Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “ARCHITECTURE”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,477 records · Page 82Linked to original sources
PubMed1989

Microscopical investigation of canine anterior cruciate ligament and patellar tendon: collagen fascicle morphology and architecture.

The collagen structure of the canine anterior cruciate ligament (ACL) and patellar tendon (PT) was examined by using light and scanning electron microscopy. The collagen waviness known as a crimping was found to occur in ACL and PT fascicles. This waviness, seen at the periphery of fascicles, is very smooth, and its amplitude seems to decrease from the periphery toward the fascicular center. It appears as a periodic collapse of the fascicle in two dimensions. Two models of the architectural patterns of the ACL and PT wavy fascicles are presented. The constituent collagen fibrils are either parallel or twisted relative to the fascicle axis, giving rise to planar and helical wave patterns, respectively. There is a distinct difference between the ACL and PT collagen structure. The helical wave pattern occurs in both PT and ACL while the planar waveform is found only in the centrally located ACL fascicles. In addition, there is less variability in fascicular size and density over the PT cross-section than in ACL.

Animals↗
PubMed1995

Changes of cytoskeletal architecture and incorporation of 3H-proline in contracted anterior cruciate ligament.

Changes of cytoskeletal architecture and incorporation of 3H-proline were investigated in contracted anterior cruciate ligaments with use of a model of contracture. In control ligaments, fibroblasts were shown by immunofluorescence microscopy to contain actin, vimentin, and myosin in their cytoplasm. Cytoskeletons were visualized by electron microscopy as a mesh network of microfilaments among cell organelles. In contracted anterior cruciate ligaments, fibroblasts were spindle-shaped and their cytoplasm could not be observed clearly in sections stained with hematoxylin and eosin. Actin staining was distributed irregularly and extensively, whereas vimentin and myosin staining was not scattered so extensively. When compared electromyographically, the actin staining appeared in cytoplasmic pseudopods of the fibroblasts. It was thought that these cytoplasmic pseudopods contained mainly actin and little or no other cytoskeletal elements such as vimentin and myosin. In autoradiographs, contracted anterior cruciate ligaments were shown, with use of 3H-proline, to experience a decrease in the number of labeled cells. On the basis of these findings of cytoskeletal rearrangement and of decreased incorporation of 3H-proline, we hypothesized that fibroblasts of the anterior cruciate ligament had the capacity to change their character during knee immobilization and to play a role in ligament contracture.

Actins↗
PubMed2005

Abnormal sleep architecture is an early feature in the E46K familial synucleinopathy.

We examined 7 patients from a family harboring a novel mutation in the alpha-synuclein gene (E46K) that segregated with a phenotype of parkinsonism and dementia with Lewy bodies. An abnormal restless sleep was the presenting symptom in 2 of them. Polysomnographic (PSG) studies were performed in 4 of the 7 patients and in 2 asymptomatic carriers of the mutation. A severe loss of both rapid eye movement (REM) and non-REM sleep was observed in 2 patients complaining of insomnia and in a third parkinsonian member of the family who did not complain of trouble with sleeping. Another parkinsonian family member had a mild disorganization of the sleep architecture. The 2 asymptomatic carriers also had minor changes in the PSG findings. Episodes of bizarre behavior at night were reported historically in the 2 symptomatic patients, but we did not observed the behaviors during the PSG studies. REM sleep behavior disorder could not be recorded in any case. Our findings expand the spectrum of sleep disorders reported in synucleinopathies whether sporadic or familial.

Adult↗
PubMed2006

Architectural reorganization of the nuclei upon transfer into oocytes accompanies genome reprogramming.

