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PubMed2004

[Inspiration to basic researches of traditional Chinese medicine from the 2001 Nobel Prize].

The contributions of the three winners (L Hartwell, RT Hunt and PM Nurse) of the 2001 Nobel Prize for physiology or medicine revealed the mystical veil of cell cycle control. It was of far-reaching significance for exploring new method for cancer treatment. It will also give a good deal of enlightenment to the basic research of traditional Chinese medicine. Their understanding about the cause and development of cancers changed from the static view to dynamic dialectical analysis, from simplex study to comprehensive analysis; they stressed regulation, instead of killing in the treatment of cancer; and they thought that the numerous factors driving the normal process of the cell cycle could be summarized as positive and negative factors. These opinions were similar to some theories of traditional Chinese medicine, such as treatment based on syndrome differentiation, integrative treatment, and keeping the balance between yin and yang, and established a connection between traditional Chinese medicine and the western medicine, which would further widen the research on compound prescriptions of Chinese herbs.

Animals↗
PubMed1998

[Optimization of non-gel sieving capillary electrophoretic separation of DNA fragments of hundreds of base pairs].

Non-gel sieving capillary electrophoresis has been employed in the biological sciences for the size-based separation of macromolecules such as nucleic acids. In this paper, four factors i.e. electric field strength, capillary length, capillary diameter and hydroxy-propylmethylcellulose (HPMC) concentration were integratively evaluated to select the optimal condition of separating DNA fragments of a few hundreds of base pairs through orthogonal analysis. Conclusion was made through comprehensive analysis: better separation could be achieved in longer capillary, smaller inside diameter of capillary and less field strength. In practical application, effective separation in short time is important. We preferred to employ 8 g/L HPMC in coated capillary (37 cm x 75 microns i.d.) and electric field strength of 324 V/cm in separating DNA fragments of hundreds of base pairs. From sampling to getting results only a few more than ten minutes were needed in capillary electrophoresis. It needs less amount of sample (a few nanoliters) and shows higher sensitivity (0.1 pmol in UV detection) than polyacrylamide gel electrophoresis (PAGE). pBR322/Msp I fragments were completely resolved in both capillary electrophoresis and PAGE, and four-bases resolution was obtained. When the concentration of the PCR product is too low (< 20 mg/L), PCR reaction system is used as a negative control to make sure of the peak generated by the unpurified PCR products, avoiding interference made by PCR buffer and polymerase.

Apolipoprotein B-100↗
PubMed2000

Sensitivity analysis of mercury human exposure.

We present a comprehensive analysis of the sensitivity of mercury (Hg) human exposure to environmental variables using a multimedia model of the fate and transport of Hg in the environment. The results of the analysis show that the Hg dose is most sensitive to the lake pH, the burial rate of Hg adsorbed to sediments, and the chemical speciation of Hg emissions to the atmosphere. The lake pH has a strong non-linear effect on the methylation rate and bioaccumulation of Hg in fish. The burial of sediments is a major pathway for removing Hg from the lake cycling. The speciation of Hg emissions is important because Hg(II) is deposited much more rapidly than Hg(0). These results highlight the importance of key variables that should be investigated through well-designed field programs, so that we can minimize the overall uncertainties associated with the modeling of mercury fate and transport.

Confounding Factors, Epidemiologic↗
PubMed1986

Music research in medical/dental treatment: meta-analysis and clinical applications.

This article is a comprehensive analysis and application of music therapy research in the general field of music in medicine, and consists of a thorough review of the literature and a meta-analysis of all empirical studies using music in actual medical/dental treatments. It also transfers research results to clinical applications of music therapy techniques and program development in a general hospital setting.

Adult↗
PubMed2001

Molecular cloning and characterization of Kremen, a novel kringle-containing transmembrane protein.

Kringle domain, a triple-disulfide-linked domain, is conserved in diverse proteins which play important roles in various biological processes. We cloned Kremen, a novel member of kringle-containing proteins, using a newly developed unique strategy, 'Kringle-SAGE (serial analysis of gene expression)', which enables comprehensive analysis of kringle-containing proteins. Kremen is likely to be a type-I transmembrane protein composed of 473 amino acid residues. Kremen has a kringle domain, a WSC domain, and CUB domains in the extracellular region, while the intracellular region has no conserved motif involved in signal transduction. In the mouse embryo, the Kremen mRNA level, which was increased during embryonic development, was localized in the apical ectodermal ridge of limb buds, myotome, and sensory organs (e.g. optic vesicle, otic vesicle, nasal pit). In the adult mouse, Kremen mRNA was expressed in a variety of tissues with a relatively strong expression in the lung, heart, and skeletal muscle. Kremen mRNA expression in C2C12 and NIE-115 cells increased during respective differentiation into muscular and neural cells. These results suggest a potential role for Kremen in the regulation of cellular responses upon extracellular stimulus or cell-cell interaction in neuronal and/or muscle cells. Kringle-SAGE is expected to facilitate further elucidation of structure and functions of kringle proteins.

