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PubMed2005

Concepts in nuclear architecture.

Genomes are defined by their primary sequence. The functional properties of genomes, however, are determined by far more complex mechanisms and depend on multiple layers of regulatory control processes. A key emerging contributor to genome function is the architectural organization of the cell nucleus. The spatial and temporal behavior of genomes and their regulatory proteins are now being recognized as important, yet still poorly understood, control mechanisms in genome function. Combined cell biological, molecular and computational analysis of architectural aspects of genome function has added a further dimension to the investigation of some of the most fundamental cellular processes including transcription and maintenance of genome integrity. The complete elucidation of the contribution that nuclear architecture makes to gene expression will be required to fully understand physiological processes such as differentiation, development and disease at the cellular level. Here I give an overview of some of the emerging concepts in the study of in vivo genome organization and function.

Animals↗
PubMed2006

Effect of spatial architecture on cellular colonization.

The spatial cell-material interaction remains vital issue in forming biodegradable scaffolds in Tissue Engineering. In this study, to understand the influence of spatial architecture on cellular behavior, 2D and 3D chitosan scaffolds of 50-190 kD and >310 kD MW were synthesized through air drying and controlled rate freezing/lypohilization technique, respectively. In addition, chitosan was emulsified with 19, 76, and 160 kD 50:50 poly lactide-co-glycolide (PLGA) using 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC) as stabilizer. 2D and 3D scaffolds were formed by air drying and lyophilization as before. Tensile and compressive properties of films and scaffolds were analyzed in wet conditions at 37 degrees C. Alterations in the cell spreading, proliferation, and cytoskeletal organization of human umbilical vein endothelial cells (HUVECs) and mouse embryonic fibroblasts (MEFs) were studied. These results showed that the formed 3D chitosan scaffolds had interconnected open pore architecture (50-200 microm size). HUVECs and MEFs had reduced spreading areas and circular morphology on 2D chitosan membranes compared with 3D chitosan scaffolds. The fluorescence photomicrographs for actin (using Alexa Fluor 488 phalloidin) and cytoplasm staining (using carboxyfluorescein diacetate-succinimidyl ester) demonstrated that the cells spread within 3D chitosan matrix. 2D and 3D emulsified chitosan and chitosan/PLGA scaffolds reduced the spreading of HUVECs and MEFs even further. Proliferation results, analyzed via MTT-Formazan assay and BrdU uptake assay, correlated with the spreading characteristics. The reductions in cell spreading area on emulsified surfaces were not detrimental to the viability and endocytic activity but to proliferation. The observed alterations in cellular colonization are in part due to the substrate stiffness and surface topography. In summary, these results suggest a significant influence of spatial architecture on cellular colonization.

Cell Culture Techniques↗
PubMed2004

Architectural analysis of oral cancer, dysplastic, and normal epithelia.

BACKGROUND: We present a novel, automated, and quantitative approach to evaluate local epithelial tissue architecture based on mathematical graph theory. METHODS: Four hundred forty-one images of three diagnostic classes of oral epithelium (normal, dysplastic, and neoplastic) were analysed. The epithelial compartment was partitioned into exclusive areas associated with each nucleus to approach the theoretical cell extents. The spatial arrangement of cells in neighbourhoods of two sizes was characterised by constructing graph networks based on the cell centroids and recording 29 statistical properties. We analysed 104,627 and 67,590 neighbourhoods of diameters 37.5 and 75 microm, respectively. RESULTS: The discrimination power of the architectural descriptors was evaluated by using discriminant analysis. The best neighbourhood discrimination rate was 75% for normal versus carcinoma. For the pooled data, discrimination into three classes based on largest number of neighbourhoods associated with each class was 100% correct. Case-wise, discrimination rates were 67%, 100%, and 80% correct for normal, premalignant, and malignant. When considering two classes, discrimination rates was 89% (normal) and 100% (malignant) correct, with 71% of premalignant cases assigned to the malignant class. CONCLUSIONS: The results indicate that unbiased and reproducible quantification of tissue architectural features is possible and may provide valuable morphological information for diagnostic purposes.

Cytodiagnosis↗
PubMed2002

Impact of human bladder cancer cell architecture on autologous T-lymphocyte activation.

