Specific Spatial Organization Research Articles

Davydov Splitting and Self-Organization in a Porphyrin Layer Noncovalently Attached to Single Wall Carbon Nanotubes.

We study the ability of porphyrin molecules to cooperate upon adsorption on the sp2 curved surface of carbon nanotube. We discuss the role of the phenyl substituents in the cooperativity of the functionalization reaction. Moreover, a specific spatial organization of the molecules around the nanotube is unveiled through polarization sensitive experiments. Furthermore, we observe an increase of the energy splitting of the porphyrin main transition upon the adsorption on the nanotube. This effect, interpreted as a Davydov splitting, is analyzed quantitatively using a dipole-dipole coupling model. This study demonstrates the ability of porphyrin molecules to create an organized self-assembled layer at the surface of the nanotubes where molecules are electronically coupled together.

Low-abundant species facilitates specific spatial organization that promotes multispecies biofilm formation.

Microorganisms frequently co-exist in matrix-embedded multispecies biofilms. Within biofilms, interspecies interactions influence the spatial organization of member species, which likely play an important role in shaping the development, structure and function of these communities. Here, a reproducible four-species biofilm, composed of Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus, was established to study the importance of individual species spatial organization during multispecies biofilm development. We found that the growth of species that are poor biofilm formers, M. oxydans and P. amylolyticus, were highly enhanced when residing in the four-species biofilm. Interestingly, the presence of the low-abundant M. oxydans (0.5% of biomass volume) was observed to trigger changes in the composition of the four-species community. The other three species were crucially needed for the successful inclusion of M. oxydans in the four-species biofilm, where X. retroflexus was consistently positioned in the top layer of the mature four-species biofilm. These findings suggest that low abundance key species can significantly impact the spatial organization and hereby stabilize the function and composition of complex microbiomes.

Spatial organization of the cytoskeleton enhances cargo delivery to specific target areas on the plasma membrane of spherical cells

Intracellular transport is vital for the proper functioning and survival of a cell. Cargo (proteins, vesicles, organelles, etc) is transferred from its place of creation to its target locations via molecular motor assisted transport along cytoskeletal filaments. The transport efficiency is strongly affected by the spatial organization of the cytoskeleton, which constitutes an inhomogeneous, complex network. In cells with a centrosome microtubules grow radially from the central microtubule organizing center towards the cell periphery whereas actin filaments form a dense meshwork, the actin cortex, underneath the cell membrane with a broad range of orientations. The emerging ballistic motion along filaments is frequently interrupted due to constricting intersection nodes or cycles of detachment and reattachment processes in the crowded cytoplasm. In order to investigate the efficiency of search strategies established by the cell’s specific spatial organization of the cytoskeleton we formulate a random velocity model with intermittent arrest states. With extensive computer simulations we analyze the dependence of the mean first passage times for narrow escape problems on the structural characteristics of the cytoskeleton, the motor properties and the fraction of time spent in each state. We find that an inhomogeneous architecture with a small width of the actin cortex constitutes an efficient intracellular search strategy.

Probing the Spatial Organization of Molecular Complexes Using Triple-Pair-Correlation.

Super-resolution microscopy coupled with multiplexing techniques can resolve specific spatial arrangements of different components within molecular complexes. However, reliable quantification and analysis of such specific organization is extremely problematic because it is frequently obstructed by random co-localization incidents between crowded molecular species and the intrinsic heterogeneity of molecular complexes. To address this, we present a Triple-Pair-Correlation (TPC) analysis approach for unbiased interpretation of the spatial organization of molecular assemblies in crowded three-color super-resolution (SR) images. We validate this approach using simulated data, as well as SR images of DNA replication foci in human cells. This demonstrates the applicability of TPC in deciphering the specific spatial organization of molecular complexes hidden in dense multi-color super-resolution images.

Morphological Diversity of the Rod Spherule: A Study of Serially Reconstructed Electron Micrographs.

