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Results for “Association and function analysis”

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PubMed1981

An introduction to the coherence function and its use in EEG signal analysis.

The coherence function quantifies the association between pairs of signals as a function of frequency and has been shown to be useful for measuring changes in EEG topography related to cognitive tasks, psychopathology, and other aspects of brain organisation. For a narrow frequency band, its magnitude is analogous to the correlation coefficient between the signals limited by that band, but its value may differ because of the way that smoothing over frequency is achieved. The coherence function is described in physical terms using simple waveforms.

Brain↗

PubMed1993

Behavioural techniques to reduce self-injurious behaviour in children with autism.

This paper is part of a special section on 'self-injurious behaviour and autism' and concentrates on behavioural treatment techniques available and useful to reduce self-injurious behaviour in children with autism (e.g. extinction, time-out, differential reinforcement, alternative forms of stimulation, sensory deprivation, physical restraint, crisis management, environmental modifications). It has become increasingly evident that the successful treatment of self-injurious behaviour requires, first, a systematic and detailed (functional) analysis of the variables associated with the behaviour and, second, a hypothesis-testing approach on an individual, naturalistic basis to increase the acquisition of alternative skills and self-control.

Autistic Disorder↗

PubMed2001

Structural and functional genomics in domestic animals: the way to understand the phenotype.

Molecular approaches to genome analysis in livestock are reviewed by discussing the contribution of molecular genome analysis to the identification of the genetic variation underlying phenotypic variation (structural genome analysis) and to the definition of the trait-associated and environment-affected gene expression (functional genome analysis) as an important prerequisite to understanding the formation of a phenotype. Aspects of using mapped 'quantitative trait loci' (QTL) or gene variants as well as the identified trait-associated and environment-affected gene expression profile in livestock production are expounded.

Journal Article↗

PubMed1995

Functional domain analysis of interferon consensus sequence binding protein (ICSBP) and its association with interferon regulatory factors.

Interferon consensus sequence binding protein (ICSBP) is a member of the interferon regulatory factor (IRF) family of proteins that include IRF-1, IRF-2, and ISGF3gamma which share sequence similarity at the putative DNA binding domain (DBD). ICSBP is expressed exclusively in cells of the immune system and acts as a repressor of interferon consensus sequence (ICS) containing promoters that can be alleviated by interferons. In this communication, we have searched for functional domains of ICSBP by dissecting the DBD from the repression activity. The putative DBD of ICSBP (amino acids 1-121) when fused in frame to the transcriptional activation domain of the herpes simplex VP16 (ICSBP-VP16) is a very strong activator of ICS-containing promoters. In addition, ICSBP-VP16 fusion construct transfected into adenovirus (Ad) 12 transformed cells enabled cell surface expression of major histocompatibility complex class I antigens as did treatment with interferon. On the other hand, the DBD of the yeast transcriptional activator GAL4 was fused in frame to a truncated ICSBP in which the DBD was impaired resulting in a chimeric construct GAL4-ICSBP. This construct is capable of repressing promoters containing GAL4 binding sites. Thus, ICSBP contains at least two independent domains: a DBD and a transcriptional repressor domain. Furthermore, we have tested possible interactions between ICSBP and IRFs. The chimeric construct GAL4-ICSBP inhibited the stimulated effect of IRF-1 on a reporter gene, implying for a possible interaction between IRF-1 and ICSBP. Electromobility shift assays, demonstrated that ICSBP can associate with IRF-2 or IRF-1 in vitro as well as in vivo. Thus, ICSBP contains a third functional domain that enables the association with IRFs. These associations are probably important for the fine balance between positive and negative regulators involved in the interferon-mediated signal transduction pathways in cells of the immune system.

Base Sequence↗

PubMed1998

Affinity and kinetic analysis of the molecular interaction of ICAM-1 and leukocyte function-associated antigen-1.

