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PubMed2001

Retinal vascular architecture is maintained in retinal degeneration: corrosion cast and electron microscope study.

PURPOSE: To demonstrate the changes of the retinal vascular architecture in the diffusely degenerated thin retina. METHODS: Three-week-old weanling Wistar Kyoto rats were divided randomly into two groups. One group (n = 20) was fed a vitamin E-deficient solid diet and the other group (n = 20) was fed a solid rat chow diet. Rats were maintained on their respective diets for 14 months and then killed for scanning electron microscopy of vascular corrosion casts, light and electron microscopy and biochemical determinations. RESULTS: The serum level of vitamin E in the E-deficient rats was 1.0 +/- 0.49 microg/ml, while that in the rats fed a normal diet was 13.7 +/- 1.0 microg/ml (Student's t-test, p = 0.0001). In vitamin E-deficient rats, light microscopy showed degenerated retinas only half as thick as normal. Corrosion casts and scanning electron microscopy revealed that the retinal capillaries of the entire retina were decreased in number and scattered with localised narrowing, calibre irregularity and frequent loop formation. In the posterior pole of the retina, some capillaries clustered into small tortuous knots. However, the two-layered architecture of the capillary network in the retina was maintained. The differences in calibre of retinal capillaries between the vitamin E-deficient and normal rats were statistically significant (p < 0.0001). No remarkable abnormal changes were observed in the large retinal vessels other than arterial calibre differences (p < 0.022). No arteriovenous shunts, crossing defects or microaneurysms were seen. Transmission electron microscopy revealed complete disappearance of the photoreceptor outer and inner segments and nuclei. The retinal pigment epithelium contained lipofuscin granules and retinal capillaries with narrow lumens. The capillary endothelial cells were thickened and had scarce cytoplasmic components with vacuoles and irregularly thickened basement membranes. The capillary pericytes had vacuoles. No abnormalities were seen in the control normal rats. CONCLUSION: These findings indicate that the decrease in retinal capillaries in vitamin E-deficient rats is secondary to retinal degeneration. It was assumed that the morphological changes in the capillary network reflected structural damage to the retinal vascular cells caused by free radicals and lipid peroxides generated by oxidation. However, even in such severe degeneration the retinal vascular architecture, including the main artery and vein and two-layer capillary networks, was maintained. This is may be because of the basic anatomical arrangement of the blood vessels.

Animals↗
PubMed2004

The role of barren stalk1 in the architecture of maize.

The architecture of higher plants is established through the activity of lateral meristems--small groups of stem cells formed during vegetative and reproductive development. Lateral meristems generate branches and inflorescence structures, which define the overall form of a plant, and are largely responsible for the evolution of different plant architectures. Here, we report the isolation of the barren stalk1 gene, which encodes a non-canonical basic helix-loop-helix protein required for the initiation of all aerial lateral meristems in maize. barren stalk1 represents one of the earliest genes involved in the patterning of maize inflorescences, and, together with the teosinte branched1 gene, it regulates vegetative lateral meristem development. The architecture of maize has been a major target of selection for early agriculturalists and modern farmers, because it influences harvesting, breeding strategies and mechanization. By sampling nucleotide diversity in the barren stalk1 region, we show that two haplotypes entered the maize gene pool from its wild progenitor, teosinte, and that only one was incorporated throughout modern inbreds, suggesting that barren stalk1 was selected for agronomic purposes.

Amino Acid Sequence↗
PubMed2006

Condensin and Repo-Man-PP1 co-operate in the regulation of chromosome architecture during mitosis.

The reversible condensation of chromosomes during cell division remains a classic problem in cell biology. Condensation requires the condensin complex in certain experimental systems, but not in many others. Anaphase chromosome segregation almost always fails in condensin-depleted cells, leading to the formation of prominent chromatin bridges and cytokinesis failure. Here, live-cell analysis of chicken DT40 cells bearing a conditional knockout of condensin subunit SMC2 revealed that condensin-depleted chromosomes abruptly lose their compact architecture during anaphase and form massive chromatin bridges. The compact chromosome structure can be preserved and anaphase chromosome segregation rescued by preventing the targeting subunit Repo-Man from recruiting protein phosphatase 1 (PP1) to chromatin at anaphase onset. This study identifies an activity critical for mitotic chromosome structure that is inactivated by Repo-Man-PP1 during anaphase. This activity, provisionally termed 'regulator of chromosome architecture' (RCA), cooperates with condensin to preserve the characteristic chromosome architecture during mitosis.

