basis than the effects within the latency data. Again, the data support this assumption showing clear dissociations of accuracy and latency data. With respect to the stimulus modality variation, the whole data pattern shows that explanations which rely on modality-specific codings are not justifiable.

Adult↗

PubMed1998

Secretion in Escherichia coli and phage-display of recombinant insulin-like growth factor binding protein-2.

Insulin-like growth factors (IGFs) promote cell growth and differentiation. Their actions are regulated by six different, but related, binding proteins (IGFBPs). To investigate the molecular interactions between IGFs and IGFBPs, an Escherichia coli based production method and a phage display system has been developed. The cDNA for bovine IGFBP-2 was inserted between regions coding for the pelB signal sequence and geneIII product, g3p, of bacteriophage fd in a phagemid vector to generate pGF14. The coding sequences of IGFBP-2 and g3p were separated by an amber stop codon and a flexible linker containing the cleavage recognition site for H64A subtilisin. Using this system in BL21, a non-supE strain lacking ompT, most product, approximately 4 mg 1(-1) of IGFBP-2, was obtained in the growth medium. The bacterially derived IGFBP-2 had a correct N-terminal sequence, molecular mass on SDS-PAGE and the same affinity for IGF-1 and IGF-II as IGFBP-2 from mammalian cells. In a supE strain of E. coli, IGFBP-2 was produced as an IGF-binding fusion to g3p. Procedures for display and approximately 10000 fold enrichment of IGFBP-2 bearing phage using adsorption to IGF-II coated microtitre plates were developed. Thus IGFBP-2 can be secreted in E. coli and displayed on filamentous phage. These can be selectively enriched by binding to immobilised IGF-II.

Amino Acid Sequence↗

PubMed1991

Molecular structure of the human muscle-specific enolase gene (ENO3).

The single human gene for muscle-specific enolase was isolated and its structure was characterized, from which the mature mRNA transcript and encoded protein were also deduced. The gene contains 12 exons, spans approx. 6 kb and encodes a protein of 433 residues. The gene structure is similar to that found for the rat neuron-specific enolase gene, and the deduced protein aligns precisely with other enolase sequences, including the sequence of the only published crystallized enolase, yeast eno-1. The 5' boundary of the gene includes a 5' non-coding exon and is characterized by an upstream TATA-like box and CpG-rich region. This region contains potential recognition motifs for general transcriptional regulation involving Sp1, activator protein 1 and 2, CCAAT box transcription factor/nuclear factor I and cyclic AMP, and for muscle-specific transcriptional regulation involving a CC(A + T-rich)6GG box, M-CAT-box CAATCCT and two myocyte-specific enhancer-binding factor 1 boxes.

Amino Acid Sequence↗

PubMed1980

Could poly(A) align the splicing sites of messenger RNA precursors?

In general, poly(A)-mRNA appears to be derived from larger nuclear RNA precursors. The maturation of these precursors involves excision of sequences of variable length from within the molecule and splicing of the remaining structural and coding sequences. The mechanism by which this process occurs is not known. It does not appear to operate solely through the recognition of a defined primary sequence or through the formation of a consistent secondary structure. We propose an alternative model in which poly(A) facilitates the splicing event by promoting the formation of triple-stranded structures within the mRNA precursor.

Animals↗

PubMed1998

A decision tree system for finding genes in DNA.

MORGAN is an integrated system for finding genes in vertebrate DNA sequences. MORGAN uses a variety of techniques to accomplish this task, the most distinctive of which is a decision tree classifier. The decision tree system is combined with new methods for identifying start codons, donor sites, and acceptor sites, and these are brought together in a frame-sensitive dynamic programming algorithm that finds the optimal segmentation of a DNA sequence into coding and noncoding regions (exons and introns). The optimal segmentation is dependent on a separate scoring function that takes a subsequence and assigns to it a score reflecting the probability that the sequence is an exon. The scoring functions in MORGAN are sets of decision trees that are combined to give a probability estimate. Experimental results on a database of 570 vertebrate DNA sequences show that MORGAN has excellent performance by many different measures. On a separate test set, it achieves an overall accuracy of 95 %, with a correlation coefficient of 0.78, and a sensitivity and specificity for coding bases of 83 % and 79%. In addition, MORGAN identifies 58% of coding exons exactly; i.e., both the beginning and end of the coding regions are predicted correctly. This paper describes the MORGAN system, including its decision tree routines and the algorithms for site recognition, and its performance on a benchmark database of vertebrate DNA.