LFA-1 is a member of the beta2 integrin family, and interacts with ICAM-1, a member of the Ig superfamily containing five Ig-like domains. Interaction of LFA-1 with ICAM-1 is important in a number of cellular events, including Ag-specific T cell activation and leukocyte transendothelial migration, which are known to be typically transient and highly regulated. In this study, we have used surface plasmon resonance technology to study the ICAM-1/LFA-1 interaction at the molecular level. A soluble form of LFA-1 (sLFA-1), normally expressed as two noncovalently associated membrane-bound subunits, has been produced, and its interaction with ICAM-1 has been examined. The kinetic analysis of a monomeric sLFA-1 binding to the first two domains of ICAM-1 expressed as a chimeric IgG fusion protein (D1D2-IgG) revealed that sLFA-1 was bound to the D1D2-IgG chimera with a Kd of 500 nM and dissociated with a k(diss) of 0.1 s(-1). Monomeric membrane-bound LFA-1 purified from plasma membranes showed a similar kinetic to sLFA-1. These results suggest that the monovalent interaction between ICAM-1 and LFA-1 has a primarily high affinity and a slow dissociation rate constant as compared with other adhesion molecules, suggesting a potential mechanism for firm adhesion.

Animals↗

PubMed1993

Epidemiology of low cholesterol levels in older adults. The Cardiovascular Health Study.

BACKGROUND: Low cholesterol levels have been associated with increased mortality from stroke, cancer, and other noncardiovascular diseases, but the reasons for this association remain unclear. One explanation is that persons with low cholesterol levels have early or occult disease that eventually leads to their deaths. METHODS AND RESULTS: This possibility was explored in 2,091 men and 2,714 women 65-100 years old in the Cardiovascular Health Study, a multicenter observational study of risk factors for heart disease and stroke in older adults. Cholesterol levels < or = 160 mg/dL were present in 11.6% of men and 3.7% of women and increased in prevalence with age. After adjustment for age, total cholesterol levels in this range were associated with a twofold increased prevalence of treated diabetes in men and women and with a twofold increased prevalence of cancer diagnosed in the preceding 5 years in women only. Low cholesterol was also associated with lower levels of hemoglobin, albumin, and factor VII, suggesting a link with hepatic synthetic function. On multivariate analysis, factors most strongly associated with low cholesterol levels in men and women were decreased factor VII levels, decreased albumin, and diabetes. CONCLUSIONS: Cross-sectional associations with low cholesterol levels differ by sex and suggest poorer health by some measures. The observed relations with treated diabetes and impaired hepatic synthetic function should be examined for risk of mortality in longitudinal data from this and other observational studies.

Aged↗

PubMed1998

Linkage and association analysis of chromosomal regions containing genes related to neuroendocrine or serotonin function in families with early-onset, recurrent major depression.

Recurrent unipolar depression with an early age of onset is a severe form of unipolar depression that has both genetic and environmental components. We genotyped the members of 16 families identified by probands with early onset (< or = 25 years), recurrent unipolar, major depression for 38 simple sequence tandem repeat polymorphisms (SSTRPs) from chromosomal regions containing 12 genes involved in neuroendocrine or serotonergic functioning. Pairwise linkage analysis was performed with the software package FASTLINK. The affected phenotype was defined four ways, and both dominant and recessive models of depression were analyzed. Seven SSTRPs showed lod scores > 1.00 at theta values between 0.10-0.20. The members of an additional 18 families were genotyped for these seven SSTRPs, and the complete sample of 34 families was evaluated using lod score analysis, affected pedigree member linkage analysis, and within-family association analysis. Evidence for linkage between D11S929 and affective illness remained positive, necessitating the analysis of four additional SSTRPs within 3 cM of D11S929. After all confirmatory analyses were completed, no evidence suggestive of linkage remained between any of the 38 SSTRPs and the affected phenotypes.

Depressive Disorder↗

PubMed2001

Identification and functional analysis of an interaction between domains of the 126/183-kDa replicase-associated proteins of tobacco mosaic virus.

