Distribution and use of burrows and tunnels ofChaetophractus villosus (Mammalia, Xenarthra) in the eastern Argentinean pampas

Burrows and tunnels built byChaetophractus villosus (Desmarest, 1804) (hairy armadillo) were studied in a farming area located in the Argentinean pampas, Buenos Aires Province, Argentina. Fifty-six structures were selected and carefully excavated for this study. Data on diameter, form, and orientation of the entrance, angle, length, and depth of the galleries, and spatial distribution of the structures were recorded. The structures were separated into two types: simple and complex, both located in high terrain. Simple structures are shorter than complex ones and are built when animals are in search of food or as temporary shelters. Complex structures are built as home burrows. The orientation of the entrances of both kinds of burrows is related to the prevalent wind direction.     

Homology modeling: an important tool for the drug discovery

In the last decades, homology modeling has become a popular tool to access theoretical three-dimensional (3D) structures of molecular targets. So far several 3D models of proteins have been built by this technique and used in a great diversity of structural biology studies. But are those models consistent enough with experimental structures to make this technique an effective and reliable tool for drug discovery? Here we present, briefly, the fundamentals and current state-of-the-art of the homology modeling techniques used to build 3D structures of molecular targets, which experimental structures are not available in databases, and list some of the more important works, using this technique, available in literature today. In many cases those studies have afforded successful models for the drug design of more selective agonists/antagonists to the molecular targets in focus and guided promising experimental works, proving that, when the appropriate templates are available, useful models can be built using some of the several software available today for this purpose. Limitations of the experimental techniques used to solve 3D structures allied to constant improvements in the homology modeling software will maintain the need for theoretical models, establishing the homology modeling as a fundamental tool for the drug discovery.     

A proposal for a specific double-helical structure in which the polynucleotide strands intercalate instead of forming base-pairs

Double helices, since the discovery of the DNA structure by Watson and Crick, represent the single most important secondary structural form of nucleic acids. The secondary structures of a variety of polynucleotide helices have now been well characterised with hydrogen-bonded base-pairs as building blocks. We wish to propose here the possibility, in a specific case, of a double stranded helical structure without any base-pair, but having a repeat unit of two nucleotides with their bases stacked through intercalation. The proposal comes from the initial models we have built for poly(dC) using the stacking patterns found in the crystal structures of 5'-dCMPNa2 which crystallises in two forms depending on the degree of hydration. These structures have pairs of nucleotides with the cytosine rings partially overlapping and separated by 3.3A. Using these as repeat units one could generate a model for poly(dC) with parallel strands, having a turn angle of 30 degrees and a base separation of 6.6A along each strand. Both right and left handed models with these parameters can be built in a smooth fashion without any obviously unreasonable stereochemical contacts. The helix diameter is about 13.5A, much smaller than that of normal helices with base-pair repeats. The changes in the sugar-phosphate backbone conformation in the present models compared to normal duplexes only reflect the torsional flexibility available for extension of polynucleotide chains as manifested by the crystal structures of drug-inserted oligonucleotide complexes. Intercalation proposed here could have some structural relevance elsewhere, for instance to the base-mismatched regions on the double helix and the packing of noncomplementary single strands as found in the filamentous bacteriophage Pf1.     

Effect of salinity on nest building behaviour in the nine-spined stickleback Pungitius sinensis

The authors evaluated the adaptability of male nine-spined sticklebacks (Pungitius sinensis) at three salinity levels (0, 5 and 10 psu) by comparing nest building success rates with nest structures. Successful nest building decreased as salinity increased. In addition, nests built in fresh water (i.e., 0 psu) were glued together, whereas those built in brackish water (5 and 10 psu) broke easily and fell from the nest site to the gravel bottom. Based on these findings, the authors suggest that P. sinensis adapts to freshwater environments.     

The structure of the outer shell layer in radiolitid rudists, a morphoconstructional approach

Radiolitids (Bivalvia, Radiolitidae) built the calcite outer layer of their shell with compact structure as many other bivalves, or with repetitively layered non-compact structure following different patterns: continuous radial ridges, discontinuous radial ridges, normal cellular, cellular with radially elongate cells, discontinuous cellular, and discontinuous cellular with elongate cells. Some special structures may develop in localized parts: radial structures and inner-marginal or radial grooves. All these structures are currently used in the diagnosis of the family and for the characterization of subfamilies. Constructional morphology analyses and re-evaluation of all these structures reveal that they were misunderstood in some important aspects in the bivalve Treatise and that, consequently, the diagnosis of the family has to be emended and their subfamilies reconsidered. All outer shell layer structure related characters are described, illustrated, and interpreted under a constructional approach, some characters are proposed to emend the diagnosis of the family, and two possible clades are preliminarily distinguished.     

