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 937 records · Page 52Linked to original sources
PubMed2006

Fluorescent core-shell silica nanoparticles: towards "Lab on a Particle" architectures for nanobiotechnology.

Novel nanoscale fluorescent materials are integral to the progress of emergent fields such as nanobiotechnology and facilitate new research in a variety of contexts. Sol-gel derived silica is an excellent host material for creating fluorescent nanoparticles by the inclusion of covalently-bound organic dyes. Significant enhancements in the brightness and stability of organic dye emission can be achieved for silica-based core-shell nanoparticle architectures at length scales down to tens of nanometers with narrow size distributions. This tutorial review will highlight these findings and describe the evolution of the fluorescent core-shell silica nanoparticle concept towards integration of multiple functionalities including mesoporosity, metal nanoshells and quantitative chemical sensing. These developments point towards the development of "lab on a particle" architectures with promising prospects for nanobiotechnology, drug development and beyond.

Animals↗
PubMed2001

Functional architecture in the cell nucleus.

The major functions of the cell nucleus, including transcription, pre-mRNA splicing and ribosome assembly, have been studied extensively by biochemical, genetic and molecular methods. An overwhelming amount of information about their molecular mechanisms is available. In stark contrast, very little is known about how these processes are integrated into the structural framework of the cell nucleus and how they are spatially and temporally co-ordinated within the three-dimensional confines of the nucleus. It is also largely unknown how nuclear architecture affects gene expression. In order to understand how genomes are organized, and how they function, the basic principles that govern nuclear architecture and function must be uncovered. Recent work combining molecular, biochemical and cell biological methods is beginning to shed light on how the nucleus functions and how genes are expressed in vivo. It has become clear that the nucleus contains distinct compartments and that many nuclear components are highly dynamic. Here we describe the major structural compartments of the cell nucleus and discuss their established and proposed functions. We summarize recent observations regarding the dynamic properties of chromatin, mRNA and nuclear proteins, and we consider the implications these findings have for the organization of nuclear processes and gene expression. Finally, we speculate that self-organization might play a substantial role in establishing and maintaining nuclear organization.

Animals↗
PubMed2003

Blood vascular architecture of the palatine tonsil in the musk shrew (Suncus murinus): scanning electron microscopic study of corrosion casts.

The musk shrew, Suncus murinus, is one of the primitive mammals and has a pair of palatine tonsils. In the present study, we investigated the blood microvascular architecture of the tonsil in this animal by scanning electron microscopy of corrosion casts. The paranodular arterioles entered the lymph nodule to form a coarse capillary plexus within the nodule. Some of the arterioles reached the dome region to give rise to a fine meshwork of dome subepithelial capillaries. This dome subepithelial capillary network did not show any hairpin or switch-back patterns, as seen in human and rabbit tonsils. Both of the nodular and dome capillaries were drained into the postcapillary venules in the periphery of the nodular or the paranodular region. On the surface of these cast venules, oval-shaped indentations were seen corresponding to the luminal surface of the high endothelial venules. These venules were collected into the large vein at the bottom of the tonsil. The blood vascular architecture of the musk shrew tonsil is basically the same as those of other mucosa-associated lymphoid tissues in mammals.

Animals↗
PubMed2003

Three-dimensional architecture of the intrinsic tongue muscles, particularly the longitudinal muscle, by the chemical-maceration method.

