A conceptual framework for the study of modular responses to local environmental heterogeneity within the plant crown and a review of related concepts

Plants respond to local heterogeneity in abiotic and biotic conditions by changing module-level morphology, growth, and reproductive patterns. This paper presents a conceptual framework for the study of modular responses in plant crowns, clarifies the points that should be considered for scaling up from modular responses to the consequences at the whole-plant level, characterizes the interspecific differences in modular response patterns, and discusses their ecological significance. The modular response was defined as either autonomous or interactive, depending on whether the response of a module to its local condition is independent from the conditions of other modules. For evaluation of the autonomy of the modular response, the importance of considering positional relationships and organizational levels of modules was then proposed as these internally affect the modular response pattern, and their interspecific differences were characterized using several concepts. The identification of an autonomous modular unit is essential for scaling up module-level studies to the whole plant. For understanding the ecological significance of the modular response, further interspecific comparisons and assessments of the scale and the predictability of environmental heterogeneity are required. The conceptual framework will be useful for such purposes.     

Cost of reproduction in the perennial herb Asphodelus albus (Liliaceae)

The cost of reproduction has been studied in two populations of the polycarpic herb Asphodelus albus under natural conditions The percentage of plants with flowers was determined in four sites and varied markedly among them The occurrence of reproduction was size-dependent, increasing flowering probability with plant size The cost of reproduction was assessed in terms of modular growth in reproductive plants relative to modular growth in vegetative ones I compared the modular growth of vegetative and reproductive plants considering two different densities m each of two populations Neither incidence of flowering nor modular growth were affected by density Flowering plants exhibited a withinramet demographic cost (in terms of modular growth) relative to non-flowering ramets in one population but not in the other This cost was greater in larger plants These results were concordant with the occurrence of flowering at both sites Both populations exhibited size-dependent patterns of allocation to reproduction, but no significant relationships were found between allocation to reproduction and cost of reproduction The data presented demonstrate differences in the cost of reproduction within a species This cost might determine whether a plant begins the reproduction, but probably have no effect on the reproductive allocation since the weight of the reproductive structures was not related to modular growth     

Synergistic Structure in the Speed Dependent Modulation of Muscle Activity in Human Walking

Recently, a modular organisation has been proposed to simplify control of the large number of muscles involved in human walking. Although previous research indicates that a single set of modular activation patterns can account for muscle activity at different speeds, these studies only provide indirect evidence for the idea that speed regulation in human walking is under modular control. Here, a more direct approach was taken to assess the synergistic structure that underlies speed regulation, by isolating speed effects through the construction of gain functions that represent the linear relation between speed and amplitude for each point in the time-normalized gait cycle. The activity of 13 muscles in 13 participants was measured at 4 speeds (0.69, 1.00, 1.31, and 1.61 ms^-1) during treadmill walking. Gain functions were constructed for each of the muscles, and gain functions and the activity patterns at 1.00 ms^-1 were both subjected to dimensionality reduction, to obtain modular gain functions and modular basis functions, respectively. The results showed that 4 components captured most of the variance in the gain functions (74.0% ± 1.3%), suggesting that the neuromuscular regulation of speed is under modular control. Correlations between modular gain functions and modular basis functions (range 0.58–0.89) and the associated synergistic muscle weightings (range 0.6–0.95) were generally high, suggesting substantial overlap in the synergistic control of the basic phasing of muscle activity and its modulation through speed. Finally, the combined set of modular functions and associated weightings were well capable of predicting muscle activity patterns obtained at a speed (1.31 ms^-1) that was not involved in the initial dimensionality reduction, confirming the robustness of the presently used approach. Taken together, these findings provide direct evidence of synergistic structure in speed regulation, and may inspire further work on flexibility in the modular control of gait.     

