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Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter.

We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends split the IGS into domains of common but different helical features. Local parameters at inter-domain junctions exhibit a high variability with respect to intrinsic curvature, bendability and thermal stability. Secondly, the repeated sequence blocks of the IGS exhibit right-handed supercoiled structures which could be related to their enhancer properties. Thirdly, the gene promoter presents both inherent curvature and minor groove narrowing which may be viewed as motifs of a structural code for protein recognition and binding. Such pre-existing deformations could simply be remodeled during the binding of the transcription complex. Alternatively, these deformations could pre-shape the promoter in such a way that further remodeling is facilitated. Mutations shown to abolish promoter curvature as well as intrinsic minor groove narrowing, in a variant which maintained full transcriptional activity, bring circumstantial evidence for structurally-preorganized motifs in relation to transcription regulation and promotion. Using well documented X. laevis rDNA regulatory sequences we showed that computer modeling may be of invaluable assistance in assessing encrypted architectural motifs. The evidence of these DNA topological motifs with respect to the concept of structural code is discussed.

Animals↗

An architectural role of the Escherichia coli chromatin protein FIS in organising DNA.

The Escherichia coli chromatin protein FIS modulates the topology of DNA in a growth phase-dependent manner. In this study we have investigated the global effect of FIS binding on DNA architecture in vitro. We show that in supercoiled DNA molecules FIS binds at multiple sites in a non-random fashion and increases DNA branching. This global DNA reshaping effect is independent of the helical phasing of FIS binding sites. We propose, in addition to the previously inferred stabilisation of tightly bent DNA microloops in the upstream regions of certain promoters, that FIS may perform the distinct architectural function of organising branched plectonemes in the E.coli nucleoid.

Carrier Proteins↗

Working memory for sign language: a window into the architecture of the working memory system.

Traditionally, working memory has been divided into two major domains: verbal and visuo-spatial. The verbal domain of working memory can be characterized either by its relationship to language or by its grounding in auditory processing. Because of this ambiguity, languages that are not auditory and vocal (i.e., signed languages) pose a challenge to this conception of working memory. We describe several experiments with deaf users of American Sign Language (ASL) that explore the extent to which the architecture of working memory is determined by the constraints of auditory and visual processing and the extent to which it is determined by the characteristics of language. Various working memory effects were investigated: phonological similarity, word length, and articulatory suppression. The pattern of evidence strongly supports the existence of a sign-based 'rehearsal loop' mechanism parallel to the speech-based rehearsal loop. However, we also discuss evidence pointing to differences between the speech loop and the sign loop from forward and backward digit span tasks with deaf and hearing subjects. Despite their similarities based on linguistic properties, the speech loop and the sign loop appear to diverge due to the differing processing demands of audition and vision. Overall, the results suggest that the architecture of working memory is shaped both by the properties of language structure and by the constraints imposed by sensorimotor modality.

Journal Article↗

Cytoskeleton in vitro: preparation of isolated cytoskeletons with three-dimensional architecture.

Cytoskeletons with three-dimensional architecture were isolated from cultured normal rat kidney cells. The preparation procedure consisted of Triton-demembranization of suspended cells followed by differential and sucrose density gradient centrifugation. By using higher (0.5%) and lower (0.1%) Triton concentrations for demembranization, two kinds of isolated cytoskeletons (CSK), called H-CSK and L-CSK, respectively, were prepared. H-CSK and L-CSK displayed unique morphology and protein composition. Three classes of cytoskeletal filaments, microfilaments, intermediate filaments, and microtubules were shown to be major components in the electron microscopic images of the H-CSK. Stereoscopic electron microscopy of the H-CSK, dried by the critical point method, revealed that the cytoskeletal filaments are arranged in three-dimensional configurations even after isolation in vitro. Two-dimensional gel electrophoresis demonstrated that the H-CSK was composed mainly of actin, tubulin, and vimentin, reflecting its basic architecture. Electron microscopic images of L-CSK were more intricate than images of the H-CSK and showed, in addition to the filament types discussed above, anastomosing networks of short filamentous structures. These short filaments, with diameters of 3-8 nm and lengths of 30-150 nm, seemed to cross-link other elements of the cytoskeleton. The morphology of these short filaments resembles that of microtrabeculae observed in situ. Two-dimensional gels of the L-CSK showed over 100 protein spots when the gels were stained by the silver method. Subsequent treatment of the L-CSK with 0.5% Triton removed the microtrabeculae-like materials leaving as a residue the basic cytoskeleton similar to the H-CSK. Our observations indicate that microtrabeculae are composed of heterogenous proteins associated, in some instances, with a core structure of actin.