Muscle bundles of the transverse and vertical muscles of the tongue become flat when they enter the longitudinal muscle layers of the tongue, where they form a tunnel-like structure that surrounds the longitudinal muscle of the tongue. However, the three-dimensional architecture of longitudinal muscle fibers of the tongue has not been clarified. In the present study, we evaluated the function of the intrinsic muscles of the tongue by studying the three-dimensional architecture of the longitudinal muscle. Muscle bundles of the longitudinal muscle of the anterior part of a rabbit's tongue were exposed by the chemical-maceration and modified chemical-maceration methods and examined by scanning electron microscopy. In the longitudinal muscle of the tongue, muscle bundles running in the anteroposterior direction were arranged at regular intervals. These muscle bundles bifurcated or ramified at a sharp angle at each level from the superficial layer to the deep layer and joined or fused with adjacent muscle bundles. In addition, these ramified muscle bundles ran obliquely into shallower or deeper layers of the muscle, as well as in the same plane. Consequently, the longitudinal muscle of the tongue as a whole had a three-dimensional mesh-like structure. The transverse and vertical muscles of the tongue entered this mesh-like structure of muscle bundles of the longitudinal muscle as flat muscle bundles. The transverse and vertical muscles showed no ramification in the center of the tongue, where there is no longitudinal muscle. These results suggest that the three intrinsic muscles of the tongue are interlaced with one another and are bound tightly in the longitudinal muscle. This structure may enable the dorsum of the tongue to harden for pressing food during mastication and shifting the food posteriorly for swallowing.

Animals↗
PubMed1996

Architectural flexibility in lambda site-specific recombination: three alternate conformations channel the attL site into three distinct pathways.

BACKGROUND: In the phage lambda life cycle, the Integrase (Int) protein carries out recombination between two different sets of DNA substrates: attP and attB in integration, attL and attR in excision. In each case, the partners are very different in structure from each other and the recombination reaction between them is effectively irreversible. For comparison, we have studied the recombination mediated by Int between two identical attL sites. Both in vitro and in vivo, recombination between two attL sites can be mediated inefficiently by Int alone. But, while IHF can stimulate recombination 5-10-fold in vivo (to the level of excision and integration), this stimulation is not observed under standard conditions in vitro. RESULTS: We find that IHF can stimulate the in vitro recombination between two attLs that are modified to be defective in one of the high affinity binding sites for Int, P'1. With such substrates, the efficiency of IHF-stimulated recombination is comparable to that seen in vivo. The requirements for this reaction distinguish it from other lambda recombination pathways, as does the performance of several mutant Int proteins. Recombination of attL sites on intracellular plasmids suggests that this pathway is effective in vivo, but that some unknown factor or condition permits it to operate on wild-type as well as mutated attL sites. CONCLUSIONS: The recombination pathway described in this work apparently uses a unique attL architecture, one which requires bending by IHF and is inhibited by Int bound at the P'1 site. In addition to demonstrating the architectural flexibility of the lambda system, this pathway should be a valuable resource for separating the basic requirements of strand exchange chemistry from the features which impart directionality.

Attachment Sites, Microbiological↗
PubMed1999

Genetic architecture of fitness and nonfitness traits: empirical patterns and development of ideas.

Comparative studies of the genetic architecture of different types of traits were initially prompted by the expectation that traits under strong directional selection (fitness traits) should have lower levels of genetic variability than those mainly under weak stabilizing selection (nonfitness traits). Hence, early comparative studies revealing lower heritabilities of fitness than nonfitness traits were first framed in terms of giving empirical support for this prediction, but subsequent treatments have effectively reversed this view. Fitness traits seem to have higher levels of additive genetic variance than nonfitness traits - an observation that has been explained in terms of the larger number loci influencing fitness as compared to nonfitness traits. This hypothesis about the larger functional architecture of fitness than nonfitness traits is supported by their higher mutational variability, which is hard to reconcile without evoking capture of mutational variability over many loci. The lower heritabilities of fitness than nonfitness traits, despite the higher additive genetic variance of the former, occur because of their higher residual variances. Recent comparative studies of dominance contributions for different types of traits, together with theoretical predictions and a large body of indirect evidence, suggest an important role of dominance variance in determining levels of residual variance for fitness-traits. The role of epistasis should not be discounted either, since a large number of loci increases the potential for epistatic interactions, and epistasis is strongly implicated in hybrid breakdown.

