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PubMed2002

Mining microarray expression data by literature profiling.

BACKGROUND: The rapidly expanding fields of genomics and proteomics have prompted the development of computational methods for managing, analyzing and visualizing expression data derived from microarray screening. Nevertheless, the lack of efficient techniques for assessing the biological implications of gene-expression data remains an important obstacle in exploiting this information. RESULTS: To address this need, we have developed a mining technique based on the analysis of literature profiles generated by extracting the frequencies of certain terms from thousands of abstracts stored in the Medline literature database. Terms are then filtered on the basis of both repetitive occurrence and co-occurrence among multiple gene entries. Finally, clustering analysis is performed on the retained frequency values, shaping a coherent picture of the functional relationship among large and heterogeneous lists of genes. Such data treatment also provides information on the nature and pertinence of the associations that were formed. CONCLUSIONS: The analysis of patterns of term occurrence in abstracts constitutes a means of exploring the biological significance of large and heterogeneous lists of genes. This approach should contribute to optimizing the exploitation of microarray technologies by providing investigators with an interface between complex expression data and large literature resources.

Cluster Analysis↗
PubMed2006

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli.

BACKGROUND: Comparisons of complete bacterial genomes reveal evidence of lateral transfer of DNA across otherwise clonally diverging lineages. Some lateral transfer events result in acquisition of novel genomic segments and are easily detected through genome comparison. Other more subtle lateral transfers involve homologous recombination events that result in substitution of alleles within conserved genomic regions. This type of event is observed infrequently among distantly related organisms. It is reported to be more common within species, but the frequency has been difficult to quantify since the sequences under comparison tend to have relatively few polymorphic sites. RESULTS: Here we report a genome-wide assessment of homologous recombination among a collection of six complete Escherichia coli and Shigella flexneri genome sequences. We construct a whole-genome multiple alignment and identify clusters of polymorphic sites that exhibit atypical patterns of nucleotide substitution using a random walk-based method. The analysis reveals one large segment (approximately 100 kb) and 186 smaller clusters of single base pair differences that suggest lateral exchange between lineages. These clusters include portions of 10% of the 3,100 genes conserved in six genomes. Statistical analysis of the functional roles of these genes reveals that several classes of genes are over-represented, including those involved in recombination, transport and motility. CONCLUSION: We demonstrate that intraspecific recombination in E. coli is much more common than previously appreciated and may show a bias for certain types of genes. The described method provides high-specificity, conservative inference of past recombination events.

Alleles↗
PubMed1999

Activation of the insulin-like growth factor-binding protein-5 promoter in osteoblasts by cooperative E box, CCAAT enhancer-binding protein, and nuclear factor-1 deoxyribonucleic acid-binding sequences.

Insulin-like growth factor (IGF)-binding protein-5 (IGFBP-5) has IGF-dependent and -independent actions. PGE2 rapidly increases IGFBP-5 expression by osteoblasts through cAMP-dependent processes. A minimal DNA sequence required for basal and PGE2-stimulated IGFBP-5 promoter activity spans -69 to -35 bp. This region adjoins a functional TATA box and contains E box, CCAAT enhancer-binding protein (C/EBP), nuclear factor-1 (NF-1), and activator protein-2 (AP-2) transcription factor related binding motifs. In this study we compared minimal promoter sequences of -74 to +120 bp, without or with mutations in each potential regulatory element, by reporter gene expression and electrophoretic mobility shift assays. Mutation of the E box-related element reduced basal promoter activity by 50% and eliminated the 2-fold stimulatory effect of PGE2. In contrast, mutations in the C/EBP- or NF-1-related elements also reduced basal promoter activity without fully eliminating the PGE2 effect. Overexpression of C/EBPdelta stimulated basal IGFBP-5 promoter activity, and this effect was eliminated by mutating the C/EBP-binding site. However, mutation of the AP-2-binding site or overexpression of AP-2 did not correlate with basal or PGE2-induced promoter activation. By electrophoretic mobility shift assay, prominent gel shift complexes occurred with osteoblast nuclear extracts and 32P-labeled probes spanning the E box-, C/EBP-, and NF-1-related motifs. These gel shift complexes were depleted by specific binding site mutations and were enhanced by PGE2. Increased binding by extracts from PGE2-treated cultures was blocked by cycloheximide treatment. These results identify several elements as integral binding sequences for both basal and PGE2-stimulated IGFBP-5 promoter activity. They further reveal that multiple sequences within this cluster form a basic transcription unit where nuclear factors can accumulate in a protein synthesis-dependent way and enhance IGFBP-5 expression by osteoblasts in response to PGE2.