PurposeRod spherules are the site of the first synaptic contact in the retina’s rod pathway, linking rods to horizontal and bipolar cells. Rod spherules have been described and characterized through electron micrograph (EM) and other studies, but their morphological diversity related to retinal circuitry and their intracellular structures have not been quantified. Most rod spherules are connected to their soma by an axon, but spherules of rods on the surface of the Mus musculus outer plexiform layer often lack an axon and have a spherule structure that is morphologically distinct from rod spherules connected to their soma by an axon. Retraction of the rod axon and spherule is often observed in disease processes and aging, and the retracted rod spherule superficially resembles rod spherules lacking an axon. We hypothesized that retracted spherules take on an axonless spherule morphology, which may be easier to maintain in a diseased state. To test our hypothesis, we quantified the spatial organization and subcellular structures of rod spherules with and without axons. We then compared them to the retracted spherules in a disease model, mice that overexpress Dscam (Down syndrome cell adhesion molecule), to gain a better understanding of the rod synapse in health and disease.MethodsWe reconstructed serial EM images of wild type and DscamGoF (gain of function) rod spherules at a resolution of 7 nm in the X-Y axis and 60 nm in the Z axis. Rod spherules with and without axons, and retracted spherules in the DscamGoF retina, were reconstructed. The rod spherule intracellular organelles, the invaginating dendrites of rod bipolar cells and horizontal cell axon tips were also reconstructed for statistical analysis.ResultsStereotypical rod (R1) spherules occupy the outer two-thirds of the outer plexiform layer (OPL), where they present as spherical terminals with large mitochondria. This spherule group is highly uniform and composed more than 90% of the rod spherule population. Rod spherules lacking an axon (R2) were also described and characterized. This rod spherule group consists of a specific spatial organization that is strictly located at the apical OPL-facing layer of the Outer Nuclear Layer (ONL). The R2 spherule displays a large bowl-shaped synaptic terminal that hugs the rod soma. Retracted spherules in the DscamGoF retina were also reconstructed to test if they are structurally similar to R2 spherules. The misplaced rod spherules in DscamGoF have a gross morphology that is similar to R2 spherules but have significant disruption in internal synapse organization.ConclusionWe described a morphological diversity within Mus musculus rod spherules. This diversity is correlated with rod location in the ONL and contributes to the intracellular differences within spherules. Analysis of the DscamGoF retina indicated that their R2 spherules are not significantly different than wild type R2 spherules, but that their retracted rod spherules have abnormal synaptic organization.

Genetic Variability in Island Populations of Two Rodent Species: Bank Vole (Myodes glareolus) and Yellow-Necked Mouse (Apodemus flavicollis)

We examined changes in genetic diversity in populations of two small mammal species inhabiting islands on a lake. We hypothesized that a less mobile species, such as the bank vole, would lose genetic diversity quicker than the yellow-necked mouse, which can more easily cross habitat barriers. In contrast to this we found that the effects of isolation were much more prominent in the case of the mouse than the vole. In the vole population, on the larger island, genetic diversity remained constant over subsequent years in spite of marked isolation. On the smaller island, we noted an increase in genetic diversity which was probably caused by immigration of a small group of individuals. Genetic diversity in the mouse population decreased markedly over the course of the study. In the bank vole, the preservation of genetic diversity, especially on the larger island, may have been possible due to the specific spatial and social organization of this species, which allows the maintenance of a relatively stable numb...

The role of spatial organization of cells in erythropoiesis

Erythropoiesis, the process of red blood cell production, occurs mainly in the bone marrow. The functional unit of mammalian erythropoiesis, the erythroblastic island, consists of a central macrophage surrounded by adherent erythroid progenitor cells (CFU-E/Pro-EBs) and their differentiating progeny, the erythroblasts. Central macrophages display on their surface or secrete various growth or inhibitory factors that influence the fate of the surrounding erythroid cells. CFU-E/Pro-EBs have three possible fates: (a) expansion of their numbers without differentiation, (b) differentiation into reticulocytes that are released into the blood, (c) death by apoptosis. CFU-E/Pro-EB fate is under the control of a complex molecular network, that is highly dependent upon environmental conditions in the erythroblastic island. In order to assess the functional role of space coupled with the complex network behavior in erythroblastic islands, we developed hybrid discrete-continuous models of erythropoiesis. A model was developed in which cells are considered as individual physical objects, intracellular regulatory networks are modeled with ordinary differential equations and extracellular concentrations by partial differential equations. We used the model to investigate the impact of an important difference between humans and mice in which mature late-stage erythroblasts produce the most Fas-ligand in humans, whereas early-stage erythroblasts produce the most Fas-ligand in mice. Although the global behaviors of the erythroblastic islands in both species were similar, differences were found, including a relatively slower response time to acute anemia in humans. Also, our modeling approach was very consistent with in vitro culture data, where the central macrophage in reconstituted erythroblastic islands has a strong impact on the dynamics of red blood cell production. The specific spatial organization of erythroblastic islands is key to the normal, stable functioning of mammalian erythropoiesis, both in vitro and in vivo. Our model of a simplified molecular network controlling cell decision provides a realistic functional unit of mammalian erythropoiesis that integrates multiple microenvironmental influences within the erythroblastic island with those of circulating regulators of erythropoiesis, such as EPO and glucocorticosteroids, that are produced at remote sites.

