Plant structural complexity and host-finding by a parasitoid

Summary There are three major components to plant structure relevant to searching parasitoids: 1) plant size or surface area, 2) the variation among plant parts (structural heterogeneity), such as seed heads, flowers and nectaries, and heterogeneous surfaces (e.g. glabrous, hirsute), and 3) the connectivity of parts or plant form (structural complexity). We examined the effect of structural complexity, while controlling for size and structural heterogeneity, on searching behaviors of Trichogramma nubilale in controlled environments. Females were presented with a structurally simple surface and a structurally complex one. Parasitism rates were 2.9 times higher on simple surfaces than on complex ones. Unexpectedly, when no hosts were present, searching time on simple surfaces was 1.2 times higher than on complex surfaces. This implies that structural complexity per se can affect the giving-up-time of a searching parasitoid. Searching efficiency, however, was the dominant process, and females found hosts on simple surfaces 2.4 times faster than on complex surfaces. Structural complexity can have a dramatic effect on the success of parasitoid search.     

Assessing the structural complexity of manufacturing systems configurations

Modern manufacturing systems are increasingly required to be flexible and adaptable to changing market demands, which adds to their structural and operational complexity. One of the major challenges at the early design stages is to select a manufacturing system configuration that both satisfies the production functional requirements and is easy to operate and manage. A new metric for assessing the structural complexity of manufacturing system configurations is presented in this paper. The proposed complexity metric incorporates the quantity of information using an entropy approach. It accounts for the complexity inherent in the various modules in the manufacturing system through the use of an index derived from a newly developed manufacturing systems classification code. The code captures the effect of various component types and technologies used in a manufacturing system on the system’s structural complexity. The presented metric would be helpful in selecting the least complex manufacturing system configuration that meets the requirements. An engine cylinder head production system is used to illustrate the application of the proposed methodology in comparing feasible but different manufacturing system configurations capable of producing the cylinder head based on their structurally inherent complexity.     

On the syntactic structure of protein sequences and the concept of grammar complexity

It is shown that the concepts of grammar complexity and syntactic structure provide a useful mathematical framework for the investigation of some current problems in protein structure. Grammar complexity gives a measure of the degree of aperiodicity of a sequence and also an optimization criterion for evaluating amino acid categorizations. Three systems of amino acid categorization are compared in relation to their value for describing molecular architecture.     

The structural complexity of DNA templates—Implications on cellular complexity

A previously formulated procedure for the quantitative evaluation of the complexities of molecules and biostructures is applied to assess the complexities of selected genomic DNA sequences. These include: (1) Several E. coli genes, including lacI, as examples of DNA sequences which are nearly as complex as possible (relative complexity=∼1). This is verified by the Lempel-Ziv (LZ) complexity analysis. (2) The telomere of a yeast chromosome, which has a considerable number of regular features that reduce complexity; the telomere shows indeed a lower structural complexity value. (3) A segment of human DNA, gene p53, which has a certain number of regular features such as 29 interspersed alu elements; these features cause a certain reduction in the complexity of the p53 gene, but do not invalidate the (previous) overall conclusion that template complexity is very high. The close to maximal complexity of the transcribed regions of p53 is validated by the LZ compression analysis. The general conclusion is that DNA base sequence composition is the dominant factor determining cellular complexity. The high complexity of DNA arrived at is a direct consequence of the template character of DNA and reflects the role of genomic DNA as a principal regulating element of a cell. It will be a challenge to find systems of lower complexity with the ability to respond to challenges from the environment to the extent that DNA templated systems do. Cellular complexity and template directed activity are thus highly intertwined properties, at the heart of many developmental, behavioral and evolutionary processes.     

Taming the complexity of protein folding

Protein folding is an important problem in structural biology with significant medical implications, particularly for misfolding disorders like Alzheimer's disease. Solving the folding problem will ultimately require a combination of theory and experiment, with theoretical models providing a comprehensive view of folding and experiments grounding these models in reality. Here we review progress towards this goal over the past decade, with an emphasis on recent theoretical advances that are empowering chemically detailed models of folding and the new results these technologies are providing. In particular, we discuss new insights made possible by Markov state models (MSMs), including the role of non-native contacts and the hub-like character of protein folded states.     

