Ribosomal RNA phylogenetics: the third dimension

With integration of secondary structures, ribosomal genes have once again become very popular for phylogenetic analyses. This additional source of information to the nucleotide sequence provides a massive boost for taxonomic inferences. Herein, we propose that in the near future a further benefit for phylogenetics with such genes will be very likely by inclusion of the third dimension. For the first time, we determined the tertiary structure of the ribosomal internal transcribed spacer 2 for Chlamydomonas rheinhardtii by application of two different in silico prediction algorithms. We compared these methods with focus on phylogenetic usability. Further, we determined the tertiary structures for closely related green algae to provide a small phylogenetic example. The results suggest that the tertiary structure inherits evolutionary information observable neither within the sequence nor in the secondary structure.     

Palaeontology in a molecular world: the search for authentic ancient DNA

The survival of ancient DNA in specimens up to several thousands of years old is established. However, there have been several claims concerning the recovery of geologically ancient DNA from fossil material many millions of years old. The authenticity of these fossil DNA sequences is questionable on theoretical and empirical grounds, and the existence of authentic geologically ancient DNA remains to be proven.     

Death in the third dimension: apoptosis regulation and tissue architecture

Tissue development, homeostasis and tumor pathogenesis all depend upon a complex dialogue between multiple cell types operating within a dynamic three-dimensional (3D) tissue extracellular matrix microenvironment. A major issue is whether the spatial organization of a cell within this 3D tissue microenvironment could modulate cell responsiveness to regulate cell fate decisions such as survival, and if so how. Classic developmental model systems and transgenic animals are instructive but pose special challenges for investigators conducting signaling studies and biochemical assays in tissues. As an alternative, 3D culture model systems exist in which cell-adhesion dependent tissue architecture, heterotypic cell-cell interactions and tissue differentiation can be recapitulated with good fidelity. 3D cell culture models are slowly revealing how tissue architecture can dramatically influence how a cell responds to exogenous stimuli to modify its apoptotic behavior and hence should prove instrumental for identifying novel cell death pathways.     

Rho family GTPases: Making it to the third dimension

The role of Rho family GTPases in controlling the actin cytoskeleton and thereby regulating cell migration has been well studied for cells migrating on 2D surfaces. In vivo, cell migration occurs within three-dimensional matrices and along aligned collagen fibers with rather different spatial requirements. Recently, a handful of studies coupled with new approaches have demonstrated that Rho GTPases have unique regulation and roles during cell migration within 3D matrices, along collagen fibers, and in vivo. Here we propose that migration on aligned matrices facilitates spatial organization of Rho family GTPases to restrict and stabilize protrusions in the principle direction of alignment, thereby maintaining persistent migration. The result is coordinated cell movement that ultimately leads to higher rates of metastasis in vivo.     

Distance estimation in the third dimension in desert ants

Desert ants of the genus Cataglyphis perform large-scale foraging excursions from which they return to their nest by path integration. They do so by integrating courses steered and the distances travelled into a continually updated home vector. While it is known that the angular orientation is based on skylight cues, it still is largely enigmatic how the ants measure distances travelled. We extended the ants' task into the third dimension by training them to walk within an array of uphill and downhill channels, and later testing them on flat terrain, or vice versa. In these tests the ants indicated homing distances that did not correspond to the distances actually travelled, but to the ground distances; that is, to the sum of the horizontal projections of the uphill and downhill segments of the ants' paths. These results suggest a much more sophisticated mechanism of distance estimation than hitherto thought. The ants must be able to measure the slopes of undulating terrain and to integrate this information into their "odometer" for the distance estimation process.     

Adding a third dimension to the edge of a species' range: altitude and genetic structuring in mountainous landscapes

In addition to the topographical and ecological barriers, other landscape features may also subtly influence the patterns of gene flow and spatial genetic structuring at species' borders. This paper focuses on the role played by altitudinal gradients that characterize mountainous landscapes. We formulate and test the hypothesis that when the distribution boundaries of plant species intersect mountainous landscapes, altitudinal gradients in ecological conditions may considerably enhance population subdivision and genetic structuring at the regional level. Using amplified fragment length polymorphism markers, we studied genetic diversity and differentiation in a set of 21 peripheral populations of the evergreen shrub Lavandula latifolia Med. (Labiatae) at its southernmost distribution limit in the Betic mountain ranges of southern Spain. Population size and abundance, and within-population genetic diversity, varied predictably with altitude, being highest at middle elevations and declining steadily towards both the upper and lower altitudinal distribution margins. Genetic differentiation tended to follow the opposite trend. These altitudinal patterns result from variation with elevation in the relative influence of gene flow and drift on the distribution of genetic variation. Genetic drift prevails around the upper and lower altitudinal limits, whereas a situation closer to a drift-gene flow equilibrium exists at the center of the altitudinal distribution. Altitudinal variation in the relative influences of gene flow and drift appears as an essential element in the interpretation of regional genetic structuring of L. latifolia at its mountainous distribution edge, and a factor which may influence the evolutionary potential of peripheral populations and the likelihood of local adaptation.     