Adenosine Triphosphatases↗
PubMed2026

Allele-specific chromatin architecture shapes imprinted domains and coordinates a distal enhancer and antisense transcription at the mouse Mest-Copg2 domain.

Genomic imprinting results in parent-of-origin-dependent gene expression, but how three-dimensional genome organization contributes to imprinted gene regulation remains unclear. Using Capture Hi-C in mouse cortex and primary cortical neurons, we identified parental allele-specific chromatin architectures across multiple imprinted domains. These architectures largely originate from imprinting control regions and correlate with DNA methylation-sensitive CTCF binding. Active and inactive alleles of imprinted genes show distinct promoter interaction profiles and differential engagement with distal regulatory elements in both contact frequency and the epigenetic state of distal regions. A CRISPR interference screen identified a distal enhancer that regulates Mest-Copg2 imprinted expression through allele-specific chromatin interactions. In neurons, this enhancer activates Copg2 on the maternal allele, whereas on the paternal allele it drives Mest isoforms transcribed antisense to Copg2 and contributes to Copg2 repression. In summary, we show that allele-specific chromatin architecture coordinates maternal enhancer activity and paternal antisense transcription to control imprinted expression in neurons.

Animals↗
PubMed2004

The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model.

We investigated the gene coexpression network in Saccharomyces cerevisiae, in which genes are linked when they are coregulated. This network is shown to have a scale-free, small-world architecture. Such architecture is typical of biological networks in which the nodes are connected when they are involved in the same biological process. Current models for the evolution of intracellular networks do not adequately reproduce the features that we observe in the network. We therefore derive a new model for its evolution based on the observation that there is a positive correlation between the sequence similarity of paralogues and their probability of coexpression or sharing of transcription factor binding sites (TFBSs). The simple, neutralist's model consists of (1) coduplication of genes with their TFBSs, (2) deletion and duplication of individual TFBSs and (3) gene loss. A network is constructed by connecting genes that share multiple TFBSs. Our model reproduces the scale-free, small-world architecture of the coregulation network and the homology relations between coregulated genes without the need for selection either at the level of the network structure or at the level of gene regulation.

Binding Sites↗
PubMed2006

Using mating designs to uncover QTL and the genetic architecture of complex traits.

Analysis of quantitative trait loci (QTL) affecting complex traits is often pursued in single-cross experiments. For most purposes, including breeding, some assessment is desired of the generalizability of the QTL findings and of the overall genetic architecture of the trait. Single-cross experiments provide a poor basis for these purposes, as comparison across experiments is hampered by segregation of different allelic combinations among different parents and by context-dependent effects of QTL. To overcome this problem, we combined the benefits of QTL analysis (to identify genomic regions affecting trait variation) and classic diallel analysis (to obtain insight into the general inheritance of the trait) by analyzing multiple mapping families that are connected via shared parents. We first provide a theoretical derivation of main (general combining ability (GCA)) and interaction (specific combining ability (SCA)) effects on F(2) family means relative to variance components in a randomly mating reference population. Then, using computer simulations to generate F(2) families derived from 10 inbred parents in different partial-diallel designs, we show that QTL can be detected and that the residual among-family variance can be analyzed. Standard diallel analysis methods are applied in order to reveal the presence and mode of action (in terms of GCA and SCA) of undetected polygenes. Given a fixed experiment size (total number of individuals), we demonstrate that QTL detection and estimation of the genetic architecture of polygenic effects are competing goals, which should be explicitly accounted for in the experimental design. Our approach provides a general strategy for exploring the genetic architecture, as well as the QTL underlying variation in quantitative traits.