To investigate the influence of tumor cell architecture on T-cell activation, we used an autologous human model based on 2 bladder tumor cell lines as targets for cytotoxic tumor-infiltrating lymphocytes (TILs). These tumor cell lines were grown in vitro as either standard 2-dimensional (2D) monolayers or 3-dimensional (3D) spheroids. T-cell activation was determined by measuring the production of three major cytokines (tumor necrosis factor, granulocyte/macrophage colony-stimulating factor and interferon-gamma), known to be secreted by most activated TILs. Changes in the architecture of target cells from 2D to 3D induced a dramatic decrease in their capacity for stimulating TILs. Interestingly, neither TIL infiltration nor MHC class I, B7.1 costimulatory or lymphocyte function-associated factor-3 adhesion molecule downregulation played a major role in this decrease. These findings demonstrate that tumor architecture has a major impact on T-cell activation and might be implicated in the escape of tumor cells from the immune system.

CD58 Antigens↗
PubMed2006

Human discs large and scrib are localized at the same regions in colon mucosa and changes in their expression patterns are correlated with loss of tissue architecture during malignant progression.

Loss of cell polarity is one of the hallmarks of malignant carcinomas. Most of the understanding about the link between cell polarity and proliferation control comes from studies on the Drosophila tumor suppressors discs large (Dlg), scribble (Scrib) and lethal giant larvae (lgl). Mammalian homologues of these proteins have been described and are conserved in sequence and function. Human Dlg (hDlg) and Scrib were independently shown to be down-regulated during malignant progression. This, and other lines of evidence, points toward the participation of both hDlg and hScrib in a common pathway involved in polarity control and tumor suppression. We investigated the correlation between the expression of both proteins in tissues and their relative contributions to the maintenance of tissue architecture during colon cancer development. We analyzed the levels and distribution of hDlg and hScrib by immunohistochemistry, using serial sections of the same sample. We used normal and neoplastic colon mucosa, since it offers a good model for analyzing these features in progressive dysplastic stages. The results demonstrate that both proteins localize at the same regions in polarized colon epithelia, and that in normal samples the proteins' distribution varies as cells differentiate at the surface mucosa. In neoplasia, alterations in the expression pattern of hDlg and of hScrib increase during tumor progression; down-regulation of both proteins being associated with lack of epithelial cell polarity and disorganized tissue architecture. The results, therefore, demonstrate that there is an inverse relationship between the levels of hDlg and hScrib expression and the loss of cell polarity and tissue architecture in the colon.

Adaptor Proteins, Signal Transducing↗
PubMed2003

Nano-fibrous scaffolding architecture selectively enhances protein adsorption contributing to cell attachment.

Tissue engineering aims at resolving problems such as donor shortage and immune rejection faced by transplantation. Scaffolds (artificial extracellular matrices) have critical roles in tissue engineering. Recently, we developed nano-fibrous poly(L-lactic acid) scaffolds under the hypothesis that synthetic nano-fibrous scaffolding, mimicking the structure of natural collagen fibers, could create a more favorable microenvironment for cells. This is the first report that the nano-fibrous architecture built in three-dimensional scaffolds improved the features of protein adsorption, which mediates cell interactions with scaffolds. Scaffolds with nano-fibrous pore walls adsorbed four times more serum proteins than scaffolds with solid pore walls. More interestingly, the nano-fibrous architecture selectively enhanced protein adsorption including fibronectin and vitronectin, even though both scaffolds were made from the same poly(L-lactic acid) material. Furthermore, nano-fibrous scaffolds also allowed >1.7 times of osteoblastic cell attachment than scaffolds with solid pore walls. These results demonstrate that the biomimetic nano-fibrous architecture serves as superior scaffolding for tissue engineering.

Animals↗
PubMed2004

Architecture control of three-dimensional polymeric scaffolds for soft tissue engineering. I. Establishment and validation of numerical models.