Amino Acid Sequence↗
PubMed2006

Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data.

The rapid accumulation of microarray data translates into an urgent need for tools to perform integrative microarray analysis. Integrative Array Analyzer is a comprehensive analysis and visualization software toolkit, which aims to facilitate the reuse of the large amount of cross-platform and cross-species microarray data. It is composed of the data preprocess module, the co-expression analysis module, the differential expression analysis module, the functional and transcriptional annotation module and the graph visualization module.

Algorithms↗
PubMed2002

HapScope: a software system for automated and visual analysis of functionally annotated haplotypes.

We have developed a software analysis package, HapScope, which includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. The HapScope analysis pipeline supports: (i) computational haplotype construction with an expectation-maximization or Bayesian statistical algorithm; (ii) SNP classification by protein coding change, homology to model organisms or putative regulatory regions; and (iii) minimum SNP subset selection by either a Brute Force Algorithm or a Greedy Partition Algorithm. The HapScope viewer displays genomic structure with haplotype information in an integrated environment, providing eight alternative views for assessing genetic and functional correlation. It has a user-friendly interface for: (i) haplotype block visualization; (ii) SNP subset selection; (iii) haplotype consolidation with subset SNP markers; (iv) incorporation of both experimentally determined haplotypes and computational results; and (v) data export for additional analysis. Comparison of haplotypes constructed by the statistical algorithms with those determined experimentally shows variation in haplotype prediction accuracies in genomic regions with different levels of nucleotide diversity. We have applied HapScope in analyzing haplotypes for candidate genes and genomic regions with extensive SNP and genotype data. We envision that the systematic approach of integrating functional genomic analysis with population haplotypes, supported by HapScope, will greatly facilitate current genetic disease research.

Algorithms↗
PubMed2005

SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites.

SEARCHGTr is a web-based software for the analysis of glycosyltransferases (GTrs) involved in the biosynthesis of a variety of pharmaceutically important compounds like adriamycin, erythromycin, vancomycin etc. This software has been developed based on a comprehensive analysis of sequence/structural features of 102 GTrs of known specificity from 52 natural product biosynthetic gene clusters. SEARCHGTr is a powerful tool that correlates sequences of GTrs to the chemical structures of their corresponding substrates. This software indicates the donor/acceptor specificity and also identifies putative substrate binding residues. In addition, it provides interfaces to other public databases like GENBANK, SWISS-PROT, CAZY, PDB, PDBSum and PUBMED for extracting various information on GTrs homologous to the query sequence. SEARCHGTr would provide new dimension to our previously developed bioinformatics tool NRPS-PKS. Together, these tools facilitate comprehensive computational analysis of proteins involved in biosynthesis of aglycone core and its downstream glycosylations. Apart from presenting opportunities for rational design of novel natural products, these tools would assist in the identification of biosynthetic products of secondary metabolite gene clusters found in newly sequenced genomes. SEARCHGTr can be accessed at http://www.nii.res.in/searchgtr.html.

Anti-Bacterial Agents↗
PubMed2003

Comparison of oligonucleotide-microarray and serial analysis of gene expression (SAGE) in transcript profiling analysis of megakaryocytes derived from CD34+ cells.

For the comprehensive analysis of transcript expression, the array-based hybridization analysis and the serial analysis of gene expression (SAGE) are commonly used platforms. The SAGE is based on a high-throughput sequencing of ditags derived from the transcript. DNA microarrays are a powerful tool for monitoring thousands of transcripts simultaneously, whereas the Genechip (Affimatrix microarray) technology is based on the hybridization of a single probe or other manufacturer's microarrays (cDNA- or oligonucleotide-microarray) procedures include the competitive hybridization of two probes. In this study, the quantitative accuracy of expression using oligonucleotide-microarray was determined by comparing data set from the SAGE. In previous study the microSAGE was performed for the megakaryocytes and non- megakaryocytes derived from human cord blood CD34+ cells by ex vivo expansion using thrombopoietin, and a total of 38,909 tags representing 8,976 unique genes were obtained. On the identical RNA, expression profiling was also carried out using oligonucleotide-microarray (MAGIC II 10K chip, Macrogen). The most frequently expressed genes in human megakaryocytes were identified as platelet factor 1 followed by annexin A1, ribosomal protein S23. The majority of the 50 most highly expressed genes in the CD34+-derived megakaryocytes were those involved in protein synthesis, e.g., ribosomal proteins. The expression level through the single channel of oligonucleotide-microarray and SAGE have a fairly good correlation in terms of absolute analyses and that the correlation is higher for the genes with higher expression levels.

