Modular control of human walking: Adaptations to altered mechanical demands

Studies have suggested that the nervous system may adopt a control scheme in which synergistic muscle groups are controlled by common excitation patters, or modules, to simplify the coordination of movement tasks such as walking. A recent computer modeling and simulation study of human walking using experimentally derived modules as the control inputs provided evidence that individual modules are associated with specific biomechanical subtasks, such as generating body support and forward propulsion. The present study tests whether the modules identified during normal walking could produce simulations of walking when the mechanical demands were substantially altered. Walking simulations were generated that emulated human subjects who had their body weight and/or body mass increased and decreased by 25%. By scaling the magnitude of five module patterns, the simulations could emulate the subjects’ response to each condition by simply scaling the mechanical output from modules associated with specific biomechanical subtasks. Specifically, the modules associated with providing body support increased (decreased) their contribution to the vertical ground reaction force when body weight was increased (decreased) and the module associated with providing forward propulsion increased its contribution to the positive anterior–posterior ground reaction force and positive trunk power when the body mass was increased. The modules that contribute to controlling leg swing were unaffected by the perturbations. These results support the idea that the nervous system may use a modular control strategy and that flexible modulation of module recruitment intensity may be sufficient to meet large changes in mechanical demand.     

Is a Persistent Global Bias Necessary for the Establishment of Planar Cell Polarity?

Planar cell polarity (PCP)–the coordinated polarisation of a whole field of cells within the plane of a tissue–relies on the interaction of three modules: a global module that couples individual cellular polarity to the tissue axis, a local module that aligns the axis of polarisation of neighbouring cells, and a readout module that directs the correct outgrowth of PCP-regulated structures such as hairs and bristles. While much is known about the molecular components that are required for PCP, the functional details of–and interactions between–the modules remain unclear. In this work, we perform a mathematical and computational analysis of two previously proposed computational models of the local module (Amonlirdviman et al., Science, 307, 2005; Le Garrec et al., Dev. Dyn., 235, 2006). Both models can reproduce wild-type and mutant phenotypes of PCP observed in the Drosophila wing under the assumption that a tissue-wide polarity cue from the global module persists throughout the development of PCP. We demonstrate that both models can also generate tissue-level PCP when provided with only a transient initial polarity cue. However, in these models such transient cues are not sufficient to ensure robustness of the resulting cellular polarisation.     

Dynamic-module redundancy confers robustness to the gene regulatory network involved in hair patterning of Arabidopsis epidermis

Redundancy among dynamic modules is emerging as a potentially generic trait in gene regulatory networks. Moreover, module redundancy could play an important role in network robustness to perturbations. We explored the effect of dynamic-module redundancy in the networks associated to hair patterning in Arabidopsis root and leaf epidermis. Recent studies have put forward several dynamic modules belonging to these networks. We defined these modules in a discrete dynamical framework that was previously reported. Then, we addressed whether these modules are sufficient or necessary for recovering epidermal cell types and patterning. After defining two quantitative estimates of the system's robustness, we also compared the robustness of each separate module with that of a network coupling all the leaf or root modules. We found that, considering certain assumptions, all the dynamic modules proposed so far are sufficient on their own for pattern formation, but reinforce each other during epidermal development. Furthermore, we found that networks of coupled modules are more robust to perturbations than single modules. These results suggest that dynamic-module redundancy might be an important trait in gene regulatory networks and point at central questions regarding network evolution, module coupling, pattern robustness and the evolution of development.     

Module demography does not mirror differentiation among populations of Stellaria longipes along an elevational gradient

Available evidence suggests that vegetative and reproductive plant growth should decrease with climatic severity. This was tested first with observations of Stellaria longipes ramets established naturally along an 1100 m gradient of elevation in the Rocky Mountains of Southern Canada, and secondly with ramets collected from the same sites but grown in climate-controlled cabinets under long warm days. Growth cabinet plants yielded three times as many new modules and biomass, at a rate twice as fast as that of field plants. In addition the mortality of field-grown modules was approximately 40 times that of growth cabinet plants. This points to a very high `cost' of living in a natural environment. Contrary to anticipated results, the considerable change in habitat generated by the gradient in elevation was not matched by an equally dramatic gradient in vegetative or reproductive module growth in the field. Plants grown in cabinets also failed to show any clinal trends in module growth. Measures of vegetative module growth, such as rate of module accumulation and biomass per module, were generally conserved among sites. By contrast, production of reproductive modules was highly variable, both within and among sites. The failure to predict module behaviour from climatic severity may have been caused by unanticipated complexities of the gradient such as soil moisture and soil pH which were distributed independently of elevation. On the other hand, differentiation in growth among ecotypes along the gradient may be explained by changes in the characteristics of individual modules, not the demography of the modules that make up the plants.     

