Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Computational prediction”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 649 records · Page 36Linked to original sources
PubMed2002

Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs.

BACKGROUND: We describe the development, validation, and use of a highly redundant 120,000 oligonucleotide microarray (MuscleChip) containing 4,601 probe sets representing 1,150 known genes expressed in muscle and 2,075 EST clusters from a non-normalized subtracted muscle EST sequencing project (28,074 EST sequences). This set included 369 novel EST clusters showing no match to previously characterized proteins in any database. Each probe set was designed to contain 20-32 25 mer oligonucleotides (10-16 paired perfect match and mismatch probe pairs per gene), with each probe evaluated for hybridization kinetics (Tm) and similarity to other sequences. The 120,000 oligonucleotides were synthesized by photolithography and light-activated chemistry on each microarray. RESULTS: Hybridization of human muscle cRNAs to this MuscleChip (33 samples) showed a correlation of 0.6 between the number of ESTs sequenced in each cluster and hybridization intensity. Out of 369 novel EST clusters not showing any similarity to previously characterized proteins, we focused on 250 EST clusters that were represented by robust probe sets on the MuscleChip fulfilling all stringent rules. 102 (41%) were found to be consistently "present" by analysis of hybridization to human muscle RNA, of which 40 ESTs (39%) could be genome anchored to potential transcription units in the human genome sequence. 19 ESTs of the 40 ESTs were furthermore computer-predicted as exons by one or more than three gene identification algorithms. CONCLUSION: Our analysis found 40 transcriptionally validated, genome-anchored novel EST clusters to be expressed in human muscle. As most of these ESTs were low copy clusters (duplex and triplex) in the original 28,000 EST project, the identification of these as significantly expressed is a robust validation of the transcript units that permits subsequent focus on the novel proteins encoded by these genes.

Algorithms↗
PubMedDate not supplied

[A new method of global search for functional DNA segments using a fractal representation of nucleotide texts].

New global method for computer prediction of functional sites in nucleotide sequences, based on the fractal representation, is presented. Fractal representation of set of sequences (FRS) provides simple way for generating recognitions matrix of functionally similar sequences and simple estimations of its efficiency for searching homologous regions in new sequences. Other advantages of the method are absence of the necessity of sequences alignment during generating based set and searching new homologous regions and small CPU time. Usage of the method illustrated for searching globin and histone genes, for ALU repeats in human genome and long terminal repeats in virus genome.

Computer Simulation↗
PubMed1998

A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome.

A major mode of gene regulation occurs via the binding of specific proteins to specific DNA sequences. The availability of complete bacterial genome sequences offers an unprecedented opportunity to describe networks of such interactions by correlating existing experimental data with computational predictions. Of the 240 candidate Escherichia coli DNA-binding proteins, about 55 have DNA-binding sites identified by DNA footprinting. We used these sites to construct recognition matrices, which we used to search for additional binding sites in the E. coli genomic sequence. Many of these matrices show a strong preference for non-coding DNA. Discrepancies are identified between matrices derived from natural sites and those derived from SELEX (Systematic Evolution of Ligands by Exponential enrichment) experiments. We have constructed a database of these proteins and binding sites, called DPInteract (available at http://arep.med.harvard.edu/dpinteract).

Bacterial Proteins↗
PubMed1998

Regulation of vascular endothelial growth factor (VEGF) expression is mediated by internal initiation of translation and alternative initiation of transcription.

