Marker-free image registration of electron tomography tilt-series

Background  

Tilt series are commonly used in electron tomography as a means of collecting three-dimensional information from two-dimensional projections. A common problem encountered is the projection alignment prior to 3D reconstruction. Current alignment techniques usually employ gold particles or image derived markers to correctly align the images. When these markers are not present, correlation between adjacent views is used to align them. However, sequential pairwise correlation is prone to bias and the resulting alignment is not always optimal.     

Ab initio and homology based prediction of protein domains by recursive neural networks

Background  

Proteins, especially larger ones, are often composed of individual evolutionary units, domains, which have their own function and structural fold. Predicting domains is an important intermediate step in protein analyses, including the prediction of protein structures.     

Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks

Background

Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3–4 Å from the native structure). Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure.

Results

We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that C _α trace reconstructions based on 4-class native maps are significantly better than those from residue contact maps. We then build two predictors of 4-class maps based on recursive neural networks: one ab initio, or relying on the sequence and on evolutionary information; one template-based, or in which homology information to known structures is provided as a further input. We show that virtually any level of sequence similarity to structural templates (down to less than 10%) yields more accurate 4-class maps than the ab initio predictor. We show that template-based predictions by recursive neural networks are consistently better than the best template and than a number of combinations of the best available templates. We also extract binary residue contact maps at an 8 Å threshold (as per CASP assessment) from the 4-class predictors and show that the template-based version is also more accurate than the best template and consistently better than the ab initio one, down to very low levels of sequence identity to structural templates. Furthermore, we test both ab-initio and template-based 8 Å predictions on the CASP7 targets using a pre-CASP7 PDB, and find that both predictors are state-of-the-art, with the template-based one far outperforming the best CASP7 systems if templates with sequence identity to the query of 10% or better are available. Although this is not the main focus of this paper we also report on reconstructions of C _α traces based on both ab initio and template-based 4-class map predictions, showing that the latter are generally more accurate even when homology is dubious.

Conclusion

Accurate predictions of multi-class maps may provide valuable constraints for improved ab initio and template-based prediction of protein structures, naturally incorporate multiple templates, and yield state-of-the-art binary maps. Predictions of protein structures and 8 Å contact maps based on the multi-class distance map predictors described in this paper are freely available to academic users at the url http://distill.ucd.ie/.     

Establishment and characterization of baboon embryonic stem cell lines: An Old World Primate model for regeneration and transplantation research

Here we have developed protocols using the baboon as a complementary alternative Old World Primate to rhesus and other macaques which have severe limitations in their availability. Baboons are not limited as research resources, they are evolutionarily closer to humans, and the multiple generations of pedigreed colonies which display complex human disease phenotypes all support their further optimization as an invaluable primate model. Since neither baboon-assisted reproductive technologies nor baboon embryonic stem cells (ESCs) have been reported, here we describe the first derivations and characterization of baboon ESC lines from IVF-generated blastocysts. Two ESCs lines (BabESC-4 and BabESC-15) display ESC morphology, express pluripotency markers (Oct-4, hTert, Nanog, Sox-2, Rex-1, TRA1-60, TRA1-81), and maintain stable euploid female karyotypes with parentage confirmed independently. They have been grown continuously for > 430 and 290 days, respectively. Teratomas from both lines have all three germ layers. Availabilities of these BabESCs represent another important resource for stem cell biologists.     

PKCtheta is a key player in the development of insulin resistance

Activation of PKCtheta is associated with lipid-induced insulin resistance and PKCtheta knockout mice are protected from the lipid-induced defects. However, the exact mechanism by which PKCtheta contributes to insulin resistance is not known. To investigate whether an increase in PKCtheta expression leads to insulin resistance, C2C12 skeletal muscle cells were transfected with PKCtheta DNA and treated with different concentrations of insulin for 10 min. PKCtheta overexpression induced reduction of IRS-1 protein levels with a decrease in insulin-induced p85 binding to IRS-1, phosphorylation of PKB and its substrates, p70 and GSK3. Pretreatment of these cells with GF-109203X (a non-specific PKC inhibitor, IC50 for PKCtheta = 10 nM) recovered insulin signaling. PKCtheta was found to be expressed in liver and treatment of human hepatoma cells (HepG2) with high insulin and glucose resulted in an increase in PKCtheta expression that correlated with a decrease in IRS-1 protein levels and the development of insulin resistance. Reduction of PKCtheta expression using RNAi technology significantly inhibited the degradation of IRS-1 and enhanced insulin-induced IRS-1 tyrosine phosphorylation, p85 association to IRS-1 and PKB phosphorylation. In conclusion, by overexpressing PKCtheta or using RNAi technology to downregulate PKCtheta, we have demonstrated that PKCtheta has a key role in the development of insulin resistance. These findings suggest that PKCtheta mediates not only insulin resistance in muscle but also in liver, which may contribute to the development of whole body insulin resistance and diabetes.     