Algorithms↗

PubMed2003

Genetic screening in haemolytic uraemic syndrome.

PURPOSE OF REVIEW: Haemolytic uraemic syndrome (HUS) is a disease of diverse origin. The last year has witnessed the identification of a novel genetic marker of this disease, the description of the frequency of the factor H associated form of HUS in a registry of over 100 patients and a better understanding of the pathophysiology of the disease. RECENT FINDINGS: In patients with atypical HUS, heterozygous mutations in the gene coding for the soluble complement regulator factor H are reported and most of the mutations cluster in the C-terminal recognition domain of the protein. A novel genetic marker for HUS has also been identified. Mutations occurring in the gene of the von Willebrand factor cleaving protease, ADAMTS13, which were previously linked to thrombotic thrombocytopenic purpura have now been identified in HUS patients. The frequency of factor H-associated HUS was established as 14% in a registry of German speaking countries and also 16 novel disease associated mutations were reported. The pathophysiology of factor H-associated HUS was analysed. Three analysed mutant proteins show normal complement regulatory activities but display defective recognition functions: reduced binding to surface attached C3b, to heparin/polyanions and to endothelial cells. SUMMARY: The identification of effector molecules of the complement as well as the coagulation cascade as disease associated molecules indicate a regulatory protein network, which maintains integrity of endothelial cells during stress or infection. Defining the individual components and how their functional interaction causes microangiopathies will identify additional disease markers and will allow the design of proper diagnostic and therapeutic approaches.

Complement Factor H↗

PubMed1994

The nucleotide sequence of potato virus A genomic RNA and its sequence similarities with other potyviruses.

The complete nucleotide sequence of potato virus A (PVA) was obtained from six independent cDNA clones. The RNA genome of PVA is 9565 nucleotides long and contains one open reading frame (ORF) of 9177 bases encoding a large polyprotein of 3059 amino acids with a calculated M(r) of 340K. Seven potential proteinase NIa, one HC-pro and one P1 proteinase recognition sites were found in PVA polyprotein by searching for cleavage site consensus sequences amongst the potyvirus group. The non-coding region preceding the ORF is 161 nucleotides long. The termination codon is followed by a 227-nucleotide sequence. Overall nucleotide sequence identity compared with several completely sequenced potyvirus genomes is between 53 and 58%, with overall amino acid sequence identity between 65 and 71%. When the putative amino acid sequences of individual proteins of PVA were compared with the corresponding proteins of other potyviruses, P1 and P3 appeared the least conserved (34 to 53%) whereas the other proteins were in most cases from 63 to 80% identical to each other.

Amino Acid Sequence↗

PubMed2006

A global assembly of cotton ESTs.

Approximately 185,000 Gossypium EST sequences comprising >94,800,000 nucleotides were amassed from 30 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including drought stress and pathogen challenges. These libraries were derived from allopolyploid cotton (Gossypium hirsutum; A(T) and D(T) genomes) as well as its two diploid progenitors, Gossypium arboreum (A genome) and Gossypium raimondii (D genome). ESTs were assembled using the Program for Assembling and Viewing ESTs (PAVE), resulting in 22,030 contigs and 29,077 singletons (51,107 unigenes). Further comparisons among the singletons and contigs led to recognition of 33,665 exemplar sequences that represent a nonredundant set of putative Gossypium genes containing partial or full-length coding regions and usually one or two UTRs. The assembly, along with their UniProt BLASTX hits, GO annotation, and Pfam analysis results, are freely accessible as a public resource for cotton genomics. Because ESTs from diploid and allotetraploid Gossypium were combined in a single assembly, we were in many cases able to bioinformatically distinguish duplicated genes in allotetraploid cotton and assign them to either the A or D genome. The assembly and associated information provide a framework for future investigation of cotton functional and evolutionary genomics.