Quantitative investigation of the modular primer effect for DNA and peptide nucleic acid hexamers

The effect on oligonucleotide-template duplex stability upon cohybridization of adjacently annealing oligonucleotides, the modular primer effect, was studied with biosensor technology. DNA and peptide nucleic acid (PNA) hexamer modules and sensor chip-immobilized template DNA strands were designed for analysis of nick, overlap, and gap modular hybridization situations. The fast hybridization kinetics for such hexamer modules allowed for the determination of apparent duplex affinities from equilibrium responses. The results showed that the hybridizational stability of modular hexamer pairs is strongly dependent on the positioning, concentration, and inherent affinity of the adjacently annealing hexamer module. Up to 80-fold increases in apparent affinities could be observed for adjacent modular oligonucleotide pairs compared to affinities determined for single hexamer oligonucleotide hybridizations. Interestingly, also for coinjections of different module combinations where DNA hexamer modules were replaced by their PNA counterparts, a modular primer effect was observed. The introduction of a single base gap between two hexamer modules significantly reduced the stabilization effect, whereas a gap of two bases resulted in a complete loss of the effect. The results suggest that the described biosensor-based methodology should be useful for the selection of appropriate modules and working concentrations for use in different modular hybridization applications.     

Reproductive diversity and survival of the potential annual Diplotaxis harra (Forssk.) Boiss (Brassicaceae) in Egypt

Diplotaxis harra is a common annual species in the desert of Egypt, The investigated population was located in Wadi Hof near Helwan city. Additional water in relatively wet years cause these ephemeral plants to live longer and become perennials. The species has ephemeral, modular and coppiced life‐cycles and may shift from a r‐ to a K‐selected strategy. The germinable seed bank represented 15,6% of the total seed rain, out of which only 0,03% established as adult plants. About 72.7% of the adult plants were ephemeral. 27.0% modular and 0.3% coppiced plants. The highest contribution of the seed rain came from modular plants and the lowest contribution from coppiced plants. The survivorship curve of the coppiced plants exhibited a combination of Deevey type I and III curves. The ephemeral and modular plants showed steep curves. In contrast to ephemeral plants, the coppiced plants attained the highest reproductive value and the lowest reproductive effort, while the modular plants demonstrated intermediate values. The active phonological cycle started earlier in coppiced plants than in the modular and ephemeral plants. The period from the start of vegetative growth lo shoot‐die back extends from mid‐December to early June in coppiced plants, from February to May in modular plants, and from late February to early May in ephemeral plants. The living stumps of the coppiced plants remained dormant during summer and autumn months. Seeds collected from coppiced plants attained high germinability and viability, while those from ephemeral and modular plants attained low values. Seed longevity was higher in the modular plants (> 10 yr) than in seeds of ephemeral and coppiced plants (7–8 yr). The high energy content of the seeds produced from different cohorts over ten years of storage enabled the population to maximize the germinability. viability and longevity of seeds despite the unpredictable environment. The potential annual behaviour of D. harra is mainly attained by the persistence of viable seed bank and root‐shoot stock. The ability to shift from a r‐ to a K‐selected life‐cycle, phenological variations among the different cohorts of the population, variations in seed longevity and energy content strengthen intra‐population interactions.     

Adhesive modular proteins occur in the extracellular mucilage of the motile, pennate diatom Phaeodactylum tricornutum

This Letter reports on adhesive modular proteins recorded by atomic force microscopy on live cells from the extracellular mucilage secreted from, and deposited around, the motile form of the pennate diatom Phaeodactylum tricornutum. This is the first report of modular proteins and their supramolecular assemblies, called adhesive nanofibers (ANFs), to be found on diatoms that use adhesives not only for substratum adhesion, but as a conduit for cell motility. The permanent adhesive pads secreted by Toxarium undulatum, a sessile centric diatom, were previously shown to possess ANFs with a modular protein backbone. Our results reported here suggest that modular proteins may be an important component of diatom adhesives in general, and that diatoms utilize the tensile strength, toughness, and flexibility of ANFs for multiple functions. Significantly, the genome of P. tricornutum has recently been sequenced; this will allow directed searches of the genome to be made for genes with modular protein homologs, and subsequent detailed studies of their molecular structure and function.     

Modular organization of finger movements by the human central nervous system

The motor system may generate automated movements, such as walking, by combining modular spinal motor synergies. However, it remains unknown whether a modular neuronal architecture is sufficient to generate the unique flexibility of human finger movements, which rely on cortical structures. Here we show that finger movements evoked by transcranial magnetic stimulation (TMS) of the primary motor cortex reproduced distinctive features of the spatial representation of voluntary movements as identified in previous neuroimaging studies, consistent with naturalistic activation of neuronal elements. Principal component analysis revealed that the dimensionality of TMS-evoked movements was low. Principal components extracted from TMS-induced finger movements resembled those derived from end-postures of voluntary movements performed to grasp imagined objects, and a small subset of them was sufficient to reconstruct these movements with remarkable fidelity. The motor system may coordinate even the most dexterous movements by using a modular architecture involving cortical components.     