A three-dimensional working model for a guide RNA from Trypanosoma brucei.

RNA editing in protozoan parasites is a mitochondrial RNA processing reaction in which exclusively uridylate residues are inserted into, and less frequently deleted from, pre-mRNAs. Molecules central to the process are so-called guide RNAs (gRNAs) which function as templates in the reaction. For a detailed molecular understanding of the mechanism of the editing process knowledge of structural features of gRNAs will be essential. Here we report on a computer-assisted molecular modelling approach to construct the first three-dimensional gRNA model for gND7-506, a ND7-specific gRNA from Trypanosoma brucei. The modelling process relied on chemical modification and enzymatic probing data and was validated by in vitro mutagenesis experiments. The model predicts a reasonably compact structure, where two stem/loop secondary structure elements are brought into close proximity by a triple A tertiary interaction, forming a core element within the centre of the molecule. The model further suggests that the surface of the gRNA is primarily made up of the sugar-phoshate backbone. On the basis of the model, footprinting experiments of gND7-506 in a complex with the gRNA binding protein gBP21 could successfully be interpreted and provide a first picture for the assembly of gRNAs within a ribonucleoprotein complex.     

Integrating the third dimension into the concept of urban ecosystem services: A review

The spatial configuration of urban environments and its impact on local and global ecological functions were the subject of recent urban ecosystem service (UES) research projects. The outcomes of these projects with respect to the data they used, however, mainly consisted of two dimensions (2D). Studies that assess aspects of the third dimension (3D) of UES – such as height, volume and shadowing effects – were absent. The objective of this paper is to contribute to a better understanding of the local ecological functions based on knowledge of three-dimensional UES. 298 articles were selected for in-depth critical analyses. The technical and computational approaches for extracting urban 3D structures and 3D structures of vegetation were the focus of the reviewed literature. Authors’ affiliations would be a better indicator for assessing the spatial distribution of articles. Uneven distribution of knowledge among countries is related to the technical and scientific advancement of countries. There was a shift in the sub-theme of reviewed publications discussing the concept of ecosystem services in the first few years, while later researchers’ interests moved towards UES and adaptation of cities to the changing climate. Further studies should progress in the development of both 3D data and results. Implementing 3D data and results helps to better understand the coupling of humans and their environs. It will be then a critically important step toward developing ecologically friendly cities.     

Communication in the third dimension: song perch height of rivals affects singing response in nightingales

Many animals use long-range signals to compete over mates and resources. Optimal transmission can be achieved by choosing efficient signals, or by choosing adequate signalling perches and song posts. High signalling perches benefit sound transmission and reception, but may be more risky due to exposure to airborne predators. Perch height could thus reflect male quality, with individuals signalling at higher perches appearing as more threatening to rivals. Using playbacks on nightingales (Luscinia megarhynchos), we simulated rivals singing at the same height as residents, or singing three metres higher. Surprisingly, residents increased song output stronger, and, varying with future pairing success, overlapped more songs of the playback when rivals were singing at the same height than when they were singing higher. Other than expected, rivals singing at the same height may thus be experienced as more threatening than rivals singing at higher perches. Our study provides new evidence that territorial animals integrate information on signalling height and thus on vertical cues in their assessment of rivals.     

Holothuria triterpene glycosides: a comprehensive guide for their structure elucidation and critical appraisal of reported compounds

Phytochemistry Reviews - Sea cucumbers or holothurians are marine invertebrates, belonging to the phylum Echinodermata (kingdom Animalia). In Asia, they are commonly used as food, while they are...     

On the relationship between fractal dimension and encounters in three-dimensional trajectories

The encounter of individuals-prey, predators and mates-living in the surrounding environment is a fundamental process in the life of an organism. Along with the sensory abilities, this process will be regulated by the movement rules adopted by the individual. In this work we discuss the encounter-enhancement effect due to different natatorial modes by calculating the number of encounters realised by differently convoluted trajectories in two homogeneous distributions of particles. Using numerically generated trajectories representative of specific swimming behaviour, we demonstrate that high values of three-dimensional fractal dimension D(3D)(>1.9) are beneficial only at high concentration, whereas at low concentration less tortuous tracks (D(3D) approximately 1.5) are almost equally efficient. In the light of our results it is possible to better understand the behavioural adaptations evolved by individuals to thrive in their environment.     

Correction to: Holothuria triterpene glycosides: a comprehensive guide for their structure elucidation and critical appraisal of reported compounds

Phytochemistry Reviews -