Animals↗
PubMed1993

Thyroid hormone resistance syndrome: correlation of dominant negative activity and location of mutations.

Generalized resistance to thyroid hormone (GRTH) is caused by multiple distinct mutations that cluster in two regions of the hormone-binding domain of the thyroid hormone beta-receptor. The mutant receptors are functionally inactive, but nevertheless inhibit normal receptor activity in a dominant negative manner. Four different GRTH mutants were studied in the transient expression assays to further examine their functional properties. The transcriptional activity of the mutant receptors correlated with their T3 binding affinities. Two distal region mutants with partial T3 binding were transcriptionally active at high T3 concentrations, but exhibited potent dominant negative activity at low T3 concentrations. Two proximal region mutants that did not bind to T3 were 5- to 10-fold less effective inhibitors of normal receptor function, indicating that dominant negative inhibition is not correlated with T3 binding activity. Each of the proximal and distal region mutants retain the ability to form heterodimers with accessory proteins and to bind to DNA effectively. Because the non-T3 binding thyroid hormone receptor isoform alpha 2 also exists in most tissues, its effects on mutant receptor function were also examined. The inhibitory activity of each of the GRTH mutants was potentiated by alpha 2 but only in the context of a positively regulated reporter gene. Thus, alpha 2 may selectively alter the degree of dominant negative activity that occurs for different target genes. We conclude that the locations of GRTH mutations may influence dominant negative activity by altering transactivating or other functions of the receptor, providing a potential basis for the phenotypic variability in different kindreds with GRTH.

Base Sequence↗
PubMed1994

Transcriptional synergism between the vitamin D3 receptor and other nonreceptor transcription factors.

Small changes in the concentrations and/or combinations of trans-acting factors can result in profound alterations in gene expression. Synergistic interaction between different classes of transcription factors bound to distinct sites within a promoter/enhancer region is one mechanism by which this can occur. Reflecting this, hormone response elements, DNA recognition sites for steroid/nuclear receptors, are often found in promoter regions organized as multiple copies or are clustered among binding sites for other trans-acting factors. To systematically examine the potential interactions between one such receptor, the vitamin D3 receptor (VDR), and other nonreceptor transcription factors, we constructed a series of reporter plasmids containing one copy of the osteopontin (Spp1) vitamin D response element (VDRE), consisting of two direct repeats spaced by 3 base pairs, and one binding site for the transcription factors SP1, NF-1, Oct-1, or AP-1. We also generated reporters either under the control of two copies of Spp1 VDRE, or a distinct VDRE from the human osteocalcin gene promoter. The various reporters were used to transiently transfect HeLa or CV-1 cells in the presence and absence of 1,25-dihydroxyvitamin D3. Our results show that VDR transactivates 12-20 times more strongly from two Spp1-VDREs than from one, indicating that VDR synergizes with itself. VDR also synergizes with the other nonreceptor factors, since we observe a 6- to 12-fold degree of synergistic induction after ligand addition, depending on the particular factor. The functional basis for the transcriptional synergism appears to be at the level of cooperative DNA binding, at least for VDR alone and VDR-Oct-1, as demonstrated in vitro by gel mobility shift assays using purified factors. Consistent with this, we show that the minimal requirement for transcriptional synergism in vivo by VDR is its DNA-binding domain.

Base Sequence↗
PubMed2005

Damage within a network of white matter regions underlies executive dysfunction in CADASIL.

