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At least 1,261 records · Page 70Linked to original sources
PubMed2001

Recombination and spontaneous mutation at the major cluster of resistance genes in lettuce (Lactuca sativa).

Two sets of overlapping experiments were conducted to examine recombination and spontaneous mutation events within clusters of resistance genes in lettuce. Multiple generations were screened for recombinants using PCR-based markers flanking Dm3. The Dm3 region is not highly recombinagenic, exhibiting a recombination frequency 18-fold lower than the genome average. Recombinants were identified only rarely within the cluster of Dm3 homologs and no crossovers within genes were detected. Three populations were screened for spontaneous mutations in downy mildew resistance. Sixteen Dm mutants were identified corresponding to spontaneous mutation rates of 10(-3) to 10(-4) per generation for Dm1, Dm3, and Dm7. All mutants carried single locus, recessive mutations at the corresponding Dm locus. Eleven of the 12 Dm3 mutations were associated with large chromosome deletions. When recombination could be analyzed, deletion events were associated with exchange of flanking markers, consistent with unequal crossing over; however, although the number of Dm3 paralogs was changed, no novel chimeric genes were detected. One mutant was the result of a gene conversion event between Dm3 and a closely related homolog, generating a novel chimeric gene. In two families, spontaneous deletions were correlated with elevated levels of recombination. Therefore, the short-term evolution of the major cluster of resistance genes in lettuce involves several genetic mechanisms including unequal crossing over and gene conversion.

Base Sequence↗
PubMed1994

Activity-induced changes in synaptic release sites at the crayfish neuromuscular junction.

Crustacean motor axons provide a model in which activity-dependent changes in synaptic physiology and synaptic structure can be concurrently observed in single identifiable neurons. In response to a train of stimulation, crustacean neuromuscular junctions undergo pronounced facilitation of transmitter release. The effects of maintained high-frequency stimulation may persist for at least several hours ("long-term facilitation"). Electrophysiological studies suggest that the number of "active" synapses contributing transmitter quanta at low frequencies of stimulation increases during and after a train of high-frequency stimulation. However, at different terminal recording sites the effect of stimulation varies, and it was observed that not all released quanta produce a voltage change in the postsynaptic muscle cell. Electron microscopic examinations of serial sections from nerve terminals subjected to stimulation were made to determine whether changes in synaptic structure could be correlated with activity-induced long-lasting enhancement of transmission. A procedure was introduced for marking a recorded terminal with fluorescent polystyrene microspheres, which are visible in electron micrographs of the recording site. Crustacean nerve terminals possess a large number of discrete synapses, a small fraction of which have multiple presynaptic "active zones" (dense bodies with clustered synaptic vesicles, thought to represent sites of evoked transmitter release). In terminals previously stimulated, the proportion of synapses with multiple "active zones" is greater than in control unstimulated terminals. Total synaptic vesicle counts and readily releasable vesicles at synapses are not significantly different in previously stimulated terminals and controls. In terminals fixed during stimulation a few synapses show evidence of division in "active zones," and synaptic vesicle counts are lower than in controls.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2002

OrthoGUI: graphical presentation of Orthostrapper results.

SUMMARY: Orthostrapper is a program that calculates orthology support values for pairs of sequences in a multiple alignment (Storm and Sonnhammer, Bioinformatics, 18, 92-99, 2002). Here we present OrthoGUI, a web interface and display tool for Orthostrapper analysis. OrthoGUI visualizes the Orthostrapper output in both tabular and tree representations, and can also apply a clustering algorithm to identify groups of multiple orthologs, which are indicated by colour coding. AVAILABILITY: http://www.cgb.ki.se/OrthoGUI CONTACT: erik.sonnhammer@cgb.ki.se

ATP-Binding Cassette Transporters↗
PubMed2006

Effect of pulse duration on resonant heating of laser-irradiated argon and deuterium clusters.