The Tobacco mosaic virus (TMV) 126-kDa and read-through 183-kDa replicase-associated proteins have been shown to interact [Watanabe, T., Honda, A., Iwata, A., Ueda, S., Hibi, T., Ishihama, A. (1999). J. Virol. 73, 2633-2640]. To identify and investigate the sequence required for this interaction, five segments covering different portions of the 126/183-kDa open reading frame, including the methyl-transferase, intervening region (IR), helicase-like (HEL), and polymerase domains, were screened via the yeast two-hybrid system against a library of TMV protein segments. Only one specific interaction between the HEL domain clone and a TMV library clone, IRnHEL, encoding the C-terminal half of the IR and the N-terminal portion of the HEL domain was identified. Sequence and deletion analysis revealed that the interacting clones share a region containing the helicase NTP-binding motif and that this region was essential for the interaction. To determine the functional significance of this interaction, mutants of the HEL domain segment that conferred a temperature-sensitive (ts) defect in the yeast interaction were identified and cloned into a recombinant TMV strain. Of the five selected mutants, three (V823I/S824N/V1042M, A877V, V1087I) produced a ts replication phenotype in protoplasts while the other two (A1073V, T884I) abolished TMV replication at both the permissive and the nonpermissive temperatures. An additional mutation, K839S, designed to disrupt the shared NTP-binding motif, nearly abolished the two-hybrid interaction and prevented virus replication, suggesting that NTP-binding and/or the structure of this motif is a contributing factor in the interaction. Taken together, these results provide support for an interaction between TMV replicase-associated proteins that involves specific structural features of the HEL and IR domains.

Amino Acid Motifs↗

PubMed2003

Loss of CBP acetyltransferase activity by PHD finger mutations in Rubinstein-Taybi syndrome.

Disruption of one copy of the human CREB binding protein (CBP or CREBBP) gene leads to the Rubinstein-Taybi syndrome (RTS), a developmental disorder characterized by retarded growth and mental functions, broad thumbs, broad big toes and typical facial abnormalities. The CREB binding protein (CBP) is an essential transcriptional coactivator for many different transcription factors. CBP has the intrinsic ability to acetylate histones and other proteins, which is regarded as an important step in transcription activation. In vitro studies have shown that this enzymatic activity critically depends on the integrity of a plant homeodomain (PHD)-type zinc finger in the HAT domain of CBP. We therefore investigated whether PHD finger mutations are present in RTS patients. Mutational analysis of 39 patients revealed eight novel heterozygous mutations in the HAT domain of CBP, one of which alters a conserved PHD finger amino acid (E1278K), while a second mutation deletes exon 22, which encodes the central region of the PHD finger. Functional analysis of these RTS-associated PHD finger mutants showed that they lacked in vitro acetyltransferase activity towards histones and CBP itself and displayed reduced coactivator function for the transcription factor CREB. Importantly, in EBV-transformed lymphoblastoid cells from the exon 22 deletion patient we found approximately 50% less endogenous CBP HAT activity. These findings therefore underscore the functional importance of the PHD finger in vivo and imply that reduction of CBP HAT activity, as exemplified here by disruption of the PHD finger, is sufficient to cause RTS.

Acetyltransferases↗

PubMed2007

Association of cystatin C and estimated GFR with inflammatory biomarkers: the Heart and Soul Study.

BACKGROUND: Cystatin C is a marker of kidney function that may also be associated with inflammation. In this study, we compared the relative strengths of association of cystatin C and estimated glomerular filtration rate (eGFR) with inflammatory biomarkers. METHODS: We measured serum cystatin C and creatinine in 990 outpatients with coronary artery disease enrolled in the Heart and Soul Study. GFR was estimated (eGFR) by the abbreviated Modification of Diet in Renal Disease (MDRD) equation. We compared the associations of serum cystatin C and eGFR with C-reactive protein (CRP) and fibrinogen, after adjustment for 24 h creatinine clearance. RESULTS: Cystatin C concentrations had moderate correlations with CRP (r=0.15, P<0.001) and fibrinogen (r=0.26, P<0.0001); eGFR had similar correlations with CRP (r=-0.17, P=0.01) and fibrinogen (r=-0.25, P<0.001) among persons with eGFR 60 ml/min (r=0.04, P=0.32; r=-0.03, P=0.38). Quartiles of cystatin C were strongly and directly associated with CRP (P=0.02) and fibrinogen (P<0.007) after multivariate adjustment. However, these associations disappeared after adjustment for creatinine clearance (P=0.26 and 0.23, respectively). CONCLUSIONS: Cystatin C concentrations have moderate associations with CRP and fibrinogen that are not independent of creatinine clearance. Although a gold standard of kidney function is lacking, this analysis suggests that cystatin C captures an association of mildly impaired kidney function with increased inflammation.

