Functional features and ontogenetic changes in reproductive allocation and partitioning strategies of plant modules

In the concept of modularity, plant modules are considered as iterative units and their changes are analyzed in terms of number or size. This paper, however, analyses changes with respect to the reproductive functional performance of modules and individual plant age. Patterns of resource allocation and partitioning in reproductive modules (fruits) are compared between two different age groups of a bushy perennial plant, Cistus ladanifer.Although modules do not differ in their allocation strategies (young plant modules produce the same seed and packing/protective structure biomass as old plant modules), their partitioning strategies change with plant age: young plant modules produce a larger number of lighter seeds than old plants. These differences have a direct consequence on the plant pre-dispersal fitness, which is not counteracted by insect predation on reproductive modules. These results are empirical evidence of a differentiation in the performance of reproductive modules with the ontogenetic development of this plant species. We think that the consideration of such kind of changes in module features is essential in the analysis of the iterative construction of plants.     

Modular organization of protein interaction networks

MOTIVATION: Accumulating evidence suggests that biological systems are composed of interacting, separable, functional modules. Identifying these modules is essential to understand the organization of biological systems. RESULT: In this paper, we present a framework to identify modules within biological networks. In this approach, the concept of degree is extended from the single vertex to the sub-graph, and a formal definition of module in a network is used. A new agglomerative algorithm was developed to identify modules from the network by combining the new module definition with the relative edge order generated by the Girvan-Newman (G-N) algorithm. A JAVA program, MoNet, was developed to implement the algorithm. Applying MoNet to the yeast core protein interaction network from the database of interacting proteins (DIP) identified 86 simple modules with sizes larger than three proteins. The modules obtained are significantly enriched in proteins with related biological process Gene Ontology terms. A comparison between the MoNet modules and modules defined by Radicchi et al. (2004) indicates that MoNet modules show stronger co-clustering of related genes and are more robust to ties in betweenness values. Further, the MoNet output retains the adjacent relationships between modules and allows the construction of an interaction web of modules providing insight regarding the relationships between different functional modules. Thus, MoNet provides an objective approach to understand the organization and interactions of biological processes in cellular systems. AVAILABILITY: MoNet is available upon request from the authors.     

Ultrafiltration of enzyme solutions by means of blood dialyzers

Hollow fibres with a symmetrical pore structure as used in artifical kidneys are tested for other purposes. The modules are shown to be suitable for the processing of enzymes such as thermitase, penicillin acylase, uratoxidase, and phosphatase by means of ultrafiltration and diafiltration. These hollow fibre modules are compared with other modules used in laboratory or in small technical devices. Similar values and material transfer coefficients are calculated.     

Prospects for the Practical Application of Substrate-Binding Modules of Glycosyl Hydrolases

The properties of substrate-binding modules of glycosyl hydrolases have been reviewed. The variation of the properties of these modules makes them promising as components of chimeric proteins, which is a rapidly developing field of biotechnology. Examples of applying substrate-binding modules of glycosyl hydrolases to the immobilization of proteins and whole cells on polysaccharides and the purification of proteins are described. Promising methods for (1) detecting various compounds using hybrids of substrate-binding modules with antibodies and (2) locating polysaccharides in live tissues are reviewed as well.     

Revealing the Hidden Relationship by Sparse Modules in Complex Networks with a Large-Scale Analysis

One of the remarkable features of networks is module that can provide useful insights into not only network organizations but also functional behaviors between their components. Comprehensive efforts have been devoted to investigating cohesive modules in the past decade. However, it is still not clear whether there are important structural characteristics of the nodes that do not belong to any cohesive module. In order to answer this question, we performed a large-scale analysis on 25 complex networks with different types and scales using our recently developed BTS (bintree seeking) algorithm, which is able to detect both cohesive and sparse modules in the network. Our results reveal that the sparse modules composed by the cohesively isolated nodes widely co-exist with the cohesive modules. Detailed analysis shows that both types of modules provide better characterization for the division of a network into functional units than merely cohesive modules, because the sparse modules possibly re-organize the nodes in the so-called cohesive modules, which lack obvious modular significance, into meaningful groups. Compared with cohesive modules, the sizes of sparse ones are generally smaller. Sparse modules are also found to have preferences in social and biological networks than others.     

Modules, kinds, and homology

Developmental modules are best conceptualized as homeostatic property cluster natural kinds. As is true in other fields of biology, an individual may instantiate properties of various natural kinds. Through their dissociability, developmental modules can be recruited to function as evolutionary modules. The proper analogy to developmental modules, atoms, or biological species depends on the scope over which specific developmental modules allow generalizations. The nature of the relationship between developmental modules, evolutionary modules, and taxic (phylogenetic) homology are explored. Similarity of gene expression patterns and developmental pathways as captured by biological homology may support hypotheses of taxic homology, but not the other way around.     

On the Classification and Evolution of Protein Modules

Our efforts to classify the functional units of many proteins, the modules, are reviewed. The data from the sequencing projects for various model organisms are extremely helpful in deducing the evolution of proteins and modules. For example, a dramatic increase of modular proteins can be observed from yeast to C. elegans in accordance with new protein functions that had to be introduced in multicellular organisms. Our sequence characterization of modules relies on sensitive similarity search algorithms and the collection of multiple sequence alignments for each module. To trace the evolution of modules and to further automate the classification, we have developed a sequence and a module alerting system that checks newly arriving sequence data for the presence of already classified modules. Using these systems, we were able to identify an unexpected similarity between extracellular C1Q modules with bacterial proteins.     