We study the effect of pulse duration on the heating of single van der Waals bound argon and deuterium clusters by a strong laser field using a two-dimensional (2D) electrostatic particle-in-cell (PIC) code in the range of laser-cluster parameters such that kinetic as well as hydrodynamic effects are active. Heating is dominated by a collisionless resonant absorption process that involves energetic electrons transiting through the cluster. A size-dependent intensity threshold defines the onset of this resonance [T. Taguchi, Physical Review Letters, 92, 20 (2004)]. It is seen that increasing the laser pulse duration lowers this intensity threshold and the energetic electrons take multiple laser periods to transit the cluster instead of one laser period. Our simulations also show that strong electron heating is accompanied by the generation of a high-energy peak in the ion energy distribution function. We also calculate the yield of thermonuclear fusion neutrons from exploding deuterium clusters using the PIC model with periodic boundary conditions that allows for the interaction of ions from neighboring clusters.

Journal Article↗
PubMed1997

Random-effects models for analyzing clustered data from a nutrition education intervention.

When evaluating the effects of public health intervention, larger units, or clusters, of individuals are often the unit of randomization and implementation. Ignoring dependency in the data due to clustering can misrepresent intervention effects. Random-effects models (REMs) may be a useful way to analyze such data. The present study compares results of analyses of data from a nutrition intervention program using four different methods: (a) usual multiple regression analysis using individual subject data, (b) usual multiple regression analysis using the classroom cluster as the unit of analysis, (c) two-level REM model with subjects clustered within classrooms, and (d) two-level REM model with subjects clustered within sites.

Adult↗
PubMed1999

Cultures of human liver cells in simulated microgravity environment.

We used microgravity-simulated bioreactors that create the unique environment of low shear force and high-mass transfer to establish long-term cultures of primary human liver cells (HLC). To assess the feasibility of establishing HLC cultures, human liver cells obtained either from cells dissociated by collagenase perfusion or minced tissues were cultured in rotating vessels. Formation of multidimensional tissue-like spheroids (up to 1.0 cm) comprised of hepatocytes and biliary epithelial cells that arranged as bile duct-like structures along newly formed vascular sprouts were observed. Electron microscopy revealed clusters of round hepatocytes and bile canaliculi with multiple microvilli and tight junctions. Scanning EM revealed rounded hepatocytes that were organized in tight clusters surrounded by a complex mesh of extracellular matrix. Also, we observed that co-culture of hepatocytes with endothelial cells stimulate albumin mRNA expression. In summary, a simulated microgravity environment is conducive for the establishment of long-term HLC cultures and allows the dissection of the mechanism of liver regeneration and cell-to-cell interactions that resembles in vivo conditions.

Albumins↗
PubMed2006

Towards clustering of incomplete microarray data without the use of imputation.

MOTIVATION: Clustering technique is used to find groups of genes that show similar expression patterns under multiple experimental conditions. Nonetheless, the results obtained by cluster analysis are influenced by the existence of missing values that commonly arise in microarray experiments. Because a clustering method requires a complete data matrix as an input, previous studies have estimated the missing values using an imputation method in the preprocessing step of clustering. However, a common limitation of these conventional approaches is that once the estimates of missing values are fixed in the preprocessing step, they are not changed during subsequent processes of clustering; badly estimated missing values obtained in data preprocessing are likely to deteriorate the quality and reliability of clustering results. Thus, a new clustering method is required for improving missing values during iterative clustering process. RESULTS: We present a method for Clustering Incomplete data using Alternating Optimization (CIAO) in which a prior imputation method is not required. To reduce the influence of imputation in preprocessing, we take an alternative optimization approach to find better estimates during iterative clustering process. This method improves the estimates of missing values by exploiting the cluster information such as cluster centroids and all available non-missing values in each iteration. To test the performance of the CIAO, we applied the CIAO and conventional imputation-based clustering methods, e.g. k-means based on KNNimpute, for clustering two yeast incomplete data sets, and compared the clustering result of each method using the Saccharomyces Genome Database annotations. The clustering results of the CIAO method are more significantly relevant to the biological gene annotations than those of other methods, indicating its effectiveness and potential for clustering incomplete gene expression data. AVAILABILITY: The software was developed using Java language, and can be executed on the platforms that JVM (Java Virtual Machine) is running. It is available from the authors upon request.

Algorithms↗
PubMed1985

A genetic locus closely linked to a protease inhibitor gene complex controls the level of multiple RNA transcripts.