One of the most important functions of artificial three-dimensional (3D) polymeric scaffolds is to serve as a physical support to provide tissues with an appropriate architecture for in vitro cell culture as well as in vivo tissue regeneration. The production of three-dimensional (3D) polymeric scaffolds with tailored macroporous architecture is thus a crucial step in promoting controlled vascularization and tissue growth within host environments. In this study, 3D poly(lactic-co-glycolic acid) (PLGA) scaffolds were manufactured by a thermally induced phase-separation (TIPS) technique. By controlling the quenching strategy, 3D interconnected PLGA scaffolds with tunable pore size and alignment were obtained and characterized with the use of scanning electron microscopy (SEM). A series of numerical heat-transfer models were established in an effort to describe the cooling process within the PLGA freezing regime. Among them, a two-dimensional (2D) solidification model has proved to be the most successful in describing the quenching of the polymer solution and has the potential to be used to infer the various 3D macroporous architectures created from different quenching conditions.

Biocompatible Materials↗
PubMed2007

Grafting amine-terminated branched architectures from poly(L-lactide) film surfaces for improved cell attachment.

Poly(L-lactide) (PLL) has been used as a bioabsorbable material in the medical and pharmaceutical fields. The unmodified hydrophobic PLL surface generally has low cell affinity; thus, modification of PLL film surface properties is necessary to improve its use as a biomaterial. Our surface modification method involved the use of photografting and typical wet chemistry to create branched architectures containing amine functionalities on the periphery of the grafted layers. Amine (-NH2) groups were first introduced on the PLL film surface by photoinduced grafting of 4,4'-diaminobenzophenone and the grafted branched architectures were created by subsequent reactions with succinic acid and tris(2-aminoethyl) amine. The resulting film surface was analyzed using contact angle goniometry and X-ray photoelectron spectroscopy. MC3T3 fibroblasts were cultured on unmodified PLL film and PLL films grafted with the branched structures and the films were subsequently analyzed by optical microscopy. The contact angle goniometry results showed an initial decrease and subsequent plateau in the water contact angles for the PLL films with each successive generation of the branched architectures. The X-ray photoelectron spectroscopy data provided insight into the structure of the grafted layer and revealed an increase in the nitrogen content with each generation. Optical micrographs showed enhanced cell attachment and viability on the surface-modified PLL films.

Amines↗
PubMed1989

Fine architecture of the splenic terminal vascular bed as revealed by arterial and venous pressure-loading perfusion fixation.

The three-dimensional fine architecture of the red pulp of human and animal spleens, which as fixed by a modified version of the arterial and venous pressure-loading perfusion fixation (AVPL perfusion fixation) method, is demonstrated by scanning and transmission electron microscopy. In the human spleen, changes in splenomegalias associated with hereditary spherocytosis and chronic portal hypertension are also introduced in addition to the normal architecture of the red pulp of spleens removed from patients with stomach cancer. The AVPL perfusion fixation of these spleens clearly visualized complicated three-dimensional fine architecture of the red pulp and provided much important information on in situ morphology and dynamic change of the terminal vascular bed, including venous pressure-dependent size change of the stomata and three-dimensional shapes of the capillary terminal, with positive proof of their opening into the cordal reticular tissue. In studies of the spleen associated with portal hypertension, the AVPL perfusion fixation is considered a necessary technique for analysis of the structural deviation closely relating to a very high venous pressure.

Animals↗
PubMed2007

Enhanced gene expression through temperature profile-induced variations in molecular architecture of thermoresponsive polymer vectors.

BACKGROUND: Successful non-viral gene targeting requires vectors to meet two conflicting needs-strong binding to protect the genetic material during transit and weak binding at the target site to enable release. Responsive polymers could fulfil such requirements through the switching of states, e.g. the chain-extended coil to chain-collapsed globule phase transition that occurs at a lower critical solution temperature (LCST), in order to transport nucleic acid in one polymer state and release it in another. METHODS: The ability of new synthetic polycations based on poly(ethyleneimine) (PEI) with grafted neutral responsive poly(N-isopropylacrylamide) (PNIPAm) chains to condense DNA into particles with architectures varying according to graft polymer LCST was assessed using a combination of fluorescence spectroscopy, dynamic light scattering (DLS), zeta sizing, gel retardation and atomic force microscopy studies. Transfection assays were conducted under experimental conditions wherein the polymer components were able to cycle across their LCST. RESULTS: Two PEI-PNIPAm conjugate polymers with different LCSTs displayed coil-globule transitions when complexed to plasmid DNA, leading to variations in molecular architecture as shown by changes in emission maxima of an environment-sensitive fluorophore attached to the PNIPAm chains. Gel retardation assays demonstrated differences in electrophoretic mobilities of polymer-DNA complexes with temperatures below and above polymer LCSTs. Atomic force micrographs showed changes in the structures of polymer-DNA complexes for a polymer undergoing a phase transition around body temperature but not for the polymer with LCST outside this range. Transfection experiments in C2C12 and COS-7 cells demonstrated that the highest expression of transgene occurred in an assay that involved a 'cold-shock' below polymer LCST during transfection. CONCLUSIONS: Designed changes in thermoresponsive polycation vector configuration via temperature-induced phase transitions enhanced transgene expression. The results indicate that changes in molecular architecture induced by a carefully chosen stimulus during intracellular trafficking can be used to enhance gene delivery.

