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At least 433 records · Page 24Linked to original sources
PubMed2006

Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice.

By constructing nearly isogenic lines (NILs) that differ only at a single quantitative trait locus (QTL), we fine-mapped the yield-improving QTL qGY2-1 to a 102.9-kb region on rice chromosome 2. Comparison analysis of the genomic sequences in the mapped QTL region between the donor (Dongxiang wild rice, Oryza rufipogon Griff.) and recurrent (Guichao2, Oryza sativa ssp. indica) parents used for the development of NILs identified the haplotypes of a leucine-rich repeat receptor kinase gene cluster, which showed extensive allelic variation. The sequences between genes in the cluster had a very high rate of divergence. More importantly, the genes themselves also differed between two haplotypes: Only 92% identity was observed for one allele, and another allele was found to have completely lost its allelic counterpart in Guichao2. The other six shared genes all showed >98% identity, and four of these exhibited obvious regulatory variation. The same haplotype segments also differed in length (43.9-kb in Guichao2 vs. 52.6-kb in Dongxiang wild rice). Such extensive sequence variation was also observed between orthologous regions of indica (cv. 93-11) and japonica (cv. Nipponbare) subspecies of Oryza sativa. Different rates of sequence divergence within the cluster have resulted in haplotype variability in 13 rice accessions. We also detected allelic expression variation in this gene cluster, in which some genes gave unequal expression of alleles in hybrids. These allelic variations in structure and expression suggest that the leucine-rich repeat receptor kinase gene cluster identified in our study should be a particularly good candidate for the source of the yield QTL.

Alleles↗
PubMed1995

Effects of normal and their branched alcohols with structurally minimal variation on kinetic parameters in thermolysin-catalyzed peptide hydrolysis and synthesis of N-(benzyloxycarbonyl)-L-phenylalanyl-L-phenylalanine and its methyl ester.

When higher alcoholic solvents were added to the reaction medium, and the enhancement of the enzyme activity, followed by its reduction then inactivation, were observed in thermolysin-catalyzed peptide hydrolysis and synthesis. The organic solvent content used was less than the saturating concentration in the buffer (i.e., water-organic one-phase system). The kinetic parameters, Km and kcat, at the alcoholic concentration giving maximal enzyme activity in these reactions changed linearly with increasing logP values of the alcohols and consequently kcat/Km as well. When the branched isomers of alcohols with structurally minimal variation of which logP was equivalent theoretically, were used as annexments, the kinetic parameters were also changed. The results, especially the changes of Km for each organic solvent, suggested that each alcohol should act at the active site of the enzyme in its own effective mode.

Alcohols↗
PubMed2002

Automated assignment and 3D structure calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY spectra.

The NOAH/DIAMOD suite uses feedback filtering and self-correcting distance geometry to generate 3D structures from unassigned NOESY spectra. In this study we determined the minimum set of experiments needed to generate a high quality structure bundle. Different combinations of 3D 15N-edited, 13C-edited HSQC-NOESY and 2D homonuclear 1H-1H NOESY spectra of the 77 amino acid protein, myeloid progenitor inhibitory factor-1 (MPIF-1) were used as input for NOAH/DIAMOD calculations. The quality of the assignments of NOESY cross peaks and the accuracy of the automatically generated 3D structures were compared to those obtained with a conventional manual procedure. Combining data from two types of experiments synergistically increased the number of peaks assigned unambiguously in both individual spectra. As a general trend for the accuracy of the structures we observed structural variations in the backbone fold of the final structures of about 2 A for single spectral data, of 1 A to 1.5 A for double spectral data, and of 0.6 A for triple spectral data sets. The quality of the assignments and 3D structures from the optimal data using all three spectra were similar to those obtained from traditional assignment methods with structural variations within the bundle of 0.6 A and 1.3 A for backbone and heavy atoms, respectively. Almost all constraints (97%) of the automatic NOESY cross peak assignments were cross compatible with the structures from the conventional manual assignment procedure, and an even larger proportion (99%) of the manually derived constraints were compatible with the automatically determined 3D structures. The two mean structures determined by both methods differed only by 1.3 A rmsd for the backbone atoms in the well-defined regions of the protein. Thus NOAD/DIAMOD analysis of spectra from labeled proteins provides a reliable method for high throughput analysis of genomic targets.

Animals↗
PubMed1983

Individual variations in structure and function of human eccrine sweat gland.