The ability of cloned embryos to sustain full-term development depends on the ability of the recipient ooplasm to reprogram the donor cell genome. As the nuclear architecture has recently emerged as a key-factor in the regulation of gene expression, we questioned whether early embryos obtained from transfer of ES metaphasic chromosomes into mouse ooplasm would adopt the somatic or embryonic type of nuclear organization. We have particularly focused on the arrangement of chromosomal territories with respect to the nucleolar compartment, and the pericentric heterochromatin domains called chromocenters. We found that nuclear transfer triggers profound chromatin rearrangements including the dispersion of the donor cell chromocenters components. These rearrangements lead to a typical 1-cell pronuclear organization, namely a radial arrangement of the chromosome territories with centromeres attached to the nucleoli, which adopt the compact fibrillar structure of nucleolar precursor bodies (NPBs). Subsequently, during the second cycle, the cloned embryos undergo further reorganization with the establishment of new chromocenters, clustered in one part of the nucleus, as during normal embryogenesis. We could also establish that the adequate distribution of chromosomal territories at the pronuclear stage seems important for the development until blastocyst.

Animals↗
PubMed1995

Imaging myocardial fiber architecture in vivo with magnetic resonance.

Methods are presented to image the fiber architecture of the human myocardium in vitro and in vivo. NMR images are obtained of the diffusion anisotropy tensor, indicative of local myofiber orientation. Studies of cardiac necropsy specimens demonstrate classic features of ventricular myoarchitecture including the continuous endocardial to epicardial variation of fiber helix angles (angles to the ventricular circumferential direction) of approximately +1.3 to -1.3 radians. Cross-fiber anisotropy is also observed. In the beating heart, NMR diffusion data must be corrected for the effects of myocardial deformation during the cardiac cycle. This correction can be performed using an independent MRI method to map the strain-rate tensor field of the myocardium through time. Combining fiber orientation with local myocardial strain rate, local rates of myocardial fiber shortening may be computed.

Anisotropy↗
PubMed2004

Postcontraction changes of muscle architecture in human quadriceps muscle.

Maximal voluntary contraction changes the mechanical properties of skeletal muscle. Using ultrasound, we investigated whether these changes are reflected by changes in muscle architecture in the vastus lateralis muscle of 8 healthy volunteers. The mean pennation angle during the time interval from 3 to 6 min after maximal voluntary contraction (late postcontraction state) was 14.4 +/- 1.11 degrees (mean +/- SEM) and differed significantly from the precontraction state (16.2 +/- 1.39 degrees ), but the pennation angle in the early postcontraction state did not change statistically from the precontraction angle. Thus, postcontraction changes of the muscle-tendon interface appeared for 6 min after a maximal contraction, which may be important for biomechanical optimization of force transmission in vivo.

Adult↗
PubMed1994

Association between muscle architecture and quadriceps femoris H-reflex.

The purpose of the present study was to establish the relationship between muscle architecture and H-reflex recordings in quadriceps femoris muscle. H-reflexes were elicited in human quadriceps femoris muscle over a broad area of skin to document the shape and amplitude of the H-potentials. This, in combination with recording monopolar and bipolar H-potentials, was performed to determine the location and method for measuring maximum-amplitude H-reflexes. The influence of neural and peripheral factors on the H-potential during passive length changes was studied by comparing the amplitude of H-potentials to motor unit action potentials. Monopolar recordings of the H-potential were found to be preferable to bipolar recordings because of the reproducibility of shape and easier distinction between the M- and H-potentials. The location for recording maximum H-potentials was in the distal one third of the quadriceps femoris muscle, over the border between vastus lateralis and rectus femoris. The inferred relationship between H-potential amplitude and reflex excitability must be made with caution in quadriceps femoris muscle because the amplitude of both the motor unit potential and H-potential change as a function of muscle length.

Action Potentials↗
PubMed2005

Maturation of dendritic architecture: lessons from insect identified neurons.

