Artificial intelligence approach in analysis of DNA sequences.

Abstract:

:We present an approach for designing a knowledge-based system, called Sequence Acquisition In Context (SAIC), that will be able to cooperate with a biologist in the analysis of DNA sequences. The main task of the system is the acquisition of the expert knowledge that the biologist uses for solving ambiguities from gel autoradiograms, with the aim of re-using it later for solving similar ambiguities. The various types of expert knowledge constitute what we call the contextual knowledge of the sequence analysis. Contextual knowledge deals with the unavoidable problems that are common in the study of the living material (eg noise on data, difficulties of observations). Indeed, the analysis of DNA sequences from autoradiograms belongs to an emerging and promising area of investigation, namely reasoning with images. The SAIC project is developed in a theoretical framework that is shared with other applications. Not all tasks have the same importance in each application. We use this observation for designing an intelligent assistant system with three applications. In the SAIC project, we focus on knowledge acquisition, human-computer interaction and explanation. The project will benefit research in the two other applications. We also discuss our SAIC project in the context of large international projects that aim to re-use and share knowledge in a repository.

journal_name

Biochimie

journal_title

Biochimie

authors

Brézillon PJ,Zaraté P,Saci F

doi

10.1016/0300-9084(93)90167-q

subject

Has Abstract

pub_date

1993-01-01 00:00:00

pages

337-45

issue

5

eissn

0300-9084

issn

1638-6183

pii

0300-9084(93)90167-Q

journal_volume

75

pub_type

杂志文章
  • Thiolation of low-density lipoproteins and their interaction with L2C leukemic lymphocytes.

    abstract::We present here, a new method for coupling sulfhydryl groups (SH) to low-density lipoprotein (LDL) surface. This method uses homocysteine thiolactone (HCTL) which reacts with lysine residues in a very mild manner, and permits the selection of the number of SH bound per LDL. Under our experimental conditions (8 SH/LDL)...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/s0300-9084(86)80166-3

    authors: Vidal M,Sainte-Marie J,Philippot J,Bienvenue A

    更新日期:1986-05-01 00:00:00

  • Purification of the catalytic subunit of adenylate cyclase in vertebrates: state of the art in 1987.

    abstract::After 30 years of effort, the mammalian adenylate cyclase catalytic subunit has now been purified. It is a glycoprotein of 155 kDa, representing less than 0.01% of synaptosomal membrane protein. As measured in the presence of forskolin, its specific activity is 10-20 mumol of cAMP X mg-1 X min-1. The enzyme obtained i...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/0300-9084(87)90016-2

    authors: Monneron A,d'Alayer J,Coussen F

    更新日期:1987-04-01 00:00:00

  • Conformational change at the active center of serine-proteases upon their binding to alpha 2-macroglobulin.

    abstract::The inhibition rates and spectral characteristics of 2 probes specific for the active-site serine residue of proteases were examined for evidence of conformational change of the proteases upon their binding to alpha 2-macroglobulin (alpha 2M). Elastase, chymotrypsin, trypsin, and plasmin were reacted with (7-nitrobenz...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/0300-9084(89)90004-7

    authors: Martini JL,Pochon F

    更新日期:1989-03-01 00:00:00

  • How botulinum and tetanus neurotoxins block neurotransmitter release.

    abstract::Botulinum neurotoxins (BoNT, serotypes A-G) and tetanus neurotoxin (TeNT) are bacterial proteins that comprise a light chain (M(r) approximately 50) disulfide linked to a heavy chain (M(r) approximately 100). By inhibiting neurotransmitter release at distinct synapses, these toxins cause two severe neuroparalytic dise...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/s0300-9084(00)00216-9

    authors: Humeau Y,Doussau F,Grant NJ,Poulain B

    更新日期:2000-05-01 00:00:00

  • Formation of protein complexes containing plant virus movement protein TGBp3 is necessary for its intracellular trafficking.

    abstract::Cell-to-cell movement of Poa semilatent virus (genus Hordeivirus) in infected plants is mediated by three viral 'triple gene block' (TGB) proteins. One of those termed TGBp3 is an integral membrane protein essential for intracellular transport of other TGB proteins and viral genomic RNA to plasmodesmata. TGBp3 targeti...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2011.01.002

    authors: Shemyakina EA,Erokhina TN,Gorshkova EN,Schiemann J,Solovyev AG,Morozov SY

    更新日期:2011-04-01 00:00:00

  • Peptide synthesis by recombinant Fasciola hepatica cathepsin L1.

