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PubMed1992

Association of efferent neurons to the compartmental architecture of the superior colliculus.

The superior colliculus is a layered structure in the mammalian midbrain serving multimodal sensorimotor integration. Its intermediate layers are characterized by a compartmental architecture. These compartments are apparent through the clustering of terminals of major collicular afferents, which in many instances match the heterogeneous distribution of tissue components such as acetylcholinesterase, choline acetyltransferase, substance P, and parvalbumin. The present study was undertaken to determine whether efferent cells observe this compartmental architecture. It was found that subpopulations of both descending and ascending collicular efferents originate from perikarya situated in characteristic positions relative to the collicular compartments defined by elevated acetylcholinesterase activity and that their dendrites appear to be specifically coordinated with the heterogeneous environment. With the specific interlocking of afferent and efferent neurons through spatially distinguished neural networks, the compartmental architecture apparently constitutes an essential element for the determination of information flow in the superior colliculus.

Acetylcholinesterase↗
PubMed1998

"Hidden" sequence periodicities and protein architecture.

I demonstrate the existence in protein domain sequences of sets of statistically significant periodic signals, characteristic of the architectures of those domains. It is shown that, although the frequencies of the signals characteristic of a particular architecture have definite wave numbers, they can occur in any physical property. The characteristic signals define sequence units, which may correspond to specific structural features. Study of signals in different architectures suggests that symmetric structures are characterized by sets of sequence signals, which are members of harmonic series and which therefore impose commensurate periodicities on the structure. Asymmetric structures are characterized by mutually incommensurate sets of sequence signals. It is pointed out that, although these periodic sequence units can be very short, their existence is a property of the entire sequence.

Fourier Analysis↗
PubMed1996

The architecture of human acetylcholinesterase active center probed by interactions with selected organophosphate inhibitors.

The role of the functional architecture of human acetylcholinesterase (HuAChE) active center in facilitating reactions with organophosphorus inhibitors was examined by a combination of site-directed mutagenesis and kinetic studies of phosphorylation with organophosphates differing in size of their alkoxy substituents and in the nature of the leaving group. Replacements of residues Phe-295 and Phe-297, constituting the HuAChE acyl pocket, increase up to 80-fold the reactivity of the enzymes toward diisopropyl phosphorofluoridate, diethyl phosphorofluoridate, and p-nitrophenyl diethyl phosphate (paraoxon), indicating the role of this subsite in accommodating the phosphate alkoxy substituent. On the other hand, a decrease of up to 160-fold in reactivity was observed for enzymes carrying replacements of residues Tyr-133, Glu-202, and Glu-450, which are constituents of the hydrogen bond network in the HuAChE active center, which maintains its unique functional architecture. Replacement of residues Trp-86, Tyr-337, and Phe-338 in the alkoxy pocket affected reactivity toward diisopropyl phosphorofluoridate and paraoxon, but to a lesser extent that toward diethyl phosphorofluoridate, indicating that both the alkoxy substituent and the p-nitrophenoxy leaving group interact with this subsite. In all cases the effects on reactivity toward organophosphates, demonstrated in up to 10,000-fold differences in the values of bimolecular rate constants, were mainly a result of altered affinity of the HuAChE mutants, while the apparent first order rate constants of phosphorylation varied within a narrow range. This finding indicates that the main role of the functional architecture of HuAChE active center in phosphorylation is to facilitate the formation of enzyme-inhibitor Michaelis complexes and that this affinity, rather than the nucleophilic activity of the enzyme catalytic machinery, is a major determinant of HuAChE reactivity toward organophosphates.

Acetylcholinesterase↗
PubMed2003

Juvenile nitrogen uptake capacities and root architecture of two open-pollinated families of Picea abies. Effects of nitrogen source and ectomycorrhizal symbiosis.

