Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy

The comparison of a pair of electron microscope images recorded at different specimen tilt angles provides a powerful approach for evaluating the quality of images, image-processing procedures, or three-dimensional structures. Here, we analyze tilt-pair images recorded from a range of specimens with different symmetries and molecular masses and show how the analysis can produce valuable information not easily obtained otherwise. We show that the accuracy of orientation determination of individual single particles depends on molecular mass, as expected theoretically since the information in each particle image increases with molecular mass. The angular uncertainty is less than 1° for particles of high molecular mass (∼ 50 MDa), several degrees for particles in the range 1-5 MDa, and tens of degrees for particles below 1 MDa. Orientational uncertainty may be the major contributor to the effective temperature factor (B-factor) describing contrast loss and therefore the maximum resolution of a structure determination. We also made two unexpected observations. Single particles that are known to be flexible showed a wider spread in orientation accuracy, and the orientations of the largest particles examined changed by several degrees during typical low-dose exposures. Smaller particles presumably also reorient during the exposure; hence, specimen movement is a second major factor that limits resolution. Tilt pairs thus enable assessment of orientation accuracy, map quality, specimen motion, and conformational heterogeneity. A convincing tilt-pair parameter plot, where 60% of the particles show a single cluster around the expected tilt axis and tilt angle, provides confidence in a structure determined using electron cryomicroscopy.     

Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending protein Hbb

The genome of the Lyme disease-causing spirochete Borrelia burgdorferi encodes only a single polypeptide from the integration host factor (IHF)/HU or 'DNABII' family of nucleoid-associated proteins - Hbb. DNABII proteins induce large bends in DNA and serve as architectural factors in a variety of prokaryotic cellular processes. We have solved the crystal structure of an Hbb-DNA complex in which the DNA is bent by over 180 degrees . We find that like IHF, Hbb relies exclusively on indirect readout to recognize its cognate site. Additional binding studies show that the sequence preferences of Hbb are related to, yet distinct from those of IHF. Defining these binding characteristics may help to uncover additional roles for Hbb in Borrelia DNA metabolism as well as further our understanding of the mechanism of indirect readout.     

Cell integrins: commonly used receptors for diverse viral pathogens

When searching for their favorite host tissues, animal viruses frequently attach to cell-surface receptors that have key roles in normal cell physiology. Integrins are prime examples of physiologically important receptors that have been usurped by nonenveloped and enveloped viruses for attachment and/or cell entry. This family of heterodimeric receptors mediates cell adhesion, cell migration, tumor metastasis and cell differentiation. Recent investigations have shed new light on integrin structure as well as on the underlying molecular features of their association with viral ligands. In this review, we discuss several examples of virus-integrin interactions that highlight recent advances in this field. The continuing improvements in virus and cell imaging techniques have helped to uncover the molecular basis of how integrins are recognized by such a wide range of microbial pathogens to invade host cells.     

Prediction of mean adult survival rates of southern African birds from demographic and ecological covariates

Estimates of annual survival rates of birds are valuable in a wide range of studies of population ecology and conservation. These include modelling studies to assess the impacts of climatic change or anthropogenic mortality for many species for which no reliable direct estimates of survival are available. We evaluate the performance of regression models in predicting adult survival rates of birds from values of demographic and ecological covariates available from textbooks and databases. We estimated adult survival for 67 species using dead recoveries of birds ringed in southern Africa and fitted regression models using five covariates: mean clutch size, mean body mass, mean age at first breeding, diet and migratory tendency. Models including these explanatory variables performed well in predicting adult survival in this set of species, both when phylogenetic relatedness of the species was taken into account using phylogenetic generalized least squares (51% of variation in logit survival explained) and when it was not (48%). Two independent validation tests also indicated good predictive power, as indicated by high correlations of observed with expected values in a leave‐one‐out cross validation test performed using data from the 67 species (35% of variation in logit survival explained), and when annual survival rates from independent mark–recapture studies of 38 southern African species were predicted from covariates and the regression using dead recoveries (48%). Clutch size and body mass were the most influential covariates, both with and without the inclusion of phylogenetic effects, and a regression model including only these two variables performed well in both of the validation tests (39 and 48% of variation in logit survival explained). Our regression models, including the version with only clutch size and body mass, are likely to perform well in predicting adult survival rate for southern African species for which direct survival estimates are not available.     

Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways

Background

Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6).

Results

Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity.

Conclusion

The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1014) contains supplementary material, which is available to authorized users.     