Vascular Endothelial Growth Factor (VEGF) is a very potent angiogenic agent that has a central role in normal physiological angiogenesis as well as in tumor angiogenesis. VEGF expression is induced by hypoxia and hypoglycemia, and thus was suggested to promote neovascularization during tumor outgrowth. Yet, the molecular mechanism that governs VEGF expression is not fully characterized. VEGF induction is attributed in part to increased levels of transcription and RNA stability. Previously, we demonstrated that the 5' Untranslated Region (5' UTR) of VEGF has an important regulatory role in its expression. VEGF has an exceptionally long 5' UTR (1038 bp) which is highly rich in G+C nucleotides. This suggests that secondary structures in the 5' UTR might be essential for VEGF expression through transcriptional and post-transcriptional control mechanisms, as demonstrated for other growth factors. In this communication, we provide evidence that a computer predicted Internal Ribosome Entry Site (IRES) structure is biologically active and is located at the 3' end of the UTR. In addition, the results demonstrate that an alternative transcriptional initiation site for VEGF exists in the 5' UTR of VEGF. This alternative initiation site is 633 bp downstream of the main transcription start site and the resulting 5' UTR includes mainly the IRES structure. Therefore, our results suggest that VEGF is subjected to regulation at either translational level through a mechanism of ribosome internal initiation and/or transcriptional level through alternative initiation.

Base Sequence↗
PubMed2005

Strategies for characterising cis-regulatory elements in Xenopus.

Understanding the cis-regulatory architecture of metazoan organisms is the greatest challenge facing genome biology today. In vertebrate organisms, distinct sequence elements mediate transcriptional regulation and are scattered throughout the genome, either proximal or distal to promoters. The identification of transcriptional enhancers has proven rather difficult by conventional experimental approaches. In the past decade, the rapid generation of genomic sequences for multiple vertebrate organisms, accompanied by sophisticated comparative tools, has facilitated the identification of non-coding evolutionarily conserved regions that may encode cis-regulatory elements. Validating computational predictions and characterising cis-regulatory elements in vivo, however, has been a major bottleneck, mainly because the most commonly used organism for these experiments has been the mouse, and generating transgenic mice or modifying the mouse genome continues to be a labour-intensive, low-throughput, expensive process. This has led to the use of Xenopus, which holds great promise for high-throughput interrogation of putative cis-regulatory elements. In particular, Xenopus tropicalis may become particularly powerful for elucidating regulatory networks, chiefly because it is amenable to genetic manipulations, and its genome is being sequenced.

Animals↗
PubMed2005

In silico design and adaptive evolution of Escherichia coli for production of lactic acid.

The development and validation of new methods to help direct rational strain design for metabolite overproduction remains an important problem in metabolic engineering. Here we show that computationally predicted E. coli strain designs, calculated from a genome-scale metabolic model, can lead to successful production strains and that adaptive evolution of the engineered strains can lead to improved production capabilities. Three strain designs for lactate production were implemented yielding a total of 11 evolved production strains that were used to demonstrate the utility of this integrated approach. Strains grown on 2 g/L glucose at 37 degrees C showed lactate titers ranging from 0.87 to 1.75 g/L and secretion rates that were directly coupled to growth rates.

Adaptation, Physiological↗
PubMed1997

Experimental confirmation of a hepatitis B virus (HBV) epsilon-like bulge-and-loop structure in avian HBV RNA encapsidation signals.

Hepatitis B viruses replicate via reverse transcription of an RNA intermediate. This RNA pregenome serves as mRNA and is packaged into capsids and reverse transcribed. Both processes require the interaction of the viral reverse transcriptase, P protein, with the 5'-proximal epsilon-signals on the pregenome. For epsilon of human hepatitis B virus (HBV), the presence of a functionally important stem-loop structure with a central bulge, part of which acts as template for a short primer of first-strand DNA synthesis, has been experimentally confirmed. Based on phylogeny and its functional similarities to epsilon, the D epsilon-signal of duck hepatitis B virus (DHBV) had been proposed to have a similar structure which does not, however, correspond to the most stable computer prediction. We have therefore experimentally determined the secondary structures of D epsilon and of the H epsilon-signal of heron hepatitis B virus which differs considerably from D epsilon in primary sequence yet interacts productively with DHBV P protein. Our data support an HBV epsilon-like structure for both D epsilon and H epsilon; in particular the bulge is highly conserved, in accord with its special function in replication. However, the apical loop in H epsilon is much enlarged suggesting that, by an induced-fit mechanism, both RNAs may adopt a new, probably similar conformation in the complex with P protein.