OBJECTIVE: To identify the important sites of white matter disruption that underpin executive dysfunction in CADASIL (cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy), a genetic model of pure subcortical vascular disease. METHODS: The anatomic pattern of correlation between tissue integrity and executive function was explored with diffusion tensor imaging (DTI), which provides quantitative measures of tissue integrity. Eighteen nondemented patients with CADASIL underwent DTI and cognitive assessment. DTI was normalized to a standard template and correlations assessed at every voxel across the brain with Statistical Parametric Mapping with cluster-level correction for multiple comparisons. RESULTS: For executive tasks, correlations were found in a number of discrete regions in the white matter of the frontal lobes. A distinct, nonoverlapping pattern of correlation was seen for verbal memory. Significant independent correlations remained in some regions after co-varying for age and IQ. CONCLUSIONS: Different cognitive functions correlate with structural integrity at different sites in the white and subcortical gray matter. The distribution of regions correlating specifically with executive function provides clues to the organization of the relevant cognitive networks and their important white matter projections. The cingulum bundle is one candidate tract that may carry anteroposterior connections important for executive processes.

Adult↗
PubMed1994

Morphological analysis of cervical vertebrae in ataxic foals.

Morphological differences between cervical vertebrae were statistically analyzed in ataxic foals to clarify abnormal structural factors in the pathogenesis of this problem. At first, multiple regression analysis and cluster analysis were performed with 28 variables in C3-C7 of 39 control foals without lameness. As a result, there were no sex differences in the growth of all cervical vertebral sites, and the most suitable categorization of the age of the foals was 3 clusters of 8 months old or younger, 9-12 months old and 13 months old or older in any sites in the cervical vertebrae. Twenty-eight ataxic and 19 control foals at the age of 13 months or older were then used for discriminant analysis with 20 variables. As a result, 1-7 variables on C3-C7 were selected for sufficient discrimination, in which the heights of the cranial and caudal orifices of the spinal canal, longitudinal length of the vertebral head and height of the vertebral fossa strongly contributed to the discrimination of all the cervical vertebrae. In addition, the widths and longitudinal diameters of the articular processes on articular surfaces strongly contributed to the discrimination of the caudal region of the neck. In conclusion, it was suggested that the lesion in the cervical spinal cord observed in ataxic foals was caused by morphological abnormalities including osteochondrosis and subsequent degenerative joint disease in the cervical vertebrae.

Animals↗
PubMed2026

Hypervirulence-associated pseudo-compound transposons as fundamental mobile units driving cross-species virulence dissemination in Enterobacteriaceae.

BACKGROUND: The rapid global spread of hypervirulence in Enterobacteriaceae, particularly in carbapenem-resistant Klebsiella pneumoniae, poses a significant public health threat. However, the key genetic vehicles and mechanisms driving horizontal transfer of hypervirulence-associated genes (iucA, iroB, rmpA, rmpA2, and peg-344) remain poorly defined, limiting effective surveillance. METHODS: We performed a large-scale genomic survey of 2,869 virulence-associated plasmid sequences and 2,337 complete Enterobacteriaceae chromosomes. Using comparative genomics and evolutionary analyses, we systematically identified and characterized Hypervirulence-associated Pseudo-Compound Transposons (Hva-PCTs), defined as structured mobile elements in which hypervirulence-associated genes are flanked by insertion sequences. RESULTS: Our results demonstrate that hypervirulence-associated genes are transmitted primarily as discrete IS-bounded units, which we term Hva-PCTs. We identified 29 distinct plasmid-borne Hva-PCTs (pHva-PCTs) and 30 chromosomal Hva-PCTs (cHva-PCTs). These modules show clear species-specific patterns: iucA/iroB-associated Hva-PCTs mainly originate in Escherichia coli and spread through IncFIB-containing multi-replicon plasmids (commonly combined with IncFIC(FII) and/or IncFII, while rmpA/rmpA2/peg-344-containing modules originate in K. pneumoniae and are disseminated via IncHI1B/repB plasmids. Three Hva-PCTs were detected on both plasmids and chromosomes (xHva-PCTs). In one clinical K. pneumoniae isolate (LS356), the identical composite module was present on both replicons. Simpler sub-modules, such as ISKqu3-rmpA2-iucA_1-IS102 and IS102-rmpA-peg-344-iroB_1-IS1A, frequently co-occur on the same plasmid; when positioned in tandem, they reconstitute the full composite structure. This assembly pattern is further supported by a partial duplication event in plasmid pP901. CD-HIT clustering (80% nucleotide identity and 90% coverage) showed that 13 of 22 major clusters contained both plasmid and chromosomal copies, with intra-cluster identities >80% across multiple sequence types and host species. CONCLUSION: Hypervirulence-associated genes in Enterobacteriaceae are disseminated mainly as IS-flanked Hva-PCTs rather than solely through intact virulence plasmids. These modules exhibit strong but not absolute host specificity. The presence of identical Hva-PCTs on plasmids and chromosomes suggests inter-replicon mobility, while their stepwise assembly from simpler sub-modules highlights modular accretion as a key evolutionary process. Tracking Hva-PCTs as distinct mobile units may complement existing plasmid- and gene-centric surveillance approaches for hypervirulent and convergent strains. Experimental validation of their transposition activity and phenotypic effects is still required.

