Side-chain control of folding of the homologous alpha-, beta-, and gamma-peptides into "mixed" helices (beta-helices)

A systematic analysis of the substituent influence on the formation of the unique secondary structure type of "mixed" helices in the homologous alpha-, beta-, and gamma-peptides was performed on the basis of ab initio molecular orbital theory. Contrary to the common periodic peptide helices, mixed helices have an alternating periodicity and their hydrogen-bonding pattern is similar to those of beta-sheets. They belong, therefore, to the family of beta-helices. It is shown that folding of peptide sequences into mixed helices is energetically preferred over folding into their periodic counterparts in numerous cases. The influence of entropy and solvents on the formation of the various competitive mixed and periodic helix types is discussed. Among the oligomers of the various homologous amino acids, beta-peptides show the highest tendency to form beta-helices. The rules of substituent influence derived from the analysis of a wide variety of backbone substitution patterns might be helpful for a rational design of mixed helix structures, which could be important for mimicking membrane channels.     

A role for Fringe in segment morphogenesis but not segment formation in the grasshopper, Schistocerca gregaria

Studies of somitogenesis in vertebrates have identified a number of genes that are regulated by a periodic oscillator that patterns the pre-somitic mesoderm. One of these genes, hairy, is homologous to a Drosophila segmentation gene that also shows periodic spatial expression. This, and the periodic expression of a zebrafish homologue of hairy during somitogenesis, has suggested that insect segmentation and vertebrate somitogenesis may use similar molecular mechanisms and possibly share a common origin. In chicks and mice expression of the lunatic fringe gene also oscillates in the presomitic mesoderm. Fringe encodes an extracellular protein that regulates Notch signalling. This, and the finding that mutations in Notch or its ligands disrupt somite patterning, suggests that Notch signalling plays an important role in vertebrate somitogenesis. Although Notch signalling is not known to play a role in the formation of segments in Drosophila, we reasoned that it might do so in other insects such as the grasshopper, where segment boundaries form between cells, not between syncytial nuclei as they do in Drosophila. Here we report the cloning of a single fringe gene from the grasshopper Schistocerca. We show that it is not detectably expressed in the forming trunk segments of the embryo until after segment boundaries have formed. We conclude that fringe is not part of the mechanism that makes segments in Schistocerca. Thereafter it is expressed in a pattern which shows that it is a downstream target of the segmentation machinery and suggests that it may play a role in segment morphogenesis. Like its Drosophila counterpart, Schistocerca fringe is also expressed in the eye, in rings in the legs, and during oogenesis, in follicle cells. Received: 14 October 1999 / Accepted: 18 January 2000     

The evolution of chordate neural segmentation

Amphioxus is the closest relative to vertebrates but lacks key vertebrate characters, like rhombomeres, neural crest cells, and the cartilaginous endoskeleton. This reflects major differences in the developmental patterning of neural and mesodermal structures between basal chordates and vertebrates. Here, we analyse the expression pattern of an amphioxus FoxB ortholog and an amphioxus single-minded ortholog to gain insight into the evolution of vertebrate neural segmentation. AmphiFoxB expression shows cryptic segmentation of the cerebral vesicle and hindbrain, suggesting that neuromeric segmentation of the chordate neural tube arose before the origin of the vertebrates. In the forebrain, AmphiFoxB expression combined with AmphiSim and other amphioxus gene expression patterns shows that the cerebral vesicle is divided into several distinct domains: we propose homology between these domains and the subdivided diencephalon and midbrain of vertebrates. In the Hox-expressing region of the amphioxus neural tube that is homologous to the vertebrate hindbrain, AmphiFoxB shows the presence of repeated blocks of cells along the anterior-posterior axis, each aligned with a somite. This and other data lead us to propose a model for the evolution of vertebrate rhombomeric segmentation, in which rhombomere evolution involved the transfer of mechanisms regulating neural segmentation from vertical induction by underlying segmented mesoderm to horizontal induction by graded retinoic acid signalling. A consequence of this would have been that segmentation of vertebrate head mesoderm would no longer have been required, paving the way for the evolution of the unsegmented head mesoderm seen in living vertebrates.     