The two major protease inhibitors in mouse plasma are alpha 1-protease inhibitor (alpha 1-PI), putative inhibitor of neutrophil elastase, and contrapsin, an inhibitor in vitro of trypsinlike proteases. We have shown by nucleotide sequence analysis that these two inhibitors are related (R. E. Hill, P. H. Shaw, P. A. Boyd, H. Baumann, and N. D. Hastie, Nature (London) 311:175-177, 1984). Here, we show that the contrapsin and alpha 1-PI genes are members of two different multigene families, each containing at least three genes in mice and rats. We established the chromosomal locations of these genes by analyzing the segregation of restriction fragment length polymorphisms in recombinant inbred mouse strains. These experiments show that the multiple genes in each family are clustered and that the two gene families are closely linked on chromosome 12. Thus the genes for contrapsin and alpha 1-PI are likely to have evolved by duplication of a common ancestral gene. The contrapsin multigene family codes for multiple mRNA transcripts in the liver. There is a genetic difference among inbred mouse strains in the regulation of two of these transcripts. In some inbred strains the transcripts are synthesized constitutively; in others they are induced by inflammation. We mapped in recombinant inbred strains the regulatory locus responsible for this genetic variation and found it is linked to the contrapsin multigene family, which suggests a cis-acting regulatory element. We also found that the contrapsin and the alpha 1-PI multigene families have acquired very different regulatory responses since the time of the gene duplication event.

Animals↗
PubMed1996

Clustering of dyslipidemia, hyperuricemia, diabetes, and hypertension and its association with fasting insulin and central and overall obesity in a general population. Atherosclerosis Risk in Communities Study Investigators.

Clustering of elevated triglycerides, decreased high-density lipoprotein cholesterol (HDL-C), hyperuricemia, diabetes, and hypertension has been related to insulin resistance/high insulin levels and central and/or overall obesity. The extent to which these abnormalities cluster and whether hyperinsulinemia, central adiposity, and overall obesity each independently associate with this clustering were evaluated in 14,481 US whites and African-Americans 45 to 64 years of age. With the exception of hypertension, abnormalities rarely existed in isolated form. Clustering greatly exceeded chance association (P < .001). Although this clustering was greater in relative terms (ratio of observed to expected cluster frequency) in the lean and less centrally obese, it was greater in absolute terms (observed minus expected cluster frequency as a percent of total population) in the more centrally and more generally obese. The greatest excesses were found for clusters that included both hypertriglyceridemia and low HDL-C. Multiple logistic regression models showed strong and independent graded relationships of clusters with quintiles of fasting insulin (fifth quintile odds ratio, 10 to 54, P < .001) and to a lesser degree with quintiles of the waist to hip ratio (2.2 to 5.4, P < .001 for most) and of body mass index (1.6 to 4.5, P < .05 for most). In conclusion, all abnormalities cluster in excess of that predicted by chance, with clusters showing remarkable and graded independent associations with fasting hyperinsulinemia and to a lesser extent with central and overall obesity. Thus, a metabolic syndrome occurs in both lean and obese middle-aged US adults.

Cluster Analysis↗
PubMedDate not supplied

A cluster of symptoms over time in patients with lung cancer.

BACKGROUND: Patients with lung cancer present late in the disease and have multiple symptoms. Previous research has shown the symptom cluster of fatigue, weakness, weight loss, appetite loss, nausea, vomiting, and altered taste to be present at time of lung cancer diagnosis. OBJECTIVES: The study determined whether the symptom cluster identified at the time of diagnosis remained 3 and 6 months later, and whether there was a difference in the mean number of symptoms and the mean level of symptom severity over time. The relation of the severity rating for individual symptoms at the time of diagnosis and at 3 and 6 months after diagnosis was examined. Predictors for the number of symptoms and whether the symptom cluster was predictive of death were determined. METHODS: Secondary analysis of an existing data set for 112 patients with newly diagnosed lung cancer assessed at diagnosis and at 3 and 6 months was performed and determined whether they were alive or dead 19 months after diagnosis. RESULTS: The cluster of seven symptoms had internal consistency that remained at 3 and 6 months. The mean symptom severity and the number of symptoms at diagnosis were correlated with later ratings, but decreased in severity over time. A similar decrease in severity rating was seen for the individual symptoms in the cluster. The stage of cancer at diagnosis was the most predictive of the number of cluster symptoms reported. Death 6 to 19 months after diagnosis was predicted by age, stage of cancer at diagnosis, and symptom severity at 6 months. CONCLUSIONS: The symptom cluster remains over the course of lung cancer and is an independent predictor of the patient's death. Symptom severity, the number of symptoms reported, and the severity of the individual symptoms decreased over time. The stage of cancer at diagnosis is the best predictor of symptoms later in the disease.