A comprehensive analysis of the Greek key motifs in protein beta-barrels and beta-sandwiches

The Greek key motifs are the topological signature of many beta-barrels and a majority of beta-sandwich structures. An updated survey of these structures integrates many early observations and newly emerging patterns and provides a better understanding of the unique role of Greek keys in protein structures. A stereotypical Greek key beta-barrel accommodates five or six strands and can have 12 possible topologies. All except one six-stranded topologies have been observed, and only one five-stranded topologies have been seen in actual structures. Of the representative beta-barrel structures analyzed here, half have left-handed Greek keys. This result challenges the empirical claim of the handedness regularity of Greek keys in beta-barrels. One of the five-stranded topologies that has not been observed in beta-barrels comprises two overlapping Greek keys. The two three-dimensional forms of this topology constitute a structural unit that is present in a vast majority of known beta-sandwich structures. Using this unit as the root, we have built a new taxonomy tree for the beta-sandwich folds and deduced a set of rules that appear to constrain how other beta-strands adjoin the unit to form a larger double-layered structure. These rules, though derived from a larger data set, are essentially the same as those drawn from earlier studies, suggesting that they may reflect the true topological constraints in the design of beta-sandwich structures. Finally, a novel variant of the Greek key motif (defined here as the twisted Greek key) has emerged which introduces loop crossings into the folded structures. Proteins 2000;40:409-419.     

A global resource for computational chemistry

A modular distributable system has been built for high-throughput computation of molecular structures and properties. It has been used to process 250,000 compounds from the NCI database and to make the results searchable by structures and properties. The IUPAC/NIST InChI specification and algorithm has been used to index the structures and enforce integrity during computation. A number of novel features of the PM5 Hamiltonian were identified as a result of the high-throughput approach. The system and the data can be redistributed and reused and promote the value of computed data as a primary chemical resource.     

Quaternary structure built from subunits combining NMR and small-angle x-ray scattering data

A new principle in constructing molecular complexes from the known high-resolution domain structures joining data from NMR and small-angle x-ray scattering (SAXS) measurements is described. Structure of calmodulin in complex with trifluoperazine was built from N- and C-terminal domains oriented based on residual dipolar couplings measured by NMR in a dilute liquid crystal, and the overall shape of the complex was derived from SAXS data. The residual dipolar coupling data serves to reduce angular degrees of freedom, and the small-angle scattering data serves to confine the translational degrees of freedom. The complex built by this method was found to be consistent with the known crystal structure. The study demonstrates how approximate tertiary structures of modular proteins or quaternary structures composed of subunits can be assembled from high-resolution structures of domains or subunits using mutually complementary NMR and SAXS data.     

Fine structure of the egg envelope and the supporting stalk in the dipliran Campodea (Apterygota : Campodeidae)

The eggs and supporting stalks of one Campodea (Apterygota : Campodeidae) species were studied by scanning and transmission electron microscopes. Each egg batch is attached to the substrate by a supporting stalk. The stalk is composed of tangled lamellae and dense annular structures. Both elements are strongly PAS-positive. The eggs are covered by one envelope only. It is built of fine granular, PAS-negative material. The surface of the envelope is smooth and possesses 2–4 ring-like structures, which are likely involved in the attachment of the eggs within a batch.     

The contribution of the vegetable material layer to the insulation capacities and water proofing of artificial Mus spicilegus mounds

Successful overwintering of small mammals in temperate and cold climates requires behavioural and physiological adaptations. There are several strategies to survive food shortages and the cold. Most species of small mammals use multiple methods simultaneously but nest building and burrowing are the most widespread among them. A well-constructed, dry nest insulates animals from harsh ambient conditions. Mound-building mice build large banks in the autumn and establish a burrow system with nest chambers beneath them. These overwintering structures are built from soil and a considerable amount of plant material. Recent studies presume that the stored vegetable matter does not, or not exclusively, serve as food and indicate that the mounds might have insulating role. To investigate the function of their plant fill, we built artificial mounds with varying plant content, similar to those built by mound-building mice. We measured temperature change at three levels, at the surface, under the mound and at the nest depth, and investigated their water retaining properties. We showed that the plant fill plays a major role in their thermal insulation and waterproofing properties. Mounds reduced temperature variation of the soil and may protect the nest from absorbing precipitation during the winter.     