Acrylic Resins↗
PubMed2004

Comparative analysis of masseter fiber architecture in tree-gouging (Callithrix jacchus) and nongouging (Saguinus oedipus) callitrichids.

Common marmosets (Callithrix jacchus) and cotton-top tamarins (Saguinus oedipus) (Callitrichidae, Primates) share a broadly similar diet of fruits, insects, and tree exudates. Common marmosets, however, differ from tamarins by actively gouging trees with their anterior teeth to elicit tree exudate flow. During tree gouging, marmosets produce relatively large jaw gapes, but do not necessarily produce relatively large bite forces at the anterior teeth. We compared the fiber architecture of the masseter muscle in tree-gouging Callithrix jacchus (n = 10) to nongouging Saguinus oedipus (n = 8) to determine whether the marmoset masseter facilitates producing these large gapes during tree gouging. We predict that the marmoset masseter has relatively longer fibers and, hence, greater potential muscle excursion (i.e., a greater range of motion through increased muscle stretch). Conversely, because of the expected trade-off between excursion and force production in muscle architecture, we predict that the cotton-top tamarin masseter has more pinnate fibers and increased physiological cross-sectional area (PCSA) as compared to common marmosets. Likewise, the S. oedipus masseter is predicted to have a greater proportion of tendon relative to muscle fiber as compared to the common marmoset masseter. Common marmosets have absolutely and relatively longer masseter fibers than cotton-top tamarins. Given that fiber length is directly proportional to muscle excursion and by extension contraction velocity, this result suggests that marmosets have masseters designed for relatively greater stretching and, hence, larger gapes. Conversely, the cotton-top tamarin masseter has a greater angle of pinnation (but not significantly so), larger PCSA, and higher proportion of tendon. The significantly larger PCSA in the tamarin masseter suggests that their masseter has relatively greater force production capabilities as compared to marmosets. Collectively, these results suggest that the fiber architecture of the common marmoset masseter is part of a suite of features of the masticatory apparatus that facilitates the production of relatively large gapes during tree gouging.

Animals↗
PubMed2004

Neuromuscular partitioning, architectural design, and myosin fiber types of the M. vastus lateralis of the llama (Lama glama).

The llama (Lama glama) is one of the few mammals of relatively large body size in which three fast myosin heavy chain isoforms (i.e., IIA, IIX, IIB) are extensively expressed in their locomotory muscles. This study was designed to gain insight into the morphological and functional organization of skeletal musculature in this peculiar animal model. The neuromuscular partitioning, architectural design, and myosin fiber types were systematically studied in the M. vastus lateralis of adult llamas (n = 15). Four nonoverlapping neuromuscular partitions or compartments were identified macroscopically (using a modified Sihler's technique for muscle depigmentation), although they did not conform strictly to the definitions of "neuromuscular compartments." Each neuromuscular partition was innervated by primary branches of the femoral nerve and was arranged within the muscle as paired partitions, two in parallel (deep-superficial compartmentalization) and the other two in-series (proximo-distal compartmentalization). These neuromuscular partitions of the muscle varied in their respective architectural designs (studied after partial digestion with diluted nitric acid) and myosin fiber type characteristics (identified immunohistochemically with specific anti-myosin monoclonal antibodies, then examined by quantitative histochemistry and image analysis). The deep partitions of the muscle had longer fibers, with lower angles of pinnation, and higher percentages of fast-glycolytic fibers than the superficial partitions of the muscle. These differences clearly suggest a division of labor in the whole M. vastus lateralis of llamas, with deep partitions exhibiting features well adapted for dynamic activities in the extension of stifle, whereas superficial portions seem to be related to the antigravitational role of the muscle in preserving the extension of the stifle during standing and stance phase of the stride. This peculiar structural and functional organization of the llama M. vastus lateralis does not confirm the generalized idea that deep muscles or the deepest portions within the same muscles somehow develop postural and/or low-intensity isometric functions. Rather, it suggests a primacy of architecture over intramuscular location in determining fiber type composition and hence division of labor within the muscle. A compartmentalization in the distribution of the three fast-subtype fibers (IIA, IIX, and IIB) also occurred, and this could also be relevant functionally, since these fiber types differed significantly in size (IIA < IIX < IIB), oxidative capacity (IIA > IIX > IIB), and capillarization (IIA = IIX > IIB). Furthermore, a typical spatial pattern in fiber type distribution was encountered in llama muscle (i.e., fiber types were consistently ranked in the order I --> IIA --> IIX --> IIB from the center to the periphery of fascicles), suggesting again peculiar and not well understood functional adaptations in these species.