Virulence↗
PubMed1999

Spatial variability in release at the frog neuromuscular junction measured with FM1-43.

We quantified the spatial variability in release properties at different synaptic vesicle clusters in frog motor nerve terminals, using a combination of fluorescence and electron microscopy. Individual synaptic vesicle clusters labeled with FM1-43 varied more than 10-fold in initial intensity (integrated FM1-43 fluorescence) and in absolute rate of dye loss during tetanic electrical nerve stimulation. Most of this variability arose because large vesicle clusters spanned more than one presynaptic active zone (inferred from postsynaptic acetylcholine receptor stripes labeled with rhodamine-conjugated alpha-bungarotoxin); when the rate of dye loss was normalized to the length of receptor stripe covered, variability from spot to spot was greatly reduced. In addition, electron microscopic measurements showed that large vesicle clusters (i.e., those spanning multiple active zones) were also thicker, and the increased depth of vesicles led to increased total spot fluorescence without a corresponding increase in the rate of dye loss during stimulation. These results did not reveal the presence of "hot zones" of secretory activity.

Animals↗
PubMed2001

[DNA chip data mining].

DNA chip data routinely contain gene expression levels of thousands of genes and the analysis should be supported by various computational tools. To be brief, the analysis procedure consists of four steps including image scanning, image processing, mathematical interpretation and biological interpretation. In image processing step, we should detect the spots and measure the signals of the spots and the background. In mathematical interpretation step, first of all we should massage the measured signals to make them appropriate for further mathematical analysis. The massaged data could be analyzed by various computational methods especially when the data were generated for multiple samples comparisons. The clustering techniques including hierarchical clustering, k-means clustering, SOTA, SOM are the most popular methods in this step. Various other multivariate statistics and related machine learning techniques are being introduced and applied to DNA chip data analysis recently. And finally the most important step we should tackle is the biological interpretation task. Although the depth of the domain knowledge about the biological situation under which the data were generated is the most important factor to elucidate the biological context, it could be supported by various bioinformatics tools including MEDLINE abstract processing by NLP techniques or genetic network models constructed by Boolean networks algorithms.

Algorithms↗
PubMed2001

[Factors determining dental plaque and their relation to the assessment of caries among 7-year-old Flemish children].

The present investigation aimed to assess the impact of a number of variables on the variation on the amount of dental plaque present in the mixed dentition of 7-year-old Flemish children and to investigate a potential correlation between caries experience and the amount of dental plaque. Analyses were performed with ordinal plaque index as outcome measure, considering the children's school (i.e. class) as a random effect. This random effect turned out to be of great importance when dealing with large clustered samples. From the multiple logistic regression analysis, it was concluded that the older the subjects the more dental plaque was observed (or = 1.35; CI: 1.08-1.68; P = 0.0081). Four exploratory variables, could be identified as important risk indicators for dental plaque accumulation in the mixed dentition: 'start of brushing after the age of 2 years' (or = 1.161; CI: 1.09-1.23; P < 0.0001), 'brushing frequency of < 1 x/day (or = 1.37; CI: 1.12-1.66; P = 0.0019), more than two in between meal snacks (or = 1.18; CI: 1.03-1.36; P = 0.02) and daily intake of sugar containing drinks (or = 1.24; CI: 1.08-1.42; P = 0.002). Further, being male was linked to a higher amount of plaque (or = 1.16; CI: 1.00-1.34; P = 0.0506). Finally a weak but significant correlation (spearman's rho: r = 0.23; P < 0.0001) between caries experience and the amount of cervical plaque was shown.

Belgium↗
PubMed2002

Using local authority data for action on health inequalities: the Caerphilly Health and Social Needs Study.