Behaviour is not Reliably Inferred from End-Product Structure in Caddisflies

Many animals engage in elaborate behavioural sequences in order to build structures. The ‘end‐products’ (e.g., nests of birds, cases of caddisflies) of these behaviours have occasionally been used either to infer details of building behaviour or to infer that structures similar in appearance are constructed by similar behavioural sequences. However, behavioural information can be extrapolated from end‐products only if there is congruence between the end‐product structure and the animal's movements. Case building behaviour was studied in caddisflies (Trichoptera) to examine the relationship between end‐products and behaviour. We found examples of taxa that built similar structures using different behavioural patterns, and taxa that built different structures using similar behaviours, regardless of whether these taxa were closely or distantly related. These findings question the reliability of behavioural inferences based solely on details of their associated end‐products and suggest that end‐product structure should be removed from the definition of animal behaviour.     

MOFOID--not only the protein modeling server

MOFOID is a new server developed mainly for automated modeling of protein structures by their homology to the structures deposited in the PDB database. Selection of a template and calculation of the alignment is performed with the Smith-Waterman or Needleman-Wunsch algorithms implemented in the EMBOSS package. The final model is built and optimised with programs from the JACKAL package. The wide spectrum of options in the web-based interface and the possibility of uploading user's own alignment make MOFOID a suitable platform for testing new approaches in the alignment building. The server is available at https:// valis.ibb.waw.pl/mofoid/.     

Stability of loops in the structure of lactose permease

Structural analysis of peptide fragments has provided useful information on the secondary structure of integral membrane proteins built from a helical bundle (up to seven transmembrane segments). Comparison of those results to recent X-ray crystallographic results showed agreement between the structures of the fragments and the structures of the intact proteins. Lactose permease of Escherichia coli (lac Y) offers an opportunity to test that hypothesis on a substantially larger integral membrane protein. Lac Y contains a bundle of 12 transmembrane segments connected by 11 loops. Eleven segments, each corresponding to one of the loops in this protein, were studied. Five of these segments form defined structures in solution as determined by multidimensional nuclear magnetic resonance. Four peptides form turns, and one peptide reveals the end of one of the transmembrane helices. These results suggest that some loops in helical bundles are stabilized by short-range interactions, particularly in smaller bundles, and such intrinsically stable loops may contribute to protein stability and influence the pathway of folding. Greater conformational flexibility may be found in large integral membrane proteins.     

Adherens junctions in the Drosophila embryo: The role of E-cadherin in their establishment and morphogenetic function

The integrity of epithelia depends largely on specialised adhesive structures, the adherens junctions. Several of the components required for building these structures are highly conserved between vertebrates and insects (e.g. E-cadherin and α- and β-catenin), while others have so far been found only in invertebrates (e.g. crumbs). Two recent papers^(1,2) show that the Drosophila E-cadherin is encoded by the gene shotgun. Phenotypic analyses of shotgun as well as armadillo (β-catenin) and crumbs mutants provide new insights into the mechanisms by which adherens junctions are built and, further, show that the requirement for E-cadherin largely depends on the morphogenetic activity of an epithelium.     

Canine capillary formation in vitro

Microvascular endothelial cells derived from canine subcutaneous adipose tissue formed knob-like and tube-like structures in vitro without tumor-conditioned medium or special substrate. The knob-like structures consisted of acidic and basic glycosaminoglycans arranged in order. Knob-like structures were built from cell extrudates and were responsible for capillary lumen formation in vitro. Transmission electron microscopy confirmed the endothelial nature of the cells which expressed extensive phagolysosomal activity.     

Semiotics of a Superorganism

Darwinian evolution, as it was first conceived, has two dimensions: adaptation, that is, selection based upon “apt function”, defined as the “good fit” between an organism’s metabolic and biological demands and the environment in which it is embedded; and heredity, the transmissible memory of past apt function. Modern Darwinism has come to focus almost exclusively on hereditary memory, eclipsing the—arguably still-problematic—phenomenon of adaptation. As a result, modern Darwinism retains, at its core, certain incoherencies that, as long as they remain unresolved, preclude the emergence of a fully-coherent theory of evolution. Resolving the incoherencies will involve clarifying the relationship between embodied memory and apt function. In short, adaptation is a problem of semiotics: the organism must interpret the environment to fit well into it. This is well-illustrated by the constructed environments built by colonies of social insects, such as hives or nests, and the ancillary structures that contain them, forming an organism-like system known as a superorganism. The superorganism is marked by a kind of extended physiology, in that these constructed environments often serve as adaptive interfaces between the nest and ambient environment, and are constructed to manage the matter and energy flows between environments that constitute the process of adaptation. These constructed environments are also semiotic phenomena: interpretive structures, governed by information flow between the member insects and the structures they build. I review our findings on one such example: the mounds built by the fungus-cultivating termites of the genus Macrotermes. These structures are dynamic forms that are sustained by flows of soil from deep horizons up into the mound. The form, and hence the function, of the mound is determined by several environmental cues, most notably water and wind, as well as how termites interpret these cues, and signals that flow between termites, both directly and vicariously through the structures they build.     