Multineuronal spike sequences repeat with millisecond precision

Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging (fMCI) technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and non-spiking neurons. Multineuronal spike sequences (MSSs) were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

Orientation-reversal VEP: Comparison of phase and peak latencies in adults and infants

The peak latency of pattern-reversal (PR)-VEP has been found to develop rapidly, reaching the adult level around 15weeks of age. However, the development of orientation-reversal (OR)-VEP, reflecting the specific spatial organization of cortical receptive fields, still remains unknown.OR-VEP was tested in 81 adults at 1–12reversals/sec (r/s) and 94 infants (age 4–79weeks) at 2–8r/s. OR data at 4r/s from an additional 123 infants (age 4.0–20.3weeks) studied previously were also analyzed. In addition to peak transient latencies at 1–4r/s, latency values derived from the gradient of phase against temporal frequency in steady-state recording were also calculated.For both adults and infants, no significant latency differences in the initial positive peaks were found among the low reversal rates. The calculated latency was statistically longer than the transient latency in both groups. While the transient latency asymptoted to adult value of 102ms at around 50weeks of age, the calculated latency, unlike that for PR-VEP, showed little variation across the age span.The data suggest a dominant effect of transmission delay on the initial peak in infancy, which reduces with age. However, the overall timing of the cortical response to orientation change remains slower than for pattern reversal in the fully developed visual cortex. Upon reaching maturity, the latencies of the initial positive peak in both pattern and orientation VEPs may arise from the same level of cortical processing in V1, but the overall time course reflected in the steady-state phase continues to show a much more prolonged response to orientation change than the transmission delay seen in the transient VEPs.

Nuclear actin depolymerization in transcriptionally active avian and amphibian oocytes leads to collapse of intranuclear structures

Actin, which is normally depleted in the nuclei of somatic cells, accumulates in high amounts in giant nuclei of amphibian oocytes. The supramolecular organization and functions of this nuclear pool of actin in growing vertebrate oocyte are controversial. Here, we investigated the role of nuclear actin in the maintenance of the spatial architecture of intranuclear structures in avian and amphibian growing oocytes. A meshwork of filamentous actin was not detected in freshly isolated or fixed oocyte nuclei of Xenopus, chicken or quail. We found that the actin meshwork inside the oocyte nucleus could be induced by phalloidin treatment. Actin polymerization is demonstrated to be required to stabilize the specific spatial organization of nuclear structures in avian and amphibian growing oocytes. In experiments with the actin depolymerizing drugs cytochalasin D and latrunculin A, we showed that disassembly of nuclear actin polymers led to chromosome condensation and their transportation to a limited space within the oocyte nucleus. Experimentally induced “collapsing” of chromosomes and nuclear bodies, together with global inhibition of transcription, strongly resembled the process of karyosphere formation during oocyte growth.

Correction: CTCF Mediates the Cell-Type Specific Spatial Organization of the Kcnq5 Locus and the Local Gene Regulation

Correction: CTCF Mediates the Cell-Type Specific Spatial Organization of the Kcnq5 Locus and the Local Gene Regulation

A unified level set based methodology for fast generation of complex microstructural multi-phase RVEs

In the frame of the multi-scale computational analysis of complex materials, the generation of Representative Volume Elements (RVE) is often a crucial step. Various microstructure generation tools may be used, depending on the material to be considered, such as Discrete Element Methods (DEM), Random Sequential Addition (RSA) based methods for particulate media requiring important computation times; or Voronoï tessellation methods for polycrystalline materials. Besides being material specific, some of these methods may become unaffordable when considering complex microstructures, large inclusions numbers or high volume fractions. The present contribution presents a unified level set based methodology for complex, periodic (or not) and random RVE generations. The presented methodology allows RVE generation for particulate granular media, polycrystalline aggregates with large size distribution and arbitrary shapes, as well as for complex three-phase or poly-phase microstructures. A level set controlled Random Sequential Addition algorithm is used for particle distribution generation, allowing increasing the RSA algorithm efficiency, generating large and dense populations of arbitrary shaped inclusions with precise control on neighboring distances. Starting from this, several methods are presented to add specific realistic features to the generated RVEs. Modifications and densifications allow the distribution pattern to fit observed real samples or to present a specific spatial organization. The addition of one (or more) phase(s) obtained from the growth of the initial inclusions allows reproducing some typical microstructural patterns such as grain bridging in clayey soils, interfacial transition zones in concrete or hydrated gel in cement paste. The versatility of the proposed RVE generation method is illustrated by means of various examples, reproducing realistic microstructural arrangements of clayey soils, irregular masonry and polycrystalline aggregates with bimodal size distributions.