Early expressed genes showing a dichotomous developing pattern in the lancelet embryo

Lancelets (amphioxus), although showing the most similar anatomical features to vertebrates, never develop a vertebrate-like head but rather several structures specific to this animal. The lancelet anatomical specificity seems to be traceable to early developmental stages, such as the vertebrate dorsal and anterior-posterior determinations. The BMP and Wnt proteins play important roles in establishing the early basis of the dorsal structures and the head in vertebrates. The early behavior of BMP and Wnt may be also related to the specific body structures of lancelets. The expression patterns of a dpp-related gene, Bbbmp2/4, and two wnt-related genes, Bbwnt7 and Bbwnt8, have been studied in comparison with those of brachyury and Hnf-3beta class genes. The temporal expression patterns of these genes are similar to those of vertebrates; Bbbmp2/4 and Bbwnt8 are first expressed in the invaginating primitive gut and the equatorial region, respectively, at the initial gastrula stage. However, spatial expression pattern of Bbbmp2/4 differs significantly from the vertebrate cognates. It is expressed in the mid-dorsal inner layer of gastrulae and widely in the anterior region, in which vertebrates block BMP signaling. The present study suggests that the lancelet embryo may have two distinct developmental domains from the gastrula stage, the domains of which coincide later with the lateral diverticular and the somitocoelomic regions. The embryonic origin of the anterior-specific structures in lancelets corresponds to the anterior domain where Bbbmp2/4 is continuously expressed.     

Arthropod-like expression patterns of engrailed and wingless in the annelid Platynereis dumerilii suggest a role in segment formation

The origin of animal segmentation, the periodic repetition of anatomical structures along the anteroposterior axis, is a long-standing issue that has been recently revived by comparative developmental genetics. In particular, a similar extensive morphological segmentation (or metamerism) is commonly recognized in annelids and arthropods. Mostly based on this supposedly homologous segmentation, these phyla have been united for a long time into the clade Articulata. However, recent phylogenetic analysis dismissed the Articulata and thus challenged the segmentation homology hypothesis. Here, we report the expression patterns of genes orthologous to the arthropod segmentation genes engrailed and wingless in the annelid Platynereis dumerilii. In Platynereis, engrailed and wingless are expressed in continuous ectodermal stripes on either side of the segmental boundary before, during, and after its formation; this expression pattern suggests that these genes are involved in segment formation. The striking similarities of engrailed and wingless expressions in Platynereis and arthropods may be due to evolutionary convergence or common heritage. In agreement with similarities in segment ontogeny and morphological organization in arthropods and annelids, we interpret our results as molecular evidence of a segmented ancestor of protostomes.     

Comparing disturbance and generalism in birds and mammals: A hump-shaped pattern

Using indices as proxies, we observed that comparing a large number of common birds and mammals, the level of generalism peaks in species inhabiting habitats at intermediate disturbance levels. This pattern might be universal, at least in these homeothermic vertebrates. Birds show nonetheless some differences in pattern from mammals, where specialization at intermediate levels of disturbance is not present. Differences in ecological and evolutionary traits between birds and mammals might determine different adaptive responses to historical anthropogenic changes, explaining these taxa-specific hump-shaped patterns.     

Regeneration studies on a crayfish neuromuscular system. I. Connectivity changes after intersegmental nerve transplants

The superficial flexor muscles of the crayfish are a neuromuscular system of a few muscle cells innervated by six neurons in a precise position-dependent pattern. The neurons are capable of regenerating their normal connectivity patterns within a short span of time when conditions are favorable. The superficial flexor muscles of the second and third segments, despite their similarities in neuronal and muscle cell size and number, have distinctive connectivity patterns; some homologous neurons form similar patterns but other homologous neurons form patterns that are reversed between segments. We transplanted each segment's nerve into each other's muscle in order to observe regeneration of the nerves into a target area that differed in connectivity patterns from their original muscle. During the first weeks of regeneration all neurons formed a connectivity pattern with more connections medially and declining connections laterally, a pattern determined by the medial location of the nerve transplant. This pattern is maintained for most of the neurons, but for some there is an eventual reduction in medial connections as maximum synapse formation shifts to the lateral muscle fibers. Three of the eight neurons studied were able to regenerate connectivity patterns that corresponded to their segment of origin and not to their host muscle. This suggests that intersegmental muscle differences are not influencing the formation of these connectivity patterns, so the neurons will follow their inherent synaptogenesis program.     