Thioredoxin - structural and functional complexity

Thioredoxins are small globular proteins that proved to be excellent model for investigating the relationship between the structure of protein and their physico-chemical and functional properties. The results from the experiments on thioredoxins offer the basic for the development of the new paradigms in the field of chemistry, biophysics and biology of proteins, with special attention to redox reaction in living cells, protein stability and design. It is a good example of broad class of sulphur-containing redox proteins.     

Bone modeling and structural measures of complexity

We test sensitivity and powerfulness of recently suggested Structure Measures of Complexity (SMC) with simulated test objects, represented by simple structures or modelled on the basis of a real bone image. We check how these SMC reflect the local and global disordering processes, as well as a deterioration of the bone structure. We show that applications of SMC provide additional information about any changes of the bone structure in comparison to bone mineral density (BMD), and that they can be potentially helpful in the diagnosis of osteoporosis.     

Sequence complexity of disordered protein

Intrinsic disorder refers to segments or to whole proteins that fail to self-fold into fixed 3D structure, with such disorder sometimes existing in the native state. Here we report data on the relationships among intrinsic disorder, sequence complexity as measured by Shannon's entropy, and amino acid composition. Intrinsic disorder identified in protein crystal structures, and by nuclear magnetic resonance, circular dichroism, and prediction from amino acid sequence, all exhibit similar complexity distributions that are shifted to lower values compared to, but significantly overlapping with, the distribution for ordered proteins. Compared to sequences from ordered proteins, these variously characterized intrinsically disordered segments and proteins, and also a collection of low-complexity sequences, typically have obviously higher levels of protein-specific subsets of the following amino acids: R, K, E, P, and S, and lower levels of subsets of the following: C, W, Y, I, and V. The Swiss Protein database of sequences exhibits significantly higher amounts of both low-complexity and predicted-to-be-disordered segments as compared to a non-redundant set of sequences from the Protein Data Bank, providing additional data that nature is richer in disordered and low-complexity segments compared to the commonness of these features in the set of structurally characterized proteins.     

The structural and mechanical complexity of cell-growth control

Tight control of cell proliferation is required to ensure normal tissue patterning and prevent cancer formation. The analysis of cultured cells has led to an explosion in our understanding of the molecules that trigger growth and mediate cell-cycle progression. However, the mechanism by which the local growth differentials that drive morphogenesis are established and maintained still remains unknown. Here we review recent work that reveals the importance of cell binding to the extracellular matrix, and associated changes in cell shape and cytoskeletal tension, to the spatial control of cell-cycle progression. These findings change the paradigm of cell-growth control, by placing our understanding of molecular signalling cascades in the context of the structural and mechanical complexity of living tissues.     

Habitat structural complexity mediates food web dynamics in a freshwater macrophyte community

A considerable amount of research has investigated the influence of habitat structure on predator success, yet few studies have explored the implications for community structure and food-web dynamics. The relative importance of macrophyte structure and fish predation on the composition of the macroinvertebrate and periphyton communities in a lowland river was investigated using a multifactorial caging experiment. We hypothesised that: (1) fish predators are less effective in a more structurally complex macrophyte analogue; (2) strong direct and indirect effects of fish predators (e.g. trophic cascades) are less likely to occur in a structurally complex habitat; and (3) the strength of these patterns is influenced by the composition of the prevailing community assemblage. We measured the abundance and composition of the macroinvertebrate and periphyton communities associated with three different-shaped macrophyte analogues, under different fish predator treatments and at different times. Macrophyte analogue architecture had strong, consistent effects on both the macroinvertebrate and periphyton communities; both were most abundant and diverse on the most structurally complex plant analogue. In contrast, the fish predators affected only a subset of the macroinvertebrate community and there was a suggestion of minor indirect effects on periphyton community composition. Contrary to expectations, the fish predators had their strongest effects in the most structurally complex macrophyte analogue. We conclude that in this system, macrophyte shape strongly regulates the associated freshwater assemblage, resulting in a diverse community structure less likely to exhibit strong effects of fish predation.     