This study was carried out to find early physiological differences occurring in young seedlings between two contrasting Picea abies open-pollinated families (OPF), one with high- and one with low-growth performance in the field by, determining their N uptake capacities and their root architecture. We used three potential N-sources in forest soil solution, NO3-, NH4+ and amino acids, to establish N uptake rates by the plants, whether or not associated with a fungus isolated from the field and identified as Paxillus involutus. NO3- fluxes were determined locally at the root surface using NO3(-)-selective microelectrodes whereas NH4+ and amino acid (L-glutamate and L-aspartate) uptake rates were calculated from their depletion of the incubation solution by the whole root system. Root systems were digitised in order to determine the number and the length of different root types. In non-mycorrhizal plants, the results showed that the most distinguishing parameters between OPF were NO3- uptake rates measured in the white tip of the secondary roots and the root architecture, with higher values determined in high-growth than in low-growth field performance OPF. The presence of the mycorrhizal fungus decreased NO3- uptake rates in both OPF and had an opposite effect on root architecture by increasing it in low-growth and decreasing it in high-growth field performance OPF, respectively. In non-mycorrhizal plants, NH4+ and amino-acid uptake rates were not different between OPF. Mycorrhizal symbiosis did not change NH4+ uptake rates whereas it increased that of amino acids, specifically that of L-aspartate in the low-growth field performance OPF. Taken together these results suggest that the measurement of local fluxes in roots of young plants could be a good potential tool for the early evaluating of growth capacity of Picea abies OPF.

Amino Acids↗
PubMed2006

Effects of nutritional level on muscle development, histochemical properties of myofibre and collagen architecture in the pectoralis muscle of male broilers.

1. The effects of nutritional level on muscle development, histochemical properties of myofibre and collagen architecture in the pectoralis muscle were evaluated using male broilers of Red Cornish x New Hampshire stock, reared on diets of high nutritional value for up to 80 d (H80d) and low nutritional value for up to 80 d (L80d, same age as H80d) or 95 d (L95d, same body weight as H80d). 2. The total live weight and the weight of pectoralis muscle were lower in L80d than in both H80d and L95d. The muscle weight as a percentage of live weight was 8.7% in L80d, 10.7% in H80d and 11.5% in L95d. 3. Pectoralis muscle was composed only of type IIB myofibres and showed no differences in myofibre type composition among the chicken groups. The largest diameter of type IIB myofibres was observed in L95d, followed by H80d and the smallest in L80d. 4. The total amount of intramuscular collagen did not differ among the chicken groups (1.92 to 1.99 mg/g). Types I and III collagens were immunohistochemically detected in both the perimysia and endomysia. The thin perimysia around the primary myofibre fascicles showed larger width in H80d than L80d and L95d, and also the thick perimysia around the secondary fascicles in H80d than L80d. 5. The collagen structure of the perimysium was most developed in H80d, followed by L95d and on the least in L80d. The development of perimysial collagen fibres could be enhanced by a rapid growth rate of the muscle induced by high nutritional level and depressed by a slow growth rate with low nutritional foods. 6. The endomysial collagen architecture was observed as a felt-like tissue of the fibril bundles with many slits. The thinnest endomysial wall was observed in L80d, followed by H80d and the thickest in L95d. 7. From these results, it was indicated that foods of high nutritional value could enhance growth of the pectoralis muscle of broilers, and this is accompanied by hypertrophy of the type IIB myofibres and development of the perimysial collagen architecture.

Animal Feed↗
PubMedDate not supplied

GASTON: an architecture for the acquisition and execution of clinical guideline-application tasks.

Recently, studies have shown the benefits of using clinical guidelines in the practice of medicine. There have been numerous efforts to develop clinical decision support systems that support guideline-based care in an automated fashion, covering a wide range of clinical settings and tasks. Despite these efforts, only a few systems progressed beyond the prototype stage and the research laboratory. For guideline-based clinical decision support systems to be successful, a balance must be made between intuitive but imprecise representations usually encountered by most of today's systems and representations that support a strong underlying clinical performance model. The project described in this paper tries to achieve such a balance. It presents the GASTON architecture that contains a set of reusable software components for the application of guidelines, including design-time components to facilitate the guideline authoring process based on guideline representation models along with execution-time components for building decision support systems that incorporate these guidelines. This architecture was used to develop several guideline representation models such as a rule-based representation to model rule-based guidelines and guideline representation models that address more complex tasks. Also, decision support systems that incorporate these models were developed with the architecture. For the representation and application of various classes of guidelines, rules were also viewed as instances of more complex tasks. By identifying similar characteristics of sets of rules, we developed several tasks such as a drug intera ction and drug contraindication task. Based on these models, we have developed and validated guidelines and decision support systems for use in several application domains such as intensive care, family physicians and psychiatry. In order to be able to represent more complex time-oriented plans, new guideline representation models are being developed.