BACKGROUND: Primary care organisations in the United Kingdom have been given new and challenging population health responsibilities to improve health and address health inequality in local communities through partnership working with local authorities. This requires robust health and social needs assessment data for effective local planning. AIM: To assess the use and value of local authority data shared through partnership working between Caerphilly Local Health Group and Caerphilly County Borough Council. DESIGN OF STUDY: Cross-sectional analysis of aggregate electoral division data. SETTING: Caephilly County Borough, south-east Wales. METHOD: Local authority datasets identified were categorised into one of six domains: income, unemployment, housing, health, education, and social services. Data were presented at electoral division level as rates in thematic maps and correlations between the variables within and between each domain were explored using Spearman's rank correlation coefficient, with particular focus on children in families. Local planning documents were scrutinised to ascertain the use and value of the data. RESULTS: A broad range of data described a comprehensive picture of health and social inequalities within the borough. Multiple deprivation tended to cluster in electoral divisions, particularly for data relating to children, painting an overwhelming picture of inequality in life chances. The data were used in a wide range of local partnership planning initiatives, including the Health Improvement Programme, Children's Services Plan, and a successful Healthy Living Centre bid. CONCLUSION: Local authority data can help primary care organisations in a population approach to needs assessment for use in local partnership planning targeted at reducing health inequalities.

Cross-Sectional Studies↗
PubMed2003

Symptom experiences of children and adolescents with cancer.

This paper examines nursing research focused on the symptom experiences of children and adolescents with cancer, and the extent to which the perspective and methods of developmental science have been used in this research. CINALH, MEDLINE, and PSYCHLIT were searched for publications between 1990 and 2002. The researcher or research team had to include a nurse or developmentally oriented researchers from other disciplines. Studies focused exclusively on pain were excluded because of recent published reviews. While nurse researchers have contributed influential knowledge related to symptom experiences and symptom distress in children and adolescents with cancer, this research is still in a formative but exciting stage. Two nurse researchers and their teams laid the foundation for this research through their individual studies and collaborative multisite studies. In general, children and adolescents from 10 through 18 years of age were primarily studied; few studies focused on preschool children. Given the fact that these are rare populations, sample sizes were generally small, limiting power and generalizability. Gender, ethnicity, and socioeconomic status were rarely considered in analyses. Most studies used cross-sectional designs, although several included short-term longitudinal or repeated measure designs. To date, longitudinal designs focused on long-term outcomes have not been conducted. There were only a few qualitative studies. There was limited use of conceptual models or theories, and inadequate attention was paid to broader ecological perspectives in the children's lives. Studies included a focus on global symptoms and on individual symptoms, particularly pain and fatigue. Few focused on nausea and vomiting. Operationalization of symptom distress generally involved adapting instruments designed for adults. A more explicit employment of a developmental science perspective in future studies would call for more longitudinal designs that conceptualize the symptom experience from the perspective of the child and that view their responses as complex and multidimensional in nature. This would necessitate measuring clusters of symptoms at multiple levels (e.g., emotional, behavioral, and biophysiological) using developmental data collection methods. Furthermore, attention needs to be paid in conceptualizing studies to ecological factors related to families, social networks, communities, and ethnicity, as well as to the ecology of the health care system, which likely influences the symptom experience of children.

Adolescent↗
PubMed1992

Identification and sequence analysis of the promoter for the leukocyte integrin beta-subunit (CD18): a retinoic acid-inducible gene.

Leukocyte adhesion receptors (LFA-1; Mac-1; p150,95) are a family of heterodimeric cell-surface adhesion molecules expressed exclusively in granulocytes, lymphocytes, and macrophages. Expression of these proteins is under complex regulatory control, but to date promoters for these genes have not been identified. The CD18 gene codes for the common beta-subunit of the leukocyte adhesion receptors. Transcription of CD18 is highly tissue-specific, hormonally inducible (by retinoic acid [RA]), and coordinately regulated with leukocyte integrin alpha-chains. To identify the CD18 promoter, we screened a human genomic phage library with a human CD18 cDNA probe and obtained a clone that contains an exon coding for the 5' untranslated region (UTR). Using rapid amplification of cDNA ends (RACE), RNAse protection, S1 nuclease, and primer extension assays, we demonstrated the existence of multiple transcription start sites clustered in a 45-nt region. We investigated the transcription-promoting activity of the genomic sequences 5' to the CD18 gene by performing transient expression assays with a growth hormone reporter gene in various hematopoietic cell lines. The CD18 promoter was active in Jurkat cells, a lineage that normally expresses CD18 but was considerably less active in K562, an early erythroid line that does not normally express CD18. The genomic sequences upstream of the start site cluster lack CAAT and TATA boxes, but have two Sp1 binding sites and 10 T(G/C)AC(C/A) boxes, which may represent binding sites for RA receptors (RAR). These features distinguish the CD18 promoter from the promoters of other tissue-specific, hormone-inducible genes, and may be representative of leukocyte integrin promoters in general.