    abstract::Synthesis of the tripeptide Z-Phe-Arg-SerNH2 has been accomplished by a recombinant cysteine protease, cathepsin L1 from liver fluke (Fasciola hepatica), using Z-Phe-Arg-OMe as acyl acceptor and SerNH2 as nucleophile in 0.1 M ammonium acetate pH 9.0-12.5% v/v acetonitrile at 37 degrees C. LC-MS detection indicated tri...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2005.06.004

    authors: Ruth DM,McMahon G,O'Fágáin C

    更新日期:2006-01-01 00:00:00

  • A stochastic approach to serotonergic fibers in mental disorders.

    abstract::Virtually all brain circuits are physically embedded in a three-dimensional matrix of fibers that release 5-hydroxytryptamine (5-HT, serotonin). The density of this matrix varies across brain regions and cortical laminae, and it is altered in some mental disorders, including Major Depressive Disorder and Autism Spectr...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2018.07.014

    authors: Janušonis S,Detering N

    更新日期:2019-06-01 00:00:00

  • Complete sequence of one of the mRNAs coding for the small subunit of ribulose bisphosphate carboxylase of Nicotiana sylvestris.

    abstract::The combination of cDNA and RNA sequencing techniques has enabled determination of the complete sequence of one of the mRNAs coding for the precursor of the small subunit of ribulose bisphosphate carboxylase of Nicotiana sylvestris. In this 898-nucleotide-long mRNA, 540 nucleotides code for the entire 180-amino-acid-l...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/0300-9084(84)90148-2

    authors: Pinck M,Guilley E,Durr A,Hoff M,Pinck L,Fleck J

    更新日期:1984-07-01 00:00:00

  • Fragile X mental retardation protein: A paradigm for translational control by RNA-binding proteins.

    abstract::Translational control is a common mechanism used to regulate gene expression and occur in bacteria to mammals. Typically in translational control, an RNA-binding protein binds to a unique sequence in the mRNA to regulate protein synthesis by the ribosomes. Alternatively, a protein may bind to or modify a translation f...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/j.biochi.2015.02.005

    authors: Chen E,Joseph S

    更新日期:2015-07-01 00:00:00

  • Phospholipid fatty acid pattern and D-glucose metabolism in muscles from omega3 fatty acid-depleted rats.

    abstract::A depletion in long-chain polyunsaturated omega3 fatty acids may affect fuel homeostasis. In such a perspective, the present study deals mainly with the in vitro fate of D-[U-(14)C]glucose in hemidiaphragms, stretched soleus and plantaris muscle pieces obtained from normal and omega3-depleted rats (second generation) ...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2006.10.004

    authors: Agascioglu E,Zhang Y,Sener A,Portois L,Chardigny JM,Malaisse WJ,Carpentier YA

    更新日期:2007-03-01 00:00:00

  • Escherichia coli DnaA protein--phospholipid interactions: in vitro and in vivo.

    abstract::DNA replication in Escherichia coli is controlled at the initiation stage, possibly by regulation of the essential activity of DnaA protein. The cellular membrane has long been hypothesized to be involved in chromosomal replication. Accumulating evidence, both in vitro and in vivo, that supports the importance of memb...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/s0300-9084(00)01224-4

    authors: Crooke E

    更新日期:2001-01-01 00:00:00

  • Characterization of DOPA decarboxylase mRNA in rat pheochromocytoma.

    abstract::Total poly (A+) RNA has been extracted from rat pheochromocytoma and translated in vitro by means of a reticulocyte lysate system. We show that two antisera, prepared against pig kidney DOPA decarboxylase (DDC) or rat pheochromocytoma DDC, immunoprecipitate an in vitro synthetized 50 kDa polypeptide identified as DDC ...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/0300-9084(90)90175-g

    authors: Bruneau G,Krieger-Poullet M,Coge F,Borri-Voltattorni C,Gros F,Thibault J

    更新日期:1990-01-01 00:00:00

  • Characterization of conserved microRNAs from five different cucurbit species using computational and experimental analysis.

    abstract::MicroRNAs (miRNAs) are ∼21 nt non-coding small RNAs which regulate gene expression at the post-transcriptional level in plants and animals. Until recently, only limited numbers of miRNAs were identified in Cucurbitaceae, a large flowering plant family. In this study, 220 potential miRNA candidates were identified from...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2014.03.002

    authors: Hu J,Sun L,Zhu Z,Zheng Y,Xiong W,Ding Y

    更新日期:2014-07-01 00:00:00

  • Isocitrate dehydrogenase 1 from Acinetobacter baummanii (AbIDH1) enzymatic characterization and its regulation by phosphorylation.