Algorithms↗
PubMed2006

A phylogenetic analysis of sleep architecture in mammals: the integration of anatomy, physiology, and ecology.

Among mammalian species, the time spent in the two main "architectural" states of sleep--slow-wave sleep (SWS) and rapid-eye-movement (REM) sleep--varies greatly. Previous comparative studies of sleep architecture found that larger mammals, those with bigger brains, and those with higher absolute basal metabolic rates (BMR) tended to engage in less SWS and REM sleep. Species experiencing a greater risk of predation also exhibited less SWS and REM sleep. In all cases, however, these studies lacked a formal phylogenetic and theoretical framework and used mainly correlational analyses. Using independent contrasts and an updated data set, we extended existing approaches with path analysis to examine the integrated influence of anatomy, physiology, and ecology on sleep architecture. Path model structure was determined by nonmutually exclusive hypotheses for the function of sleep. We found that species with higher relative BMRs engage in less SWS, whereas species with larger relative brain masses engage in more REM sleep. REM sleep was the only sleep variable strongly influenced by predation risk; mammals sleeping in riskier environments engage in less REM sleep. Overall, we found support for some hypotheses for the function of sleep, such as facilitating memory consolidation or learning, but not others, such as energy conservation.

Animals↗
PubMed2005

Towards an inline reconstruction architecture for micro-CT systems.

Recent developments in micro-CT have revolutionized the ability to examine in vivo living experimental animal models such as mouse with a spatial resolution less than 50 microm. The main requirements of in vivo imaging for biological researchers are a good spatial resolution, a low dose induced to the animal during the full examination and a reduced acquisition and reconstruction time for screening purposes. We introduce inline acquisition and reconstruction architecture to obtain in real time the 3D attenuation map of the animal fulfilling the three previous requirements. The micro-CT system is based on commercially available x-ray detector and micro-focus x-ray source. The reconstruction architecture is based on a cluster of PCs where a dedicated communication scheme combining serial and parallel treatments is implemented. In order to obtain high performance transmission rate between the detector and the reconstruction architecture, a dedicated data acquisition system is also developed. With the proposed solution, the time required to filter and backproject a projection of 2048 x 2048 pixels inside a volume of 140 mega voxels using the Feldkamp algorithm is similar to 500 ms, the time needed to acquire the same projection.

Algorithms↗
PubMed2005

Architectures for high-performance FPGA implementations of neural models.

As the complexity of neural models continues to increase (larger populations, varied ionic conductances, more detailed morphologies, etc) traditional software-based models have difficulty scaling to reach the performance levels desired. This paper describes the use of FPGAs, or field programmable gate arrays, to easily implement a wide variety of neural models with the performance of custom analogue circuits or computer clusters, the reconfigurability of software, and at a cost rivalling personal computers. FPGAs reach this level of performance by enabling the design of neural models as parallel processed data paths. These architectures provide for a wide range of single-compartment, multi-compartment and population models to be readily converted to FPGA implementations. Generalized architectures are described for the efficient modelling of a first-order, nonlinear differential equation in throughput maximizing or latency minimizing data-path configurations. The homogeneity of population and multicompartment models is exploited to form deep pipelines for improved performance. Limitations of FPGA architectures and future research areas are explored.

Animals↗
PubMed1999

Cardiac organogenesis in vitro: reestablishment of three-dimensional tissue architecture by dissociated neonatal rat ventricular cells.