Animals↗
PubMed2001

The contrasting genetic architecture of wing size and shape in Drosophila melanogaster.

Surprisingly little is known about the genetic architecture of body size in natural populations of Drosophila melanogaster. Using both generation means and triple-test-cross analyses, we investigated the genetic architecture of wing size (an indicator of body size) and wing shape in a naturally occurring body size cline. For wing size, we found significant epistatic genetic variance and evidence of past directional selection for increased body size. While wing shape also exhibits significant epistatic genetic variance, there was no indication of directional selection, suggesting instead a history of optimizing selection. Our results support the idea that epistatic variance may be more common in natural populations than was once suspected. Also, our results suggest substantial directional selection on wing size but not shape.

Animals↗
PubMed2003

Microvessel densities and microvascular architecture in colorectal carcinomas and their liver metastases: significant correlation of high microvessel densities with better survival.

AIMS: Microvessel densities in cancers have been shown to be a prognostic factor for some types of cancer. For colorectal cancer, however, the situation is far from clear. METHODS: A consecutive series of 173 colorectal carcinomas was investigated, and to these were added 55 liver metastases originating from colorectal cancer. Microvessels were counted in hotspots (factor VIII immunostaining, 0.74 mm2). The capillary architecture was scored according to the degree of order and envelopment of the neoplastic glands. Endothelial proliferation was determined by factor VIII/Ki67 double labelling. RESULTS: Mean microvessel densities were 51.8 for colorectal carcinomas (range 8-140) and 31.9 for liver metastases (range 3-101). Stratification according to stage, depth of infiltration and nodal involvement showed a significant inverse relation with increase. Mean microvessel densities in primaries were significantly higher than in metastases. Kaplan-Meier analysis showed a significantly higher cancer-specific survival for high microvessel densities (median as cut-off) and for a more ordered microvascular architecture. Endothelial proliferation in carcinomas was significantly higher than in normal mucosa. CONCLUSIONS: Contrary to other types of cancer, for colorectal cancer high microvessel densities confer good rather than poor prognosis. We hypothesize that neoangiogenesis, though extant in colorectal cancer, is not rate-limiting in the metastatic cascade.

Adenocarcinoma↗
PubMed2002

Sin recombinase from Staphylococcus aureus: synaptic complex architecture and transposon targeting.

The Sin recombinase from Staphylococcus aureus builds a distinctive DNA-protein synaptic complex to regulate strand exchange. Sin binds at two sites within an 86 basepair (bp) recombination site, resH. We propose that inverted motifs at the crossover site, and tandem motifs at the regulatory site, are recognized by structurally disparate Sin dimers. An essential architectural protein, Hbsu, binds at a discrete central site in resH. Positions of Hbsu-induced DNA deformation coincide with natural targets for Tn552 integration. Remarkably, Sin has the same topological selectivity as Tn3 and gammadelta resolvases. Our model for the recombination synapse has at its core an assembly of four Sin dimers; Hbsu plays an architectural role that is taken by two resolvase dimers in models of the Tn3/gammadelta synapse.

Bacterial Proteins↗
PubMed2003

Architecture and transcriptional activity of the initiator element of the TATA-less RPL21 gene.

The nuclear RPL21 gene coding for the plastid ribosomal protein L21 is a TATA-less gene that is overexpressed in a leaf-dependent manner by the specific usage of a strong initiator called P1. We have previously shown that the RPL21 core promoter spanning from -23 to +104 relative to P1 start site activates transcription in the same manner as does the full promoter. Here, we present results of experiments aimed at deciphering the RPL21 core promoter architecture. Results of transient expression using various 5' deletions of the core promoter fused to a chloramphenicol acetyl transferase (CAT) reporter gene show that 34 bp encompassing the P1 initiation site (from -23 to +11) are required for full transcription activation. Gel-shift analysis shows that five DNA/protein complexes (C1-C5) are formed on this 34-bp fragment with protein extracts from green tissues. C1 is the major complex present during seed germination. The other complexes are present in young leaf tissues suggesting a role in transcription activation. Linker scanning mutagenesis experiments show that the five complexes form two independent groups: I (C1-C3) and II (C4 and C5), with a common binding site located on P1. Using transgenic plants, we show that three nucleotides encompassing the P1 start site and three trinucleotides necessary for group I binding are determinant for RPL21 activation. These results identify an unusually compact core structure, which is centred on P1 initiation site and is responsible for transcription activation. A model of the architecture of this region is presented.