The mechanisms underlying variations in perspiration rate at the glandular level are still poorly understood. Human eccrine sweat glands were dissected from the back of 12 adults, cannulated, and stimulated in vitro with methacholine (Mch). The maximal sweat rate and pKA for Mch determined from the dose-response curve for each individual were compared with the anatomic dimensions of the isolated secretory tubules. There was significant correlation between Mch sensitivity (pKA) and the size of the sweat gland, sweat rate per gland, sweat rate per unit length of the secretory tubule, and sweat rate per unit glandular volume. The sweat glands from individuals judged to be poor sweaters exhibited smaller size, lower secretory activity both in vivo and in vitro, and decreased Mch sensitivity compared with glands from physically fit individuals. We conclude that the increased Mch sensitivity and glandular hypertrophy are the two important features of functionally active sweat glands and infer that these parameters could improve as a result of acclimatization to physical exercise and/or heat.

Adult↗
PubMed2004

Genetic structure and variation in the relict populations of Alsophila spinulosa from southern China based on RAPD markers and cpDNA atpB-rbcL sequence data.

RAPD markers and sequences of chloroplast DNA (cpDNA) atpB-rbcL intergenic spacers were used to characterize the pattern of genetic variation and the phylogenetic relationships of the relict populations of Alsophila spinulosa located in Jian Feng Ling (JFL) and Diao Luo Shan (DLS), Hainan, and Tang Lang Shan (TLS), Ding Hu Shan (DHS), and Da Xi Shan (DXS), Guangdong, of southern China. 28 random primers generated 118 bands, out of which 26 (22.03%) were polymorphic loci, distinguishing 17 different RAPD phenotypes. Percentage of polymorphic loci, Shannon phenotypic diversity and Nei's gene diversity comprehensively indicated that JFL possessed the highest diversity, TLS and DHS in intermediate and DLS or DXS the least; the corresponding values of the population appeared correlated with the population size. Differentiation was detected among populations of A. spinulosa (1-Hpop/Hsp=0.7453, GST=0.7763, and phist=0.8145). AMOVA showed that 47.44% of the variance was partitioned among regions (Hainan and Guangdong), 34.01% attributed among populations within regions, whereas only 18.55% occurring within populations. Low level of intra-specific diversity was maintained in A. spinulosa with Shannon diversity and gene diversity merely 0.0560 and 0.0590, repectively. Sequence length of atpB-rbcL intergenic spacer varied from 724 bp to 730 bp. Base composition was with A+T content between 63.17% and 63.70%. 13 haplotypes of atpB-rbcL noncoding spacers were identified. UPGMA dendrogram of RAPD phenotypes, principal components analysis based on RAPD patterns, minimum spanning network and neighbour-joining (NJ) tree established on atpB-rbcL haplotypes consistently suggested the geographical subdivision of populations of A. spinulosa between Hainan and Guangdong. Breeding system and conservation strategy of A. spinulosa was discussed based on the information of population genetic structure and variation.

Base Composition↗
PubMed1995

Average core structures and variability measures for protein families: application to the immunoglobulins.

A variety of methods are currently available for creating multiple alignments, and these can be used to define and characterize families of related proteins, such as the globins or the immunoglobulins. We have developed a method for using a multiple alignment to identify an average structural "core", a subset of atoms with low structural variation. We show how the means and variances of core-atom positions summarize the commonalities and differences with a family, making them particularly useful in compiling libraries of protein folds. We show further how it is possible to describe the rotation and translation relating two core structures, as in two domains of a multi-domain protein, in a consistent fashion in terms of a "mean" transformation and a deviation about this mean. Once determined, our average core structures (with their implicit measure of structural variation) allow us to define a measure of structural similarity more informative than the usual root-mean-square (RMS) deviation in atomic position, i.e. a "better RMS." Our average structures also permit straightforward comparisons between variation in structure and sequence at each position in a family. We have applied our core-finding methodology in detail to the immunoglobulin family. We find that the structural variability we observe just within the VL and VH domains anticipates the variability that others have observed throughout the whole immunoglobulin superfamily; that a core definition based on sequence conservation, somewhat surprisingly, does not agree with one based on structural similarity; and that the cores of the VL and VH domains vary about 5 degrees in relative orientation across the known structures.

Algorithms↗
PubMed1998

Alzheimer disease: quantitative H-1 MR spectroscopic imaging of frontoparietal brain.