Animals↗

Microinjection methods for visualization of the vascular architecture of the mouse embryo for light and scanning electron microscopy.

Injection of certain materials into blood vessels enables three dimensional visualization of vascular architecture and has provided abundant information which is not available by reconstruction of serial sections. By injection methods, the vascular architecture can be visualized either with scanning electron microscopy (SEM) after injection of resin and tissue digestion or with light microscopy (LM) after injection of barium sulfate and tissue clearing. The author has successfully observed whole blood vessels of 13.5-18.5 day mouse embryos using the collodion cast method in SEM. In mouse embryos younger than 12.5 embryonic days, a part, not whole, of blood vessels was obtained using cast colloiding. When the X-ray contrast medium was injected, the whole vasculature of the 9.5 day embryo was elucidated with LM, and the backscattered electron image and the secondary electron image of the identical area in the lung alveolar capillaries of the 17.5 day embryo were obtained with SEM, which showed the spatial relationship between the capillaries and their circumferential cells three dimensionally. Cast and injection methods are reviewed with respect to their application for investigating the development of mouse embryo.

Animals↗

Action of xyloglucan hydrolase within the native cell wall architecture and its effect on cell wall extensibility in azuki bean epicotyls.

Xyloglucan hydrolase (XGH) has recently been purified from the cell wall of azuki bean (Vigna angularis Ohwi et Ohashi) epicotyls as a new type of xyloglucan-degrading enzyme [Tabuchi et al. (2001) Plant Cell Physiol. 42: 154]. In the present study, the effects of XGH on the mechanical properties of the cell wall and on the level and the molecular size of xyloglucans within the native wall architecture were examined in azuki bean epicotyls. When the epidermal tissue strips from the growing regions of azuki bean epicotyls were incubated with XGH, the mechanical extensibility of the cell wall dramatically increased. XGH exogenously applied to cell wall materials (homogenates) or epidermal tissue strips decreased the amount of xyloglucans via the solubilization of the polysaccharides. Also, XGH substantially decreased the molecular mass of xyloglucans in both materials. These results indicate that XGH is capable of hydrolyzing xyloglucans within the native cell wall architecture and thereby increasing the cell wall extensibility in azuki bean epicotyls.

Biomechanical Phenomena↗

Sleep architecture and continuity measures of neonates with chronic lung disease.

Electroencephalographic (EEG) sleep studies of 25 preterm neonates with chronic lung disease (CLD) corrected to a fullterm postconceptional age were compared with recordings from two groups of neonates without CLD: a fullterm appropriate for gestational age group (9 patients) and a preterm group studied at a corrected term postconceptional age (15 patients). Electrographic/polygraphic studies were obtained using 21-channel EEG recordings. Scores were tabulated based on minute-by-minute visual analyses of sleep state, number and duration of arousals, body movements and rapid eye movements (REM). A significant reduction in the percentage of active sleep was noted in the CLD group compared to both control groups (31.15% vs. 47.01% and 52.9%, respectively). The mean percentage of indeterminate sleep was significantly increased in the study group as compared to both control groups (31.23% vs. 15.18% and 11.5%). In addition, significant differences were noted between the CLD group and the healthy preterm control group with respect to the number (0.29/minute vs. 0.13/minute) and duration (4.8 seconds vs. 2.94 seconds) of arousals as well as the total number of body movements (1.57/minute vs. 0.74/minute). These data suggest that neurophysiological organization of the immature brain, as reflected in neonatal sleep architecture and continuity measures, is adversely affected in neonates with CLD. EEG sleep architecture and continuity measures may be helpful in predicting the longitudinal outcome of infants with CLD as this group is at risk for adverse neurodevelopmental outcome.

Cerebral Cortex↗

A pilot study on the effects of sodium oxybate on sleep architecture and daytime alertness in narcolepsy.