Using a multiscale image processing method to characterize the periodic growth patterns on scallop shells

The fine periodic growth patterns on shell surfaces have been widely used for studies in the ecology and evolution of scallops. Modern X‐ray CT scanners and digital cameras can provide high‐resolution image data that contain abundant information such as the shell formation rate, ontogenetic age, and life span of shellfish organisms. We introduced a novel multiscale image processing method based on matched filters with Gaussian kernels and partial differential equation (PDE) multiscale hierarchical decomposition to segment the small tubular and periodic structures in scallop shell images. The periodic patterns of structures (consisting of bifurcation points, crossover points of the rings and ribs, and the connected lines) could be found by our Space‐based Depth‐First Search (SDFS) algorithm. We created a MATLAB package to implement our method of periodic pattern extraction and pattern matching on the CT and digital scallop images available in this study. The results confirmed the hypothesis that the shell cyclic structure patterns encompass genetically specific information that can be used as an effective invariable biomarker for biological individual recognition. The package is available with a quick‐start guide and includes three examples: http://mgb.ouc.edu.cn/novegene/html/code.php .     

Lessons on pattern formation from planet WATOR

It is well known that if reacting species experience unequal diffusion rates, then dynamics that lead to a constant steady state in a "well-mixed" environment can in a spatial setting lead to interesting patterns. In this paper, we focus on complementary pattern formation mechanisms that operate even when the diffusion rates are equal. In particular, we can say that when the mean-field ODE has an attracting periodic orbit then the stochastic spatial model will have large-scale spatial structures in equilibrium. We explore this mechanism in depth through the dynamics of the simulator WATOR.     

Charged residues at protein interaction interfaces: unexpected conservation and orchestrated divergence

Protein-protein interactions play an essential role in the functioning of cell. The importance of charged residues and their diverse role in protein-protein interactions have been well studied using experimental and computational methods. Often, charged residues located in protein interaction interfaces are conserved across the families of homologous proteins and protein complexes. However, on a large scale, it has been recently shown that charged residues are significantly less conserved than other residue types in protein interaction interfaces. The goal of this work is to understand the role of charged residues in the protein interaction interfaces through their conservation patterns. Here, we propose a simple approach where the structural conservation of the charged residue pairs is analyzed among the pairs of homologous binary complexes. Specifically, we determine a large set of homologous interactions using an interaction interface similarity measure and catalog the basic types of conservation patterns among the charged residue pairs. We find an unexpected conservation pattern, which we call the correlated reappearance, occurring among the pairs of homologous interfaces more frequently than the fully conserved pairs of charged residues. Furthermore, the analysis of the conservation patterns across different superkingdoms as well as structural classes of proteins has revealed that the correlated reappearance of charged residues is by far the most prevalent conservation pattern, often occurring more frequently than the unconserved charged residues. We discuss a possible role that the new conservation pattern may play in the long-range electrostatic steering effect.     

Time Space Translation: A Hox Mechanism for Vertebrate A-P Patterning

The vertebrate A-P axis is a time axis. The head is made first and more and more posterior levels are made at later and later stages. This is different to the situation in most other animals, for example, in Drosophila. Central to this timing is Hox temporal collinearity (see below). This occurs rarely in the animal kingdom but is characteristic of vertebrates and is used to generate the primary axial Hox pattern using time space translation and to integrate successive derived patterns (see below). This is thus a different situation than in Drosophila, where the primary pattern guiding Hox spatial collinearity is generated externally, by the gap and segmentation genes.     

Reaction-diffusion microtubule concentration patterns occur during biological morphogenesis.