Aged↗

PubMed2005

A biomimetic tissue from cultured normal human urothelial cells: analysis of physiological function.

The urinary bladder and associated tract is lined by the urothelium. Once considered as just an impermeable epithelium, it is becoming evident that the urothelium not only functions as a volume-accommodating urinary barrier but has additional roles, including sensory signaling. Lack of access to normal human urothelium has hampered physiological investigation, and although cell culture systems have been developed, there has been a failure to demonstrate that normal human urothelial (NHU) cells grown in vitro retain the capacity to form a functional differentiated urothelium. The aim of this study was to develop a biomimetic human urothelium from NHU cell cultures. Urothelial cells isolated from normal human urothelium and serially propagated as monolayers in serum-free culture were homogeneous and adopted a proliferative, nondifferentiated phenotype. In the presence of serum and physiological concentrations of calcium, these cells could be reproducibly induced to form stratified urothelia consisting of basal, intermediate, and superficial cells, with differential expression of cytokeratins and superficial tight junctions. Functionally, the neotissues showed characteristics of native urothelium, including high transepithelial electrical resistance of >3,000 Omega.cm(2), apical membrane-restricted amiloride-sensitive sodium ion channels, basal expression of Na(+)-K(+)-ATPase, and low diffusive permeability to urea, water, and dextran. This model represents major progress in developing a biomimetic human urothelial culture model to explore molecular and functional relationships in normal and dysfunctional bladder physiology.

Adult↗

PubMed1998

Identification and isolation of the indole-3-pyruvate decarboxylase gene from Azospirillum brasilense Sp7: sequencing and functional analysis of the gene locus.

The root-associated bacterium Azospirillum brasilense Sp7 produces the growth-stimulating phytohormone indole-3-acetic acid (= IAA) via the indole-3-pyruvate pathway. The DNA region containing ipdC, the structural gene for indole-3-pyruvate decarboxylase, was identified in a cosmid gene library of strain Sp7 by hybridization and has been sequenced. Upstream of the gene, two other ORF homologous to gltX and cysS were sequenced that are transcribed in the opposite direction. A functional analysis of the cloned ipdC region has been performed. To test the expression of the gene, a lacZ-Km cartridge was introduced into the gene. By this construct, tryptophan-dependent stimulation of gene expression in A. brasilense Sp7 was observed. Evidences for the existence of another copy of the ipdC gene in the Azospirillum genome are also reported.

Azospirillum brasilense↗

PubMed2006

Identification and functional analysis of damage-induced neuronal endopeptidase (DINE), a nerve injury associated molecule.

Nerve regeneration is a complex process associated with the expression of hundreds of genes. To elucidate the molecular mechanism responsible for nerve regeneration, hundreds of nerve regeneration-associated genes have been hunted using differential display polymerase chain reaction (DD-PCR), random cloning, microarray and proteomics. Damage-induced neuronal endopeptidase (DINE) is a newly identified nerve regeneration-related molecule derived from normal and axotomized hypoglosssal nuclei using DD-PCR. After full-length cloning, we have found that DINE is a neuron-specific membrane-bound metalloprotease. Damage-induced neuronal endopeptidase shares homology with neprilysin and endothelin-converting enzyme, which degrade or process neuropeptides. Although DINE has some neuroprotective effects, the physiological function of, as well as the substrate for, DINE remains obscure. The most intriguing property of DINE is its extreme transcriptional response against various types of nerve injuries, including that of the peripheral and central nervous systems. Thus, a more detailed expression profile of DINE mRNA was investigated using the dorsal root ganglion (DRG) after sciatic nerve injury. In the DRG, DINE mRNA was observed in small-sized DRG neurons after axotomy. This expression profile was similar to that of the neuropeptide galanin. Both in vitro and in vivo studies revealed that leukemia inhibitory factor and nerve growth factor withdrawal additively enhanced the expression of DINE, as well as that of galanin. Damage-induced neuronal endopeptidase and galanin may use common transcriptional regulation machinery. Although functional correlation of these molecules remains unclear, their simultaneous induction may provide more successful protection for injured neurons.