Linking changes in knowledge and attitudes with successful land restoration in indigenous communities

Successful land restoration in impoverished rural environments may require adoption of new resource management strategies; however, feedbacks between local knowledge and introduced restoration technologies have rarely been articulated. We used interview scenarios to analyze the role of local knowledge in land restoration at a large‐scale, long‐term watershed rehabilitation and wet meadow restoration program in the highland Andes. Indigenous communities built over 30,000 check dams, terraces and infiltration ditches, and the density of erosion control structures and visible restoration varied greatly across participant communities. We developed a survey reaching across the highest restoration management intensity, lowest restoration management intensity, and non‐project (control) communities. We interviewed 49 respondents using 14 scenarios based on photos depicting biophysical phenomena related to land degradation and restoration. The scenarios generated 5,828 statements that were coded into 964 distinct concepts. As expected, respondents that built more erosion control structures had more detailed knowledge of check dam construction and ecosystem development following physical interventions. More significantly, there was a shift in the conceptualization of and attitudes toward land degradation and restoration. Respondents who built more erosion control structures were more likely to: attribute wetland hydrology to groundwater recharge rather than myth constructs about seeps and springs; attribute land degradation to human rather than mythological causes; and have more proactive attitudes regarding land restoration. Evidence suggests that when addressing severe land degradation or restoring ecosystem processes not readily observable by indigenous people, such as groundwater flow and wetland recharge, restoration success will depend on combining local and scientific knowledge.     

Evaluating mixture models for building RNA knowledge-based potentials

Ribonucleic acid (RNA) molecules play important roles in a variety of biological processes. To properly function, RNA molecules usually have to fold to specific structures, and therefore understanding RNA structure is vital in comprehending how RNA functions. One approach to understanding and predicting biomolecular structure is to use knowledge-based potentials built from experimentally determined structures. These types of potentials have been shown to be effective for predicting both protein and RNA structures, but their utility is limited by their significantly rugged nature. This ruggedness (and hence the potential's usefulness) depends heavily on the choice of bin width to sort structural information (e.g. distances) but the appropriate bin width is not known a priori. To circumvent the binning problem, we compared knowledge-based potentials built from inter-atomic distances in RNA structures using different mixture models (Kernel Density Estimation, Expectation Minimization and Dirichlet Process). We show that the smooth knowledge-based potential built from Dirichlet process is successful in selecting native-like RNA models from different sets of structural decoys with comparable efficacy to a potential developed by spline-fitting - a commonly taken approach - to binned distance histograms. The less rugged nature of our potential suggests its applicability in diverse types of structural modeling.     

Building proteins from C alpha coordinates using the dihedral probability grid Monte Carlo method.

Dihedral probability grid Monte Carlo (DPG-MC) is a general-purpose method of conformational sampling that can be applied to many problems in peptide and protein modeling. Here we present the DPG-MC method and apply it to predicting complete protein structures from C alpha coordinates. This is useful in such endeavors as homology modeling, protein structure prediction from lattice simulations, or fitting protein structures to X-ray crystallographic data. It also serves as an example of how DPG-MC can be applied to systems with geometric constraints. The conformational propensities for individual residues are used to guide conformational searches as the protein is built from the amino-terminus to the carboxyl-terminus. Results for a number of proteins show that both the backbone and side chain can be accurately modeled using DPG-MC. Backbone atoms are generally predicted with RMS errors of about 0.5 A (compared to X-ray crystal structure coordinates) and all atoms are predicted to an RMS error of 1.7 A or better.     

A look into DGAT1 through the EM lenses

With the advent of modern detectors and robust structure solution pipeline, cryogenic electron microscopy has recently proved to be game changer in structural biology. Membrane proteins are challenging targets for structural biologists. This minireview focuses a membrane embedded triglyceride synthesizing machine, DGAT1. Decades of research had built the foundational knowledge on this enzyme's activity. However, recently solved cryo-EM structures of this enzyme, in apo and bound form, has provided critical mechanistic insights. The flipping of the catalytic histidine is critical of enzyme catalysis. The structures explain why the enzyme has preference to long fatty acyl chains over the short forms.