Host discrimination in modular mutualisms: a theoretical framework for meta-populations of mutualists and exploiters

Plants in multiple symbioses are exploited by symbionts that consume their resources without providing services. Discriminating hosts are thought to stabilize mutualism by preferentially allocating resources into anatomical structures (modules) where services are generated, with examples of modules including the entire inflorescences of figs and the root nodules of legumes. Modules are often colonized by multiple symbiotic partners, such that exploiters that co-occur with mutualists within mixed modules can share rewards generated by their mutualist competitors. We developed a meta-population model to answer how the population dynamics of mutualists and exploiters change when they interact with hosts with different module occupancies (number of colonists per module) and functionally different patterns of allocation into mixed modules. We find that as module occupancy increases, hosts must increase the magnitude of preferentially allocated resources in order to sustain comparable populations of mutualists. Further, we find that mixed colonization can result in the coexistence of mutualist and exploiter partners, but only when preferential allocation follows a saturating function of the number of mutualists in a module. Finally, using published data from the fig–wasp mutualism as an illustrative example, we derive model predictions that approximate the proportion of exploiter, non-pollinating wasps observed in the field.     

Growth of clonal modules on <i>Agropyron michnoi</i> in the Songnen Plain of Northeast China

Spatial expansion of clonal plants and growth of their modules are of concern in the field of plant ecology. After measuring a large number of samples, we analyzed the module components and the growth patterns of vegetatively propagated Agropyron michnoi clones in the Songnen Plain on Northeast China. The results showed that the plasticity of clonal growth was large; the coefficients of variation of both extensive areas and the quantitative characters of modules were more than 20%. The numbers of ramets, seedlings, and buds and the cumulative length of the rhizomes showed exponentially and linearly increasing patterns with increases of the area and the total number of modules. The biomass of each module, total number of modules and total biomass showed an allometric growth pattern, which was best described by power functions. For A. michnoi, there was a relatively stable investment to sexual reproduction; it showed a priority for allocating biomass to reproductive ramets, and also to rhizomes and buds formation.     

Domain structure and domain-domain interactions in the carboxy-terminal heparin binding region of fibronectin.

The domain structures and stabilities of fragments isolated from the so-called 'hep 2' region of plasma fibronectin have been investigated by differential scanning calorimetry (DSC) and fluorescence spectroscopy. The 30 kDa hep-2A fragment contains three type III modules (III12 to III14), whereas the 40 kDa hep-2B fragment contains four such modules (III12 to III15). Melting of these fragments at neutral pH was irreversible and accompanied by rapid aggregation. In contrast, melting was completely reversible in 50 mM-glycine at pH 2.7, where DSC measurements revealed the presence of three independently folded domains in 30kDa hep-2A and four in 40 kDa hep-2B. That each domain represented a single module was confirmed by measurements with four single-module subfragments, all of which melted reversibly, even at neutral pH. At neutral pH in the presence of 6 M-urea, 30 kDa hep-2A melted reversibly in a sharp peak from which only two transitions could be resolved by deconvolution. Only the larger of these was stabilized by heparin and was assigned to modules III13 and III14. Upon isolation, module III13 melted at lower temperature than in the parent fragment where it is stabilized through an interaction with module III14. We conclude that all type III modules in the hep-2 region of fibronectin constitute independently folded domains. Modules III13 and III14 form a highly co-operative structure through functionally significant interactions that can be disrupted with acid or sufficient concentrations of urea or guanidinium chloride.     