Producing Gestures Facilitates Route Learning

The present study investigates whether producing gestures would facilitate route learning in a navigation task and whether its facilitation effect is comparable to that of hand movements that leave physical visible traces. In two experiments, we focused on gestures produced without accompanying speech, i.e., co-thought gestures (e.g., an index finger traces the spatial sequence of a route in the air). Adult participants were asked to study routes shown in four diagrams, one at a time. Participants reproduced the routes (verbally in Experiment 1 and non-verbally in Experiment 2) without rehearsal or after rehearsal by mentally simulating the route, by drawing it, or by gesturing (either in the air or on paper). Participants who moved their hands (either in the form of gestures or drawing) recalled better than those who mentally simulated the routes and those who did not rehearse, suggesting that hand movements produced during rehearsal facilitate route learning. Interestingly, participants who gestured the routes in the air or on paper recalled better than those who drew them on paper in both experiments, suggesting that the facilitation effect of co-thought gesture holds for both verbal and nonverbal recall modalities. It is possibly because, co-thought gesture, as a kind of representational action, consolidates spatial sequence better than drawing and thus exerting more powerful influence on spatial representation.     

The effects of insects,nutrients, and plant invasion on community structure and function above‐ and belowground

Soil nutrient availability, invasive plants, and insect presence can directly alter ecosystem structure and function, but less is known about how these factors may interact. In this 6‐year study in an old‐field ecosystem, we manipulated insect abundance (reduced and control), the propagule pressure of an invasive nitrogen‐fixing plant (propagules added and control), and soil nutrient availability (nitrogen added, nitrogen reduced and control) in a fully crossed, completely randomized plot design. We found that nutrient amendment and, occasionally, insect abundance interacted with the propagule pressure of an invasive plant to alter above‐ and belowground structure and function at our site. Not surprisingly, nutrient amendment had a direct effect on aboveground biomass and soil nutrient mineralization. The introduction of invasive nitrogen‐fixing plant propagules interacted with nutrient amendment and insect presence to alter soil bacterial abundance and the activity of the microbial community. While the larger‐scale, longer‐term bulk measurements such as biomass production and nutrient mineralization responded to the direct effects of our treatments, the shorter‐term and dynamic microbial communities tended to respond to interactions among our treatments. Our results indicate that soil nutrients, invasive plants, and insect herbivores determine both above‐ and belowground responses, but whether such effects are independent versus interdependent varies with scale.     

Conformational features of topologically classified RNA secondary structures

Background

Current RNA secondary structure prediction approaches predict prevalent pseudoknots such as the H-pseudoknot and kissing hairpin. The number of possible structures increases drastically when more complex pseudoknots are considered, thus leading to computational limitations. On the other hand, the enormous population of possible structures means not all of them appear in real RNA molecules. Therefore, it is of interest to understand how many of them really exist and the reasons for their preferred existence over the others, as any new findings revealed by this study might enhance the capability of future structure prediction algorithms for more accurate prediction of complex pseudoknots.

Methodology/Principal Findings

A novel algorithm was devised to estimate the exact number of structural possibilities for a pseudoknot constructed with a specified number of base pair stems. Then, topological classification was applied to classify RNA pseudoknotted structures from data in the RNA STRAND database. By showing the vast possibilities and the real population, it is clear that most of these plausible complex pseudoknots are not observed. Moreover, from these classified motifs that exist in nature, some features were identified for further investigation. It was found that some features are related to helical stacking. Other features are still left open to discover underlying tertiary interactions.

Conclusions

Results from topological classification suggest that complex pseudoknots are usually some well-known motifs that are themselves complex or the interaction results of some special motifs. Heuristics can be proposed to predict the essential parts of these complex motifs, even if the required thermodynamic parameters are currently unknown.     

Potential impacts of climatic change on southern African birds of fynbos and grassland biodiversity hotspots

Aim To examine potential impacts of climatic change on bird species richness of the fynbos and grassland biomes, especially on species of conservation concern, and to consider implications for biodiversity conservation strategy. Location Southern Africa, defined for this study as South Africa, Lesotho and Swaziland. Methods Climate response surfaces were fitted to model relationships between recorded distributions and reporting rates of 94 species and current bioclimatic variables. These models were used to project species’ potential ranges and reporting rates for future climatic scenarios derived from three general circulation models for 30‐year periods centred on 2025, 2055 and 2085. Results were summarized for species associated with each biome and examined in detail for 12 species of conservation concern. Results Species richness of fynbos and grassland bird assemblages will potentially decrease by an average of 30–40% by 2085 as a result of projected climatic changes. The areas of greatest richness are projected to decrease in extent and to shift in both cases. Attainment of projected shifts is likely to be limited by extent of untransformed habitat. Most species of conservation concern are projected to decrease in range extent, some by > 60%, and to decrease in reporting rate even where they persist, impacts upon their populations thus being greater than might be inferred from decreases in range extent alone. Two species may no longer have any areas of suitable climatic space by 2055; both already appear to be declining rapidly. Main conclusions Species losses are likely to be widespread with most species projected to decrease in range extent. Loss of key species, such as pollinators, may have far‐reaching implications for ecosystem function and composition. Conservation strategies, and identification of species of conservation concern, need to be informed by such results, notwithstanding the many uncertainties, because the certainties of climatic change make it essential that likely impacts not to be ignored.