Habitat structural complexity mediates the foraging success of multiple predator species

We investigated the role of freshwater macrophytes as refuge by testing the hypothesis that predators capture fewer prey in more dense and structurally complex habitats. We also tested the hypothesis that habitat structure not only affects the prey-capture success of a single predator in isolation, but also the effectiveness of two predators combined, particularly if it mediates interactions between the predators. We conducted a fully crossed four-factorial laboratory experiment using artificial plants to determine the separate quantitative (density) and qualitative (shape) components of macrophyte structure on the prey-capture success of a predatory damselfly, Ischnura heterosticta tasmanica, and the southern pygmy perch, Nannoperca australis. Contrary to our expectations, macrophyte density had no effect on the prey-capture success of either predator, but both predators were significantly less effective in the structurally complex Myriophyllum analogue than in the structurally simpler Triglochin and Eleocharis analogues. Furthermore, the greater structural complexity of Myriophyllum amplified the impact of the negative interaction between the predators on prey numbers; the habitat use by damselfly larvae in response to the presence of southern pygmy perch meant they captured less prey in Myriophyllum. These results demonstrate habitat structure can influence multiple predator effects, and support the mechanism of increased prey refuge in more structurally complex macrophytes.     

Social scale and structural complexity in human languages

The complexity of different components of the grammars of human languages can be quantified. For example, languages vary greatly in the size of their phonological inventories, and in the degree to which they make use of inflectional morphology. Recent studies have shown that there are relationships between these types of grammatical complexity and the number of speakers a language has. Languages spoken by large populations have been found to have larger phonological inventories, but simpler morphology, than languages spoken by small populations. The results require further investigation, and, most importantly, the mechanism whereby the social context of learning and use affects the grammatical evolution of a language needs elucidation.     

The importance of structural complexity in coral reef ecosystems

The importance of structural complexity in coral reefs has come to the fore with the global degradation of reef condition; however, the limited scale and replication of many studies have restricted our understanding of the role of complexity in the ecosystem. We qualitatively and quantitatively (where sufficient standardised data were available) assess the literature regarding the role of structural complexity in coral reef ecosystems. A rapidly increasing number of publications have studied the role of complexity in reef ecosystems over the past four decades, with a concomitant increase in the diversity of methods used to quantify structure. Quantitative analyses of existing data indicate a strong negative relationship between structural complexity and algal cover, which may reflect the important role complexity plays in enhancing herbivory by reef fishes. The cover of total live coral and branching coral was positively correlated with structural complexity. These habitat attributes may be creating much of the structure, resulting in a collinear relationship; however, there is also evidence of enhanced coral recovery from disturbances where structural complexity is high. Urchin densities were negatively correlated with structural complexity; a relationship that may be driven by urchins eroding reef structure or by their gregarious behaviour when in open space. There was a strong positive relationship between structural complexity and fish density and biomass, likely mediated through density-dependent competition and refuge from predation. More variable responses were found when assessing individual fish families, with all families examined displaying a positive relationship to structural complexity, but only half of these relationships were significant. Although only corroborated with qualitative data, structural complexity also seems to have a positive effect on two ecosystem services: tourism and shoreline protection. Clearly, structural complexity is an integral component of coral reef ecosystems, and it should be incorporated into monitoring programs and management objectives.     

On the complexity of graphs and molecules

A new formula for the complexity of graphs is proposed and applied to the points lines and ‘connections’ of some chemically relevant graphs.     