PURPOSE: To replicate previous hydrogen-1 magnetic resonance (MR) spectroscopic imaging findings of metabolic abnormalities in patients with Alzheimer disease (AD), to verify that metabolic abnormalities are not an artifact of structural variations measured at MR imaging, to determine whether metabolic changes correlate with dementia severity, and to test whether MR imaging and MR spectroscopic imaging findings together improve ability to differentiate AD. MATERIALS AND METHODS: MR spectroscopic imaging and MR imaging were performed in 28 patients with AD and 22 healthy elderly subjects. Spectroscopic imaging data were coregistered with MR imaging segmentation data to obtain volume-corrected metabolite concentrations. RESULTS: Consistent with previous results, N-acetyl aspartate (NAA) levels were statistically significantly reduced in frontal and posterior mesial cortex of AD patients, presumably due to neuronal loss. NAA level reductions were independent of structural variations measured at MR imaging and, in parietal mesial cortex, were correlated mildly with dementia severity. Spectroscopic imaging findings of NAA level combined with MR imaging measures did not improve discrimination power for AD relative to that of MR imaging alone. CONCLUSION: Reduced NAA levels in frontoparietal brain are of limited use for diagnosis of AD. However, they are not an artifact of structural variations and thus may provide useful information for the understanding of the pathologic processes underlying AD.

Aged↗
PubMed2002

Subjective health complaints in adolescence: dimensional structure and variation across gender and age.

AIMS: The aim of this study is to investigate dimensional structures in subjective health complaints in adolescents and to examine the variation in levels and dimensionality across gender and age groups. METHODS: Data from two studies were used: (1) a study based on a convenience sample, consisting of 1427 Norwegian students (11- to 15-year-olds) from schools participating in the European Network of Health Promoting Schools; (2) a nationwide survey amongst 7,059 Norwegian students (aged 11, 13, 15, and 16) from the Health Behaviour in School-aged Children (HBSC) study. Subjective health complaints were measured by revised versions of the HBSC symptoms checklist (HBSC-SCL). RESULTS: In study 1 confirmatory factor analysis revealed that a model of two highly correlated factors, which can be labelled somatic and psychological, fitted the data reasonably well (CFI = 0.91). This two-factor model was applied in study 2 and latent means were tested across sub-samples defined by gender and age. The results indicate that girls show higher mean levels compared with boys on both factors. There is also an indication of an increase in these factors with age amongst girls, while amongst boys there is less, if any, difference across age groups. The correlation between the somatic and psychological factors was virtually constant across age groups and gender. CONCLUSIONS: The identification of a somatic and a psychological factor indicates the existence of two different dimensions that may have different aetiologies. The gender difference in latent means across age groups may suggest a different developmental pattern amongst girls and boys.

Adolescent↗
PubMed1996

AF4/FEL, a gene involved in infant leukemia: sequence variations, gene structure, and possible homology with a genomic sequence on 5q31.

The most common chromosome abnormality among infants with acute lymphoblastic leukemia is a t(4;11)(q2l;q23) and patients with this 4;11 translocation have a very poor prognosis. This unique genetic rearrangement fuses the MLL/ALL-1/HRX-Htrx gene at 11q23 with the AF4/FEL gene at 4q21. The resulting chimeric mRNAs presumably encode chimeric proteins which contribute to the leukemogenic state. The AF4 gene remains poorly understood with an unknown function. In this report, we describe the cDNA sequence information from human placental tissue where AF4 mRNA is highly expressed. We identified six intron-exon boundaries in the AF4 genomic structure and discussed more than 30 AF4 cDNA sequence variations reported in the literature. In addition, we identified three overlapping genomic sequences in GenBank entitled the "interleukin growth hormone cluster on chromosome 5q31," which, when aligned and translated, had three regions that suggested homology to the predicted AF4 protein sequence (32% amino acid sequence identity over 314 amino acids, 43% over 63 amino acids, and 50% over 40 amino acids). Of interest, this same chromosome 5q31 region has also been implicated in MLL gene rearrangements in human leukemia.

Amino Acid Sequence↗
PubMed1979

[X-ray diffraction analysis of disintegration of polyglycolic acid suture material both in vivo and in model media].