Characterization of the Phd repressor-antitoxin boundary

The P1 plasmid addiction operon (a classic toxin-antitoxin system) encodes Phd, an unstable 73-amino-acid repressor-antitoxin protein, and Doc, a stable toxin. It was previously shown by deletion analysis that the N terminus of Phd was required for repressor activity and that the C terminus was required for antitoxin activity. Since only a quarter of the protein or less was required for both activities, it was hypothesized that Phd might have a modular organization. To further test the modular hypothesis, we constructed and characterized a set of 30 point mutations in the third and fourth quarters of Phd. Four mutations (PhdA36H, V37A, I38A, and F44A) had major defects in repressor activity. Five mutations (PhdD53A, D53R, E55A, F56A, and F60A) had major defects in antitoxin activity. As predicted by the modular hypothesis, point mutations affecting each activity belonged to disjoint, rather than overlapping, sets and were separated rather than interspersed within the linear sequence. A final deletion experiment demonstrated that the C-terminal 24 amino acid residues of Phd (preceded by a methionine) retained full antitoxin activity.     

Preventing Complications from High-Dose Rate Brachytherapy when Treating Mobile Tongue Cancer via the Application of a Modular Lead-Lined Spacer

PurposeTo point out the advantages and drawbacks of high-dose rate brachytherapy in the treatment of mobile tongue cancer and indicate the clinical importance of modular lead-lined spacers when applying this technique to patients.MethodsFirst, all basic steps to construct the modular spacer are shown. Second, we simulate and evaluate the dose rate reduction for a wide range of spacer configurations.ResultsWith increasing distance to the source absorbed doses dropped considerably. Significantly more shielding was obtained when lead was added to the spacer and this effect was most pronounced on shorter (i.e. more clinically relevant) distances to the source.ConclusionsThe modular spacer represents an important addition to the planning and treatment stages of mobile tongue cancer using HDR-ISBT.     

Design strategies to address the effect of hydrophobic epitope on stability and in vitro assembly of modular virus‐like particle

Virus‐like particles (VLPs) and capsomere subunits have shown promising potential as safe and effective vaccine candidates. They can serve as platforms for the display of foreign epitopes on their surfaces in a modular architecture. Depending on the physicochemical properties of the antigenic modules, modularization may affect the expression, solubility and stability of capsomeres, and VLP assembly. In this study, three module designs of a rotavirus hydrophobic peptide (RV10) were synthesized using synthetic biology. Among the three synthetic modules, modularization of the murine polyomavirus VP1 with a single copy of RV10 flanked by long linkers and charged residues resulted in the expression of stable modular capsomeres. Further employing the approach of module titration of RV10 modules on each capsomere via Escherichia coli co‐expression of unmodified VP1 and modular VP1‐RV10 successfully translated purified modular capomeres into modular VLPs when assembled in vitro. Our results demonstrate that tailoring the physicochemical properties of modules to enhance modular capsomeres stability is achievable through synthetic biology designs. Combined with module titration strategy to avoid steric hindrance to intercapsomere interactions, this allows bioprocessing of bacterially produced in vitro assembled modular VLPs.     

Pseudocyclical similarities and structural evolution of modular organisms

It was found that pseudocyclical similarities are common in modular organisms due to the peculiarities of their morphogenesis and ontogenesis and the system specifics of the modular organization. An analysis of the structural evolution in the different groups of modular living beings according to the concept of pseudocycles is topical, as it will contribute to the further development of evolutionary morphology and theoretical biology.     

On the origin of modular variation

We study the dynamics of modularization in a minimal substrate. A module is a functional unit relatively separable from its surrounding structure. Although it is known that modularity is useful both for robustness and for evolvability (Wagner 1996), there is no quantitative model describing how such modularity might originally emerge. Here we suggest, using simple computer simulations, that modularity arises spontaneously in evolutionary systems in response to variation, and that the amount of modular separation is logarithmically proportional to the rate of variation. Consequently, we predict that modular architectures would appear in correlation with high environmental change rates. Because this quantitative model does not require any special substrate to occur, it may also shed light on the origin of modular variation in nature. This observed relationship also indicates that modular design is a generic phenomenon that might be applicable to other fields, such as engineering: Engineering design methods based on evolutionary simulation would benefit from evolving to variable, rather than stationary, fitness criteria, as a weak and problem-independent method for inducing modularity.     