On the complexity measures of genetic sequences

MOTIVATION: It is well known that the regulatory regions of genomes are highly repetitive. They are rich in direct, symmetric and complemented repeats, and there is no doubt about the functional significance of these repeats. Among known measures of complexity, the Ziv-Lempel complexity measure reflects most adequately repeats occurring in the text. But this measure does not take into account isomorphic repeats. By isomorphic repeats we mean fragments that are identical (or symmetric) modulo some permutation of the alphabet letters. RESULTS: In this paper, two complexity measures of symbolic sequences are proposed that generalize the Ziv-Lempel complexity measure by taking into account any isomorphic repeats in the text (rather than just direct repeats as in Ziv-Lempel). The first of them, the complexity vector, is designed for small alphabets such as the alphabet of nucleotides. The second is based on a search for the longest isomorphic fragment in the history of sequence synthesis and can be used for alphabets of arbitrary cardinality. These measures have been used for recognition of structural regularities in DNA sequences. Some interesting structures related to the regulatory region of the human growth hormone are reported.     

On the predictability of protein database search complexity and its relevance to optimization of distributed searches

We discuss several aspects related to load balancing of database search jobs in a distributed computing environment, such as Linux cluster. Load balancing is a technique for making the most of multiple computational resources, which is particularly relevant in environments in which the usage of such resources is very high. The particular case of the Sequest program is considered here, but the general methodology should apply to any similar database search program. We show how the runtimes for Sequest searches of tandem mass spectral data can be predicted from profiles of previous representative searches, and how this information can be used for better load balancing of novel data. A well-known heuristic load balancing method is shown to be applicable to this problem, and its performance is analyzed for a variety of search parameters.     

Review of the effects of within-patch scale structural complexity on seagrass fishes

Studies on the effects of within-patch scale structure of seagrass habitats on predator–prey fish interactions and abundance/habitat use patterns were reviewed. Most laboratory experiments have employed chase-and-attack predators, usually resulting in lower foraging efficiency in (denser) seagrass. However, a few laboratory procedures employed alternative foraging tactics, resulting in no differences in prey mortality rates. Field studies did not always result in lower prey mortality rates in seagrass habitats. Accordingly, it is premature to conclude that seagrass presence is almost always negatively related to predator foraging efficiency or that increasing seagrass abundance is usually associated with a decrease in predator efficiency. Because several categories of predator and prey fishes occur in seagrass habitats, further studies are needed with all of these predator–prey combinations, in order to fully clarify predator–prey fish interactions in association with seagrass structure. Seagrass fishes have been shown to respond to alterations in seagrass structure in various ways: seagrass height and/or density reduction or clearance resulted in decreased abundance of some species but increases or no change in others. Some explanations have been proposed, not all mutually exclusive, for these phenomena. Although within-patch scale processes have been well studied, room exists for improvement. For example, predator–prey fish interactions in relation to varying within-patch scale complexity is not yet fully understand. The relationships of patch size, edge effects and within-patch scale complexity also still remain unclear. Further studies, which add to the clarification of within-patch scale process, will in turn improve our understanding of larger spatial scale processes.     

Thermodynamics elucidation of the structural stability of a thermophilic protein

The structural stability of the protein, phycocyanin isolated from two strains of cyanophyta, Synechococcus lividus (thermophile) and Phormidium luridum (mesophile), are investigated by comparative thermal and denaturant unfolding, using differential scanning calorimetry, visible absorption spectrophotometry, and circular dichroism. The thermophilic protein exhibits a much higher temperature and enthalpy of unfolding from the native to the denatured state. The concentration of urea at half-completion of thermal unfolding is essentially the same between the thermophilic and mesophilic proteins; in contrast, the corresponding temperature and the enthalpy of thermal unfolding are much higher for the thermophilic protein. In addition, the concentration of urea at which the non-thermal (denaturant) unfolding of protein is half-completed, as detected by either circular dichroism or absorption spectroscopy, is significantly higher in the thermophilic protein, while the apparent free energy of unfolding only shows a moderate difference between the two proteins. The distinct differences in the enthalpy of thermal unfolding and the free energy of denaturant unfolding are interpreted in terms of a significant entropy change associated with the unfolding of these proteins. This entropy contribution is much higher in the thermophilic protein, and may be derived from its more rigid overall structure that possesses higher internal hydrophobicity and stronger internal packing.