Animals↗
PubMed2004

Nucleocapsid protein of SARS coronavirus tightly binds to human cyclophilin A.

Severe acute respiratory syndrome coronavirus (SARS-CoV) is responsible for SARS infection. Nucleocapsid protein (NP) of SARS-CoV (SARS_NP) functions in enveloping the entire genomic RNA and interacts with viron structural proteins, thus playing important roles in the process of virus particle assembly and release. Protein-protein interaction analysis using bioinformatics tools indicated that SARS_NP may bind to human cyclophilin A (hCypA), and surface plasmon resonance (SPR) technology revealed this binding with the equilibrium dissociation constant ranging from 6 to 160nM. The probable binding sites of these two proteins were detected by modeling the three-dimensional structure of the SARS_NP-hCypA complex, from which the important interaction residue pairs between the proteins were deduced. Mutagenesis experiments were carried out for validating the binding model, whose correctness was assessed by the observed effects on the binding affinities between the proteins. The reliability of the binding sites derived by the molecular modeling was confirmed by the fact that the computationally predicted values of the relative free energies of the binding for SARS_NP (or hCypA) mutants to the wild-type hCypA (or SARS_NP) are in good agreement with the data determined by SPR. Such presently observed SARS_NP-hCypA interaction model might provide a new hint for facilitating the understanding of another possible SARS-CoV infection pathway against human cell.

Amino Acid Sequence↗
PubMed1990

Exon as well as intron sequences are cis-regulating elements for the mutually exclusive alternative splicing of the beta tropomyosin gene.

The beta tropomyosin gene contains two internal exons which are spliced in a mutually exclusive manner. Exon 6B is specifically included in the mature transcripts expressed in skeletal muscle or cultured myotubes, while exon 6A is a myoblast- or smooth muscle-specific exon. The intron between them, which is never spliced in normal conditions, contains two characteristic features: first, the unusual location of the branch point at position -105 from the acceptor, and second, the presence of a very long pyrimidine stretch upstream of the skeletal muscle exon. In this study we designed a number of sequence modifications to investigate the role of these two elements and of a computer-predicted secondary structure in the mutually exclusive splicing of the two exons. We found that mutations in the skeletal exon as well as in the upstream intron could change in vivo the tissue-specific pattern as well as the mutually exclusive character of the two exons. Our results suggest that the unusual position of the branch point does not prevent the utilization of exon 6B in myoblasts and that the region around the acceptor site of exon 6B and the polypyrimidine tract have an important role in this control. Last, we discuss the possible implications of secondary structures.

Animals↗
PubMed2024

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.

BACKGROUND: The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors. RESULTS: Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic. CONCLUSIONS: Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.

Humans↗
PubMed2000

Model study of vector-loop morphology during electrical mapping of microscopic conduction in cardiac tissue.

The large variety in loop morphology of potential differences recorded at the cardiac surface has been generally attributed to structural discontinuities of the tissue. The aim of this work was to examine if the diversity of vector loops of the electric field E found experimentally may also arise during continuous anisotrope conduction. For this purpose a monodomain computer model was used, consisting of a two-dimensional sheet of excitable tissue surrounded with an unbounded volume conductor. Close to the tissue surface our computations predicted a narrow biphasic course of phi(e) with peak-to-peak separation of less than 400 microm. We examined how accurately E could be reconstructed from measurements recorded with four-element electrode arrays and how activation sequence, interelectrode spacing, and probe orientation affects the results. We found "closed" vector loops of E in planar, and at the apex of elliptical wave fronts, whereas outside of these regions vector loops were "open." Varying probe orientation and size resulted in substantial changes of vector-loop morphology. We concluded that close to the cardiac current sources accurate measurement of E would require interelectrode distances of less than 100 microm.