Antigens, CD34↗
PubMed1998

Analysis of interferon-regulated proteins binding the interferon-alpha-stimulated response element.

Interferon mediates its biological effects of antiviral, antiproliferative, and immunomodulatory activities through induction of specific gene expression. Transcription of target genes is regulated through a set of transcription factors that bind to specific cis-acting regulatory sequences in target promoters and enhancers. The activity or abundance of these transcription factors is modulated by interferon treatment. Because of their DNA binding activity, regulatory factors can be recognized and characterized using methods to detect protein-DNA complexes. The availability of antibodies directed against common interferon regulatory proteins coupled with analysis of binding-site specificity provides comprehensive analysis.

Base Sequence↗
PubMed2002

Gene expression during acute allograft rejection: novel statistical analysis of microarray data.

High-throughput microarrays promise a comprehensive analysis of complex biological processes, yet their applicability is hampered by problems of reproducibility and data management. The current study examines some of the major questions of microarray use in a well-described model of allograft rejection. Using the Brown Norway to Lewis heterotopic heart transplant model, highly purified RNA was isolated from cardiac tissue at postoperative days (POD) 3, 5 and 7 and hybridized onto Affymetrix U34A microarrays. Using the log average ratio (LAR), changes in gene expression were monitored at each timepoint and p-values generated through statistical analysis. Microarray data were verified for 13 significant transcripts using RT-PCR. Of the 8800 transcripts studied, 2864 were increased on POD 3, 1418 on POD 5 and 2745 on POD 7. Verifying previous studies, many up-regulated genes appeared to be associated with the inflammatory process and graft infiltrating cells. Down-regulated transcripts included many novel molecules such as SC1 and decorin. LAR analysis provides a useful approach to analyze microarray data. Results were reproducible and correlated well with both RT-PCR and prior studies. Most importantly, these results provide new insights into the pathogenesis of acute rejection and suggest new molecules for future studies.

Animals↗
PubMed2002

MarC-V: a spreadsheet-based tool for analysis, normalization, and visualization of single cDNA microarray experiments.

The comprehensive analysis and visualization of data extracted from cDNA microarrays can be a time-consuming and error-prone process that becomes increasingly tedious with increased number of gene elements on a particular microarray. With the increasingly large number of gene elements on today's microarrays, analysis tools must be developed to meet this challenge. Here, we present MarC-V, a Microsoft Excel spreadsheet tool with Visual Basic macros to automate much of the visualization and calculation involved in the analysis process while providing the familiarity and flexibility of Excel. Automated features of this tool include (i) lower-bound thresholding, (ii) data normalization, (iii) generation of ratio frequency distribution plots, (iv) generation of scatter plots color-coded by expression level, (v) ratio scoring based on intensity measurements, (vi) filtering of data based on expression level or specific gene interests, and (vii) exporting data for subsequent multi-array analysis. MarC-V also has an importing function included for GenePix results (GPR) raw data files.

DNA, Complementary↗
PubMed2001

[A model for clinical study based on genome science--trials in disorders of the immune system and allergies].

Disorders of the immune system, such as allergies, have multi-factorial etiologies that include both genetic and environmental components. The recent advances in genome science have facilitated two strategies for studying the genetic basis of disease: (1) systematic analysis of gene expression profiles and (2) comprehensive analysis of gene variations, such as polymorphisms. Here, we describe a unique research institute, Genox Research Inc., that can relate the clinical profile of a patient to genotyping and molecular profiling. Systematic gene expression analyses using differential display have been performed to explore genes related to allergy, and revealed 93 differentially expressed candidate genes in T-cells. Also, a single nucleotide polymorphism(SNP) analysis project has been designed to mine disease-related and/or drug-response-related genes involved in allergic disorders using biochip technologies. As exemplified above, clinical studies based on these applications of genome science would be of considerable value in clarifying our understanding of multi-gene disorders.

Gene Expression Profiling↗
PubMed2025

Using Callus as an Ex Vivo System for Chromatin Analysis.

Next-generation sequencing has revolutionized epigenetics research, enabling a comprehensive analysis of DNA methylation and histone modification profiles to explore complex biological systems at unprecedented depth. Deciphering the intricate epigenetic mechanisms that regulate gene activity presents significant challenges, including the issue of analyzing heterogeneous cell populations in bulk. Bulk analysis introduces bias and can obscure crucial information by averaging readouts from distinct cells. Various approaches have been developed to address this issue, such as cell-type-specific enrichment or single-cell sequencing techniques. However, the need for transgenic lines with fluorescent markers, along with technical challenges such as efficient protoplast isolation and low yield, limits their widespread adoption and use in multi-omic studies. This review discusses the pros and cons of these approaches, providing a valuable basis for selecting the most suitable strategy to minimize heterogeneity. We will also highlight the use of cotyledon-derived callus as an ex vivo system as a simple, accessible, and robust platform for enabling high-throughput multi-omic analyses.