Joint Inversion of Fracture Model Properties for CO2Storage Monitoring or Oil Recovery History Matching

For oil recovery or CO2 storage, “reservoirs” are commonly used to designate geological structures where oil can be found or CO2 can be stored. All reservoirs present a heterogeneity in terms of rock type and properties (such as porosity and permeability). In addition, some of these reservoirs present fractures and faults. Fractured reservoirs are an important part of the oil reserves in the world (Middle East, Gulf of Mexico, etc.) and some of them are important reservoirs in terms of oil volume and productivity in spite of the fractures. In addition, studies of reservoirs for geologic storage of CO2 have shown the existence of diffuse fractures and faults and their strong impacts on flow.A key point in fractured reservoirs is to understand the geometry and hydraulic conductivity of the network formed by the fractures. This requires the construction of a reservoir model that integrates all available conceptual knowledge and quantitative data.The topic of the present paper deals with a new methodology able to perform the history matching of a fractured reservoir model by adapting the sub-seismic fault properties and positions. The main difficulty of this work is to generate a sub-seismic fault network whose fault positions can be easily modified while respecting the statistical fault model. The sub-seismic fault model we have chosen allows us to obtain a sub-seismic fault network that is consistent with the seismic fault network and that succeeds in capturing the specific spatial organization of the faults. In a first step, the geometry of the seismic fault network is characterized using fractal methods. Sub-seismic faults are then generated according to a stochastic algorithm. Finally, the geometry of this discrete fracture network is optimized in order to match the hydrodynamic data about the reservoir. The optimization algorithm modifies the sub-seismic fault positions, leading to the history matching of the reservoir model. Fractal properties are preserved during the deformation process. These different steps are demonstrated on a realistic synthetic case.

CTCF Mediates the Cell-Type Specific Spatial Organization of the Kcnq5 Locus and the Local Gene Regulation

Chromatin loops play important roles in the dynamic spatial organization of genes in the nucleus. Growing evidence has revealed that the multivalent functional zinc finger protein CCCTC-binding factor (CTCF) is a master regulator of genome spatial organization, and mediates the ubiquitous chromatin loops within the genome. Using circular chromosome conformation capture (4C) methodology, we discovered that CTCF may be a master organizer in mediating the spatial organization of the kcnq5 gene locus. We characterized the cell-type specific spatial organization of the kcnq5 gene locus mediated by CTCF in detail using chromosome conformation capture (3C) and 3C-derived techniques. Cohesion also participated in mediating the organization of this locus. RNAi-mediated knockdown of CTCF sharply diminished the interaction frequencies between the chromatin loops of the kcnq5 gene locus and down-regulated local gene expression. Functional analysis showed that the interacting chromatin loops of the kcnq5 gene locus can repress the gene expression in a luciferase reporter assay. These interacting chromatin fragments were a series of repressing elements whose contacts were mediated by CTCF. Therefore, these findings suggested that the dynamical spatial organization of the kcnq5 locus regulates local gene expression.

Specific Spatial and Orientational Order in Phospholipid Membranes Induced by Cholesterol

Cholesterol plays a major role in formation of laterally ordered membrane structures such as lipid rafts. These domains have been found to be involved in a variety of cellular functions, implying that there is immediate interest to understand the structure as well as the dynamics of rafts, and in particular the role of cholesterol in promoting order in rafts. Nonetheless, due to the molecular scales associated with lipid rafts and the soft nature of membrane domains overall, the atomic-level mechanisms responsible for cholesterol's specific ordering capability have remained unresolved. Our atomistic simulations [1] reveal that this ordering and the associated packing effects in membranes largely result from cholesterol's molecular structure, which differentiates cholesterol from other sterols. Cholesterol molecules are found to prefer a specific spatial and orientational molecular in-plane organization, where cholesterol molecules are located in the second coordination shell, avoiding direct cholesterol-cholesterol contacts, and forming a three-fold symmetric arrangement with proximal cholesterol molecules. At larger distances, the lateral three-fold organization is broken by thermal fluctuations. Other sterols having less structural asymmetry are found to lack the three-fold arrangement that is characteristic to cholesterol.[1] H. Martinez-Seara, T. Rog, M. Karttunen, I. Vattulainen, and R. Reigada. Manuscript under review (2009).