DNA, Complementary↗

PubMed1989

QRS feature extraction using linear prediction.

This communication proposes a method called linear prediction (a high performant technique in digital speech processing) for analyzing digital ECG signals. There are several significant properties indicating that ECG signals have an important feature in the residual error signal obtained after processing by Durbin's linear prediction algorithm. This communication also indicates that the prediction order need not be more than two for fast arrhythmia detection. The ECG signal classification puts an emphasis on the residual error signal. For each ECG's QRS complex, the feature for recognition is obtained from a nonlinear transformation which transforms every residual error signal to a set of three states pulse-code train relative to the original ECG signal. The pulse-code train has the advantage of easy implementation in digital hardware circuits to achieve automated ECG diagnosis. The algorithm performs very well in feature extraction in arrhythmia detection. Using this method, our studies indicate that the PVC (premature ventricular contraction) detection has at least a 92 percent sensitivity for MIT/BIH arrhythmia database.

Algorithms↗

PubMed1996

In vivo protective anti-HIV immune responses in non-human primates through DNA immunization.

An effective immune response involves the specific recognition of and elimination of an infectious organism at multiple levels. In this context DNA immunization can present functional antigenic proteins to the host for recognition by all arms of the immune system, yet provides the opportunity to delete any genes of the infectious organism which code for antigens or pieces of antigens that may have deleterious effects. Our group has developed the use of nucleic acid immunization as a possible method of vaccination against Human immunodeficiency virus type 1 (HIV-1) [1,2,3,10,11,12]. Sera from non-human primates immunized with DNA vectors that express the envelope proteins from HIV-1 contain antibodies specific to the HIV-1 envelope. These sera also neutralize HIV-1 infection in vitro and inhibit cell to cell infection in tissue culture. Analysis of cellular responses is equally encouraging. T cell proliferation as well as cytotoxic T cell lysis of relevant env expressing target cells were observed. In addition, evidence that DNA vaccines are capable of inducing a protective response against live virus was demonstrated using a chimeric SIV/HIV (SHIV) challenge in vaccinated cynomologous macaques. We found that nucleic acid vaccination induced protection from challenge in one out of four immunized cynomolgus macaques and viral load was lower in the vaccinated group of animals versus the control group of animals. These data encouraged us to analyze this vaccination technique in chimpanzees, the most closely related animal species to man. We observed the induction of both cellular and humoral immune responses with a DNA vaccine in chimpanzees. These studies demonstrate the utility of this technology to induce relevant immune responses in primates which may ultimately lead to effective vaccines.

AIDS Vaccines↗

PubMed1995

A vaccine-elicited, single viral epitope-specific cytotoxic T lymphocyte response does not protect against intravenous, cell-free simian immunodeficiency virus challenge.

Protection against simian immunodeficiency virus (SIV) challenge was assessed in rhesus monkeys with a vaccine-elicited, single SIV epitope-specific cytotoxic T-lymphocyte (CTL) response in the absence of SIV-specific antibody. Strategies were first explored for eliciting an optimal SIV Gag epitope-specific CTL response. These studies were performed in rhesus monkeys expressing the major histocompatibility complex (MHC) class I gene Mamu-A*01, a haplotype associated with a predominant SIV CTL epitope mapped to residues 182 to 190 of the Gag protein (p11C). We demonstrated that a combined modality immunization strategy using a recombinant Mycobacterium bovis BCG-SIV Gag construct for priming, and peptide formulated in liposome for boosting, elicited a greater p11C-specific CTL response than did a single immunization with peptide-liposome alone. Vaccinated and control monkeys were then challenged with cell-free SIVmne by an intravenous route of inoculation. Despite a vigorous p11C-specific CTL response at the time of virus inoculation, all monkeys became infected with SIV. gag gene sequencing of the virus isolated from these monkeys demonstrated that the established viruses had no mutations in the p11C-coding region. Thus, the preexisting CTL response did not select for a viral variant that might escape T-cell immune recognition. These studies demonstrate that a potent SIV-specific CTL response can be elicited by combining live vector and peptide vaccine modalities. However, a single SIV Gag epitope-specific CTL response in the absence of SIV-specific antibody did not provide protection against a cell-free, intravenous SIV challenge.