Antigens, CD↗
PubMed2003

[Study on the function localization during different brain calculation tasks].

The aim of this study is to define the anatomical localization of corresponding brain function area during calculating. The activating modes in brain during continuous silent calculating subtraction and repeated silent reading multiplication table were compared and investigated. Fourteen volunteers of right-handedness were enrolled in this experiment. The quite different reaction models in brain area during the two models of calculation revealed that there are different processing pathways in brain during these two operating tasks. During continuous silent calculating, the function areas were found localized on the posterior portion of superior and middle gyrus of frontal lobe and the lobule of posterior parietal lobe (P < 0.01, T = 5.41), demonstrating that these function areas play an important role in the performance of calculation and working memory. During repeated silent reading multiplication table, the activating cluster was found only located in in the gyri occipital lateral(P < 0.01, T = 4.77).

Adult↗
PubMed2004

[Mining gene expression microarray data of nasopharyngeal carcinoma by literature profiling].

OBJECTIVE: To study abnormal signal pathway in nasopharyngeal carcinoma (NPC). METHOD: NPC gene expression microarray data was mined by analysis of literature profiles generated by extracting the frequencies of certain terms from the abstracts stored in the Medline literature database. The terms were then filtered on the basis of both repetitive occurrence and co-occurrence among multiple gene entries. Finally, clustering analysis was performed on the retained frequency values, shaping a coherent picture of the functional relationship among large and heterogeneous lists of genes. RESULT: Sixteen function groups were found among 112 abnormally expressed genes, including 4 groups indicative of Epstein-Barr virus (EBV) infection, 6 groups indicative of normal nasopharyngeal tissues that acquired essential capabilities to develop into tumor, 2 groups involved in energy metabolism, 1 group suggesting abnormal phosphorylation of proteins, 2 groups related to other diseases, and 1 group associated with muscle activities. The pathways of p53 and Rb, which were frequently abnormal during tumor progression, were not found in these groups. CONCLUSION: Initiation and progression of NPC may be caused by special signal transduction pathways.

Humans↗
PubMed1987

[Transmission of amber mutants of bacteriophage T4. III. Thermostability of the replication of amber mutants in cells of a non-permissive host is typical for the majority of phage tail genes].

The article deals with determination of the spreading of the earlier discovered phenomenon of the temperature sensitivity of multiplication of T4 phage amber mutants. On the basis of the study of the dependence of multiplication of 50 amber mutants in 22 genes of T4 phage tail in the cells of non-permissive host on the incubation temperature in the range of 15-41 degrees C, the following conclusion is drawn: temperature sensitivity of multiplication of amber mutants appears to be gene-specific and is widely spread among T4 phage genes, i.e. in the case of amber mutants the burst size decreases, even for 14 tail genes, by several orders with the increase in incubation temperature. Temperature sensitivity of multiplication is typical of amber mutants in the genes whose proteins are either of small number in a phage particle (several molecules) or play the role of catalytic factors. Moreover, genes, amber mutants of which possess temperature sensitivity of multiplication, map in defined clusters.

Escherichia coli↗
PubMed1987

Multivariate statistical analysis of L-dopa esters as potential anti-parkinsonian prodrugs.

This paper reports a QSAR study of thirteen L-DOPA esters previously synthesised and examined for their physicochemical, biochemical and behavioural properties. Multivariate statistical analysis (principal component analysis, cluster analysis, simple and multiple linear regression) reveals favourable and unfavourable structural features of L-DOPA prodrugs. Some of the many biochemical and behavioural activities investigated are shown to be redundant. These indications may contribute to the design of novel L-DOPA prodrugs.

Analysis of Variance↗