Animals↗
PubMed2003

Aggregation of metallo-supramolecular architectures by metallo-assembled hydrogen bonding sites.

Metal-ligand interactions are used not only to design metallo-supramolecular architectures but also to assemble multiple hydrogen bond sites at the periphery of these architectures. The hydrogen bond sites aggregate the architectures into polymeric arrays with the selection of anion determining whether this is self H-bond aggregation or anion-mediated H-bond aggregation.

Journal Article↗
PubMed2006

Self-association of block copoly(oxyalkylene)s in aqueous solution. Effects of composition, block length and block architecture.

The article deals with the association behaviour in dilute aqueous solution of block copoly(oxyalkylene)s in which hydrophilic poly(ethylene oxide) is combined with hydrophobic poly(propylene oxide), poly(1,2-butylene oxide) or poly(styrene oxide). Polymers with three simple architectures are considered, i.e. copolymers of type EmAn, EmAnEm and AnEmAn, where E denotes an oxyethylene unit, A denotes a hydrophobic oxyalkylene unit, and the subscripts m and n denote number-average block lengths in repeat units. The aim is to examine how composition, block length and block architecture govern two fundamental properties, critical micelle concentration (cmc) and micelle association number (N), for systems which are in dynamic equilibrium. Copolymers with properties known to be greatly affected by heterogeneity in composition are excluded from consideration. A uniform pattern of behaviour emerges when log(cmc) is plotted against reduced hydrophobic block length (x), consistent with the micellisation equilibrium changing from one between unimers and multimolecular micelles at low values of x, to one between unimolecular micelles and multimolecular micelles at high values of x. Support for this model is provided by the enthalpy of micellisation, values of which fall effectively to zero as x is increased. Values of the micelle association number are used to define a critical hydrophobic block length for micellisation (n(cr)) for each class of diblock copolymers, values of which apply equally well to the half-length of the central block of corresponding EmAnEm triblock copolymers. Given these values, and irrespective of block architecture, the overall scaling law for the weight-average association number of the micelles is shown to be Nw = n'(1.07)m(-0.63) where m is the length (or half-length) of the hydrophilic block, and n' is the effective length of the hydrophobic block, equal to its length (or half-length) minus the critical length, i.e. n' = n-n(cr).

Algorithms↗
PubMed2006

Synthetic functional pi-stack architecture in lipid bilayers.

Neglected until recently, pi-stack architecture is rapidly emerging as a powerful strategy to create function in lipid bilayer membranes. Recent reports describe supramolecular rosettes acting as hosts of intercalating guests, to assemble in bilayer membranes and, in the case of stacked guanosine and folate quartets, to form ion channels. The introduction of rigid-rod pi-stack architecture allowed us to address one of the great challenges in the field, i.e. ligand gating. Inspiring pi-stack chemistry from related fields, covering rainbow coloration, conductivity, as well as the critical dependence of charge mobilities on the precision of supramolecular organization is summarized to zoom in on arguably the most promising application of functional pi-stack architecture in lipid bilayers, that is the creation of multifunctional photosystems.

Circular Dichroism↗
PubMed2003

Low mast cell density in the human duodenal mucosa from chronic inflammatory duodenal bowel disorders is associated with defective villous architecture.

BACKGROUND: Mast cells (MC) have recently been implicated in the processes of tissue homeostasis, remodeling and repair. DESIGN: In this study, the total and tryptase-reactive mast cell populations were quantified in the duodenal mucosa of 27 subjects suffering from chronic inflammatory bowel disorders. Mast cell density was both related to the general villous architecture (normal or defective) and to the microvascular density in the duodenal mucosa. RESULTS: Total mast cell and tryptase-positive mast cell subpopulation densities were found to be significantly reduced in the samples with defective villous architecture in comparison with those exhibiting a normal villous profile. In these last samples, a relevant proportion of mucosal mast cells exhibited ultrastructural features of secretory activity, in particular piecemeal degranulation. Finally, no correlation was established between microvascular density and tryptase activity, as it has been previously demonstrated in other pathological conditions. CONCLUSIONS: Overall, these findings indicate a significant correlation between mast cell density and the duodenal mucosal architecture.