Hierarchical thinking in network biology: the unbiased modularization of biochemical networks

As reconstructed biochemical reaction networks continue to grow in size and scope, there is a growing need to describe the functional modules within them. Such modules facilitate the study of biological processes by deconstructing complex biological networks into conceptually simple entities. The definition of network modules is often based on intuitive reasoning. As an alternative, methods are being developed for defining biochemical network modules in an unbiased fashion. These unbiased network modules are mathematically derived from the structure of the whole network under consideration.     

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.     

Homologies of process and modular elements of embryonic construction

There are several signal transduction pathways that integrate embryonic development. We find that both within species and between species, these pathways constitute homologous modules. The processes, themselves, can be considered homologous, just as structures can be considered homologous. Just like vertebrate limbs, these pathways are composed of homologous parts (in this case, the proteins of the pathway) that are organized in homologous ways. These pathways are conserved through evolutionary time, and they undergo descent with modification. Such homologies of processes become critical to the discussion of evolution and development when we consider (1) that evolution depends on heritable changes in development, (2) that development is modular such that different modules can change without affecting other modules, (3) that modules can be co-opted into new functions, and (4) that modules depend on intercellular communication.     

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.     

Secondary structural features of modules M2 and M3 of barnase in solution by NMR experiment and distance geometry calculation

Proteins consist of structural units such as globular domains, secondary structures, and modules. Modules were originally defined by partitioning a globular domain into compact regions, each of which is a contiguous polypeptide segment having a compact conformation. Since modules show close correlations with the intron positions of genes, they are regarded as primordial polypeptide pieces encoded by exons and shuffled, leading to yield new combination of them in early biological evolution. Do modules maintain their native conformations in solution when they are excised at their boundaries? In order to find answers to this question, we have synthesized modules of barnase, one of the bacterial RNases, and studied the solution structures of modules M2 (amino acid residues 24–52) and M3 (52–73) by 2D NMR studies. Some local secondary structures, α-helix, and β-turns in M2 and β-turns in M3, were observed in the modules at the similar positions to those in the intact barnase but the overall state seems to be in a mixture of random and native conformations. The present result shows that the excised modules have propensity to form similar secondary structures to those of the intact barnase. © 1993 Wiley-Liss, Inc.     

Fabrication of Micro-tissues using Modules of Collagen Gel Containing Cells

This protocol describes the fabrication of a type of micro-tissues called modules. The module approach generates uniform, scalable and vascularized tissues. The modules can be made of collagen as well as other gelable or crosslinkable materials. They are approximately 2 mm in length and 0.7 mm in diameter upon fabrication but shrink in size with embedded cells or when the modules are coated with endothelial cells. The modules individually are small enough that the embedded cells are within the diffusion limit of oxygen and other nutrients but modules can be packed together to form larger tissues that are perfusable. These tissues are modular in construction because different cell types can be embedded in or coated on the modules before they are packed together to form complex tissues. There are three main steps to making the modules: (1) neutralizing the collagen and embedding cells in it, (2) gelling the collagen in the tube and cutting the modules and (3) coating the modules with endothelial cells.Download video file.^{(58M, mov)}     

The structure and function of protein modules.

Analysis of protein sequences shows that many proteins in multicellular organisms have evolved by a process of exon shuffling, deletion and duplication. These exons often correspond to autonomously folding protein modules. Many extracellular enzymes have this modular structure; for example, serine proteases involved in blood-clotting, fibrinolysis and complement. The main role of these modules is to confer specificity by protein-protein interactions. Lack of structural information about such proteins has required a new strategy for studying the structure and function of protein modules. The strategy involves the production of individual modules by protein expression techniques, determination of their structure by high resolution nuclear magnetic resonance and definition of functional patches on the modules by site-directed mutagenesis and biological assays. The structures of the growth factor module, the fibronectin type 1 module and the complement module are briefly described. The possible functional roles of modules in various proteins, including the enzymes factor IX and tissue plasminogen activator, are discussed.     

A hierarchical model of plumage: morphology,development, and evolution

Plumage is a complex component of the avian phenotype. The plumage of an individual is composed of numerous hierarchically arranged developmental and morphological modules. We present a hierarchical model of plumage that provides an intellectual framework for understanding the development and evolution of feathers. Independence, covariation, and interaction among plumage modules create numerous opportunities for developmental and evolutionary diversification of feather complexity and function. The hierarchical relationships among plumage modules are characterized by both top-down and bottom-up effects in which properties of modules at one level of the hierarchy determine or influence the properties of modules at lower or higher levels of the hierarchy. Plumage metamodules are created by covariation or interaction among modules at different levels of the hierarchy.     

All six modules of the gelatin-binding domain of fibronectin are required for full affinity

The gelatin-binding sites of fibronectin are confined to a 42-kDa region having four type I and two type II modules in the following order: I(6)-II(1)-II(2)-I(7)-I(8)-I(9). To determine the relative importance of each module for recognition of gelatin, recombinant green fluorescent fusion proteins were prepared in which individual modules or groups of modules were deleted, and the resulting proteins were tested for binding to gelatin by analytical affinity chromatography. Deletion of both type II modules did not eliminate binding, confirming that at least some of the type I modules in this region are able to bind gelatin. It was found that deletion of type I module 6 tends to increase the affinity, whereas deletion of any other module decreases it. Deletion of module I(9) had a large effect but only if module II(2) was also present, suggesting an interaction between these two noncontiguous modules. Analysis of more than 20 recombinant fusion products led to the conclusion that all modules contribute to the interaction either directly by contacting the ligand or indirectly through module-module interactions.     

Evolution of protein complexes by duplication of homomeric interactions

Background  

Cellular functions are accomplished by the concerted actions of functional modules. The mechanisms driving the emergence and evolution of these modules are still unclear. Here we investigate the evolutionary origins of protein complexes, modules in physical protein-protein interaction networks.