STUDY OBJECTIVES: To measure the effect of nocturnal sodium oxybate administration on sleep architecture in patients with narcolepsy. DESIGN: Open-label study. SETTING: Four accredited sleep clinics. PARTICIPANTS: 25 adult patients with narcolepsy-cataplexy. INTERVENTIONS: Patients were weaned from previously used anticataplectic medications and administered increasing nightly doses of sodium oxybate over a 10-week period: 4.5 g for 4 weeks, 6 g for 2 weeks, 7.5 g for 2 weeks, and 9 g for 2 weeks. The effect of sodium oxybate was measured using nocturnal polysomnograms, the Epworth Sleepiness Scale, the Maintenance of Wakefulness Test, and a narcolepsy symptoms questionnaire. RESULTS: The nightly administration of sodium oxybate produced dose-related increases in slow-wave sleep and delta power, rapid eye movement sleep increased initially and then decreased in a dose-related manner, nocturnal awakenings decreased, and daytime sleep latency increased. Significant improvements in daytime symptoms were measured by the Maintenance of Wakefulness Test, the Epworth Sleepiness Scale, and the narcolepsy symptom questionnaire. CONCLUSIONS: Nocturnal administration of sodium oxybate in patients with narcolepsy produces significant improvements in sleep architecture, which coincide with significant improvements in daytime functioning.

Adjuvants, Anesthesia↗

Bruxism in children: effect on sleep architecture and daytime cognitive performance and behavior.

STUDY OBJECTIVES: Sleep bruxism is an involuntary mandibular movement with tooth grinding during sleep. The prevalence of sleep bruxism in children is high and may lead to frequent arousals with altered daytime functioning. We investigated the sleep architecture, the incidence of gastroesophageal reflux, and the daytime cognitive behavioral functioning in a group of children with sleep bruxism. DESIGN-PATIENTS: This prospective pilot study included 10 children. Polysomnographic data with pH-probe analysis was compared with 10 age- and sex-matched controls. Each patient completed a dental evaluation, a nighttime polysomnogram, and cognitive behavioral tests (Kaufman Brief Intelligence Test and Achenbach Child Behavior Checklist). RESULTS: Eight of 10 children had clinically significant bruxism and the 2 remaining patients had recent teeth exfoliation. There was no difference on sleep architecture between patients and controls, except for a higher arousal index for the bruxism group (36.7 vs 20.7, p < .007). Sleep bruxism occurred more frequently in stage 2 and rapid eye movement sleep, with arousals in 66% of the cases. There was no relationship of bruxism to gastroesophageal reflux or intelligence. However, 40% of the patients had elevated scores on the Achenbach Child Behavior Checklist, indicating significant attention and behavior problems, and there were moderate correlations between the arousal index and several of the behavior-problem scales from the Achenbach Child Behavior Checklist (0.5 to 0.6). CONCLUSIONS: The data suggest that children with bruxism have a higher arousal index, which may be associated with an increased incidence of attention-behavior problems. Future studies investigating pediatric sleep bruxism will need to focus on behavior issues that may be prevalent in this population.

Adolescent↗

Patterns of hydraulic architecture and water relations of two tropical canopy trees with contrasting leaf phenologies: Ochroma pyramidale and Pseudobombax septenatum.

Many authors have attempted to explain the adaptive response of tropical plants to drought based on studies of water relations at the leaf level. Little attention has been given to the role of the xylem system in the control of plant water requirements. To evaluate this role, we studied the hydraulic architecture and water relations parameters of two tropical canopy trees with contrasting leaf phenologies: deciduous Pseudobombax septenatum (Jacq.) Dug and evergreen Ochroma pyramidale (Cav. ex lamb) Urban, both in the family Bombacaceae. The hydraulic architecture parameters studied include hydraulic conductivity, specific conductivity, leaf specific conductivity, and Huber value. Water relations parameters include leaf water potential, stem and leaf water storage capacitance, transpiration, stomatal conductance, and vulnerability of stems to cavitation and loss of hydraulic conductivity by embolisms. Compared to temperate trees, both species showed a pattern of highly vulnerable stems (50% loss of conductivity due to embolism at water potentials less than 1 MPa) with high leaf specific conductivities. The vulnerability of xylem to water-stress-induced embolism was remarkably similar for the two species but the leaf specific conductivity of petioles and leaf-bearing stems of the evergreen species, Ochroma (e.g., 9.08 and 11.4 x 10(-4) kg s(-1) m(-1) MPa(-1), respectively), were 3.4 and 2.3 times higher, respectively, than those of the deciduous species, Pseudobombax (e.g., 2.64 and 5.15 x 10(-4) kg s(-1) m(-1) MPa(-1), respectively). A runaway embolism model was used to test the ability of Ochroma and Pseudobombax stems to maintain elevated transpiration rates during the higher evaporative demand of the dry season. The percent loss of leaf area predicted by the runaway embolism model for stems of Pseudobombax ranged from 5 to 30%, not enough to explain the deciduous phenology of this tree species without analysis of root resistance or leaf and petiole vulnerability to embolism.