Making scents out of how olfactory neurons are ordered in space

Many sensory brain areas are characterized by a specific spatial organization, with neurons being ordered according to their similarity in receptive field properties. A surprising new study provides evidence that the organization of glomeruli in the olfactory bulb violates this anatomical principle, suggesting that olfaction might work by a different set of rules.

Differential origin of reticulospinal drive to motoneurons innervating trunk and hindlimb muscles in the mouse revealed by optical recording

To better understand how the brainstem reticular formation controls and coordinates trunk and hindlimb muscle activity, we used optical recording to characterize the functional connections between medullary reticulospinal neurons and lumbar motoneurons of the L2 segment in the neonatal mouse. In an isolated brainstem-spinal cord preparation, synaptically induced calcium transients were visualized in individual MNs of the ipsilateral and contralateral medial and lateral motor columns (MMC, LMC) following focal electrical stimulation of the medullary reticular formation (MRF). Stimulation of the MRF elicited differential responses in MMC and LMC, according to a specific spatial organization. Stimulation of the medial MRF elicited responses predominantly in the LMC whereas stimulation of the lateral MRF elicited responses predominantly in the MMC. This reciprocal response pattern was observed on both the ipsilateral and contralateral sides of the spinal cord. To ascertain whether the regions stimulated contained reticulospinal neurons, we retrogradely labelled MRF neurons with axons coursing in different spinal funiculi, and compared the distributions of the labelled neurons to the stimulation sites. We found a large number of retrogradely labelled neurons within regions of the gigantocellularis reticular nucleus (including its pars ventralis and alpha) where most stimulation sites were located. The existence of a mediolateral organization within the MRF, whereby distinct populations of reticulospinal neurons predominantly influence medial or lateral motoneurons, provides an anatomical substrate for the differential control of trunk and hindlimb muscles. Such an organization introduces flexibility in the initiation and coordination of activity in the two sets of muscles that would satisfy many of the functional requirements that arise during postural and non-postural motor control in mammals.

The Expansions of the Pectoral Girdle Muscles onto the Brachial Fascia: Morphological Aspects and Spatial Disposition

Background/Aims: The aim of this study was to analyse the relationships between the expansions of the pectoral girdle muscles, i.e. pectoralis major, latissimus dorsi and deltoid, and the brachial fascia. Methods: Thirty shoulder specimens from 15 unembalmed adult cadavers were studied by dissection and in vivo radiological studies were performed in 20 patients using magnetic resonance (MR) imaging. Results: The clavicular part of the pectoralis major muscle sent a fibrous expansion onto the anterior portion of the brachial fascia, its costal part onto the medial portion and medial intermuscular septum. The latissimus dorsi muscle showed a triangular fibrous expansion onto the posterior portion of the brachial fascia. The posterior part of the deltoid muscle inserted muscular fibres directly onto the posterior portion of the brachial fascia, its lateral part onto the lateral portion and the lateral intermuscular septum. In MR images, the brachial fascia appeared as a low-signal-intensity sinuous line of connective tissue, sharply delineated in T₁-weighted sequences. Conclusion: The expansions of the pectoral girdle muscles onto the brachial fascia were present in all the subjects and showed a quite constant course with a specific spatial organization. During the various movements of the arm, these expansions stretch selective portions of the brachial fascia, with possible activation of specific patterns of fascial proprioceptors.

The Verny, 1887, earthquake in Central Asia: Application of the INQUA scale, based on coseismic environmental effects

The INQUA scale, based on coseismic environmental effects, appears to be a very promising tool to get long-term and reliable information on seismicity. However, it has to pass through comprehensive testing procedures. Results of the INQUA scale application to earthquake intensity calibration are presented, part of the worldwide testing of the scale. As a case study, the Verny, 1887, earthquake in Central Asia has been chosen. It was a large earthquake (felt over 2,000,000 km 2) located in a region with a specific temporal and spatial organization of seismicity. Verification of magnitudes of some large past earthquakes is important for the correct understanding of regional seismotectonics and seismic hazard assessment. The work is based on the original materials collected by the expedition soon after the earthquake in the epicentral area. It is demonstrated that assessment of epicentral intensity derived from total area of secondary environmental effects is reliable. This enables evaluation of the parameters of historical earthquakes based on generalized information of observed earthquake environmental effects (EEE). The epicentral intensity I 0 is assessed to be IX-X degrees; the highest observed local intensities are coherent with I 0 assessment.

Specific spatial organization of chromosomes in nuclei of primary human fibroblasts is maintained by nuclear matrix

Specific spatial organization of chromosomes in nuclei of primary human fibroblasts is maintained by nuclear matrix