Animals↗
PubMed1992

The use of multiple-pin peptide synthesis in an analysis of the continuous epitopes recognised by various anti-(recombinant bovine growth hormone) sera. Comparison with predicted regions of immunogenicity and location within the three-dimensional structure of the molecule.

A recently developed technology called epitope scanning permits the rapid and accurate delineation of continuous stretches of amino acids in a protein which constitute the sequential epitopes recognised by an antiserum raised to that protein. In the present report, we describe the use of this technique to identify the epitopes in the recombinant bovine growth-hormone (rbGH) molecule recognised by three polyclonal guinea-pig antisera and two polyclonal rabbit antisera. The results obtained show that, for guinea-pig antisera, 3 or 4, very-well-defined major continuous epitopes are present. As would be expected given the intrinsic genetic factors (major histocompatibility restriction, antigen processing and presentation) controlling the immune response in individual animals, subtle differences are evident in the precise location and relative reactivities of these epitopes in different guinea-pig antisera. Nevertheless, there is a large degree of overlap in these epitopes, such that immunodominant regions of the antigen can be clearly delineated. In a structural sense, these epitopes share a common motif in that they are sited in areas of the protein antigen with little secondary structure (loop/coil), although there is some contribution by neighbouring alpha-helices. For the two rabbit antisera, the response tends to be rather more heterogeneous, with recognition of more peptides and less clearly defined epitopes than was the case with the guinea-pig antiserum. Comparison of the four guinea-pig epitopes, identified by our experimental methods with computer predictions for this molecule (Jameson-Wolf antigenic index), indicate that two are strongly predicted, one is weakly predicted and one is not predicted. These observations, together with the displayed intraspecies and interspecies variation clearly indicate the limitations of these predictive methods. In conclusion, we have demonstrated that, despite the expected variation in the exact location of continuous epitopes defined by different anti-rbGH sera, there are large regions of overlap defining immunogenic core regions within the molecule. We believe that studies of this nature, together with further understanding of antigen processing and peptide presentation to immune cells, may have a role to play in the development of candidate peptide vaccines.

Amino Acid Sequence↗
PubMed2006

[Is the Berlin questionnaire an appropriate diagnostic tool for sleep medicine in pneumological rehabilitation?].

BACKGROUND: The Berlin Questionnaire is an explorative tool of 13 questions designed to identify patients with obstructive sleep apnea. The questions are targeted toward key symptoms of snoring, apneas, daytime sleepiness, hypertension and overweight. METHODS: 153 patients undergoing pulmonary rehabilitation were screened for obstructive sleep apnea via i) ApneaLink (ResMed, Munich) and ii) the Berlin Questionnaire. The Epworth Sleepiness Scale (ESS) was administered to grade daytime sleepiness. Results of ApneaLink screening and questionnaires were prospectively compared. The Respiratory Disturbance Index (RDI) was used to compute predictive performance of the Berlin Questionnaire for obstructive sleep apnea. Results were also compared to previously published data from a primary care patient cohort. RESULTS: At a cut-off RDI=10/h, the Berlin Questionnaire had a sensitivity of 62.5 %, a specificity of 53.8 %, a positive predictive value of 38.4 %, a negative predictive value of 74.2 %, a positive likelihood ratio of 1.35 and a negative likelihood ratio of 0.69. At a cut-off RDI=15/h, the Berlin Questionnaire had a sensitivity of 67.2 %, a specificity of 52.8 %, a positive predictive value of 25.1 %, a negative predictive value of 84.7 %, a positive likelihood ratio of 1.42 and a negative likelihood ratio of 0.62. There was evidence that the participants of this study suffered from an increased daytime sleepiness (ESS=8.8 +/- 4.8). The study group was more likely to snore, have apneas (men 6.7 % more often, women 12.6 % more often) and suffer from daytime sleepiness (men 19.0 % more often, women 14.6 % more often) than the control group. Also, hypertension and overweight were more prevalent (men 6.1 % more often, women 11.1 % more often). CONCLUSIONS: The Berlin Questionnaire is a poor predictor of obstructive sleep apnea in a random group of patients undergoing pulmonary rehabilitation.