Seasonal phenology of Aphis glycines (Hemiptera: Aphididae) and other aphid species in cultivated bean and noncrop habitats in Wisconsin

The occurrence of aphid-transmitted viruses in agricultural crops of the Midwest and northeastern United States has become more frequent since the arrival and establishment of the soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae). A. glycines is a competent vector of plant viruses and may be responsible for recent virus epidemics in Wisconsin snap bean, Phaseolus vulgaris L., fields. To determine whether vegetation surrounding crop fields could serve as sources of virus inocula, we examined the settling activity ofA. glycines and other aphid species in agricultural crops and noncrop field margins adjacent to snap bean fields. Noncrop field margins were made up of numerous virus-susceptible plant species within 10 m from snap bean field edges. During summers 2006 and 2007, horizontal pan traps were placed in commercial soybean [Glycine max (L.) Merr.], snap bean, and surrounding field margins to characterize aphid flight activity patterns in the different habitat types. Alate abundance and peak occurrence across years varied between crop and noncrop field margins and differed among patches of plants in field margins. Overall aphid activity peaked late in the season (21 August in 2006 and 28 July in 2007); with the majority (52%) of total aphids trapped in all habitats being A. glycines. Susceptibility to viral infection and confirmed visitation of A. glycines to these forage plants suggests the importance ofnoncrop habitats as potential sources of primary virus inoculum. Viral disease onset followed peak aphid flights and further implicates A. glycines as a likely vector of viruses in commercial bean and other crops in Wisconsin.     

Transgenerational effects of poor elemental food quality on Daphnia magna

Environmental effects on parents can strongly affect the phenotype of their offspring, which alters the heritability of traits and the offspring’s responses to the environment. We examined whether P limitation of the aquatic invertebrate, Daphnia magna, alters the responses of its offspring to inadequate P nutrition. Mother Daphnia consuming P-poor algal food produced smaller neonates having lower body P content compared to control (P-rich) mothers. These offspring from P-stressed mothers, when fed P-rich food, grew faster and reproduced on the same schedule as those from P-sufficient mothers. In contrast, offspring from P-stressed mothers, when fed P-poor food, grew more slowly and had delayed reproduction compared to their sisters born to control mothers. There was also weak evidence that daughters from P-stressed mothers are more susceptible to infection by the virulent bacterium, Pasteuria ramosa. Our results show that P stress is not only transferred across generations, but also that its effect on the offspring generation varies depending upon the quality of their own environment. Maternal P nutrition can thus determine the nature of offspring responses to food P content and potentially obfuscates relationships between the performance of offspring and their own nutrition. Given that food quality can be highly variable within and among natural environments, our results demonstrate that maternal effects should be included as an additional dimension into studies of how elemental nutrition affects the physiology, ecology, and evolution of animal consumers.     

Examining affinities of the Taung child by developmental simulation

As a well-preserved juvenile and the type specimen of Australopithecus africanus, the Taung child figures prominently in taxonomic, ontogenetic, and phylogenetic analyses of fossil hominins. Despite general agreement about allocation of Sterkfontein and Makapansgat fossils to this species, limited morphological comparisons have been possible between these adult specimens and the juvenile Taung. Here, we used developmental simulation to estimate the adult form of the Taung child, and directly compare its morphology to that of other fossil hominins. Specimens were represented by 50 three-dimensional landmarks superimposed by generalized Procrustes analysis. The simulation process applied developmental trajectories from extant hominine species to the Taung fossil in order to generate its adult form. Despite differences found in the developmental patterns of these modern species, simulations tested on extant juveniles-transforming them into "adults" using trajectories from other species-revealed that these differences have negligible impact on adult morphology. This indicates that morphology already present by occlusion of the first permanent molar is the primary determinant of adult form, thereby supporting use of extant trajectories to estimate the morphology of an extinct species. The simulated Taung adult was then compared to other adult fossils. As these comparisons required assumptions about the pattern and magnitude of developmental change, additional analyses were performed to evaluate these two parameters separately. Results of all analyses overwhelmingly rejected the possibility that the Taung child was a juvenile robust australopith, but were consistent with the hypothesis that the Taung and Sterkfontein fossils are conspecific. Between Sts 5 and Sts 71, the latter is more likely to resemble the adult form of the Taung child.     

The CD11a partner in Sus scrofa lymphocyte function-associated antigen-1 (LFA-1): mRNA cloning, structure analysis and comparison with mammalian homologues

Background  

Lymphocyte function-associated antigen-1 (LFA-1, CD11a/CD18, alphaLbeta2), the most abundant and widely expressed beta2-integrin, is required for many cellular adhesive interactions during the immune response. Many studies have shown that LFA-1 is centrally involved in the pathogenesis of several diseases caused by Repeats-in-toxin (RTX) -producing bacteria.