The mammalian heart does not regenerate in vivo. The heart is, therefore, an excellent candidate for tissue engineering approaches and for the use of biosynthetic devices in the replacement or augmentation of defective tissue. Unfortunately, little is known about the capacity of isolated heart cells to re-establish tissue architectures in vitro. In this study, we examined the possibility that cardiac cells possess a latent organizational potential that is unrealized within the mechanically active tissue but that can be accessed in quiescent environments in culture. In the series of experiments presented here, total cell populations were isolated from neonatal rat ventricles and recombined in rotating bioreactors containing a serum-free medium and surfaces for cell attachment. The extent to which tissue-like structure and contractile function were established was assessed using a combination of morphological, physiological, and biochemical techniques. We found that mixed populations of ventricular cells formed extensive three-dimensional aggregates that were spontaneously and rhythmically contractile and that large aggregates of structurally-organized cells contracted in unison. The cells were differentially distributed in these aggregates and formed architectures that were indistinguishable from those of intact tissue. These architectures arose in the absence of three-dimensional cues from the matrix, and the formation of organotypic structures was apparently driven by the cells themselves. Our observations suggest that cardiac cells possess an innate capacity to re-establish complex, three-dimensional, cardiac organization in vitro. Understanding the basis of this capacity, and harnessing the organizational potential of heart cells, will be critical in the development of tissue homologues for use in basic research and in the engineering of biosynthetic implants for the treatment of cardiac disease.

Actins↗
PubMed1999

Direct visualization of a protein nuclear architecture.

Whether the cell nucleus is organized by an underlying architecture analagous to the cytoskeleton has been a highly contentious issue since the original isolation of a nuclease and salt-resistant nuclear matrix. Despite electron microscopy studies that show that a nuclear architecture can be visualized after fractionation, the necessity to elute chromatin to visualize this structure has hindered general acceptance of a karyoskeleton. Using an analytical electron microscopy method capable of quantitative elemental analysis, electron spectroscopic imaging, we show that the majority of the fine structure within interchromatin regions of the cell nucleus in fixed whole cells is not nucleoprotein. Rather, this fine structure is compositionally similar to known protein-based cellular structures of the cytoplasm. This study is the first demonstration of a protein network in unfractionated and uninfected cells and provides a method for the ultrastructural characterization of the interaction of this protein architecture with chromatin and ribonucleoprotein elements of the cell nucleus.

Animals↗
PubMed2003

Growth and architecture of small honey mesquites under jackrabbit browsing: overcoming the disadvantage of being eaten.

Browsing is an important mortality factor in seedlings and small plants. However, the induced changes in the architecture of plant survivors may influence subsequent browsing, opening the possibility of compensating for the damage done. How jackrabbit (Lepus californicus) browsing affects the growth and architecture of small individuals of honey mesquite, Prosopis glandulosa var. torreyana, a tree/shrub that produces spines at every node, was explored. Naturally established mesquites of unknown age were selected in one site, and 2-year-old mesquites were transplanted in another site. In both cases, half of them were exposed to jackrabbits and the other half were excluded as controls. After 4 years, shoot production (height, length and number of derived shoots) and plant growth (height and cover) increased 1.4-2.5-fold in naturally established controls relative to exposed plants, depending on the measured variable. In the transplant experiment, the increases were 2.8-7.1-fold in controls relative to exposed plants 2 years after initiation of the experiment. The net loss of biomass in treatment vs. control plants in these experiments suggests a negative response to browsing which has been defined as under-compensation. Alternative architectures in honey mesquites were evident at the end of the exclusion experiments: controls had long branches and an extended crown cover, while exposed plants had short branches and a compact crown cover. Results indicated that mesquites were able to grow under browser pressure by packing many stems in a compact matrix armed with spines and producing one or more shoots tall and wide enough to escape from jackrabbits.

Animals↗
PubMed2004

A dynamic, architectural plant model simulating resource-dependent growth.