Journal Article↗

Geographical variation in water relations, hydraulic architecture and terpene composition of Aleppo pine seedlings from Italian provinces.

Ecotypic variations in leaf conductance, soil-to-leaf hydraulic conductance, components of tissue water potential, hydraulic architecture parameters and xylem embolism were examined in greenhouse-grown two-year-old Aleppo pine (Pinus halepensis Mill.) seedlings from six origins representing the geographic range of the species in Italy. Cortical resin composition of the seedlings was also determined. Measurements were made on well-watered seedlings and on seedlings subjected to recurring severe drought. Drought-stressed seedlings had lower mean leaf conductances, transpiration rates and soil-to-leaf hydraulic conductances than well-watered seedlings. They also exhibited more negative osmotic potentials, higher relative water deficit at incipient plasmolysis, but a similar maximum modulus of elasticity. Drought-stressed seedlings showed a higher degree of xylem embolism, a lower Huber value, lower leaf specific conductivity and lower specific conductivity than well-watered seedlings. Drought-stressed seedlings of provenances from more xeric habitats (Tremiti, Porto Pino and Mottola) had greater leaf conductances, transpiration rates and soil-to-leaf hydraulic conductances than drought-stressed seedlings of provenances from more mesic habitats (Imperia, Otricoli and Vico del Gargano). They also showed higher osmotic adjustment and a lower degree of xylem embolism. Among provenances, there were no significant differences in hydraulic architecture parameters in response to the drought treatment; however, Tremiti and Porto Pino seedlings displayed smaller drought-induced reductions in specific conductivity and leaf specific conductivity, respectively, than seedlings from other provenances. These differences suggest that seedlings from xeric provenances, especially Tremiti, have greater resistance to desiccation than seedlings from mesic provenances. No clear association was found between terpene variability and the other traits investigated, although terpene composition was related to the geographical distribution of the provenances. We conclude that the drought-tolerance responses of Tremiti make it a more suitable provenance than the others for establishment on sites prone to severe soil water deficits.

Journal Article↗

Relationships between hydraulic architecture and leaf photosynthetic capacity in nitrogen-fertilized Eucalyptus grandis trees.

We compared the effects of nitrogen fertilization on shoot hydraulic architecture and leaf photosynthetic properties of Eucalyptus grandis Hill ex Maiden trees in Hawaii. It was hypothesized that water transport capacity would adjust to nutrient availability, with leaf specific hydraulic conductivity (kl) increasing in fertilized trees in coordination with higher photosynthetic capacity per unit leaf area. Trees were grown from seedlings in the field for 10 months at four rates of nitrogen (N) fertilization between 0 and 336 kg x ha(-1). Leaf water potentials, photosynthetic capacity and kl were measured before whole shoots were harvested to determine total growth, leaf area and sapwood density. Mean tree height increased from 4 to 5.3 m, stem basal area increased from 27 to 67 cm2 and total leaf area increased from 15 to 40 m2 between the lowest and highest rates of fertilizer addition. When trees were compared on the basis of leaf nitrogen per unit area (N(area)), light-saturated rates of photosynthesis on an area and mass basis and the maximum rate of electron transport all increased from 50% to more than 100% as N(area) increased from 0.8 to 2.1 g x m(-2). Branch specific hydraulic conductivity (ks) and kl increased with height in the crown. However, there was no change in branch kl or the ratio of leaf area to sapwood area of the whole shoot in response to fertilization, and ks and density of the sapwood were unrelated to leaf N(area). In contrast to photosynthesis, stomatal conductance did not respond to fertilization, leading to decreased internal carbon dioxide partial pressure (p(i)/p(a)) in fertilized plants and similar leaf water potentials in all plants. Consistent with the behavior of p(i)/p(a), carbon isotope discrimination decreased by 2% with increasing leaf N(area), supporting the conclusion that intrinsic water-use efficiency was enhanced by fertilization. Increased growth in response to fertilization involved adjustment at the leaf level rather than a change in the balance between water transport capacity and leaf area. It is proposed that, when there are changes in leaf properties without any external change in water availability or evaporative demand, leaf photosynthesis and stomatal conductance are partially constrained by the hydraulic architecture of the tree.