Animals↗
PubMed1982

Architecture of the hind limb muscles of cats: functional significance.

Force, velocity, and displacement properties of a muscle are determined in large part by its architectural design. The relative effect of muscle architecture on these physiological variables was studied by determining muscle weight, fiber length, average sarcomere length, and approximate angle of pinnation of 24 cat hind limb muscles. Muscle lengths ranged from 28.3 to 144 mm, whereas fiber lengths ranged from 8.4 to 105.5 mm. Generally, fiber to muscle length ratios were similar throughout a muscle. Estimated angles of pinnation of muscle fibers varied from 0 to 21 degrees with most having an angle of less than 10 degrees. The cross-sectional area of the knee extensors was similar to the knee flexors (16.43 vs. 16.83 cm2) whereas the cross-sectional area of the ankle extensors was more than six times greater than the ankle flexors (18.59 vs. 2.83 cm2). There was a 6.7-fold difference in the maximal force between muscles, when normalized to a constant weight, that could be attributed to architectural features. Ratios of wet weight to predicted maximal tetanic tension for each muscle and muscle group were calculated to compare the relative priority of muscle force versus muscle length-velocity for a given mass of muscle. These ratios varied from 0.4 to 4.84. The ratios suggest that velocity and/or displacement is a priority for the hamstrings, whereas force is a priority for the quadriceps and lower leg muscles. As much as a 12.6-fold difference in maximal velocity between muscles can be attributed to differences in fiber lengths. This can be compared to approximately a 2.5-fold difference in maximal velocity reported to occur as a result of biochemical (intrinsic) differences.

Animals↗
PubMed2001

Membrane architecture of mitochondria in neurons of the central nervous system.

Electron tomography was used to help redefine the membrane architecture of mitochondria in neurons of the brain. Investigations were conducted on unexplored questions of structural homogeneity between mitochondria in the four intensely studied regions of the brain and in the functionally distinct neuronal sub-compartments. These mitochondria have the majority of cristae composed of both tubular and lamellar segments with the tubes arranged more peripherally and the lamellae more centrally located. Cristae that are entirely tubular were not commonly seen and those that are entirely lamellar were rare. It was determined that cristae connect through narrow, sometimes very long tubular regions to the peripheral surface of the inner membrane. A structurally distinct type of contact site was revealed in brain mitochondria, which we named the bridge contact site. These bridges may play a role in the structural integrity of the outer and inner membrane systems. It was found that the membrane architecture in the various brain regions and neuronal compartments was strikingly uniform, including consistently tubular crista junctions. The functional consequences of this junctional architecture are discussed in relation to the segregation of proteins between the inner boundary membrane and the cristae membranes, and in relation to the model of microcompartmentation of macromolecules inside cristae.

Animals↗
PubMed2005

Determination of mouse skeletal muscle architecture using three-dimensional diffusion tensor imaging.