Examined were the structural variations of polyglycolic acid surgical suture material by X-ray diffraction methods subsequent to sejour in vivo and in several model mediums. After a long stay in vivo, water and buffer at pH 2 the following structural variations in the polymer were observed: diminution of macroperiod, and certain increase of crystallinity. Rather profound, ten times faster destruction of suture material in alkaline medium at pH 12 did not cause the variation of macroperiod and crystallinity. Even in the case of extensive destruction with mass losses approaching 90% and variation of crystalline structure of the polymer was not observed. These data confirm the theory described previously by the authors on the existence of two possible methods of polymer destruction in aggressive mediums passing through total volume and on the plastic surface only.

Animals↗
PubMed1977

Variations in structure within the trabecular bone of the mandible.

A study of the intramandibular variations in bone mass, coarseness of the bone trabeculae and bone activity between incisor, premolar, and molar regions has been carried out, as well as estimation of possible differences in these variations between groups of mandibles with different dentition. The material consisted of 24 autopsy specimens of half mandibles from normal subjects. Microradiograms of ground sections from incisor, premolar, and molar regions were used. Quantitation of bone mass was done by an electronic point-counting system. The analysis indicates that (1) the variations in bone mass within same region are marked, (2) trabecular bone is denser and more delicately woven in the incisor region than in either premolar or molar regions, where mass of bone is the same, although there is probably more delicately woven trabecular bone in molar region, (3) bone activity lies on the same level all over in trabecular bone within the mandibular body and (4) the variations of these factors seem to be independent of state of dentition in the single mandible.

Bicuspid↗
PubMed1997

Structure and variation of mood in individuals with Parkinson's disease: a dynamic factor analysis.

Mood structure was examined among individuals diagnosed with Parkinson's disease. Twelve individuals completed a measure of positive and negative affect for 70 consecutive days. Mood structure was determined by using dynamic factor analysis (DFA) models that account for both concurrent and lagged relationships in repeated measurements. Five individuals had sufficient variability in positive and negative affect to conduct DFA on both sets of variables. Results showed the presence of 2 2-factor 1-lag models, 2 1-factor 1-lag models, and a P-technique model. There was sufficient variability in positive affect to conduct DFA on positive affect for the entire sample. Two individuals displayed 2-factor 1-lag models, 6 individuals had 1-factor 1-lag models, and 4 individuals showed P-technique models. Implications of lagged relationships are discussed from substantive and methodological perspectives.

Affect↗
PubMed2026

A haploid wild yeast resource for exploring the natural ecology of Saccharomyces cerevisiae.

Saccharomyces cerevisiae occurs predominantly in the diploid state in nature, limiting genetic analyses of wild populations. Here, we establish a haploid collection from 32 Taiwanese S. cerevisiae isolates through targeted HO disruption. This resource spans predomesticated Asian wild lineages and enables the investigation of reproductive isolation and ecological trait variation. Although all pairwise hybridizations formed zygotes, many yielded reduced spore viability, revealing strong postzygotic barriers. Genome analyses associated reduced hybrid fertility with lineage-specific structural variation, including elevated levels of intra-chromosomal inversions in H413-8/TW1 and inter-chromosomal rearrangements in PD35A/CHN-V, rather than sequence divergence alone. Phenotyping revealed ecological differentiation, with TW1 favoring cooler growth and a natural hybrid exhibiting heterosis with expanded thermotolerance. Most wild strains grew poorly on maltose, whereas anthropogenic strains displayed enhanced utilization linked to MAL + regulatory alleles and maltose-specific transporters. Together, this haploid collection links structural variation and metabolic divergence to ecological and reproductive differentiation in wild S. cerevisiae.

Saccharomyces cerevisiae↗
PubMed1998

Time series analysis of surveillance data of infectious diseases in Japan.

Temporal variational structures of long-term trends, recursive variations and seasonal variations were investigated, as to the incidence data of infectious diseases obtained from Infectious Diseases Surveillance Program in Japan by a newly devised procedure of time series analysis. In this procedure, three-dimensional spectral array indicates temporal variations of periodic structures of the incidence data, and is useful for investigating the long-term trend of the incidence data. Dominant spectral lines of the whole incidence data for each disease were assigned as the linear combinations of the fundamental modes. The optimum least squares fitting curve calculated with the fundamental modes essentially reproduces the recursive variation of the incidence data and an extension of the curve could be used to predict the incidence of the disease. Seasonal periodic modes of the incidences were estimated. The infectious diseases were classified into three basic groups (measles-, chickenpox- and mumps-patterns) and others, according to the resemblance of temporal variational structures of the incidence data.

Communicable Diseases↗
PubMed2003

DSSPcont: Continuous secondary structure assignments for proteins.