Animals↗

PubMedDate not supplied

A follow-up study of attentional behavior in 6-year-old children exposed prenatally to marihuana, cigarettes, and alcohol.

Attentional behavior was examined in one hundred twenty-six 72-month-old children for whom prenatal exposure to marihuana, cigarettes, and alcohol has previously been ascertained. Discriminant Function Analysis revealed a dose-response association between prenatal cigarette exposure and impulsive behavior as manifest on poorer performance on a response inhibition task and increased errors of commission on a sustained vigilance task. Performance on a series of memory tasks particularly those requiring verbal recall was also negatively associated with maternal cigarette use. Prenatal marihuana habits were associated with increased omission errors in the vigilance task, possibly reflecting a deficit in sustained attention. In addition, Discriminant Function Analysis revealed a dose-response relationship between prenatal marihuana use and a higher rating by the mothers on an impulsive/hyperactive scale. Relatively low levels of maternal alcohol consumption was related to decreased impulsive responding both in the response inhibition task and in terms of the mothers' perception of the child's behavior. The multifaceted approach of examining attentional behavior was essential to reveal the differential associations with the three prenatally used drugs. The implications of the observations and how the findings relate to and extend the existing literature is discussed.

Adult↗

PubMed1993

Analysis of peripheral blood lymphocyte cell surface density of functional and activation associated markers in young and old hemodialysis patients.

Aging has been associated with specific shifts in various peripheral blood immune competent cell subsets. As part of pre-transplant immune profile evaluation possible parallel age-related changes in mean T-cell surface density of several cluster differentiation and activation linked antigens were into 2 groups: group 1-114 patients 40 years old or younger and group 2-36 patients 55 years old or older. Peripheral blood CD3+, DR+, CD3+DR+, CD4+, CD4+DR+, CD8+, CD8+DR+, CD56+, CD8+CD56+, CD3+IL-2-R+ and CD3+TR+ (interleukin-2 and transferrin receptors bearing CD3+ cells respectively), all mononuclear cells expressing IL-2-R and TR, and CD4+CD45+ cell subsets were analyzed and enumerated by 2-color flow cytometry. Subset relative levels as well as absolute counts were recorded. Cell surface density computation was performed using a computerized mathematical model based on fluorescence intensity vector analysis and cell size score determination based on light scatter pattern from raw data obtained by flow cytometry studies. Younger age was significantly associated with higher absolute cell count of CD3+ (p < 0.001), DR+ (p < 0.05), CD4+ (p < 0.01), CD8+ (p < 0.005), CD3+IL-2-R+ (p < 0.05), CD3+TR+ (p < 0.03) and IL-2-R+ (p < 0.05). Older patients had a slightly higher mean absolute count of CD4+CD45+ subset (p not significant) and significantly higher mean count for CD8+CD56+ cell subset (p < 0.001). When cell subset levels were compared between the 2 groups as the relative fraction of cells expressing a given marker out of all mononuclear cells gated out by flow cytometry, younger age was significantly associated with higher levels of CD3+ (p < 0.005), CD8+ (p < 0.001), CD4+DR+ (p < 0.004), CD3-TR+ (p < 0.05) and CD8+IL-2-R+ (p < 0.05). In contrast, slightly higher subset levels of CD56+ (p not significant), and significantly elevated levels of CD8+CD56+ (p < 0.0019) and CD4+CD45+ (p < 0.004) were observed in the older patients. Cell surface density analysis showed that younger patients had higher mean density per cell of CD3 (p < 0.05), CD8 (p < 0.001), IL-2-R on CD3+ cells (p < 0.05) and TR on CD3+ cells (p < 0.05). Mean cell surface density of CD56 on all CD56+ cells as well as on CD8+ cells was higher in older individuals (p < 0.001 and p < 0.003, respectively).(ABSTRACT TRUNCATED AT 400 WORDS)

Adult↗

PubMed1989

Prediction of microbial aetiology at admission to hospital for pneumonia from the presenting clinical features. British Thoracic Society Pneumonia Research Subcommittee.