    abstract::Acinetobacter baumannii encodes all enzymes required in the tricarboxylic acid (TCA) cycle and glyoxylate bypass except for isocitrate dehydrogenase kinase/phosphatase (IDHKP), which can phosphorylate isocitrate dehydrogenase (IDH) at a substrate-binding Ser site and control the carbon flux in enterobacteria, such as ...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2020.12.001

    authors: Song P,Wang ML,Zheng QY,Wang P,Zhu GP

    更新日期:2020-12-05 00:00:00

  • Characterization of genetic interactions with RFA1: the role of RPA in DNA replication and telomere maintenance.

    abstract::Replication protein A (RPA) is a heterotrimeric single-stranded DNA binding protein whose role in DNA replication, recombination and repair has been mainly elucidated through in vitro biochemical studies utilizing the mammalian complex. However, the identification of homologs of all three subunits in Saccharomyces cer...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/s0300-9084(00)00183-8

    authors: Smith J,Zou H,Rothstein R

    更新日期:2000-01-01 00:00:00

  • A comparative Raman spectroscopic study of cholinesterases.

    abstract::We report Raman spectra of various cholinesterases: lytic tetrameric forms (G4) obtained by tryptic digestion of asymmetric acetylcholinesterase (AChE) from Torpedo californica and Electrophorus electricus, a PI-PLC-treated dimeric form (G2) of AChE from T marmorata, and the soluble tetrameric form (G4) of butyrylchol...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/0300-9084(91)90167-y

    authors: Aslanian D,Grof P,Bon S,Masson P,Négrerie M,Chatel JM,Balkanski M,Taylor P,Massoulié J

    更新日期:1991-11-01 00:00:00

  • An idiosyncratic serine ordering loop in methanogen seryl-tRNA synthetases guides substrates through seryl-tRNASer formation.

    abstract::Seryl-tRNA synthetases (SerRS) covalently attach serine to cognate tRNA(Ser). Atypical SerRSs, considerably different from canonical enzymes, have been found in methanogenic archaea. A crystal structure of methanogenic-type SerRS revealed a motif within the active site (serine ordering loop; SOL), which undergoes a no...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2011.06.013

    authors: Dulic M,Pozar J,Bilokapic S,Weygand-Durasevic I,Gruic-Sovulj I

    更新日期:2011-10-01 00:00:00

  • A convenient and robust method for construction of combinatorial and random mutant libraries.

    abstract::Here we describe a convenient and robust ligase-independent method for construction of combinatorial and random mutant libraries. The homologous genes flanked by plasmid-derived DNA sequences are fragmented, and the random fragments are reassembled in a self-priming polymerase reaction to obtain chimeric genes. The pr...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2010.03.016

    authors: An Y,Wu W,Lv A

    更新日期:2010-08-01 00:00:00

  • Role of membrane sialic acid and glycophorin protein in thorium induced aggregation and hemolysis of human erythrocytes.

    abstract::Thorium-232 ((232)Th), a natural radionuclide from the actinide family, is abundantly present in monazite and other ores. It is used as one of the prime fuel materials in nuclear industry and may pose an exposure risk to nuclear workers and members of the public. Human erythrocytes, as a classical cellular membrane mo...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2010.03.008

    authors: Kumar A,Ali M,Pandey BN,Hassan PA,Mishra KP

    更新日期:2010-07-01 00:00:00

  • Inhibition of glycosyltransferases by bis-(p-nitrophenyl)phosphate: general effect and relation to their membrane integration.

    abstract::The effect of bis-(p-nitrophenyl)phosphate on various glycosyltransferases involved in protein glycosylation (sialyl-, fucosyl-, galactosyl-, mannosyl- and glucosyltransferases) have been studied using crude enzyme preparations solubilized from rat spleen lymphocytes. Bis-(p-nitrophenyl)phosphate appears as a common i...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/s0300-9084(83)80106-0

    authors: Guette F,Cacan R,Montreuil J,Verbert A

    更新日期:1983-10-01 00:00:00

  • A role for calcium in Bcl-2 action?

    abstract::Changes in the cytosolic Ca(2+) concentration ([Ca(2+)](c)) translate a variety of extracellular signals into widely diverse intracellular effects, ranging from secretion to movement, proliferation and also cell death. As regards the last one, it has long been known that large [Ca(2+)](c) increases lead cells to death...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/s0300-9084(02)01373-1

    authors: Pinton P,Ferrari D,Rapizzi E,Di Virgilio F,Pozzan T,Rizzuto R

    更新日期:2002-02-01 00:00:00

  • Feedback control of ribosome function in Escherichia coli.

    abstract::We have previously proposed that the rate of ribosome function during balanced growth in E. coli, expressed as the rate of peptide chain elongation, is adjusted by a feedback mechanism: whenever that rate is submaximal (i.e. below 22 amino acid residues polymerized per active ribosome at 37 degrees C), the feedback si...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2007.10.008

    authors: Bremer H,Dennis P

    更新日期:2008-03-01 00:00:00

  • EPR determination of the oxidation-reduction potentials of the hemes in cytochrome c3 from Desulfovibrio vulgaris.