Aged↗
PubMed1990

A cluster classification for histologic diagnoses of CNS tumors in an epidemiologic study.

This paper introduces a method which was utilized to sort multiple pathologic diagnoses pertaining to brain tumors into clusters of equivalent diagnostic terms for an epidemiological study of brain cancer. The method enabled the medical record abstractors to ascertain cases for the study. It enabled the reviewing pathologist to identify differences between original and reviewed diagnoses. It identified the large range of classification systems of brain tumors used by practicing pathologists as a factor contributing to confusion of data if slide reviews are not incorporated into epidemiological studies, and demonstrated how the use of a cluster classification alleviates this problem.

Adult↗
PubMed2001

Genesis of the ILT/LIR/MIR clusters within the human leukocyte receptor complex.

The human leukocyte receptor complex (LRC) contains at least 26 genes which belong to the immunoglobulin superfamily The genes include two clusters of immunoglobulin-like transcript (ILT)/leukocyte immunoglobulin-like receptor (LIR)/monocyte-macrophage inhibitory receptor (MIR) loci, a cluster of killer cell inhibitory receptor (KIR) genes, two leukocyte-associated immunoglobulin-like receptor genes, as well as the Fc receptor for IgA and the natural cytotoxicity receptor I loci. It has already been postulated that these genes have evolved by multiple duplications, while the two ILT clusters are likely to have been generated by the inverse duplication of an ancient ILT cluster. To shed more light on the possible origin of the loci within the LRC, we have now investigated the presence of KIR and ILT loci in a variety of vertebrates by hybridizations and compared the genomic sequences of all ILT genes. Our results lead to the following conclusions: 1) the origin of KIR genes dates back to about 100 million years, but only primate and human KIRs are closely related; 2) in contrast, genes which are detectable with human ILT cDNAs are already found in birds, suggesting their presence already about 300 million years ago. Using the sequence data produced by the human genome project, we have developed a hypothesis that reconstructs the genesis of the two human ILT clusters in detail which will help to understand the function of the LRC.

Animals↗
PubMed2003

[Multiple Spitz nevus].

Benign juvenile melanoma was originally described and differentiated from malignant melanoma by Sophie Spitz in 1948. The solitary form is the most frequent and usually appears on the face and extremities of young children and adolescents as a solitary, hairless, dome-shaped papule or nodule, varying in size from 3 to 15 mm. It can be of a wide spectrum of colors including pink, yellow, red, brown, purple and black, representing 1% to 8% of melanocytic tumors in children. Histologically, Spitz nevus has been subdivided into junctional, compound and intradermal type according to the location of neoplastic melanocytes in the skin. Rarely multiple benign juvenile melanoma arranged in clusters (agminated) or widespread (disseminated) are described. Less than 50 cases have been reported in the world literature. The grouped form usually occurs on the face of children on normal, but also hyperpigmented or hypopigmented skin, while the disseminated one in adults. A case of multiple agminated Spitz nevus arised on the face of a 2 years old girl is reported. The clinical presentations with a 3 years follow-up and the histologic features of this nevus are described as well as the therapeutic approach.

Child, Preschool↗
PubMed1983

Spatial distribution of individual medial lemniscal axons in the thalamic ventrobasal complex of the cat.