Adult↗
PubMed2005

Diversification of stem cell molecular repertoire by alternative splicing.

Complete information regarding transcriptional and posttranscriptional gene regulation in stem cells is necessary to understand the regulation of self-renewal and differentiation. Alternative splicing is a prevalent mode of posttranscriptional regulation, and occurs in approximately one half of all mammalian genes. The frequency and functional impact of alternative splicing in stem cells are yet to be determined. In this study we combine computational and experimental methods to identify splice variants in embryonic and hematopoietic stem cells on a genome-wide scale. Using EST collections derived from stem cells, we detect alternative splicing in >1,000 genes. Systematic RT-PCR and sequencing studies show confirmation of computational predictions at a level of 80%. We find that alternative splicing can modify multiple components of signaling pathways important for stem cell function. We also analyze the distribution of splice variants across different classes of genes. We find that tissue-specific genes have a higher tendency to undergo alternative splicing than ubiquitously expressed genes. Furthermore, the patterns of alternative splicing are only weakly conserved between orthologous genes in human and mouse. Our studies reveal extensive modification of the stem cell molecular repertoire by alternative splicing and provide insights into its overall role as a mechanism of generating genomic diversity.

Alternative Splicing↗
PubMed2001

Pharmacokinetics of recombinant factor IX in relation to age of the patient: implications for dosing in prophylaxis.

The aims of this study were to investigate possible age-related changes in the disposition of factor IX procoagulant activity (FIX:C) after administration of recombinant factor IX (rFIX) and to translate the pharmacokinetic findings into suggestions for dosing of rFIX during prophylactic treatment of haemophilia B. Pharmacokinetic data were available from a previous study on 56 patients, aged 4-56 years (one of whom was excluded from analysis). FIX:C curves during prophylactic dosing were computer-simulated from the single-dose data. Clearance and volume of distribution at steady state of FIX:C increased linearly with body weight of the patients, consequently increasing during childhood and adolescence but remaining fairly constant during adulthood. The terminal half-life of FIX:C showed no correlation with age, while in vivo recovery (in U dL(-1) per U kg(-1) given) tended to increase. Computer-predicted trough levels of exogenous FIX:C during repeated doses of rFIX (50 U kg(-1)) and, conversely, doses (in U kg(-1)) needed to maintain a 1-U dL(-1) trough level showed little or no dependence on age. There was considerable interindividual variation in disposition and required doses of rFIX, emphasizing the need for individual dose titration. Dosing of rFIX according to lean body mass instead of body weight did not reduce this variability. During prophylaxis a 1-U dL(-1) trough level can normally be maintained by dosing every 2-3 days, the former schedule resulting in, on average, a 45% lower consumption of rFIX.

Adolescent↗
PubMed1995

A 3' untranslated region of catalase mRNA composed of a stem-loop and dinucleotide repeat elements binds a 69-kDa redox-sensitive protein.

Rat lung extract contains protein that forms redox-sensitive, specific complexes with a 1130-base catalase cRNA (J. Biol. Chem. 267, 2853-2855, 1992). The present paper reports studies aimed at delimiting the site of protein binding on the RNA and characterizing the protein. A 240-base sequence was identified as the 3' untranslated region of catalase mRNA that binds lung protein in a redox-sensitive manner. Two elements within this 240-base region bind protein; one is a 36-base element that has a computer-predicted stem-loop secondary structure and the other is a CA dinucleotide repeat. Competition studies indicate that both elements are required for specific binding. Cross-competition experiments demonstrated that catalase RNA-binding protein (CAT-BP) is not the iron-responsive element-binding protein. Ultraviolet light-induced cross-linking and two-dimensional electrophoresis showed that CAT-BP has an apparent molecular mass of 69 kDa and appears to be composed of four isoforms. Competition studies indicate that stem-loop cis element is directly involved in binding CAT-BP. In addition to rat, the 69-kDa catalase RNA-binding protein is present in mouse and human fibroblast cell lines.