The highly complex geometry of dendritic trees is crucial for neural signal integration and the proper wiring of neuronal circuits. The morphogenesis of dendritic trees is regulated by innate genetic factors, neuronal activity, and external molecular cues. How each of these factors contributes to dendritic maturation has been addressed in studies of the developing nervous systems of animals ranging from insects to mammals. This article reviews our current knowledge and understanding of the role of afferent input in the establishment of the architecture of mature dendritic trees, using insect neurons as models. With these model systems and using quantitative morphometry, it is possible to define the contributions of intrinsic and extrinsic factors in dendritic morphogenesis of identified neurons and to evaluate the impact of dendritic maturation on the integration of identified neurons into functional circuits subserving identified behaviors. The commonly held view of dendritic morphogenesis is that general structural features result from genetic instructions, whereas fine connectivity details rely mostly on substrate interactions and functional activity. During early dendritic maturation, dendritic growth cone formation produces new branches at all dendritic roots. The second phase is growth cone independent and afferent input dependent, during which branching is limited to high order distal dendrites. During the third phase, activity-dependent synaptic maturation occurs with limited or subtle remodeling of branching.

Animals↗
PubMed1987

Epithelial-cell architecture during involution of the human thymus.

One hundred thymus glands were assessed histologically as to their degree of involution. Epithelial cells were demonstrated by an immunoperoxidase method using a monoclonal antibody against cytokeratin. The distribution of these cells was studied in the medulla, the cortico-medullary junction, the cortical parenchyma and the subcapsular cortex. As involution proceeds, the loss of cells from the thymus is almost totally confined to the lymphoid-cell elements. The architecture of the epithelial-cell network remains largely intact although there is extensive collapse of the structure due to the loss of the intervening lymphocytes. Even when involution is apparently complete; sheets of epithelial cells can be demonstrated in the thymic remnant.

Adolescent↗
PubMed1997

Crystallization and preliminary X-ray diffraction studies of aSFP, a bovine seminal plasma protein with a single CUB domain architecture.

Bovine acidic seminal fluid protein (aSFP) is a 1.29 kDa polypeptide of the spermadhesin family built by a single CUB domain architecture. The CUB domain is an extracellular module present in 16 functionally diverse proteins. To determine the three-dimensional structure of aSFP, the protein was crystallized at 21 degrees C by vapor diffusion in hanging drops, using ammonium sulfate, pH 4.7, and polyethyleneglycol 4,000 as precipitants, containing 10% dioxane to avoid the formation of clustered crystals. Elongated prismatic crystals with maximal size of 0.6 x 0.3 x 0.2 mm3 diffract to beyond 1.9 A resolution and belong to space group P2(1)2(1)2(1), with cell parameters a = 52.4 A, b = 41.5 A, c = 48.2 A. There is one aSFP molecule per asymmetric unit, which corresponds to a crystal volume per unit molecular mass of 2.04 A3/Da, and analytical ultracentrifugation analysis show that aSFP is a monomeric protein.

Animals↗
PubMed2005

Molego-based definition of the architecture and specificity of metal-binding sites.

Decomposing proteins into "molegos," building blocks that are conserved in sequence and 3D-structure, can identify functional elements. To demonstrate the specificity of the decomposition method, the PCPMer program suite was used to numerically define physical chemical property motifs corresponding to the molegos that make up the metal-containing active sites of three distinct enzyme families, from the dimetallic phosphatases, DNase 1 related nucleases/phosphatases, and dioxygenases. All three superfamilies bind metal ions in a beta-strand core region but differ in the number and type of ions needed for activity. The motifs were then used to automatically identify proteins in the ASTRAL40 database that contained similar motifs. The proteins with the highest PCPMer score in the database were primarily metal-binding enzymes that were related in function to those in the alignment used to generate the PCPMer motif lists. The proteins that contained motifs similar to the dioxygenases differed from those found with PCP-motifs for phosphatases and nucleases. Relatively few metal-binding enzymes were detected when the search was done with PCP-motifs defined for interleukin-1 related proteins, which have a beta-strand core but do not bind metal ions. While the box architecture was constant in each superfamily, the specificity for the metal ion preferred for enzymatic activity is determined by the pattern of carbonyl, hydroxyl or imadazole groups in key positions in the molegos. These results have implications for the design of metal-binding enzymes, and illustrate the ability of the PCPMer approach to distinguish, at the sequence level, structural and functional elements.

