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Biomedical subjects

S Kuhara

Publications and source records attributed to S Kuhara.

At least 37 records · Page 2Linked to original sources
PubMed1999

Identification of genetic networks from a small number of gene expression patterns under the Boolean network model.

Liang, Fuhrman and Somogyi (PSB98, 18-29, 1998) have described an algorithm for inferring genetic network architectures from state transition tables which correspond to time series of gene expression patterns, using the Boolean network model. Their results of computational experiments suggested that a small number of state transition (INPUT/OUTPUT) pairs are sufficient in order to infer the original Boolean network correctly. This paper gives a mathematical proof for their observation. Precisely, this paper devises a much simpler algorithm for the same problem and proves that, if the indegree of each node (i.e., the number of input nodes to each node) is bounded by a constant, only O(log n) state transition pairs (from 2n pairs) are necessary and sufficient to identify the original Boolean network of n nodes correctly with high probability. We made computational experiments in order to expose the constant factor involved in O(log n) notation. The computational results show that the Boolean network of size 100,000 can be identified by our algorithm from about 100 INPUT/OUTPUT pairs if the maximum indegree is bounded by 2. It is also a merit of our algorithm that the algorithm is conceptually so simple that it is extensible for more realistic network models.

Algorithms↗
PubMed1999

Use of BONSAI decision trees for the identification of potential MHC class I peptide epitope motifs.

Recognition of short peptides of 8 to 10 mer bound to MHC class I molecules by cytotoxic T lymphocytes forms the basis of cellular immunity. While the sequence motifs necessary for binding of intracellular peptides to MHC have been well studied, little is known about sequence motifs that may cause preferential affinity to the T cell receptor and/or preferential recognition and response by T cells. Here we demonstrate that computational learning systems can be useful to elucidate sequence motifs that affect T cell activation. Knowledge of T cell activation motifs could be useful for targeted vaccine design or immunotherapy. With the BONSAI computational learning algorithm, using a database of previously reported MHC bound peptides that had positive or negative T cell responses, we were able to identify sequence motif rules that explain 70% of positive T cell responses and 84% of negative T cell responses.

Algorithms↗
PubMed1999

A System to Find Genetic Networks Using Weighted Network Model.

We are developing a system which finds a genetic network from data obtained by multiple gene disruptions and overexpressions. We deal with a genetic network as a weighted graph, where each weight represents the strength of activation from a gene to another gene. In this paper, we explain the overview of our system, and our strategy to visualize the weighted network. We also study the computational complexity related to the visualization.

Journal Article↗
PubMed1998

Complete nucleotide sequences of 93-kb and 3.3-kb plasmids of an enterohemorrhagic Escherichia coli O157:H7 derived from Sakai outbreak.

Enterohemorrhagic Escherichia coli (EHEC) O157:H7, derived from an outbreak in Sakai city, Japan in 1996, possesses two kinds of plasmids: a 93-kb plasmid termed pO157, found in clinical EHEC isolates world-wide and a 3.3-kb plasmid termed pOSAK1, prevalent in EHEC strains isolated in Japan. Complete nucleotide sequences of both plasmids have been determined, and the putative functions of the encoded proteins and the cis-acting DNA sequences have been analyzed. pO157 shares strikingly similar genes and DNA sequences with F-factor and the transmissible drug-resistant plasmid R100 for DNA replication, copy number control, plasmid segregation, conjugative functions and stable maintenance in the host, although it is defective in DNA transfer by conjugation due to the truncation and deletion of the required genes and DNA sequences. In addition, it encodes several proteins implicated in EHEC pathogenicity such as an EHEC hemolysin (HlyA), a catalase-peroxidase (KatP), a serine protease (EspP) and type II secretion system. pOSAK1 possesses a ColE1-like replication system, and the DNA sequence is extremely similar to that of a drug-resistant plasmid, NTP16, derived from Salmonella typhimurium except that it lacks drug resistance transposons.

DNA, Bacterial↗
PubMed1998

Molecular dynamics simulations of HLA-DR4 (DRB1*0405) complexed with analogue peptide: conformational changes in the putative T-cell receptor binding regions.