Chromatin↗
PubMed1998

[Body build related body composition and nutrition in adulthood--a comparison of skinfold thickness measurement and bioelectric impedance analysis].

The objective of the present study was to conduct a comprehensive analysis of body build, body composition and nutritional status. The study sample consists of 498 men and women aged from 35 to 65 years. Subjects underwent a detailed anthropometric examination incompassing thirty-one body measurements, eleven skinfold thickness measurements, and bioelectrical impedance analysis for determination of body composition. Dietary intake was assessed by a semiquantitative food frequency questionnaire. Body composition was clearly associated with age and body build. Somatometric differentiation by use of the metric index showed that percentage of body fat was significantly higher in pycnomorphic compared to leptomorphic subjects, whereas reported dietary energy intake was lower. Comparison of estimates of body fat showed considerably deviating results for skinfold thickness measurements and bioelectrical impedance analysis depending on the equations used. This was especially pronounced in obese subjects, where, on an average, bioelectrical impedance analysis resulted in higher values for percentage of body fat compared to skinfold thickness measurements. We conclude that for assessment of nutritional status body composition should be investigated taking into account body build in addition to age and sex.

Adult↗
PubMed1981

Oscillations and control features in glycolysis: numerical analysis of a comprehensive model.

We present an analysis of glycolysis based on experimental findings and an interpretation based on concepts of efficiency, resonance response, and control features available in highly nonlinear reaction kinetics. We begin with a model for the glycolytic mechanism that is comprehensive, includes a large number of known activations and inhibitions of enzymes by metabolites, and couples the phosphofructokinase (PFKase) and the pyruvate kinase (PKase) reactions. The PFKase and PKase reactions and the coupling between them are modeled according to experimental information, but we do not attempt to model the glyceraldehyde-3-phosphate dehydrogenase-3-phosphoglycerate kinase reaction. We use experimental data to obtain the best estimates for the kinetic parameters and test the model by calculating the concentration variations of the intermediate metabolites. We confirm oscillatory behavior and calculate the ATP/ADP ratio and the free-energy dissipation for an extended range of the kinetic parameters as a function of the driving force for the glycolytic pathway, a measure of which is the total adenine nucleotide concentration. We find agreement of the calculated results with experimental findings except for the insufficiently represented reactions. Our model shows that the average ATP/ADP ratio is increased and the average free-energy dissipation is decreased in an oscillatory compared with a steady state mode of operation. The average values of the ATP/ADP ratio and of the free energy dissipation change abruptly past the onset of sustained oscillations.

Adenosine Diphosphate↗
PubMed2006

Clustering microarray data.

Even a simple, small-scale, microarray experiment generates thousands to millions of data points. Clearly, spreadsheets or plotting programs do not suffice for analysis of such large volumes of data, and comprehensive analysis requires systematic methods for selection and organization of data. This chapter focuses on the concepts and algorithms of hierarchical clustering and the most commonly employed methods of partitioning or organizing microarray data, and freely available software that implements these algorithms.

Animals↗
PubMed2001

Combined SSCP/duplex analysis by capillary electrophoresis for more efficient mutation detection.

SSCP and heteroduplex analysis (HA) continue to be the most popular methods of mutation detection due to their simplicity, high sensitivity and low cost. The advantages of these methods are most clearly visible when large genes, such as BRCA1 and BRCA2, are scanned for scattered unknown mutations and/or when a large number of DNA samples is screened for specific mutations. Here we describe a novel combined SSCP/duplex analysis adapted to the modern capillary electrophoresis (CE) system, which takes advantage of multicolor labeling of DNA fragments and laser-induced fluorescence detection. In developing this method, we first established the optimum conditions for homoduplex and heteroduplex analysis by CE. These were determined based on comprehensive analysis of representative Tamra-500 markers and BRCA1 fragments at different concentrations of sieving polymer and temperatures in the presence or absence of glycerol. The intrinsic features of DNA duplex structures are discussed in detail to explain differences in the migration rates between various types of duplexes. When combined SSCP/duplex analysis was carried out in single conditions, those found to be optimal for analysis of duplexes, all 31 BRCA1 and BRCA2 mutations, polymorphisms and variants tested were detected. It is worth noting that the panel of analyzed sequence variants was enriched in base substitutions, which are usually more difficult to detect. The sensitivity of mutation detection in the SSCP portion alone was 90%, and that in the duplex portion was 81% in the single conditions of electrophoresis. As is also shown here, the proposed combined SSCP/duplex analysis by CE has the potential of being applied to the analysis of pooled genomic DNA samples, and to multiplex analysis of amplicons from different gene fragments. These modifications may further reduce the costs of analysis, making the method attractive for large scale application in SNP scanning and screening.

BRCA1 Protein↗