BACKGROUND AND AIMS: Physiological and architectural plant models have originally been developed for different purposes and therefore have little in common, thus making combined applications difficult. There is, however, an increasing demand for crop models that simulate the genetic and resource-dependent variability of plant geometry and architecture, because man is increasingly able to transform plant production systems through combined genetic and environmental engineering. MODEL: GREENLAB is presented, a mathematical plant model that simulates interactions between plant structure and function. Dual-scale automaton is used to simulate plant organogenesis from germination to maturity on the basis of organogenetic growth cycles that have constant thermal time. Plant fresh biomass production is computed from transpiration, assuming transpiration efficiency to be constant and atmospheric demand to be the driving force, under non-limiting water supply. The fresh biomass is then distributed among expanding organs according to their relative demand. Demand for organ growth is estimated from allometric relationships (e.g. leaf surface to weight ratios) and kinetics of potential growth rate for each organ type. These are obtained through parameter optimization against empirical, morphological data sets by running the model in inverted mode. Potential growth rates are then used as estimates of relative sink strength in the model. These and other 'hidden' plant parameters are calibrated using the non-linear, least-square method. KEY RESULTS AND CONCLUSIONS: The model reproduced accurately the dynamics of plant growth, architecture and geometry of various annual and woody plants, enabling 3D visualization. It was also able to simulate the variability of leaf size on the plant and compensatory growth following pruning, as a result of internal competition for resources. The potential of the model's underlying concepts to predict the plant's phenotypic plasticity is discussed.

Algorithms↗
PubMed2004

Root system architecture of Quercus pubescens trees growing on different sloping conditions.

BACKGROUND AND AIMS: Plant roots' growth direction has important implications for plant development and survival; moreover it plays an effective and vital role in stabilizing weathered soil on a steep slope. The aim of this work was to assess the influence of slope on the architecture of woody root systems. METHODS: Five mature, single-stemmed Quercus pubescens trees growing on a steep slope and five on a shallow slope were excavated to a root diameter of 1 cm. A very precise numeric representation of the geometry and topology of structural root architecture was gained using a low-magnetic-field digitizing device (Fastrak, Polhemus). Several characteristics of root architecture were extracted by macros, including root volume, diameter, length, number, spatial position and branching order. KEY RESULTS: The diameter at breast height (dbh) was the best predictor of the root volume but had no correlation with length and number of roots. The slope affected the root volume for each branching order, and the basal cross-sectional area (CSA), number and length of the first-order roots. Number and length of the second- and third-order laterals were closely related in both conditions, although this relationship was closer in the shallow trees, suggesting the influence of a genetic control. Sloping trees showed a clustering tendency of the first- and second-order lateral roots in the up-slope direction, suggesting that the laterals rather than the taproots provide much of the anchorage. In a steep-slope condition, the taproot tapering was positively correlated with the asymmetry magnitude of first-order roots, indicating compensation between taproot and main lateral roots' clustering tendency. CONCLUSIONS: These results suggest that on a slope, on clayey soils, root asymmetry appears to be a consequence of several environmental factors such as inclination, shallow-slides and soil compactness. In addition, this adaptive growth seems to counteract the turning moment induced by the self-loading forces acting in slope conditions, and as a consequence improves the tree stability.

Environment↗
PubMed2026

dcHiChIP: a comprehensive Nextflow-based pipeline for multiscale analysis of chromatin architecture from HiChIP data.

MOTIVATION: Despite the growing use of HiChIP to investigate protein-directed chromatin architecture, a comprehensive and reproducible pipeline for analysing these datasets-from raw reads to multiscale 3D genome features-remains lacking. Existing tools often focus on isolated components, such as loop calling or matrix generation, but fall short in integrating structural annotation, functional enrichment, and spatial modeling within a unified framework. To address this gap, we developed dcHiChIP, a modular, scalable Nextflow-based workflow that streamlines the analysis of HiChIP data, enabling both routine processing and in-depth exploration of chromatin organization and regulatory interactions. RESULTS: dcHiChIP enables robust and reproducible analysis of HiChIP datasets across multiple scales of chromatin architecture. It accepts raw sequencing data as input and generates high-quality loop calls, domain annotations, and 3D genome models. It also performs functional annotation and motif enrichment analyses. Applied to benchmark CTCF HiChIP datasets, dcHiChIP identifies major chromatin architectural features such as TADs/CCDs, A/B compartments, and chromatin stripes, and offers efficient, end-to-end execution with support for batch processing and workflow resumability. AVAILABILITY: dcHiChIP is publicly available on GitHub at https://github.com/SFGLab/dcHiChIP, with documentation at https://sfglab.github.io/dcHiChIP/. The software version used in this study is archived at Zenodo: https://doi.org/10.5281/zenodo.22030542.