Reaction-diffusion processes can lead to a macroscopic concentration pattern from an initially homogeneous solution, and thus provide a physical-chemical mechanism for biological pattern formation and morphogenesis. The central prediction of reaction-diffusion theory is that the patterns contain periodic concentration variations in some of the reactives. Microtubules assembled in vitro spontaneously self-organise and form stationary striped macroscopic structures. In agreement with reaction-diffusion theory. Here we show, in agreement with reaction-diffusion theory, that these preparations contain substantial microtubule concentration variations. Similar striped microtubule patterns arise during Drosophila embryogenesis. A characteristic of these patterns is their dependence on sample dimensions. In Drosophila eggs shortened by ligation, we found that the microtubule pattern varied with egg fragment length in the same way as the in vitro microtubule pattern varied with sample length, and as expected from theory. This is evidence that reaction-diffusion structures occur during Drosophila morphogenesis.     

Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction

The pattern of residue substitution in divergently evolving families of globular proteins is highly variable. At each position in a fold there are constraints on the identities of amino acids from both the three-dimensional structure and the function of the protein. To characterize and quantify the structural constraints, we have made a comparative analysis of families of homologous globular proteins. Residues are classified according to amino acid type, secondary structure, accessibility of the sidechain, and existence of hydrogen bonds from sidechain to other sidechains or peptide carbonyl or amide functions. There are distinct patterns of substitution especially where residues are both solvent inaccessible and hydrogen bonded through their sidechains. The patterns of residue substitution can be used to construct templates or to identify 'key' residues if one or more structures are known. Conversely, analysis of conversation and substitution across a large family of aligned sequences in terms of substitution profiles can allow prediction of tertiary environment or indicate a functional role. Similar analyses can be used to test the validity of putative structures if several homologous sequences are available.     

Micromorphology of osteoderms in Dasypodidae (Cingulata,Mammalia): Characterization and 3D-reconstructions

Osteoderms are present in a variety of extinct and extant vertebrates, but among mammals, the presence of osteoderms is essentially restricted to armadillos (Cingulata, Dasypodidae). Osteoderms have been proposed to exhibit a variety of functionalities in Dasypodidae, mainly protection and thermoregulation, and they have been considered as one of the synapomorphies of this group. In this study, we use high-resolution microcomputed tomography to describe the osteoderm micromorphology of several extant species of Dasypodidae in a comparative context. This study allowed the identification, 3D-reconstruction and volume quantification of different internal structures of osteoderms as well as their interrelations. This detailed characterization of the internal osteoderm morphology was compared in a phylogenetic context to assess the evolutionary trends of the species involved. This enables the identification of distinctive patterns for the most widely recognized clades, the Dasypodinae and Euphractinae with a morphological homogeneity in the microstructure of their osteoderms, in comparison with Tolypeutinae where it has not been possible to establish a common morphological pattern. The most important features for linage differentiation is the degree of compaction of the osteoderms, the number of cavities and the development of hairs. It is likely that the differential development of the various structures occurred as adaptive response to climate changes.     

Towards a synthetic view of axis specification mechanisms in vertebrates: insights from the dogfish

The genetic mechanisms, which control axis specification, apparently extensively diverge across vertebrates. In amphibians and teleosts, they are tightly linked to the establishment of an early dorso-ventral polarity. This polarity has no equivalent in amniotes, which unlike the former, retain a considerable plasticity for their site of axis formation until blastula stages and rely on signals secreted by extra-embryonic tissues for the establishment of their early rostro-caudal pattern. In order to better understand the links between these seemingly highly divergent mechanisms, we have used an evo-devo approach, aimed at reconstructing the gnathostome ancestral state and focussed on a chondrichthyan, the dogfish Scyliorhinus canicula. A detailed molecular characterization of the dogfish embryo at blastula and gastrula stages highlights striking similarities with all vertebrate model organisms including amniotes. It suggests the presence in the dogfish of territories homologous to the hypoblast and extra-embryonic ectoderm of the latter, which may therefore reflect the primitive condition of jawed vertebrates. In the ancestral state, these territories are specified at opposite sides of an early axis of bilateral symmetry, homologous to the dorso-ventral axis of amphibians and teleosts, and aligned with the later forming embryonic axis, from head to tail. Amniotes have diverged from this pattern through a posterior expansion of extra-embryonic ectoderm, resulting in an apparently radial symmetry at late blastula stages. These data delineate the broad outlines of the gnathostome ancestral pattern of axis specification and highlight an unexpected unity of mechanisms across jawed vertebrates. They illustrate the complementarity of comparative and genetic approaches for a comprehensive view of developmental mechanisms themselves. To cite this article: M. Coolen et al., C. R. Biologies 332 (2009).     