The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.columbia.edu/services/DSSPcont) introduces a continuous assignment of secondary structure that replaces 'static' by 'dynamic' states. Technically, the continuum results from calculating weighted averages over 10 discrete DSSP assignments with different hydrogen bond thresholds. A DSSPcont assignment for a particular residue is a percentage likelihood of eight secondary structure states, derived from a weighted average of the ten DSSP assignments. The continuous assignments have two important features: (i) they reflect the structural variations due to thermal fluctuations as detected by NMR spectroscopy; and (ii) they reproduce the structural variation between many NMR models from one single model. Therefore, functionally important variation can be extracted from a single X-ray structure using the continuous assignment procedure.

Algorithms↗
PubMed2005

Structural brain variation, age, and response time.

Response time (RT) generally slows with aging, but the contribution of structural brain changes to this slowing is unknown. We used voxel-based morphometry (VBM) to determine gray matter (GM) and white matter (WM) brain volumes in 9 middle-aged adults (38-58 years old) and 9 seniors (66-82 years old). We correlated brain volumes with RT assessed in both a simple visual stimulus-response task and a visual continuous recognition memory task. No GM correlations with simple RT were significant; there was one WM correlation in the right fusiform gyrus. In the memory task, faster RT was correlated (p < .05, corrected) with less GM in the globus pallidus, the parahippocampus, and the thalamus for both groups. Several Brodmann areas (BA) differed between the groups such that in each area, less GM was correlated with slower RTs in the middle-aged group but with faster RTs in the senior group (BAs 19, 37, 46, 9, 8, 6, 13, 10, 41, and 7). The results suggest that individual differences in specific brain structure volumes should be considered as potential moderating factors in cognitive brain imaging studies.

Adult↗
PubMed2006

Para-cavernous sinus venous structures: anatomic variations and pathologic conditions evaluated on fat-suppressed 3D fast gradient-echo MR images.

BACKGROUND: The cavernous sinus communicates with several para-cavernous sinus venous structures, receiving blood flow from the superficial middle cerebral vein (SMCV), the sphenoparietal sinus (SPS), and the superior ophthalmic vein, and draining into the superior and inferior petrosal sinuses and pterygoid and basilar plexuses. Anatomic variations of these veins have been previously reported; however, some details, such as the relationship between the SPS and the SMCV, are incompletely characterized. The anatomic variations of para-cavernous sinus veins, especially drainage patterns of the SMCV, were evaluated on MR imaging. MATERIALS AND METHODS: Thirty-seven patients, including those without any lesions affecting the cavernous sinus or para-cavernous veins and patients with carotid cavernous fistulas, were examined by using fat-suppressed contrast-enhanced 3D fast gradient-echo MR imaging. Two neuroradiologists evaluated the images on a viewer, regarding the normal anatomy and the pathologic findings of the para-cavernous sinus veins. RESULTS: The fat-suppressed 3D fast gradient-echo MR images clearly depicted the para-cavernous sinus venous structures in all patients. SMCVs had 4 variations in the drainage patterns. The most frequent pattern was drainage into the SPS (39%), and other types were draining into cavernous sinus, pterygoid plexus, and tentorial sinus. The SPS had 3 variations. The most frequent pattern was drainage into cavernous sinus (72%), and others were the hypoplastic type or those draining into pterygoid plexus. CONCLUSION: The fat-suppressed 3D fast gradient-echo MR image is useful for evaluating the venous structures in the skull base. Knowledge of the variations is important for diagnosis and endovascular treatment of the cavernous sinus lesions.

Adult↗
PubMed1977

Effects of adenine nucleotides on oxidation of phenothiazine tranquilizers.

The effects of adenosine diphosphate and triphosphate on the periodic acid oxidation of the phenothiazine tranquilizing drugs were studied. The principal effect was a marked reduction in the rate of formation and decay of the drug free radical. The oxidation rates of the nucleotide free drugs seemed to be most strongly influenced by the inductive effects of substituents at the 2-position of the phenothiazine nucleus. However, the oxidation rates of the drugs in the presence of nucleotide were most strongly influenced by the substituents at the 10-position. Variations of the structure of substituents at the 10-position have only a modest effect on the electronic state of the phenothiazine nucleus. Therefore, the marked effect of structural variation in the 10-substituents in the presence of nucleotide on the periodate oxidation rate most likely is an expression of steric effects related to an interaction between drug and nucleotide.

Adenine Nucleotides↗