Animals↗

PubMed1988

Discrimination of spatial phase changes: contrast and position codes.

Changing the relative phase of the frequency components of a stimulus usually also produces local contrast variations. Using stimuli composed of the product of a sinusoid (carrier) and a spatial envelope, an attempt was made to distinguish between the visual system's ability to code spatial phase on the one hand and local contrast and position cues on the other. The experiments assess the ability of observers to detect which of two stimuli is farther to the left. In the main experiments a large, easily detectable, envelope shift is presented on every trial and performance is measured as a function of the size of a carrier shift in the same direction. Increasing the size of the carrier shift gradually increases the size of the phase difference between the two stimuli in a trial but simultaneously reduces the contrast change in the bars of the stimulus. If the visual system can code phase directly the ability of observers to detect a change in location should improve as the size of the carrier shift increases but if local contrast is coded performance should be poorer over a small range of carrier shifts than that obtained without a carrier shift. It is shown that a region of poorer performance is obtained and therefore it is concluded that the visual system does not code spatial phase explicitly.

Contrast Sensitivity↗

PubMed2025

IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes.

The Immunoglobulin fold (Ig-fold) is found in proteins from all domains of life and represents the most populous fold in the human genome, with current estimates ranging from 2 to 3% of protein coding regions. That proportion is much higher in the surfaceome where Ig and Ig-like domains orchestrate cell-cell recognition, adhesion and signaling. The ability of Ig-domains to reliably fold and self-assemble through highly specific interfaces represents a remarkable property of these domains, making them key elements of molecular interaction systems: the immune system, the nervous system, the vascular system and the muscular system. We define a universal residue numbering scheme, common to all domains sharing the Ig-fold in order to study the wide spectrum of Ig-domain variants constituting the Ig-proteome and Ig-Ig interactomes at the heart of these systems. The "IgStrand numbering scheme" enables the identification of Ig structural proteomes and interactomes in and between any species, and comparative structural, functional, and evolutionary analyses. We review how Ig-domains are classified today as topological and structural variants and highlight the "Ig-fold irreducible structural signature" shared by all of them. The IgStrand numbering scheme lays the foundation for the systematic annotation of structural proteomes by detecting and accurately labeling Ig-, Ig-like and Ig-extended domains in proteins, which are poorly annotated in current databases and opens the door to accurate machine learning. Importantly, it sheds light on the robust Ig protein folding algorithm used by nature to form beta sandwich supersecondary structures. The numbering scheme powers an algorithm implemented in the interactive structural analysis software iCn3D to systematically recognize Ig-domains, annotate them and perform detailed analyses comparing any domain sharing the Ig-fold in sequence, topology and structure, regardless of their diverse topologies or origin. The scheme provides a robust fold detection and labeling mechanism that reveals unsuspected structural homologies among protein structures beyond currently identified Ig- and Ig-like domain variants. Indeed, multiple folds classified independently contain a common structural signature, in particular jelly-rolls. Examples of folds that harbor an "Ig-extended" architecture are given. Applications in protein engineering around the Ig-architecture are straightforward based on the universal numbering.

Humans↗

PubMed2000

Cloning of genes participating in aerobic biodegradation of p-cumate from Rhodopseudomonas palustris.