The selection of initial antimicrobial treatment in a patient with community acquired pneumonia is an important clinical decision. Because this decision is usually made before the results of specific microbiological tests are available, we attempted to determine how well the presenting clinical features would allow prediction of microbial aetiology in 441 adults admitted to hospital with pneumonia. Five of 90 variable available on admission were selected for inclusion in a multivariate discriminant function analysis because of their strong association with one or more of the major aetiological subsets (Mycoplasma pneumoniae, Streptococcus pneumoniae, "other," and undetermined). These variables were age, number of days ill before admission, presence or absence of bloody sputum and of lobar infiltration on chest radiograph, and white blood cell count. The microbial aetiology was correctly predicted by this discriminant function analysis in only 42% of cases, which gives a quantitative estimate of the degree of difficulty encountered in determining the microbial aetiology at the time of admission for pneumonia. When a similar discriminant function analysis was applied to the third of patients in whom the microbial aetiology was never determined, most of these cases were predicted to be due to Streptococcus pneumoniae.

Adolescent↗

PubMed2004

Refinement of the 6p21.3 quantitative trait locus influencing dyslexia: linkage and association analyses.

Reading disability (RD), or dyslexia, is the most common learning disability with a prevalence rate of ~5%-10% in school-age children. RD is highly heritable with evidence of a neurobiological origin. Linkage studies have identified several quantitative trait loci (QTLs) for RD. The QTL on chromosome 6p21.3 has been independently replicated by several groups and spans a 16.4-Mb (13.8 cM) interval from D6S109 to D6S291. In this study, we performed sib-pair linkage analyses with Haseman-Elston and DeFries-Fulker methods to define more accurately the QTL interval. Linkage was assessed by using five quantitative phenotypes, including a composite measure of reading performance and four component phenotypes. When probands were selected for severe scores, single- and multi-point analyses showed significant linkage with all five phenotypes, converging over an interval of ~3.24 Mb spanning D6S1597 to D6S1571. Maximal linkage converged at marker D6S1554 across phenotypes. Out of 12 genes in the linkage interval, ten clustered within ~680 kb and were selected for association analysis based on central nervous system expression and putative function. Marker-trait associations were assessed by using QTDT (a general test of association for quantitative traits) and the family-based association test (FBAT), and haplotype analysis was performed by using FBAT and the GeneHunter Transmission/Disequilibrium Test TDT. Marker associations were detected in five of the ten genes, results that were corroborated by our haplotype TDT analysis. The results of the association study have thereby allowed us to significantly reduce the number of possible candidate genes and to prioritize genes for further mutation screening.

Adolescent↗

PubMed2005

Age-related changes in cognitive domains. A population-based study.

BACKGROUND AND AIMS: The aim of the present study is to describe the effects of aging on various cognitive domains (global cognitive function, executive function, motor speed) in a population sample of elderly men, and to describe how their age-related changes are influenced by education, depression, or prevalent cerebrovascular accidents (CEVD). METHODS: A cross-sectional observational study was conducted in a cohort of 334 men, 65 to 95 years old, living in rural communities, participating in the Italian cohort of two population studies--MATISS (Malattie cardiovascolari ATerosclerotiche Istituto Superiore di Sanità) and FINE (Finland, Italy, Netherlands, Elderly). Global cognitive function was measured by the Mini-Mental State Examination (MMSE), executive function by the Stroop test, motor speed by the Purdue Pegboard test, and depression by the CES-D test. Prevalence of cerebrovascular accidents (CEVD), myocardial infarction, and diabetes were evaluated by a questionnaire and a clinical examination. Blood pressure, and total and HDL cholesterol were measured. Current smoking status was self-reported. RESULTS: An age-associated decline in global cognitive functions, executive functions, and motor speed was observed. The decline is more apparent after the age of 85 for the MMSE, and after 75 for executive functions and motor speed. Logistic regression analysis revealed that age was independently associated with altered global cognitive functions, executive functions, and motor speed, even after adjusting for education, depression or prevalent CEVD. CONCLUSIONS: In a cohort of community-living elderly men aged 65 to 95 years, age-associated changes in mental functions are more evident after the age of 85. These changes are independent of education, depression, or prevalent CEVD.

Aged↗