Adolescent↗
PubMed1998

Effects of mesenchyme on epithelial tissue architecture revealed by tissue recombination experiments between the submandibular gland and lung of embryonic mice.

Lung epithelium during morphogenesis maintains a sheet structure of polarized cells lining a lumen, in which E-cadherin, beta-catenin and tight junctional proteins are localized at the cell-cell contact sites. On the other hand, the submandibular gland epithelium at early stages of development forms a non-cavitated mass of cells where E-cadherin/beta-catenin are present on the entire cell surfaces and tight junctional proteins are almost absent or weakly scattered. In the present study, tissue recombination experiments were performed between the two organs to explore roles of mesenchyme in the architectural development of the epithelium. Homotypic recombinants of both submandibular gland and lung showed the tissue architecture as observed in the intact organs. In contrast, 11-day lung epithelium cultured with 13-day submandibular mesenchyme formed multilayers of cells with the lumen being less visible. It was accompanied by redistribution of E-cadherin/beta-catenin along the entire cell surfaces and by an irregular distribution of tight junctional proteins. A similar redistribution of these molecules was observed in 15-day lung epithelium cultured with the submandibular mesenchyme, although the epithelial sheet structure lining the lumen was formed. On the other hand, the tissue architecture of submandibular gland epithelium was little affected by lung mesenchyme, although the epithelium was flattened and showed branching morphogenesis.

Animals↗
PubMed2002

An investigation of thoracic and lumbar cancellous vertebral architecture using power-spectral analysis of plain radiographs.

The internal architecture of the vertebral bodies spanning the levels T1 to L5 in seven male columns was studied using mammographic-resolution radiographs of 2.5-mm-thick planar parasagittal slices. The overlapping radiographic shadows of vertebral trabeculae combined in the image to form a series of 'elements', broadly representative of the cancellous structure. The orientations and sizes of these elements were analysed by applying the Fast Fourier transform (FFT) to the digitized radiographic images. Elements aligned in the 'vertical' orientation, along the long axis of the column, were the most prominent for all vertebral levels. The relative prominence of horizontal to vertical elements was generally constant along the column below T5. In contrast, the relative prominence of oblique to vertical elements declined in the cranio-caudal direction, particularly in individuals aged > or = 60 years. The ratio of 'large' (x > 0.3 mm) to 'small' (0.15 mm < or = x < or = 0.3 mm) elements was unchanged cranio-caudally in specimens < 60 years. However, in individuals > or = 60 years, large elements increased in relative prominence in the caudal direction. These results suggest that a basic orthogonal pattern of trabeculae is found along the male human spine, regardless of differences in vertebral body size. Power-spectral analysis is shown to yield information summarizing the predominant orientations and sizes of radiographically rendered architectural elements of vertebral cancellous bone, to define the effects of ageing on architecture, and to identify broad structural differences between vertebral levels in the adult male spine.

Humans↗
PubMed2001

Quantitative evaluation of the posterior deltoid to triceps tendon transfer based on muscle architectural properties.

The architectural properties of the posterior deltoid muscle and the 3 heads of the triceps were measured using microdissection techniques to determine whether substitution of triceps function by the posterior deltoid is architecturally appropriate. Muscles from 10 fresh cadaver specimens were fixed by high-pressure perfusion using buffered formaldehyde. Muscle architectural properties, including pennation angle, fiber bundle length, sarcomere length, and physiologic cross-sectional area, were determined. Fiber bundle length varied significantly among the deltoid (123.1 +/- 7.8 mm), medial (64.5 +/- 3.8 mm), lateral (66.5 +/- 5.4 mm), and long (85.3 +/- 9.5) heads of the triceps. The physiologic cross-sectional area of the posterior deltoid was significantly less than the total triceps area and was predicted to provide only approximately 20% of the maximum isometric tension of the combined triceps heads. These data demonstrate that the long fibers of the posterior deltoid render it a very suitable transfer to provide elbow extension because of its tremendous excursion and also show why useful functional results seem relatively independent of posterior deltoid tension at the time of surgery.