Base Sequence↗
PubMed2000

Ultrastructure of the horse tongue: further observations on the lingual integumentary architecture.

This investigation examined primarily epidermal specializations of the adult horse tongue by light, scanning and transmission electron microscopy. Samples were collected from seven regions of the normal tongue of various breeds of horse. The filiform papillae, present on the dorsal and lateral aspects but not the ventral aspect of the tongue, were short, slender and finger-like structures with variable-shaped terminae. The epidermal thickness and height of dermal ridges were reduced on fungiform and vallate papillae, but tissue architecture and keratinocyte ultrastructure of most of the lingual epidermis corresponded to the common mammalian epidermal paradigm. One unique finding was the highly localized clustering of epidermal cells with exceptionally high content of PAS-negative trichohyalin cytoplasmic granules at a location atop the dermal ridges and beneath the base of filiform papillae. These granular cells were immediately subjacent to clusters of clear, non-granulated epidermal cells. It is believed that this integumentary specialization may enhance the structural strength at this localized site of the tissue architecture, in relationship to the mechanical papillae.

Animals↗
PubMed2000

Sleep architectures of obstructive sleep apnea syndrome in the young child.

The sleep architectures of obstructive sleep apnea syndrome (OSAS) in the young child (child-OSAS, n = 17; mean age: 5.9+/-2.7 years; male:female 14:3) were compared with that of OSAS in the adult (n = 19; mean age: 44.7+/-10.7 years; male:female 18:1) and that of primary snoring in the child (n = 5; mean age: 7.0+/-2.4 years; male:female 5:0). Child-OSAS and OSAS in the adult had the same severity in oxygen desaturation. Child-OSAS showed lower Apnea-Hypopnea Index compared with OSAS in the adult. Sleep continuity in child-OSAS was not impaired compared with OSAS in the adult. Sleep fragmentation in child-OSAS was not so remarkable. The quantity of slow wave sleep in child-OSAS was similar to that of primary snoring in the child. Both profiles of sleep architectures showed nearly the same pattern.

Cerebral Cortex↗
PubMed1998

Quantification of the collagen fibre architecture of human cranial dura mater.

The purpose of this study was to quantify and map the gross fibre architecture of the cranial dura mater (CDM) using small angle light scattering (SALS). In SALS, HeNe laser light is passed through the tissue, and the resultant scattering pattern is analysed to determine the preferred fibre direction and degree of orientation. The dura mater was found to be a complex structure with fibre orientations ranging from highly aligned to nearly random. In the temporal region, 80% of the samples (n = 20) were found to have regions composed of highly oriented fibres with a mean fibre direction of 6.3 degrees +/- 0.8 degree with respect to the sagittal plane (i.e. almost parallel to the superior sagittal sinus). These highly aligned regions were found in symmetric anatomical locations about the median sagittal sinus and had similar fibre orientations over both hemispheres. Although our sample size was small, we found that the size of the symmetric regions, which covered 14.4 +/- 1.6% of the total CDM area, was not influenced by subject's age or sex. The presence of these highly oriented fibre regions in CDM may be due to mechanical forces exerted on dura mater during its development. These forces may have induced realignment of the collagen fibres in the direction of tensile pull, although the exact basis for the unique gross fibre architecture of CDM remains unknown.

Brain↗
PubMed2003

The three-dimensional architecture of the notochordal nucleus pulposus: novel observations on cell structures in the canine intervertebral disc.