The specific recognition of foreign peptide bound to the major histocompatibility complex (MHC) molecule by T-cell receptor (TCR) leads to T-cell activation. We found that analogue peptides containing single amino acid substitutions at the third amino acid position (p3), p5, p7 and p8 of the index peptide (YWALEAAAD) induced different response patterns of T cell clones specific for the index peptide in the context of the human MHC class II molecule HLA-DR4. Analogue peptides were classified into three types, agonists, antagonists or null peptides (non-agonistic and non-antagonistic peptides). A molecular basis for how these slight changes lead to such different consequences for T cells has not been described. To explore the mechanistic basis of these observations, molecular dynamics simulations at 300 K of 300 ps duration were carried out for the DR4-index peptide, DR4-agonist, and DR4-antagonist complexes. The simulations showed that the DR4-antagonist complexes were distinguished from the DR4-index peptide and DR4-agonist complexes by relatively higher deviations of C(alpha) atoms in proposed TCR-binding regions, suggesting that subtle changes of the exposed framework of the peptide binding groove by the antagonist peptides could induce the TCR antagonistic activities.

Amino Acid Sequence↗
PubMed1998

Finding Genetic Network from Experiments by Weighted Network Model.

We study the problem of finding a genetic network from data obtained by multiple gene disruptions and overexpressions. We define a genetic network as a weighted graph, and analyze the computational complexity of the problem. We show that if there exists a weighted network which is consistent with given data, we can find it in polynomial time. Moreover, we also consider the optimization problem, where we try to find an optimally consistent weighted network with given data. We show that the problem is NP-hard. On the other hand, we give a polynomial-time approximation algorithm to solve it with approximation ratio 2. We report some simulation results on experiments.

Journal Article↗
PubMed1998

A System for Identifying Genetic Networks from Gene Expression Patterns Produced by Gene Disruptions and Overexpressions.

A hot research topic in genomics is to analyze the interactions between genes by systematic gene disruptions and gene overexpressions. Based on a boolean network model without time delay, we have been investigating efficient strategies for identifying a genetic network by multiple gene disruptions and overexpressions. This paper first shows the relationship between our boolean network model without time delay and the standard synchronous boolean network model. Then we present a simulator of boolean networks without time delay for multiple gene disruptions and gene overexpressions, which includes a genetic network identifier with a graphic interface that generates instructions for experiments of gene disruptions and overexpressions.

Journal Article↗
PubMed1997

Temporal changes in expression of transforming growth factor-beta superfamily members and their receptors during bovine preodontoblast differentiation in vitro.

Transforming growth factor (TGF)-beta superfamily members and their receptors play a part in the differentiation of pulp cells into odontoblasts during reparative dentinogenesis. Bovine primary pulp-cell culture has been used as an in vitro model for proliferation and differentiation of pulp cells into preodontoblasts. To explore the molecular cascade of odontoblast differentiation, Northern blot analyses and reverse transcriptase polymerase chain reaction were here used to investigate the expression patterns of the genes for TGF-beta superfamily members: TGF-beta 1, namely bone morphogenetic protein (BMP)-4, BMP-7, activin-beta A and activin-beta B, and their type I and type II receptors, namely activin receptor-like kinase (ALK)-2 (ActR-I), ALK-3 (BMPR-IA), ALK-4 (ActR-IB), ALK-5 (T beta R-I), BMPR-II and T beta R-II, during differentiation of pulp cells into preodontoblasts in bovine adult pulp-cell culture. TGF-beta 1 and BMP-4 mRNAs were expressed from day 14 when matrix formation increased. BMP-7 mRNA was expressed only on day 28 when osteocalcin appeared. ALK-2 mRNA was increased from the beginning of the culture. ALK-3 and ALK-5 mRNAs first decreased on day 14 and increased again on day 21. T beta R-II and BMPR-II mRNAs were almost constant. These results suggest that the differentiation of pulp cells into preodontoblasts may be regulated by changes in the temporally coordinated expression pattern of TGF-beta superfamily members and their receptors, including up-regulation of transcription of TGF-beta 1, BMP-4, BMP-7, ALK-2, ALK-3, and ALK-5.

Amino Acid Sequence↗
PubMed1997

Two closely-related left-right asymmetrically expressed genes, lefty-1 and lefty-2: their distinct expression domains, chromosomal linkage and direct neuralizing activity in Xenopus embryos.