Solution structure of a pair of modules from the gelatin-binding domain of fibronectin

BACKGROUND: Fibronectin has a role in vital physiological processes such as cell migration during embryogenesis and wound healing. It mediates the attachment of cells to extracellular matrices that contain fibrous collagens. The affinity of fibronectin for native collagen and denatured collagen (gelatin) is located within a 42 kDa domain that contains four type 1 (F1) and two type 2 (F2) modules. A putative ligand-binding site has been located on an isolated F2 module, but the accessibility of this site in the intact domain is unknown. Thus, structural studies of module pairs and larger fragments are required for a better understanding of the interaction between fibronectin and collagen. RESULTS: The solution structure of the 101-residue 6F1 1F2 module pair, which has a weak affinity for gelatin, has been determined by multidimensional NMR spectroscopy. The tertiary structures determined for each module conform to the F1 and F2 consensus folds established previously. The experimental data suggest that the two modules interact via a small hydrophobic interface but may not be tightly associated. Near-random-coil 1H NMR chemical shifts and fast dynamics for backbone atoms in the linker indicate that this region is unlikely to be involved in the overall stabilisation of the module pair. CONCLUSIONS: The modules in the 6F1 1F2 module pair interact with each other via a flexible linker and a hydrophobic patch, which lies on the opposite side of the 1F2 module to the putative collagen-binding site. The intermodule interaction is relatively weak and transient.     

The X6 "thermostabilizing" domains of xylanases are carbohydrate-binding modules: structure and biochemistry of the Clostridium thermocellum X6b domain

Many polysaccharide-degrading enzymes display a modular structure in which a catalytic module is attached to one or more noncatalytic modules. Several xylanases contain a module of previously unknown function (termed "X6" modules) that had been implicated in thermostability. We have investigated the properties of two such "thermostabilizing" modules, X6a and X6b from the Clostridium thermocellumxylanase Xyn10B. These modules, expressed either as discrete entities or as their natural fusions with the catalytic module, were assayed, and their capacity to bind various carbohydrates and potentiate hydrolytic activity was determined. The data showed that X6b, but not X6a, increased the activity of the enzyme against insoluble xylan and bound specifically to xylooligosaccharides and various xylans. In contrast, X6a exhibited no affinity for soluble or insoluble forms of xylan. Isothermal titration calorimetry revealed that the ligand-binding site of X6b accommodates approximately four xylose residues. The protein exhibited K(d) values in the low micromolar range for xylotetraose, xylopentaose, and xylohexaose; 24 microM for xylotriose; and 50 microM for xylobiose. Negative DeltaH and DeltaS values indicate that the interaction of X6b with xylooligosaccharides and xylan is driven by enthalpic forces. The three-dimensional structure of X6b has been solved by X-ray crystallography to a resolution of 2.1 A. The protein is a beta-sandwich that presents a tryptophan and two tyrosine residues on the walls of a shallow cleft that is likely to be the xylan-binding site. In view of the structural and carbohydrate-binding properties of X6b, it is proposed that this and related modules be re-assigned as family 22 carbohydrate-binding modules.     

A second generation microcomputer controlled binding system for alpine skiing research

In the study of sports biomechanics, alpine skiing injuries have always demanded significant attention. In order to aid in understanding the loading phenomena associated with alpine skiing, a new research binding system has been designed which enables both the recording of boot loading data and actively controlled release of the skier's boot from the ski. The new research binding system consists of three hardware components, a dynamometer which senses all six load components at the boot/ski interface, an electromechanical device capable of releasing the boot from the ski, and a new general purpose microprocessor-based data acquisition and release control module. Constructed integrally with the dynamometer, the release mechanism is activated by electrical command from the control module. The mechanical and electrical design features of the dynamometer/release mechanism as well as important features of the hardware and software of the data acquisition and control module are briefly discussed. The system has been tested both in the laboratory and on the ski slopes. The emphasis of this paper is on the boot loading data acquired through field testing and observations on the loading environment during common recreational skiing maneuvers. Through analysis of the data, insight into both the style and safety aspects of alpine skiing is gained.     

Positive and negative cooperativity of modularly assembled zinc fingers

One simple and widespread method to create engineered zinc fingers targeting the desired DNA sequences is to modularly assemble multiple finger modules pre-selected to recognize each DNA triplet. However, it has become known that a sufficient DNA binding affinity is not always obtained. In order to create successful zinc finger proteins, it is important to understand the context-dependent contribution of each finger module to the DNA binding ability of the assembled zinc finger proteins. Here, we have created finger-deletion mutants of zinc finger proteins and examined the DNA bindings of these zinc fingers to clarify the contributions of each finger module. Our results indicate that not only a positive cooperativity but also a context-dependent reduction in the DNA binding activity can be induced by assembling zinc finger modules.     