Biomechanical Phenomena↗
PubMed2002

Magnifying endoscopy, stereoscopic microscopy, and the microvascular architecture of superficial esophageal carcinoma.

BACKGROUND AND STUDY AIMS: In this study we clarify the microvascular architecture of superficial esophageal carcinoma as observed by ultra-high magnification endoscopy and stereoscopic microscopy with Microfil injection. PATIENTS AND METHODS: We observed two surgically resected specimens of superficial esophageal cancer under stereoscopic microscopy with Microfil injection. In addition, in the histological investigation, we measured the caliber of the vessels at the surface of the tumor. We carried out ultra-high magnification before treatment in 82 patients with superficial esophageal neoplasms. We classified the depth of tumor penetration of superficial esophageal carcinoma into four categories: m1 to m3 (mucosal cancer) and sm (submucosal cancer). RESULTS: By observing the normal esophageal mucosa under a stereoscopic microscope and an ultra-high magnification endoscope, we were able to visualize the intrapapillary capillary loops (IPCL). In cancer lesions, we observed characteristic changes in the superficial microvascular architecture according to the depth of tumor invasion. In m1 invasion, there was dilatation of the IPCL; in m2 invasion, there was dilatation and elongation of the IPCL; in m3, there was a mixed appearance of the IPCL and tumor vessels; and in sm invasion, complete replacement by tumor vessels. On the basis of the above criteria, ultra-high magnification endoscopic observation before treatment showed a rate of agreement between histological depth of invasion and magnified appearance of 60/72 cases (83.3 %) for which satisfactory pictures were obtained. The histological investigation showed the caliber of the IPCL of the m1 cancer lesions (12.9 +/- 3.9 microm) to be significantly greater than that of the normal esophageal mucosa (6.9 +/- 1.5 microm) (P < 0.0001). CONCLUSIONS: Observation of the microvascular architecture of superficial esophageal carcinoma is useful in the diagnosis of the depth of invasion.

Carcinoma↗
PubMed2005

Quantitative analysis of the microvascular architecture observed on magnification endoscopy in cancerous and benign gastric lesions.

BACKGROUND AND STUDY AIMS: Gastric cancer remains a common malignant tumor in Japan. The aim of this study was to attempt a quantitative evaluation of the microvascular architecture observed by magnification endoscopy using image analysis, and to investigate whether this method is able to distinguish between gastric cancers and benign lesions. PATIENTS AND METHODS: A total of 132 patients were studied using magnification endoscopy, and image analysis was performed in 71 patients (32 patients with early gastric cancer, 39 patients with benign lesions). Analysis was not possible in the other 61 patients because the quality of the image was not good enough. A square region of interest was selected from the magnified images of the gastric mucosa. From this we extracted the vascular images corresponding to microvessels and calculated the mean caliber of vessels in the region of interest. RESULTS: Image analysis provided good-quality images of microvessels and enabled evaluation of the microvascular architecture. The mean caliber of vessels was 4.454 pixels in 17 differentiated adenocarcinomas, 4.319 pixels in 15 undifferentiated adenocarcinomas, and 4.034 pixels in the 39 benign lesions. This represented a significant difference between gastric cancers and benign lesions (P<0.0001). Histopathological investigation of surgically resected tumors demonstrated the mean caliber of microvessels in cancerous lesions to be greater than that of microvessels in the surrounding mucosa. CONCLUSIONS: Image analysis was useful for evaluating the microvascular architecture of the gastric mucosa, and calculation of the mean caliber of the vessels may prove helpful in the differential diagnosis of gastric cancers. However, analysis was not possible in 61 of the 132 patients studied because of inadequate image quality, and this represents a significant limitation of this diagnostic method.

Adult↗
PubMed2005

A modular microfluidic architecture for integrated biochemical analysis.