BACKGROUND: Vertebrates have numerous lateral asymmetries in the position of their organs, but the molecular basis for the determination of left-right (L-R) asymmetries remains largely unknown. TGFbeta-related genes such as lefty and nodal are L-R asymmetrically expressed in developing mouse embryos, and may be involved in L-R determination. RESULTS: We have identified two highly conserved genes, lefty-1 and lefty-2, in the mouse genome. These two genes are tightly linked on mouse chromosome 1. lefty-1 and lefty-2 are both expressed in a L-R asymmetric fashion in mouse embryos. However, the major expression domains of the two genes are different: lefty-1 expression is predominantly confied to the left side of ventral neural tube, whereas lefty-2 is strongly expressed in the lateral plate mesoderm on the left side. In embryos homozygous for the iv and inv mutation, which cause situs inversus, the expression sites of both genes are affected, either reversed or bilaterally, indicating that lefty-1 and lefty-2 are downstream of iv and inv. Although Lefty-1 and Lefty-2 prepro-proteins are not readily processed in cultured cells, BMP2-Lefty chimeric proteins can be processed to a secreted form. We have examined the activities of Lefty-1 and Lefty-2 in Xenopus embryos. In animal cap explants, Lefty-1 and Lefty-2 induce neural cells in the absence of mesoderm induction. The direct neuralizing activities of Lefty-1 and Lefty-2 thus seem remarkably similar to those of BMP antagonists such as noggin and chordin, suggesting that the action of Lefty-1 and Lefty-2 may be to locally antagonize BMP (bone morphogenic protein)-mediated signals in tissues positioned on the left side of the mouse embryos. CONCLUSION: There are two lefty genes in mice (lefty-1 and lefty-2), both of which are expressed in a L-R asymmetric fashion and are downstream of iv and inv. Lefty-1 and Lefty-2 possess direct neuralizing activity in Xenopus embryos, resembling the activities of BMP antagonists.

Amino Acid Sequence↗
PubMed1997

Application of a deductive database system to search for topological and similar three-dimensional structures in protein.

A deductive database system PACADE (Protein Atomic Coordinate Analyzer with Deductive Engine) has been developed for protein structure analysis. With this system, super-secondary structures described in logical and declarative rules can be retrieved effectively. For protein structure analysis, comparison of local structures in different proteins is a necessary mean. A function to search for similar structures has, therefore, been added to the PACADE system. We describe herein the result of searches for the same topological structures and three-dimensionally similar ones. A user of PACADE can select these two levels of similarity by changing parameters. This function enables the inference system to retrieve similar structures, according to the restraints of variables defined by the user. Similar super-secondary structures among proteins can be searched for automatically, which is useful for protein structure analysis. The retrieved similar super-secondary structures can serve as criteria for protein spatial alignment.

Algorithms↗
PubMed1997

Expression of TGF-beta superfamily receptors in dental pulp.

Transforming growth factor-beta (TGF-beta) superfamily members and their cell-surface receptors may play inductive and/or regulatory roles in tooth development and repair. It will be important to identify the complete set of TGF-beta superfamily receptors, to examine their temporal and spatial localization during tooth development, and to elucidate the cascade of molecular events of tooth formation induced by the TGF-beta superfamily. In this report, we have cloned the cDNAs encoding potential receptors for TGF-beta superfamily members in rat incisor pulp and bovine adult pulp which are regarded as embryonic and adult pulp, respectively. We analyzed poly (A)+ RNA from rat incisor pulp and bovine adult pulp by reverse-transcriptase/polymerase chain-reaction (RT-PCR), using a degenerate primers corresponding to the most conserved amino acid sequences in the intracellular serine/threonine kinase of type I or type II like kinase-1 (ALK-1), ALK-2, ALK-3 (bone morphogenetic protein receptor type IA, BMPR-IA), ALK-4 (B1), ALK-5, ALK-6 (BMPR-IB), and BMPR-II (BMP type II receptor) was found to be in dental pulp. Northern blot analysis further detected TGF-beta type II receptor (T beta R-II) mRNA transcript in addition to the above-identified receptors. These results provide the first evidence of multiple type I and type II receptors for TGF-beta s, activins, and BMPs expressed in embryonic and adult pulp, implicating diverse function in tooth development and pulp tissue repair.

Activin Receptors↗
PubMed1997

Prediction of Hydrophobic Cores of Proteins Using Wavelet Analysis.