Neurons responding to deep or cutaneous stimuli are situated in different parts of the ventrobasal complex. Within the cutaneous region elongated clusters of cells with common place and modality properties project to single columns in the somatic sensory cortex. The present study sought to determine to what extent single lemniscal axons contribute terminals to different regions and to different cell clusters. Lemniscal axons, anterogradely labelled by horseradish peroxidase injected into the medial lemniscus of cats were examined light and electron microscopically. Labelled axons bore one or two, mainly anteroposteriorly oriented, terminal ramifications. These ramifications were relatively small when compared to the length of the complex. Some of the axons bore one or two collaterals that ascended towards the dorsal edge of the complex and formed an additional small ramification there. Electron microscopic analyses of labelled lemniscal axons provided further evidence to that already available that most of their boutons synapse on proximal dendrites of relay neurons and on presynaptic dendrites, presumably belonging to interneurons. A concurrent study of Golgi-impregnated ventrobasal neurons showed three morphological types all with dendritic fields of similar extent. From measurements of the lemniscal terminal ramifications and the counting of counterstained cells it was calculated that 50-120 neurons may receive input from a single terminal ramification. However, because of the restricted extent of the ramifications, the elongated clusters of cells projecting to a single cortical column probably receive input from multiple lemniscal axons and not all members of the cluster receive inputs from the same axons.

Afferent Pathways↗
PubMed2002

Responses to panic induction procedures in subjects with multiple chemical sensitivity/idiopathic environmental intolerance: understanding the relationship with panic disorder.

Idiopathic environmental intolerance (IEI), also known as multiple chemical sensitivity, is a clinical description for a cluster of symptoms of unknown etiology that have been attributed by patients to multiple environmental exposures when other medical explanations have been excluded. Because allergy has not been clearly demonstrated and current toxicological paradigms for exposure-symptom relationships do not readily accommodate IEI, psychogenic theories have been the focus of a number of investigations. A significantly higher lifetime prevalence of major depression, mood disorders, anxiety disorders, and somatization disorder has been reported among patients with environmental illness compared with that in controls. Symptoms often include anxiety, lightheadedness, impaired mentation, poor coordination, breathlessness (without wheezing), tremor, and abdominal discomfort. Responses to intravenous sodium lactate challenge or single-breath inhalation of 35% carbon dioxide versus a similar breath inhalation of clean air have shown a greater frequency of panic responses in subjects with IEI than in control subjects, although such responses did not occur in all subjects. Preliminary genetic findings suggest an increased frequency of a common genotype with panic disorder patients. The panic responses in a significant proportion of IEI patients opens a therapeutic window of opportunity. Patients in whom panic responses may at least be a contributing factor to their symptoms might be responsive to intervention with psychotherapy to enable their desensitization or deconditioning of responses to odors and other triggers, and/or may be helped by anxiolytic medications, relaxation training, and counseling for stress management.

Administration, Inhalation↗
PubMed1996

Relative frequency, heterogeneity and geographic clustering of PKU mutations in Norway.

We have analysed 236 Norwegian phenylketonuria (PKU) alleles by a combination of mutation scanning methods, restriction enzyme-based assays and DNA sequencing. Thirty-three different mutations constituted 99.6% of all mutant alleles (only 1 allele remains unidentified), 23 of these have been identified also in other European countries. Twenty were predicted missense mutations, 6 splice mutations, 4 nonsense mutations and 2 deletion mutations and 1 mutation disrupted the start codon. The 8 most common mutations represented 83.5% of the PKU alleles, with single allele frequencies ranging from 5.9 to 15.7%. Four of these mutations (R261Q, R408W, Y414C, and 1VS12nt1) are commonly occurring also in PKU patients in other European countries, while the other 4 (G46S, G272X, F299C, and R408Q) have higher frequencies in Norway than in any other country studied. Six mutations (I65T, L249F, P281L, Y356X, R158Q, and R252W) have frequencies between 0.8% and 2.1%, and 19 mutations were encountered only once. The majority of PKU mutations were found on the same RFLP/VNTR haplotype backgrounds in Norway as in other European populations, suggesting that only a few of the mutations may represent recurrent mutations (< 3.4%). Among 10 mutations only reported for our population, we detected 2 de novo mutations (0.8%) arisen in Norway. From the birthplaces of the probands' grandparents, each mutation seemed to have an individual geographic distribution within Norway, with patterns of local mutation clustering. Our observations are compatible with multiple founder effects and genetic drift for the distribution of PKU mutations within Norway.

Alleles↗