Binding Sites↗
PubMed1995

Why do protein architectures have Boltzmann-like statistics?

A theoretical study has shown that the occurrence of various structural elements in stable folds of random copolymers is exponentially dependent on the own energy of the element. A similar occurrence-on-energy dependence is observed in globular proteins from the level of amino acid conformations to the level of overall architectures. Thus, the structural features stabilized by many random sequences are typical of globular proteins while the features rarely observed in proteins are those which are stabilized by only a minor part of the random sequences.

Computer Simulation↗
PubMed2005

13C-Isotope ratio mass spectrometry as a potential tool for the forensic analysis of white architectural paint: a preliminary study.

Paints have a dual role in society, to protect materials from environmental agents such as ultraviolet light, moisture and oxygen, and to make painted materials look more attractive. Variability in paint samples is often due to binder and pigment type within the sample. The most common resin used in decorative paints is drying oil alkyd resin, which incorporates soybean oil and vinyl acrylic based latexes. Traditional analytical methods used by forensic scientists may be able to say whether two paint samples are indistinguishable but cannot conclusively say that they both originate from the same source. To find out if isotopic composition can provide an added dimension of information, 28 different white architectural paints were analysed for (13)C abundance using isotope ratio mass spectrometry. In addition, variations in application, drying time and thickness were also investigated to assess the discriminatory power of (13)C data from white paints with an unknown history. Preliminary results indicate that this method could aid screening of paint samples.

Journal Article↗
PubMedDate not supplied

Three-dimensional architecture of ribosomal DNA within barley nucleoli revealed with electron microscopy.

To elucidate the topological positioning of ribosomal RNA genes (rDNA) and nucleolar structure in three dimensions, we examined the localization of rDNA using in situ hybridization (ISH) analysis by scanning electron microscopy (SEM). The rDNA genes within the three-dimensional architecture of nucleoli were detected on chromatin fibers that connect a thick strand-like structure and a protrusion of rDNA into the inner nuclear hole where the nucleolus is formed. This novel use of ISH together with SEM is useful for the analysis of nucleolar structure in detail. Furthermore, rDNA was detected at the periphery of the fibrillar centers (FCs) of the nucleolus using immuno-gold labeling together with transmission electron microscopy (TEM). In situ hybridization with TEM confirmed that rDNA is naked and thus active in the FCs of nucleoli; ISH with SEM confirmed that rDNA is not covered with ribonucleo proteins at the protruding point and is thus inactive. We also show that the distribution pattern of FCs differs from sample to sample. These results indicate that rDNA is transcribed dynamically in a time- and region-specific manner over the course of the cell cycle.

Cell Nucleolus↗
PubMed2005

Chain-growth polycondensation for well-defined condensation polymers and polymer architecture.

The historical development of our research on polycondensation that proceeds in a chain-growth polymerization manner ("chain-growth polycondensation") for well-defined condensation polymers is described. We first studied polycondensation in which change of the substituent effect induced by bond formation drove the reactivity of the polymer end group higher than that of the monomer. In this approach, well-defined aromatic polyamides, polyesters, polyethers, and poly(ether sulfone)s were obtained. The second approach was the study of the phase-transfer polymerization of a solid monomer dispersed in an organic solvent. In this type of polymerization, the solid monomer was physically unable to react with another monomer and was carried with the phase transfer catalyst into the solution phase where it reacted with an initiator and the polymer end group in the solvent in a chain polymerization manner. We also found catalyst-transfer polycondensation as a third approach to chain-growth polycondensation. In the Ni-catalyzed polycondensation of 2-bromo-5-chloromagnesiothiophenes, the Ni catalyst transferred to the polymer end group, and a coupling reaction occurred there to yield a well-defined polythiophene. This chain-growth polycondensation was applied to the synthesis of condensation polymer architectures such as block copolymers, star polymers, graft copolymers, and so on.

Models, Molecular↗
PubMed2026

Dissecting genetic architecture and improving machine learning‑based genomic prediction of flowering time in Osmanthus fragrans by integrating structural variants.