Eucalyptus↗

Shoot growth patterns in saplings of Cleyera japonica in relation to light and architectural position.

To gain further insight into crown development, the influences of shoot architectural position (branch order) and light environment on patterns of shoot growth of Cleyera japonica Thunberg (Theaceae) were investigated. Annual shoot length and light environment were positively correlated within same-order branches. Shoot length differed significantly among branch orders: shoot length was greater for the lower-order branches when light environments were comparable. Lower-order branches lengthened to a certain extent even if light availability was relatively low, whereas higher-order branches did not grow vigorously even when light availability was relatively high. Within same-order branches, branching was independent of the light environment of the shoot. Sylleptic shoot production differed significantly among branch orders, with most sylleptic shoots being produced on second-order branches. It is concluded that both light condition and architectural position of shoots must be considered when examining the mechanisms underlying crown development.

Environment↗

Hydraulic architecture correlates with bud organogenesis and primary shoot growth in beech (Fagus sylvatica).

In beech (Fagus sylvatica L.), the number of leaf primordia preformed in the buds determines the length and the type (long versus short) of annual growth units, and thus, branch growth and architecture. We analyzed the correlation between the number of leaf primordia and the hydraulic conductance of the vascular system connected to the buds. Terminal buds of short growth units and axillary buds of long growth units on lower branches of mature trees were examined. Buds with less than four and more than five leaf primordia formed short and long growth units, respectively. Irrespective of the type of growth unit the bud was formed on, the occurrence of a large number of leaf primordia was associated with high xylem hydraulic conductance. Xylem conductance was correlated to the area of the outermost annual ring. These results suggest that organogenesis and primary growth in buds correlates with secondary growth of the growth units and thus with their hydraulic architecture. Possible causal relationships between the variables are discussed.

Carbon Isotopes↗

Patterns in hydraulic architecture and their implications for transport efficiency.

We evaluated whether patterns in hydraulic architecture increase transport efficiency. Five patterns are identified: area-preserving branching; variable trunk versus twig sap velocity; distally decreasing leaf specific conductivity (K(L)) and conduit diameter; and a decline in leaf specific conductance (k(L)) of the entire plant with maturation. These patterns coexist in innumerable combinations depending on the ratio of distal/proximal conduit number (F). The model of West and colleagues does not account for this diversity, in part by specifying F = 1 and requiring a specific conduit taper derived from the incorrect premise that k(L) is constant with plant size. We used Murray's law to identify the conduit taper that maximizes k(L)for a given vascular investment. Optimal taper requires the ratio of distal/proximal conduit diameter to equal the ratio of distal/proximal K(L). The smaller these ratios, the greater the k(L). Smaller ratios are achieved by an increase in F. Conductivity and diameter ratios < 1 and F >/= 1 in plants are therefore consistent with maximizing conducting efficiency. However, the benefit of increasing F requires area-increasing conduit branching, potentially leading to mechanical instability of trees. This trade-off may explain why tree stems were relatively inefficient with F near 1 and limited conduit taper compared with vine stems or compound leaves with F > 1 and greater taper. Within trees, the anatomies of a coniferous and a diffuse-porous species were less efficient than that of a ring-porous species, presumably because the latter allows conduit area to increase distally without also increasing total xylem area. This is consistent with decelerating sap velocities from trunk to twigs in ring-porous trees versus accelerating velocities in other types. In general, the observed architectural patterns are consistent with the maximization of transport efficiency operating within mechanical constraints.