Genome evolution and the evolution of exon-shuffling--a review

Recent studies on the genomes of protists, plants, fungi and animals confirm that the increase in genome size and gene number in different eukaryotic lineages is paralleled by a general decrease in genome compactness and an increase in the number and size of introns. It may thus be predicted that exon-shuffling has become increasingly significant with the evolution of larger, less compact genomes. To test the validity of this prediction, we have analyzed the evolutionary distribution of modular proteins that have clearly evolved by intronic recombination. The results of this analysis indicate that modular multidomain proteins produced by exon-shuffling are restricted in their evolutionary distribution. Although such proteins are present in all major groups of metazoa from sponges to chordates, there is practically no evidence for the presence of related modular proteins in other groups of eukaryotes. The biological significance of this difference in the composition of the proteomes of animals, fungi, plants and protists is best appreciated when these modular proteins are classified with respect to their biological function. The majority of these proteins can be assigned to functional categories that are inextricably linked to multicellularity of animals, and are of absolute importance in permitting animals to function in an integrated fashion: constituents of the extracellular matrix, proteases involved in tissue remodelling processes, various proteins of body fluids, membrane-associated proteins mediating cell-cell and cell-matrix interactions, membrane associated receptor proteins regulating cell cell communications, etc. Although some basic types of modular proteins seem to be shared by all major groups of metazoa, there are also groups of modular proteins that appear to be restricted to certain evolutionary lineages. In summary, the results suggest that exon-shuffling acquired major significance at the time of metazoan radiation. It is interesting to note that the rise of exon-shuffling coincides with a spectacular burst of evolutionary creativity: the Big Bang of metazoan radiation. It seems probable that modular protein evolution by exon-shuffling has contributed significantly to this accelerated evolution of metazoa, since it facilitated the rapid construction of multidomain extracellular and cell surface proteins that are indispensable for multicellularity.     

A “plug‐n‐play” modular metabolic system for the production of apocarotenoids

Apocarotenoids, such as α‐, β‐ionone, and retinol, have high commercial values in the food and cosmetic industries. The demand for natural ingredients has been increasing dramatically in recent years. However, attempts to overproduce β‐ionone in microorganisms have been limited by the complexity of the biosynthetic pathway. Here, an Escherichia coli‐based modular system was developed to produce various apocarotenoids. Incorporation of enzyme engineering approaches (N‐terminal truncation and protein fusion) into modular metabolic engineering strategy significantly improved α‐ionone production from 0.5 mg/L to 30 mg/L in flasks, producing 480 mg/L of α‐ionone in fed‐batch fermentation. By modifying apocarotenoid genetic module, this platform strain was successfully re‐engineered to produce 32 mg/L and 500 mg/L of β‐ionone in flask and bioreactor, respectively (>80‐fold higher than previously reported). Similarly, 33 mg/L of retinoids was produced in flask by reconstructing apocarotenoid module, demonstrating the versatility of the “plug‐n‐play” modular system. Collectively, this study highlights the importance of the strategy of simultaneous modular pathway optimization and enzyme engineering to overproduce valuable chemicals in microbes.     

Complex organization of the Streptomyces avermitilis genes encoding the avermectin polyketide synthase.

The avermectin (Av) polyketide synthase (PKS) and erythromycin (Er) PKS are encoded by modular repeats of DNA, but the genetic organization of the modules encoding Av PKS is more complex than Er PKS. Sequencing of several related DNA fragments from Streptomyces avermitilis that are part of the Av biosynthetic gene cluster, revealed that they encode parts of large multifunctional PKS proteins. The Av PKS proteins show strong similarity to each other, as well as similarity to Er PKS proteins [Donadio et al., Science 252 (1991) 675-679] and fatty acid synthases. Partial DNA sequencing of the 65-kb region containing all the related sequence elements in the avr genes provides evidence for twelve modular repeats encoding FAS-like domains. The genes encoding the Av PKS are organized as two sets of six modular repeats which are convergently transcribed.     