Two novel homologous proteins of Streptomyces coelicolor and Streptomyces lividans are involved in the formation of the rodlet layer and mediate attachment to a hydrophobic surface

The filamentous bacteria Streptomyces coelicolor and Streptomyces lividans exhibit a complex life cycle. After a branched submerged mycelium has been established, aerial hyphae are formed that may septate to form chains of spores. The aerial structures possess several surface layers of unknown nature that make them hydrophobic, one of which is the rodlet layer. We have identified two homologous proteins, RdlA and RdlB, that are involved in the formation of the rodlet layer in both streptomycetes. The rdl genes are expressed in growing aerial hyphae but not in spores. Immunolocalization showed that RdlA and RdlB are present at surfaces of aerial structures, where they form a highly insoluble layer. Disruption of both rdlA and rdlB in S. coelicolor and S. lividans (DeltardlAB strains) did not affect the formation and differentiation of aerial hyphae. However, the characteristic rodlet layer was absent. Genes rdlA and rdlB were also expressed in submerged hyphae that were in contact with a hydrophobic solid. Attachment to this substratum was greatly reduced in the DeltardlAB strains. Sequences homologous to rdlA and rdlB occur in a number of streptomycetes representing the phylogenetic diversity of this group of bacteria, indicating a general role for these proteins in rodlet formation and attachment.     

The global biogeography of semi‐arid periodic vegetation patterns

Aim Vegetation exhibiting landscape‐scale regular spatial patterns has been reported for arid and semi‐arid areas world‐wide. Recent theories state that such structures are bound to low‐productivity environments and result from a self‐organization process. Our objective was to test this relationship between periodic pattern occurrence and environmental factors at a global scale and to parametrize a predictive distribution model. Location Arid and semi‐arid areas world‐wide. Methods We trained an empirical predictive model (Maxent) for the occurrence of periodic vegetation patterns, based on environmental predictors and known occurrences verified on Landsat satellite images. Results This model allowed us to discover previously unreported pattern locations, and to report the first ever examples of spotted patterns in natural systems. Relationships to the main environmental drivers are discussed. Main conclusions These results confirm that periodic patterned vegetations are ubiquitous at the interface between arid and semi‐arid regions. Self‐organized patterning appears therefore to be a biome‐scale response to environmental conditions, including soil and topography. The set of correlations between vegetation patterns and their environmental conditions presented in this study will need to be reproduced in future modelling attempts.     

Segmentation and zooid formation in animals with a posterior growing region: the case for metabolic gradients and Turing waves

The discovery of periodic propagation of anteriorly moving pulses/stripes of gene expression in the presomitic mesoderm (PSM) of vertebrates has given new life to the clock and wavefront model, and other models of morphogenesis based on a molecular oscillator where the time periodicity is translated into spatial periodicity. Instead we suggest that segmentation, somitogenesis and metamerism in vertebrates and in invertebrates with a posterior growing region are based on a Turing-Child metabolic gradient that is progressively shifted posteriorly with the PSM as elongation, segmentation and somitogenesis proceed. This gradient corresponds to anteriorly propagating metabolic front in the PSM that drives the anteriorly propagating mRNA synthesis and which, together with mRNA degradation, explains stripe formation and spatial periodicity.The process of segmentation has been compared to zooid formation. We show that for annelids the metabolic profile behaves as a Turing field in the sense that an increase in the length of the system or a decrease of the Turing wavelength results in an additional peak in the posterior growing region as predicted by Turing theory. In particular, it is shown that the metabolic gradient that drives the segmentation is based on a Turing system.