Microfluidic laboratory-on-a-chip (LOC) systems based on a modular architecture are presented. The architecture is conceptualized on two levels: a single-chip level and a multiple-chip module (MCM) system level. At the individual chip level, a multilayer approach segregates components belonging to two fundamental categories: passive fluidic components (channels and reaction chambers) and active electromechanical control structures (sensors and actuators). This distinction is explicitly made to simplify the development process and minimize cost. Components belonging to these two categories are built separately on different physical layers and can communicate fluidically via cross-layer interconnects. The chip that hosts the electromechanical control structures is called the microfluidic breadboard (FBB). A single LOC module is constructed by attaching a chip comprised of a custom arrangement of fluid routing channels and reactors (passive chip) to the FBB. Many different LOC functions can be achieved by using different passive chips on an FBB with a standard resource configuration. Multiple modules can be interconnected to form a larger LOC system (MCM level). We demonstrated the utility of this architecture by developing systems for two separate biochemical applications: one for detection of protein markers of cancer and another for detection of metal ions. In the first case, free prostate-specific antigen was detected at 500 aM concentration by using a nanoparticle-based bio-bar-code protocol on a parallel MCM system. In the second case, we used a DNAzyme-based biosensor to identify the presence of Pb(2+) (lead) at a sensitivity of 500 nM in <1 nl of solution.

Biochemistry↗
PubMed2005

The architecture of pre-mRNAs affects mechanisms of splice-site pairing.

The exon/intron architecture of genes determines whether components of the spliceosome recognize splice sites across the intron or across the exon. Using in vitro splicing assays, we demonstrate that splice-site recognition across introns ceases when intron size is between 200 and 250 nucleotides. Beyond this threshold, splice sites are recognized across the exon. Splice-site recognition across the intron is significantly more efficient than splice-site recognition across the exon, resulting in enhanced inclusion of exons with weak splice sites. Thus, intron size can profoundly influence the likelihood that an exon is constitutively or alternatively spliced. An EST-based alternative-splicing database was used to determine whether the exon/intron architecture influences the probability of alternative splicing in the Drosophila and human genomes. Drosophila exons flanked by long introns display an up to 90-fold-higher probability of being alternatively spliced compared with exons flanked by two short introns, demonstrating that the exon/intron architecture in Drosophila is a major determinant in governing the frequency of alternative splicing. Exon skipping is also more likely to occur when exons are flanked by long introns in the human genome. Interestingly, experimental and computational analyses show that the length of the upstream intron is more influential in inducing alternative splicing than is the length of the downstream intron. We conclude that the size and location of the flanking introns control the mechanism of splice-site recognition and influence the frequency and the type of alternative splicing that a pre-mRNA transcript undergoes.

Alternative Splicing↗
PubMed2024

Multivariate genetic architecture reveals testosterone-driven sexual antagonism in contemporary humans.

Sex difference (SD) is ubiquitous in humans despite shared genetic architecture (SGA) between the sexes. A univariate approach, i.e., studying SD in single traits by estimating genetic correlation, does not provide a complete biological overview, because traits are not independent and are genetically correlated. The multivariate genetic architecture between the sexes can be summarized by estimating the additive genetic (co)variance across shared traits, which, apart from the cross-trait and cross-sex covariances, also includes the cross-sex-cross-trait covariances, e.g., between height in males and weight in females. Using such a multivariate approach, we investigated SD in the genetic architecture of 12 anthropometric, fat depositional, and sex-hormonal phenotypes. We uncovered sexual antagonism (SA) in the cross-sex-cross-trait covariances in humans, most prominently between testosterone and the anthropometric traits - a trend similar to phenotypic correlations. 27% of such cross-sex-cross-trait covariances were of opposite sign, contributing to asymmetry in the SGA. Intriguingly, using multivariate evolutionary simulations, we observed that the SGA acts as a genetic constraint to the evolution of SD in humans only when selection is sexually antagonistic and not concordant. Remarkably, we found that the lifetime reproductive success in both the sexes shows a positive genetic correlation with anthropometric traits, but not with testosterone. Moreover, we demonstrated that genetic variance is depleted along multivariate trait combinations in both the sexes but in different directions, suggesting absolute genetic constraint to evolution. Our results indicate that testosterone drives SA in contemporary humans and emphasize the necessity and significance of using a multivariate framework in studying SD.

Humans↗