Chromatin↗
PubMed2002

Plant architecture.

Plant architecture is species specific, indicating that it is under strict genetic control. Although it is also influenced by environmental conditions such as light, temperature, humidity and nutrient status, here we wish to focus only on the endogenous regulatory principles that control plant architecture. We summarise recent progress in the understanding of the basic patterning mechanisms involved in the regulation of leaf arrangement, the genetic regulation of meristem determinacy, i.e. the decision to stop or continue growth, and the control of branching during vegetative and generative development. Finally, we discuss the basis of leaf architecture and the role of cell division and cell growth in morphogenesis.

Gene Expression Regulation, Plant↗
PubMed2004

Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease.

The term 'genomic disorder' refers to a disease that is caused by an alteration of the genome that results in complete loss, gain or disruption of the structural integrity of a dosage sensitive gene(s). In most of the common chromosome deletion/duplication syndromes, the rearranged genomic segments are flanked by large (usually >10 kb), highly homologous low copy repeat (LCR) structures that can act as recombination substrates. Recombination between non-allelic LCR copies, also known as non-allelic homologous recombination, can result in deletion or duplication of the intervening segment. Recent findings suggest that other chromosomal rearrangements, including reciprocal, Robertsonian and jumping translocations, inversions, isochromosomes and small marker chromosomes, may also involve susceptibility to rearrangement related to genome structure or architecture. In several cases, LCRs, AT-rich palindromes and pericentromeric repeats are located at such rearrangement breakpoints. Analysis of the products of recombination at the junctions of the rearrangements reveals both homologous recombination and non-homologous end joining as causative mechanisms. Thus, a more global concept of genomic disorders emerges in which susceptibility to rearrangements occurs due to underlying complex genomic architecture. Interestingly, this architecture plays a role not only in disease etiology, but also in primate genome evolution. In this review, we discuss recent advances regarding general mechanisms for the various rearrangements of our genome, and potential models for rearrangements with non-homologous breakpoint regions.

Biological Evolution↗
PubMed2006

Role of genomic architecture in PLP1 duplication causing Pelizaeus-Merzbacher disease.

Genomic architecture, higher order structural features of the human genome, can provide molecular substrates for recurrent sub-microscopic chromosomal rearrangements, or may result in genomic instability by forming structures susceptible to DNA double-strand breaks. Pelizaeus-Merzbacher disease (PMD) is a genomic disorder most commonly arising from genomic duplications of the dosage-sensitive proteolipid protein gene (PLP1). Unlike many other genomic disorders that result from non-allelic homologous recombination utilizing flanking low-copy repeats (LCRs) as substrates, generating a common and recurrent rearrangement, the breakpoints of PLP1 duplications have been reported not to cluster, yielding duplicated genomic segments of varying lengths. This suggests a distinct molecular mechanism underlying PLP1 duplication events. To determine whether structural features of the genome also facilitate PLP1 duplication events, we analyzed extensively the genomic architecture of the PLP1 region and defined several novel LCRs (LCR-PMDs). Array comparative genomic hybridization showed that PLP1 duplication sizes differed, but revealed a subgroup of patients with apparently similar PLP1 duplication breakpoints. Pulsed-field gel electrophoresis analysis using probes adjacent to the LCR-PMDs detected unique recombination-specific junction fragments in 12 patients, enabled us to associate the LCR-PMDs with breakpoint regions, and revealed rearrangements inconsistent with simple tandem duplications in four patients. Two-color fluorescence in situ hybridization was consistent with directly oriented duplications. Our study provides evidence that PLP1 duplication events may be stimulated by LCRs, possibly non-homologous pairs at both the proximal and distal breakpoints in some cases, and further supports an alternative role of genomic architecture in rearrangements responsible for genomic disorders.

Base Sequence↗