    abstract::EPR spectroscopy in conjunction with oxidation-reduction potentiometry has been used to determine the half-reduction potentials of the four hemes of cytochrome c3. As predicted, the four hemes of cytochrome c3 have different mid-point potentials. The Em values are: Heme I,--284 mV; Heme II,--310 mV; Heme III,--324 mV ...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/s0300-9084(78)80829-3

    authors: Dervartanian DV,Xavier AV,Gall JL

    更新日期:1978-01-01 00:00:00

  • Molecular property-binding affinity relationship of flavonoids for common rat plasma proteins in vitro.

    abstract::The structural difference of flavonoids strongly affects the binding process with plasma proteins. This work in here mainly concerns about the molecular property-binding affinity relationship of dietary flavonoids for common rat plasma proteins (CRPP). The magnitudes of binding constants between flavonoids and CRPP we...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2010.08.013

    authors: Xiao J,Cao H,Chen T,Yang F,Liu C,Xu X

    更新日期:2011-02-01 00:00:00

  • New insights into the formation of HIV-1 reverse transcription initiation complex.

    abstract::HIV-1 reverse transcriptase uses the host tRNA3(Lys) as a primer for the synthesis of the minus DNA strand. The first event in viral replication is thus the annealing of tRNA to the primer binding site (PBS) in the 5' UTR of the viral RNA. This event requires a major RNA rearrangement which is chaperoned by the viral ...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2007.01.016

    authors: Barraud P,Gaudin C,Dardel F,Tisné C

    更新日期:2007-10-01 00:00:00

  • An active site mutant of Escherichia coli cyclopropane fatty acid synthase forms new non-natural fatty acids providing insights on the mechanism of the enzymatic reaction.

    abstract::We have produced and purified an active site mutant of the Escherichia coli cyclopropane fatty acid synthase (CFAS) by replacing the strictly conserved G236 within cyclopropane synthases, by a glutamate residue, which corresponds to E146 of the homologous mycolic acid methyltransferase, Hma, producing hydroxymethyl my...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2013.08.007

    authors: E G,Drujon T,Correia I,Ploux O,Guianvarc'h D

    更新日期:2013-12-01 00:00:00

  • Evidence for a phosphoenolpyruvate dependent sugar-phosphotransferase system in the mollicute Acholeplasma florum.

    abstract::In order to confirm the presence of a phosphoenolpyruvate (PEP)-dependent sugar-phosphotransferase system (PTS) in the mollicute Acholeplasma florum we studied the ability of cell free extracts of this organism to phosphorylate glucose and/or fructose in the presence of PEP. We also cloned and sequenced a DNA fragment...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/0300-9084(93)90098-d

    authors: Navas-Castillo J,Laigret F,Hocquellet A,Chang CJ,Bove JM

    更新日期:1993-01-01 00:00:00

  • Alterations of endogenous sphingolipid metabolism in cardiometabolic diseases: Towards novel therapeutic approaches.

    abstract::The increasing prevalence of obesity and metabolic diseases is a worldwide public health concern, and the advent of new analytical technologies has made it possible to highlight the involvement of some molecules, such as sphingolipids (SL), in their pathophysiology. SL are constituents of cell membranes, lipoproteins ...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/j.biochi.2019.10.003

    authors: Le Barz M,Boulet MM,Calzada C,Cheillan D,Michalski MC

    更新日期:2020-02-01 00:00:00

  • Does histone H1 bind specifically to the nuclear factor I recognition sequence?

    abstract::The issue of whether histone H1 possesses specificity of binding to certain nucleotide sequences in DNA is of fundamental importance to the suggested role of the linker histone in the regulation of gene transcription. The purpose of the present study was to reinvestigate the specificity of binding of histone H1 to the...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/0300-9084(93)90116-a

    authors: Yaneva JN,Zlatanova JS

    更新日期:1993-01-01 00:00:00

  • Complete purification and studies on the structural and kinetic properties of two forms of yeast valyl-tRNA synthetase.

    abstract::Two forms of baker's yease valyl-tRNA synthetase have been purified to apparent homogeneity by classical methods. It was demonstrated that one of the two forms of the enzyme originates from the other by proteolysis, the respective amounts of each form depending on the physiological state of the yeast. The species main...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/s0300-9084(76)80579-2

    authors: Kern D,Giegé R,Robre-Saul S,Boulanger Y,Ebel JP

    更新日期:1975-01-01 00:00:00