Information concerning the secondary structures, flexibility, epitope and hydrophobic regions of amino acid sequences can be extracted by assigning physicochemical indices to each amino acid residue, and information on structure can be derived using the sliding window averaging technique, which is in wide use for smoothing out raw functions. Wavelet analysis has shown great potential and applicability in many fields, such as astronomy, radar, earthquake prediction, and signal or image processing. This approach is efficient for removing noise from various functions. Here we employed wavelet analysis to smooth out a plot assigned to a hydrophobicity index for amino acid sequences. We then used the resulting function to predict hydrophobic cores in globular proteins. We calculated the prediction accuracy for the hydrophobic cores of 88 representative set of proteins. Use of wavelet analysis made feasible the prediction of hydrophobic cores at 6.13% greater accuracy than the sliding window averaging technique.

Journal Article↗
PubMed1997

Extraction of substructures of proteins essential to their biological functions by a data mining technique.

Correlation between the sequential, structural, and functional features of proteins is one of the most important open questions in the field of molecular biology. To this problem, we apply a technique known as data mining for discovering associations across protein sequence, structure, and function. We were able to find various association rules on the substructures essential to some protein functions. Moreover, structure-structure associations were found between proteins having different functions. The results suggest that data mining might be a powerful tool in protein analysis.

Algorithms↗
PubMed1997

Finding association rules on heterogeneous genome data.

A novel approach for discovery of knowledge from genome data, which has been recently watched with interest in the research area of database, is applied to finding unified rules spreading over sequence, structure, and function of protein. As the result of experiments using data extracted from PDB, SWISS-PROT, and PROSITE, some association rules stating sequential/structural/functional aspects of two kinds of endopeptidases were found.

Computer Simulation↗
PubMed1996

Glycine-15 in the bend between two alpha-helices can explain the thermostability of DNA binding protein HU from Bacillus stearothermophilus.

On the basis of sequence comparison of thermophilic and mesophilic DNA binding protein HUs, Bacillus stearothermophilus DNA binding protein HU (BstHU) seems to gain thermostability with a change in amino acid residues present on the molecular surface. To evaluate the contribution of exchange of each amino acid to the thermostability of BstHU, we constructed three mutants, BstHU-T13A (Thr13 to Ala), BstHU-G15E (Gly15 to Glu), and BstHU-T33L (Thr33 to Leu), in which the amino acids in BstHU were changed to the corresponding ones in Bacillus subtilis DNA binding protein HU (BsuHU). Stability of the mutant proteins was determined from thermal-denaturation curves. Replacement of Gly15 located in the turn region between alpha 1 and alpha 2 helices (HTH motif), with Glu (BstHU-G15E), resulted in a decrease in thermostability, and the Tm value was 54.0 degrees C compared to the Tm value of 63.9 degrees C for BstHU. The mutants, BstHU-T13A and BstHU-T33L, were, by contrast, slightly more stable (Tm values of 67.0 and 65.6 degrees C for BstHU-T13A and BstHU-T33L, respectively) than the wild type. We then generated the BsuHU mutant protein BsuHU-E15G, where Glu15 in BsuHU was in turn replaced by Gly, and we analyzed the thermostability. This substitution clearly enhanced the melting temperature by 11.8 degrees C (Tm value: 60.4 degrees C for BsuHU-E15G) compared to the value for BsuHU (Tm: 48.6 degrees C). Thus, Gly15 in the HTH motif of BstHU has an important role in the thermostability of BstHU. Characterization of the structure of the BstHU-G15E by 1H-NMR analysis showed that solvent accessibility of amide proton of Ala21 in the mutant was significantly increased compared with that of wild type, which means that the structure of the HTH motif in the N-terminal region in the mutant was changed to a more open conformation, thereby avoiding the interaction of Ala21 with either Ser17 by hydrogen bond or Ala11 by hydrophobic interaction.

Bacterial Proteins↗
PubMed1996

In vivo rapid magnetic field measurement and shimming using single scan differential phase mapping.

In vivo shimming is a powerful tool for alleviating subject-dependent magnetic field distortions in MRI, although the usually lengthy procedure has limited its use. A magnetic field measurement method called single scan differential phase mapping that can reduce the measurement time of conventional methods by more than half when used with multiple gradient-recalled echo imaging was developed. An automatic high-order shimming using the present method was implemented in a commercial MRI system. In vivo field inhomogeneity features and the shimming performances were investigated. The method was found to be useful for improving the quality of echo-planar images.

Abdomen↗