Animals↗
PubMed1987

Absorption of theophylline from a sustained-release theophylline tablet formulation, Theo-Dur.

The absorption kinetics of theophylline after single oral administration of a sustained-release theophylline tablet formulation, Theo-Dur, were studied in healthy volunteers. The pharmacokinetic parameters were estimated by utilizing a one-compartment model with zero-order or first-order absorption according to the procedure "Praxis". The release of theophylline from the formulation in the in vitro dissolution study was shown to be an apparent zero-order process. The in vivo studies demonstrated that the time required to reach maximum plasma concentration of theophylline was about 8 h. The mean residence time in vivo, MRT, was 18.6 h. The present study also showed that the formulation was good sustained-release properties with adequate bioavailability and that the in vitro sustained-release characteristic was confirmed to be reflected in the plasma concentration-time profile of theophylline in the in vivo. The computer-predicted concentrations of theophylline based on the zero-order absorption model fitted to the observed data points better than those based on the first-order absorption model. The regression curves obtained by nonlinear least squares method based on the first-order absorption model underestimate the maximum observed plasma concentrations of theophylline. There was a highly significant relationship between observed and calculated around the maximum plasma concentration data based on the zero-order absorption model. These results show that the drug absorption from the formulation is best described by an apparent zero-order rather than a first-order absorption model.

Absorption↗
PubMed1994

The role of arginine 143 in the electrostatics and mechanism of Cu,Zn superoxide dismutase: computational and experimental evaluation by mutational analysis.

Cu,Zn superoxide dismutase protects cells from oxidative damage by removing superoxide radicals in one of the fastest enzyme reactions known. The redox reaction at the active-site Cu ion is rate-limited by diffusion and enhanced by electrostatic guidance. To quantitatively define the electrostatic and mechanistic contributions of sequence-invariant Arg-143 in human Cu,Zn superoxide dismutase, single-site mutants at this position were investigated experimentally and computationally. Rate constants for several Arg-143 mutants were determined at different pH and ionic strength conditions using pulse radiolytic methods and compared to results from Brownian dynamics simulations. At physiological pH, substitution of Arg-143 by Lys caused a 2-fold drop in rate, neutral substitutions (Ile, Ala) reduced the rate about 10-fold, while charge-reversing substitutions (Asp, Glu) caused a 100-fold decrease. Position 143 mutants showed pH dependencies not seen in other mutants. At low pH, the acidic residue mutations exhibited protonation/deprotonation effects. At high pH, all enzymes showed typical decreases in rate except the Lys mutant in which the rate dropped off at an unusually low pH. Increasing ionic strength at acidic pH decreased the rates of the wild-type enzyme and Lys mutant, while the rate of the Glu mutant was unaffected. Increasing ionic strength at higher pH (> 10) increased the rates of the Lys and Glu mutants while the rate of the wild-type enzyme was unaffected. Reaction simulations with Brownian dynamics incorporating electrostatic effects tested computational predictability of ionic strength dependencies of the wild-type enzyme and the Lys, Ile, and Glu mutants. The calculated and experimental ionic strength profiles gave similar slopes in all but the Glu mutant, indicating that the electrostatic attraction of the substrate is accurately modeled. Differences between the calculated and experimental rates for the Glu and Lys mutants reflect the mechanistic contribution of Arg-143. Results from this joint analysis establish that, aside from the Cu ligands, Arg-143 is the single most important residue in Cu,Zn superoxide dismutase both electrostatically and mechanistically, and provide an explanation for the evolutionary selection of arginine at position 143.

Arginine↗