Muscle architecture is the main determinant of the mechanical behavior of skeletal muscles. This study explored the feasibility of diffusion tensor imaging (DTI) and fiber tracking to noninvasively determine the in vivo three-dimensional (3D) architecture of skeletal muscle in mouse hind leg. In six mice, the hindlimb was imaged with a diffusion-weighted (DW) 3D fast spin-echo (FSE) sequence followed by the acquisition of an exercise-induced, T(2)-enhanced data set. The data showed the expected fiber organization, from which the physiological cross-sectional area (PCSA), fiber length, and pennation angle for the tibialis anterior (TA) were obtained. The values of these parameters ranged from 5.4-9.1 mm(2), 5.8-7.8 mm, and 21-24 degrees , respectively, which is in agreement with values obtained previously with the use of invasive methods. This study shows that 3D DT acquisition and fiber tracking is feasible for the skeletal muscle of mice, and thus enables the quantitative determination of muscle architecture.

Animals↗
PubMed2007

Lack of human muscle architectural adaptation after short-term strength training.

The mechanisms governing the increases in force production in response to short periods of strength training have yet to be fully elucidated. We examined whether muscle architectural adaptation was a contributing factor. Ultrasound imaging techniques were used to measure quadriceps muscle architecture at 17 sites in vivo in trained and untrained legs of men and women after 2.5 and 5 weeks of unilateral knee extension training, as well as in a nontraining control group. Despite increases in knee extensor strength of the trained and untrained (women only) legs, there were no changes in muscle thickness, fascicle angle, or fascicle length in any of the muscles tested. The moderate correlation between vastus lateralis thickness (middle site) and eccentric (r = 0.55; P < 0.05) and concentric (r = 0.46; P < 0.1) torque after, but not before, training is suggestive of neural rather than architectural adaptations predominating in the early phase of training.

Adaptation, Physiological↗
PubMed1988

Architectural and nuclear morphometrical features together are more important prognosticators in endometrial hyperplasias than nuclear morphometrical features alone.

Previous studies have shown that 80-90 per cent of cases of atypical hyperplasia of the endometrium do not progress to cancer. Criteria to predict the outcome in an individual patient with hyperplasia are lacking, and hysterectomy is the usual (over)treatment in order to avoid a 10-20 per cent chance of confrontation with cancer later on in the course of the disease. A recent study has shown that using a nuclear morphometric classification rule, 15 per cent of patients without progression can be accurately separated from patients with progression. However, as it is unlikely that nuclear morphometrical features are the only morphological factors reflecting the outcome of the disease, other quantitative parameters describing the architecture of the glands have also been studied for their potential value in selecting patients who will progress to cancer. In total, 10 nuclear features and 12 glandular architectural features were studied in 39 cases of atypical endometrial hyperplasia. Among these cases, seven (18 per cent) progressed to cancer. Using linear stepwise regression analysis and discriminant analysis, the volume percentage stroma and the standard deviation of the shortest nuclear axis are the best discriminators, although the outer surface density of the glands also adds to the discriminating power. The volume percentage stroma is the best single prognosticator; this feature is highly reproducible. In total, using these combined architectural and nuclear morphometrical features, 20 of the 32 cases without progression were separated from those who subsequently progressed (62.5 per cent). This is a considerable improvement over nuclear morphometrical features alone (15 per cent separated).

Cell Nucleus↗
PubMed2006

Hypophosphorylation of the architectural chromatin protein DEK in death-receptor-induced apoptosis revealed by the isotope coded protein label proteomic platform.

During apoptosis nuclear morphology changes dramatically due to alterations of chromatin architecture and cleavage of structural nuclear proteins. To characterize early events in apoptotic nuclear dismantling we have performed a proteomic study of apoptotic nuclei. To this end we have combined a cell-free apoptosis system with a proteomic platform based on the differential isotopic labeling of primary amines with N-nicotinoyloxy-succinimide. We exploited the ability of this system to produce nuclei arrested at different stages of apoptosis to analyze proteome alterations which occur prior to or at a low level of caspase activation. We show that the majority of proteins affected at the onset of apoptosis are involved in chromatin architecture and RNA metabolism. Among them is DEK, an architectural chromatin protein which is linked to autoimmune disorders. The proteomic analysis points to the occurrence of multiple PTMs in early apoptotic nuclei. This is confirmed by showing that the level of phosphorylation of DEK is decreased following apoptosis induction. These results suggest the unexpected existence of an early crosstalk between cytoplasm and nucleus during apoptosis. They further establish a previously unrecognized link between DEK and cell death, which will prove useful in the elucidation of the physiological function of this protein.

Animals↗