MEGO: gene functional module expression based on gene ontology

Existing analysis tools to study the collective properties of gene functional modules cannot return highly homogeneous modules and do not provide quantitative measures of module activity level. By partitioning genes according to multiple gene functional categorization principles and summarizing gene expression values into module expression values, MEGO (module expression based on gene ontology), a standalone microarray data analysis program, is able to extract highly activated gene functional modules that are of much interest to microarray experimenters. With multiple functional categorization principles simultaneously introduced in MEGO, the partition of genes is more delicate, and the collective property of a group of genes is sharpened and easier to capture. The quantitative measures of module activity levels returned by MEGO give users a quick impression of the direction and degree of module regulation. MEGO efficiently determines the answers to frequently asked questions, such as which functional classes have been induced or repressed under a specific experiment and to which levels these functional classes have been affected. MEGO is available free of charge for academic use and may be downloaded from http://www.dxy.cn/mego/MEGOInstall.EXE. Supplementary information can be found on the authors' web page at http://www.dxy.cn/mego/ and at the BioTechniques' web site at http://www. BioTechniques.com/February2005/TuSupplementary.html.     

Geometrical model of spiral-cyclical self-organization of morphofunctional modules with two-dimensional (2D) transfer channels

The general model of spiral-cyclic self-organization of morphofunctional modules has been studied with the help of elliptic Riemannian geometry. Depending on the level of hierarchy cells, groups of cells, macromolecules or subcellular components can function as separate biological units. The hierarchically coordinated morphofunctional modules of biological pattern with two-dimensional (2D) channels of morphogenes transfer are formed in the process of geometric transformation. The width of 2D channel is regulated by module parameters, whereas the direction of transport is controlled by vector of module electrostatic field. The disturbance of morphogenesis in the model is regarded as a change of reciprocal hierarchically coordinated arrangement of morphofunctional modules that causes branching of 2D channels without general power- and mass transfer. The model can be used for constructing concrete analogies of self-organization of morphofunctional modules in onto- and phylogenesis.     

Localization of hydrogen-bonds within modules in barnase

Proteins in eukaryotes are composed of structural units, each encoded by discrete exons. The protein module is one such structural unit; it has been defined as the least extended or the most compact contiguous segment in a globular domain. To elucidate roles of modules in protein evolution and folding, we examined roles of hydrogen bonds and hydrophobic cores, as related to the stability of these modules. For this purpose we studied barnase, a bacterial Rnase from Bacillus amylolique-faciens. Barnase is decomposed into at least six modules, M1–M6; the module boundaries are identified at amino acid residues 24, 52, 73, 88, and 98. Hydrogen bonds are localized mainly within each of the modules, with only a few between them, thereby indicating that their locations are designed to primarily stabilize each individual module. To obtain support for this notion, an analysis was made of hypothetical modules defined as segments starting at a center of one module and ending at the center of the following one. We found that the hydrogen bonds did not localize in each hypothetical module and that many formed between the hypothetical modules. The native conformations of modules of barnase may be specified predominantly by interactions within the modules. © 1993 Wiley-Liss, Inc.     

Enhancing biological relevance of a weighted gene co-expression network for functional module identification

Relationships among gene expression levels may be associated with the mechanisms of the disease. While identifying a direct association such as a difference in expression levels between case and control groups links genes to disease mechanisms, uncovering an indirect association in the form of a network structure may help reveal the underlying functional module associated with the disease under scrutiny. This paper presents a method to improve the biological relevance in functional module identification from the gene expression microarray data by enhancing the structure of a weighted gene co-expression network using minimum spanning tree. The enhanced network, which is called a backbone network, contains only the essential structural information to represent the gene co-expression network. The entire backbone network is decoupled into a number of coherent sub-networks, and then the functional modules are reconstructed from these sub-networks to ensure minimum redundancy. The method was tested with a simulated gene expression dataset and case-control expression datasets of autism spectrum disorder and colorectal cancer studies. The results indicate that the proposed method can accurately identify clusters in the simulated dataset, and the functional modules of the backbone network are more biologically relevant than those obtained from the original approach.