Rhodopseudomonas palustris utilizes p-cumate as a carbon source both under anaerobic light and aerobic dark conditions. A gene cluster was isolated whose sequence showed high homology to genes which have been implicated the degradation of p-cumate in Pseudomonas pitida. Seven structural genes coding for dioxygenase-reductase, dihydroxy-dihydro dehydrogenase, and ring cleavage oxygenases were identified. A putative regulator and its possible recognition site was suggested on the basis of homology data. Mutant cells in which a kanamycin cassette was inserted into the dihydroxy-dihydro dehydrogenase gene could not grow aerobically on p-cumate. The mutation had no effect on growth using the para substituted benzoate derivatives 4-hydroxycinnamate, ferulate, protocatechuate, and 2,3,4-trihydroxybenzoate as sole carbon source. Moreover, mutant cells showed a growth pattern similar to wild type cells grown on these compounds under photoheterotrophic anaerobic conditions. These data suggest that genes of this operon are involved specifically in aerobic dissimilation of p-cumate. Intermediate products of p-cumate degradation could be detected from extracts of Escherichia coli heterologously expressing the first 5 genes responsible for the first two steps of p-cumate degradation in R. palustris. Primer extension analysis revealed the transcription regulation of the gene cluster which could be induced with para methyl-, ethyl- and isopropyl (cumate) benzoates. This is the first report on genes involved in aerobic degradation of these compounds in photosynthetic bacteria.

Aerobiosis↗

PubMed2004

Asymmetries in the processing of Arabic digits and number words.

Numbers can be represented as Arabic digits ("6") or as number words ("six"). The present study investigated potential processing differences between the two notational formats. In view of the previous finding (e.g., Potter & Faulconer, 1975) that objects are named slower, but semantically categorized faster, than corresponding words, it was investigated whether a similar interaction between stimulus format and task could be obtained with numbers. Experiment 1 established that number words were named faster than corresponding digits, but only if the two notation formats were presented in separate experimental blocks. Experiment 2 contrasted naming with a numerical magnitude judgment task and demonstrated an interaction between notation and task, with slower naming but faster magnitude judgment latencies for digits than for number words. These findings suggest that processing of the two notation formats is asymmetric, with digits gaining rapid access to numerical magnitude representations, but slower access to lexical codes, and the reverse for number words.

Attention↗

PubMed1982

Bacteriophage T4 gene 45. Sequences of the structural gene and its protein product.

Bacteriophage T4 gene 45 codes for a protein whose functions are required for both T4 DNA replication and T4 late gene transcription. To facilitate studies of the interactions of 45 protein with the T4 DNA replication complex and with RNA polymerase, we have determined the primary structure of 45 protein. The amino acid sequence of 45 protein has been determined by correlating nucleotide sequence analysis of gene 45 with protein chemistry studies of 45 protein. Our studies indicate that gene 45 codes for a polypeptide containing 227 amino acids, with a calculated Mr = 24,710. The coding region of gene 46 is preceded by a putative promoter containing sequences which are homologous to Escherichia coli RNA polymerase recognition and binding regions. In addition, there are sequence similarities in the translation initiation regions of gene 45 and the rIIB gene, which may relate to their common regulation by regA protein.

Base Sequence↗

PubMed1995

Modification of M1 cells by exogenous introduction of IL6 gene: a model for gene therapy of acute and chronic myeloid leukemia in mice.

A number of recent studies has shown that animals immunized with cytokine secreting primary tumors show resistance against an unmodified tumor cell challenge. In the present study we have evaluated the potential role of IL6, a myeloid differentiation inducing factor, in modifying myeloid leukemia cells, a tumor so far not challenged by this approach. M1 cells transduced with N2 based retrovirus carrying the murine IL6 gene exhibit morphological and functional alterations. Genetically modified M1 cells show significant reduction in the growth constant coefficient and in the ability to form hematopoietic colonies. Flow cytometry analysis demonstrate increased expression of CD11b, CD18, F4/80, FcR and MHC class II, suggesting driven differentiation towards commitment. Transduced cells secrete high level of autocrine IL6 and, upon activation with LPS, high levels of TNF further indicating a functional alteration and differentiation. The insertion of IL6 gene coding for signals of cell activation and improved expression of MHC antigens into myeloid leukemia cells may enable more effective tumor recognition in vivo, and boost the local as well as the systemic immune-mediated anti-leukemia response.

Acute Disease↗