Sweet osmanthus (Osmanthus fragrans), a traditional ornamental plant in China, exhibits substantial variation in autumn flowering time, which significantly affects landscape application and cultivation efficiency. Here, we performed a genome-wide association study on 127 resequenced accessions classified into early, intermediate, and late flowering types, using a set of 2,325,410 single-nucleotide polymorphisms (SNPs) and 246,824 structural variants (SVs). By integrating SNP/insertion and deletion (Indel) and SV data with weighted gene co-expression network analysis, machine learning, and genomic prediction, we dissected the genetic architecture of flowering time. We identified 24 associated SNP/Indels and six SVs, mapping to 30 candidate genes, including known flowering regulators FLK, LOS1, Y14, MIF2, and GID1B. These genes showed tissue-specific expression, with some responding to low temperature. The two hub genes, GUX1 and LYG027904, were located within modules of the co-expression network associated with low-temperature treatment. Haplotype analysis revealed a specific three-SNP haplotype associated with late flowering and linked to LOS1, and epistatic interactions among combined genotypes contributed to phenotypic variation. Notably, integrating SVs with SNP/Indels improved genomic prediction accuracy; the gradient boosting decision tree model outperformed other machine learning algorithms, achieving a mean accuracy of 0.859 and an AUC > 0.8 (where AUC is area under receiver operating characteristic curve) for all flowering types. These findings provide insights into the genetic mechanisms underlying flowering time variation in O. fragrans, offer candidate genes and haplotypes for molecular breeding, and highlight the value of integrating SVs with machine learning for genomic prediction in woody ornamentals.

Machine Learning↗
PubMed1998

Architectural DNA-binding properties of the spermatidal transition proteins 1 and 2.

Mammalian spermiogenesis is characterized by replacement of somatic histones by a set of basic nuclear transition proteins thought to be actively involved in the chromatin remodeling process. The two major transition proteins of the elongating spermatids, namely TP1 and TP2, were expressed and purified using a bacterial expression system. Both topoisomerase and ligase-mediated supercoiling assays demonstrated that TP1, as well as TP2, did not produce detectable changes in the twist and/or writhe of DNA molecules upon binding. Ligase-mediated circularization assay further demonstrated that neither of the transition proteins under study produced bends in linear DNA but that they both have the capacity to stimulate oligomerization of linear DNA fragments. We further established that the transition proteins are in vitro substrates for the Ca+2-phospholipid-dependent protein kinase (PKC) as well as the cAMP-dependent protein kinase (PKA). PKC phosphorylation was found to strongly weaken the DNA-condensing ability of TP2. These results suggest that the major transition proteins represent architectural factors able to stabilize DNA in a nonsupercoiled state, thereby promoting DNA condensation.

Amino Acid Sequence↗
PubMed1999

Helicobacter pylori vacuolating cytotoxin (VacA) disorganizes the cytoskeletal architecture of gastric epithelial cells.

Helicobacter pylori colonization of the gastric mucosa induces peptic ulcer disease and interferes with ulcer healing. Re-epithelialization is an essential component of ulcer healing. It requires cell migration and proliferation which are dependent on the cell cytoskeleton. Most H. pylori strains produce a toxin (VacA) that induces multiple structural and functional changes in epithelial cells. In this study, we investigated the effects of VacA on the gastric epithelial cell cytoskeletal architecture. Exposure of rat gastric epithelial cells to purified VacA from H. pylori 60190 significantly inhibited actin stress fiber formation (83 +/- 5% reduction; p < 0.0001) and disorganized microtubule pattern (90 +/- 8%; p < 0.001). Furthermore, VacA treatment significantly reduced tyrosine phosphorylation of focal adhesion kinase (FAK) (by 45 +/- 6%; p < 0.002) and its expression in focal adhesions (73 +/- 8%; p < 0.0001). These findings suggest that H. pylori VacA interferes with cytoskeleton-dependent cell functions and with the transmission of signals related to cell spreading and growth.

Actin Cytoskeleton↗