Cells from the nucleus pulposus of young (< 2 years) and old (> 5 years) non-chondrodystrophoid dogs were studied using routine histology, confocal laser scanning microscopy and transmission electron microscopy. The architecture of cell structures--from the tissue scale down to subcellular scale--was reported. Clusters of notochordal cells were observed in young nuclei pulposi, ranging from 10 to 426 cells each. These clusters resisted mechanical disruption and showed evidence of cell-cell signalling via gap junctions. Cells (30-40 microm in diameter) within the clusters had a physaliferous appearance, containing numerous large inclusions which ranged from 1 to 20 microm in diameter. The inclusions were surrounded by a dense actin cortex but were not contained by a lipid bilayer. The contents of the inclusions were determined not to be predominantly carbohydrate or neutral lipid as assessed by histochemical staining, but the exact composition of the contents remained uncertain. There were striking differences in the cell architecture of young vs. old nuclei pulposi, with a loss of both cell clusters and physaliferous cells during ageing. These observations demonstrate unique cell structures, which may influence our understanding of the differences between notochordal and chondrocytic cells in the nucleus pulposus. Such differences could have substantial impact upon how we think about development, degeneration and repair of the intervertebral disc.

Aging↗
PubMed1999

Factors maintaining a pH gradient within the kidney: role of the vasculature architecture.

BACKGROUND: The architecture of the vasa rectae produces significant oxygen (O2) "shunting" and marked decreases in renal medullary pO2 values. We hypothesized that carbon dioxide (CO2) trapping and increases in medullary pCO2 along with decreases in medullary pH values should also accompany this O2 shunting. METHODS: We developed computer simulations employing a model of gas exchange through the countercurrent vasculature that predicted trapping of CO2 along with O2 shunting. To test the validity of this model directly, medullary pH was measured by using needle electrodes in the in situ kidney before and after the administration of mannitol or furosemide, or by decreasing blood flow with a transient decrease of renal perfusion pressure with a suprarenal clamp. Data are expressed as mean +/- SD. RESULTS: Medullary pH was lower than cortical pH (7.20 +/- 0.09 vs. 7.39 +/- 0.08, P < 0.01). Mannitol caused a decrease in medullary pH to 7.02 +/- 0.07 (P < 0.01), whereas furosemide increased medullary pH to 7. 31 +/- 0.09 (P < 0.01). Brief periods of severe hypotension decreased medullary pH to 6.90 +/- 0.09 (P < 0.01). CONCLUSIONS: These data demonstrate that a significant pH gradient exists within the kidney parenchyma. This gradient is related to the metabolic activity of the thick ascending limb of Henle and the countercurrent vascular architecture, and may be relevant to a variety of physiological phenomena involved in volume, electrolyte, and acid-based homeostasis.

Animals↗
PubMed2005

Helicobacter felis eradication restores normal architecture and inhibits gastric cancer progression in C57BL/6 mice.

BACKGROUND & AIMS: The impact of Helicobacter eradication therapy on the progression or regression of gastric lesions is poorly defined. This study examined the effects of eradication therapy on inflammation, atrophy, metaplasia, dysplasia, and cancer progression. METHODS: C57BL/6 mice were infected with Helicobacter felis and received bacterial eradication therapy after 2, 6, or 12 months of infection. The gastric mucosa was examined at early, mid, and late intervals after eradication and graded for histology, expression pattern of alpha-catenin and beta-catenin, and IQGAP1. RESULTS: Eradication of Helicobacter infection after 2 or 6 months of infection led to a regression of inflammation, restoration of parietal cell mass, and reestablishment of normal architecture. Progression to adenocarcinoma was prevented. Bacterial eradication at 1 year was associated with the reappearance of parietal cells, partial regression of inflammation, and restoration of architecture. Hyperplasia scores significantly improved, and dysplasia did not progress. Infected mice developed antral adenocarcinoma and gastric outlet obstruction by 24 months. Only 30% of the mice receiving bacterial eradication therapy at 12 months developed antral carcinoma. Bacterial eradication at any time during the first year of infection prevented death due to gastric outlet obstruction. The expression pattern of alpha-catenin, beta-catenin, and IQGAP1 varied with cell type and paralleled histologic changes. CONCLUSIONS: Inflammation, metaplasia, and dysplasia are reversible with early eradication therapy; progression of dysplasia was arrested with eradication therapy given as late as 1 year and prevented gastric cancer-related deaths.