Cellular fate of a modular DNA delivery system mediated by silica nanoparticles

Development of efficient molecular medicines, including gene therapeutics, RNA therapeutics, and DNA vaccines, depends on efficient means of transfer of DNA or RNA into the cell. Potential problems, including toxicity and immunogenicity, surrounding viral methods of DNA delivery have necessitated the use of nonviral, synthetic carriers. To better design synthetic carriers, or transfection reagents, the modular design of viruses has inspired a modular approach to DNA and RNA delivery. Each modular component can be designed to circumvent each of the many barriers. The modular approach will allow modification of individual components for a specific application. By utilizing a dense silica nanoparticle to form a ternary complex, transfection efficiency of a DNA-transfection reagent complex was increased by a factor of approximately 10 by concentrating the DNA at the surface of cells. Surface modification of the silica nanoparticles allowed determination of the cellular uptake mechanism with only minor alteration of transfection efficiency. Nanoparticles are internalized by an endosome-lysosomal route followed by perinuclear accumulation. The modification mechanism confirms that surface modification of the modular system can allow specific moieties to be incorporated into the modular system without significant alteration of the transfection efficiency. By showing that the modular system based upon concentration of DNA at the level of the cell can be used to increase transfection efficiency, we have shown that further modification of the system may better target DNA delivery and overcome other barriers of DNA expression.     

A biological transporter for the delivery of peptide nucleic acids (PNAs) to the nuclear compartment of living cells

To facilitate nuclear delivery of biomolecules we describe the synthesis of a modular transporter bearing a cellular membrane transport peptide (pAntp) and, as a cargo, a 16-mer peptide nucleic acid (PNA) covalently linked to a nuclear localisation signal (NLS[SV40-T]). Transport peptide and PNA are connected via N-terminal activated cysteine to form cleavable disulphide bonds. Internalization and subsequent delivery of PNA to the nucleus was verified in living and fixed cells by confocal laser scanning microscopy (CLSM) and fluorescence correlation spectroscopy (FCS). Double-labelling experiments indicate the cytoplasmic cleavage of the two modules and the effective nuclear import of the chromophore-tagged cargo. A non-degradable linker between transport module and cargo as well as a construct without NLS did not enable nuclear PNA import under the described experimental conditions. FCS-measurements revealed that most of the PNAs delivered into the cytoplasm by the modular transporter are anchored or encapsulated, indicating that intracellular transport of these compounds is not governed by molecular diffusion. Our results clearly demonstrate efficient compartment-directed transport using a synthetic, non-toxic modular transporter in living cells.     

A ribonucleopeptide module for effective conversion of an RNA aptamer to a fluorescent sensor

Ribonucleopeptide (RNP) is a new class of scaffold for modular fluorescent sensors. We report here a short RNA motif that induces an efficient communication between the structural changes associated with the ligand-binding event of RNA aptamer and an optical response of a fluorescent RNP module. An optimized short RNA motif was used as a communication module for the rational design of modular RNP sensors. A modular combination of a GTP-binding RNA aptamer, the short RNA motif and the fluorophore-labeled RNP module afforded a fluorescent GTP sensor that retain the ligand-binding affinity of the parent aptamer.     

Emergence of Bursting Activity in Connected Neuronal Sub-Populations

Uniform and modular primary hippocampal cultures from embryonic rats were grown on commercially available micro-electrode arrays to investigate network activity with respect to development and integration of different neuronal populations. Modular networks consisting of two confined active and inter-connected sub-populations of neurons were realized by means of bi-compartmental polydimethylsiloxane structures. Spontaneous activity in both uniform and modular cultures was periodically monitored, from three up to eight weeks after plating. Compared to uniform cultures and despite lower cellular density, modular networks interestingly showed higher firing rates at earlier developmental stages, and network-wide firing and bursting statistics were less variable over time. Although globally less correlated than uniform cultures, modular networks exhibited also higher intra-cluster than inter-cluster correlations, thus demonstrating that segregation and integration of activity coexisted in this simple yet powerful in vitro model. Finally, the peculiar synchronized bursting activity shown by confined modular networks preferentially propagated within one of the two compartments (‘dominant’), even in cases of perfect balance of firing rate between the two sub-populations. This dominance was generally maintained during the entire monitored developmental frame, thus suggesting that the implementation of this hierarchy arose from early network development.