Models, Biological↗

A dynamic model for water flow in a single tree: evidence that models must account for hydraulic architecture.

A model is presented for the dynamics of water flow in a single eastern white cedar tree (Thuja occidentalis L.). The model takes into account the spatial and temporal dependence of the evaporative flux from leaves in the crown. It also accounts for the quantitative hydraulic architecture of the tree, i.e., the model characterizes the tree as a branched catena of > 4000 stem segments in which account is taken of the segment length, diameter, hydraulic resistance, and the total area of leaves attached to the segment. Input values needed to run the model are measurements of evaporative flux, hydraulic conductance of stems versus stem diameter, and leaf and stem water storage capacitances. Output parameters are the spatial and temporal characterization of stem and leaf water potentials, stem and leaf water deficits, sap flow rate, and relative sap velocity. The input and output values of the branched catena model are compared and contrasted to that of an unbranched catena model. It is shown that the branched catena model fits independently measured field parameters better than an unbranched catena model. Close correspondence is found between model predictions and field measurements of shoot water potential, pressure gradients in stems, hysteresis in sap velocity between the lower and upper parts of the tree, and diurnal changes in stem and leaf water deficits. This model is discussed in terms of both the hydraulic architecture of trees and the potential application of the model to questions of tree morphology, ecology, physiology and evolution.

Journal Article↗

Architectural distribution of foliage in individual Pinus radiata D. Don crowns and the effects of clumping on radiation interception.

The architectural arrangement and leaf area of representative branch units, on one branch complex from each cluster on the stem, were measured on six trees in a widely spaced 7-year-old Pinus radiata D. Don plantation. There was a linear relationship between leaf area and the basal area of branch complexes. Assuming similarity in the arrangement of branch units within concomitant branch complexes at each cluster, the 3-dimensional distribution of leaf area density (leaf area per unit volume) in an array of cubic cells, each 10(-3) m(3), comprising the volume of each tree crown, was reconstructed. The fraction of cells in which foliage was present varied from 0.08 to 0.23 in the crowns with the highest (Tree 4) and lowest (Tree 3) degree of clumping, respectively. This difference was related to the number, length, and leaf area per unit length of Order 3 branch units, in particular. The actual distributions of leaf area density were used with a simple radiative transfer model to estimate the probability of penetration of beam and diffuse photosynthetically active radiation (PAR) through individual tree crowns. The average probability of beam penetration was greater for the tree with the most clumped foliage than for the tree with the least clumped foliage. For both trees, the average probabilities of penetration were greater than the values that would have resulted if a random distribution of foliage had been assumed. The negative binomial model was used to estimate an index of foliage dispersion for the tree crowns. For beam PAR, the index of foliage dispersion was 3.3 and 2.3 for the trees with the most, and the least clumped foliage, respectively. These results were supported by analysis of the architectural arrangement of foliage in the tree crowns. For two days in summer, the assumption that leaf area density was randomly distributed would have resulted in a 20 to 30% overestimation of intercepted PAR flux by the tree crowns.

Journal Article↗

Molecular architecture of basement membranes.

Basement membranes are specialized extracellular matrices with support, sieving, and cell regulatory functions. The molecular architectures of these matrices are created through specific binding interactions between unique glycoprotein and proteoglycan protomers. Type IV collagen chains, using NH2-terminal, COOH-terminal, and lateral association, form a covalently stabilized polygonal framework. Laminin, a four-armed glycoprotein, self-assembles through terminal-domain interactions to form a second polymer network, Entactin/nidogen, a dumbbell-shaped sulfated glycoprotein, binds laminin near its center and interacts with type IV collagen, bridging the two. A large heparan sulfate proteoglycan, important for charge-dependent molecular sieving, is firmly anchored in the basement membrane and can bind itself through a core-protein interaction to form dimers and oligomers and bind laminin and type IV collagen through its glycosaminoglycan chains. Heterogeneity of structure and function occur in different tissues, in development, and in response to different physiological needs. The molecular architecture of these matrices may be regulated during or after primary assembly through variations in compositions, isoform substitutions, and the modifying influence of exogenous macromolecules such as heparin and heparan sulfate.

Animals↗