Adenocarcinoma↗
PubMed2006

[MDCT after balloon kyphoplasty: analysis of vertebral body architecture one year after treatment of osteoporotic fractures].

PURPOSE: To evaluate the value of MDCT in the monitoring of vertebral body architecture after balloon kyphoplasty and observe morphological changes of the vertebral body. MATERIAL AND METHODS: During a period of 26 months, 66 osteoporotic fractures of the vertebral bodies were treated with percutanous balloon kyphoplasty. The height of the vertebral body, width of spinal space, sagittal indices, kyphosis und COBB angle, and cement leakage were evaluated by computed tomography before and after treatment and in a long-term follow up. Statistical analysis was performed by calculating quantitative constant parameters of descriptive key data. In addition, parametric and distribution-free procedures were performed for all questions. RESULTS: After kyphoplasty, the treated vertebral bodies showed a significant gain in the height of the leading edge (0.15 cm; p < 0.0001) and in the central part of the vertebral body (0.17 cm; p < 0.0001). The height of the trailing edge did not change significantly. A corresponding gain in the sagittal index was found. The index remained stable during follow-up. Treated vertebral bodies as well as untreated references showed a comparable loss of height over the period of one year. The shape of the vertebral bodies remained stable. In comparison to these findings, treated vertebral bodies showed a reduced loss of height. A significant change in kyphosis und the COBB angle was noted. In total, pallacos leakage was detected in 71 % of cases. CONCLUSION: MDCT is an accurate method for evaluating vertebral body architecture after treatment with balloon kyphoplasty. Morphological changes in the vertebral bodies, and complications such as pallacos leakage and progression of osteoprosis can be accurately documented. The significant increase in the vertebral body height after treatment is closely correlated with a gain in the sagittal index and reduced kyphosis and COBB angle.

Adult↗
PubMed2005

Studies on the behavior of nanoconfined homopolymers with cyclic chain architecture.

We have performed Monte Carlo simulations to study the effect of cyclic architecture on the behavior of homopolymer chains under several conditions of confinement. The collapse of the rings in two stages, a coil-to-globule and a liquidlike-to-solidlike transition, was observed even at extreme confinement. Both transitions were observed at lower temperatures than for linear chains of the same length, 2%-5% lower for unconfined systems, and 10%-15% lower for wall separations below three bond lengths due to the effect of confinement. When the plates separation approached the two-dimensional regime, the coil-to-globule transition shifted to lower temperatures. The inverse trend was observed when the chain length was increased. In the collapsed state, the average size and conformations of linear and cyclic molecules of same length were similar independently of confinement. At temperatures near the coil-to-globule transition, the radius of gyration of unconfined linear chains, [R(g)(2)](linear), became larger than for the cyclic chains, [R(g)(2)](cyclic), and this difference increased considerably with confinement. The radius of gyration ratio [R(g)(2)](linear)/[R(g)(2)](cyclic) in this region decreased rapidly. The decrease was more pronounced and occurred at lower temperatures for slit width confinements. At higher temperatures, in the coil state, the radius of gyration ratio became nearly constant for a given separation, and varied from 0.56 for unconfined systems to 0.47 when the chain was completely confined between the walls. This reduction was attributed to the higher increase in the average size of linear chains with confinement when compared with cyclic chains, due to architectural restrictions.

Algorithms↗