Echocardiographic quantification of myocardial function using tissue deformation imaging, a guide to image acquisition and analysis using tissue Doppler and speckle tracking

Recent developments in the field of echocardiography have allowed the cardiologist to objectively quantify regional and global myocardial function. Regional deformation (strain) and deformation rate (strain-rate) can be calculated non-invasively in both the left and right ventricle, providing information on regional (dys-)function in a variety of clinical settings. Although this promising novel technique is increasingly applied in clinical and preclinical research, knowledge about the principles, limitations and technical issues of this technique is mandatory for reliable results and for implementation both in the clinical as well as the scientific field. In this article, we aim to explain the fundamental concepts and potential clinical applicability of strain and strain-rate for both tissue Doppler imaging (TDI) derived and speckle tracking (2D-strain) derived deformation imaging. In addition, a step-by-step approach to image acquisition and post processing is proposed. Finally, clinical examples of deformation imaging in hypertrophic cardiomyopathy (HCM), cardiac resynchronization therapy (CRT) and arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C) are presented.     

Suppressed Deep Traps and Bandgap Fluctuations in Cu2CdSnS4 Solar Cells with ≈8% Efficiency

The identification of performance‐limiting factors is a crucial step in the development of solar cell technologies. Cu₂ZnSn(S,Se)₄‐based solar cells have shown promising power conversion efficiencies in recent years, but their performance remains inferior compared to other thin‐film solar cells. Moreover, the fundamental material characteristics that contribute to this inferior performance are unclear. In this paper, the performance‐limiting role of deep‐trap‐level‐inducing 2Cu_Zn+Sn_Zn defect clusters is revealed by comparing the defect formation energies and optoelectronic characteristics of Cu₂ZnSnS₄ and Cu₂CdSnS₄. It is shown that these deleterious defect clusters can be suppressed by substituting Zn with Cd in a Cu‐poor compositional region. The substitution of Zn with Cd also significantly reduces the bandgap fluctuations, despite the similarity in the formation energy of the Cu_Zn+Zn_Cu and Cu_Cd+Cd_Cu antisites. Detailed investigation of the Cu₂CdSnS₄ series with varying Cu/[Cd+Sn] ratios highlights the importance of Cu‐poor composition, presumably via the presence of V_Cu, in improving the optoelectronic properties of the cation‐substituted absorber. Finally, a 7.96% efficient Cu₂CdSnS₄ solar cell is demonstrated, which shows the highest efficiency among fully cation‐substituted absorbers based on Cu₂ZnSnS₄.     

Identification of a glycosylphosphatidylinositol anchor-modifying β1-3 N-acetylglucosaminyl transferase in Trypanosoma brucei

Trypanosoma brucei expresses complex glycoproteins throughout its life cycle. A review of its repertoire of glycosidic linkages suggests a minimum of 38 glycosyltransferase activities. Of these, five have been experimentally related to specific genes and a further nine can be associated with candidate genes. The remaining linkages have no obvious candidate glycosyltransferase genes; however, the T. brucei genome contains a family of 21 putative UDP sugar-dependent glycosyltransferases of unknown function. One representative, TbGT8 , was used to establish a functional characterization workflow. Bloodstream and procyclic-form TbGT8 null mutants were created and both exhibited normal growth. The major surface glycoprotein of the procyclic form, the procyclin, exhibited a marked reduction in molecular weight due to changes in the procyclin glycosylphosphatidylinositol (GPI) anchor side-chains. Structural analysis of the mutant procyclin GPI anchors indicated that TbGT8 encodes a UDP-GlcNAc: β-Gal-GPI β1-3 GlcNAc transferase. This is only the second GPI-modifying glycosyltransferase to have been identified from any organism. The glycosylation of the major glycoprotein of bloodstream-form T. brucei , the variant surface glycoprotein, was unaffected in the TbGT8 mutant. However, changes in the lectin binding of other glycoproteins suggest that TbGT8 influences the processing of the poly N-acetyllactosamine-containing asparagine-linked glycans of this life cycle stage.     

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/.     

ABC50 Promotes Translation Initiation in Mammalian Cells

ABC50 is an ATP-binding cassette (ABC) protein, which, unlike most ABC proteins, does not possess membrane-spanning domains. ABC50 interacts with eukaryotic initiation factor 2 (eIF2), which plays a key role in translation initiation and its control. ABC50 binds to ribosomes, and this interaction requires both the N-terminal domain and at least one ABC domain. Knockdown of ABC50 by RNA interference impaired translation of both cap-dependent and -independent reporters, consistent with a positive role for ABC50 in the function of eIF2, which is required for both types of translation initiation. Mutation of the Walker box A or B motifs in both ABC regions of ABC50 yielded a mutant protein that exerted a dominant-interfering phenotype with respect to protein synthesis and translation initiation. Importantly, although dominant-interfering mutants of ABC50 impaired cap-dependent translation, translation driven by certain internal ribosome entry segments was not inhibited. ABC50 is located in the cytoplasm and nucleoplasm but not in the nucleolus. Thus, ABC50 is not likely to be directly involved in early ribosomal biogenesis, unlike some other ABC proteins. Taken together, the present data show that ABC50 plays a key role in translation initiation and has functions that are distinct from those of other non-membrane ABC proteins.ABC50 was first reported as a protein whose expression is increased following treatment of synoviocytes with tumor necrosis factor α (1). ABC50 was subsequently identified independently as a protein that co-purified extensively with eukaryotic initiation factor 2 (eIF2)² (2). In common with other members of the ATP-binding cassette (ABC) family of proteins, ABC50 contains two ATP-binding cassettes (also termed nucleotide-binding domains (NBDs)) (1). Unlike most other members of the group, however, it lacks recognizable trans-membrane domains.Sequence analysis revealed that ABC50 is a close relative of the yeast protein Gcn20p, which is required for the control by amino acids of the yeast eIF2 kinase, Gcn2p, which is activated by binding to uncharged tRNA molecules (3). Gcn20p is thought to cooperate with Gcn1p to bring uncharged tRNAs to Gcn2p during the elongation process; this couples the availability of amino acids for tRNA charging to the control of Gcn2p (4). However, Gcn20p and ABC50 differ in important respects. For example, whereas Gcn20p associates with ribosomes that are engaged in elongation, ABC50 apparently binds ribosomes involved in initiation as well as elongation (2). Its association with ribosomes is stimulated by ATP. In addition, although Gcn20p and ABC50 are similar in their ABC domains, they differ markedly in their N termini. Since it is only the N terminus of Gcn20p that is required to support the function of Gcn2p in yeast (4), it seems likely that ABC50 and Gcn20p play distinct roles.Tyzack et al. (2) have provided initial data indicating that ABC50 stimulates the formation of complexes between eIF2, GTP, and the initiator methionyl-tRNA in vitro. It did so without affecting the binding of guanine nucleotides to eIF2, indicating that the effect is likely to be on the association of initiator methionyl-tRNA with eIF2. The available data thus suggested that ABC50 might play a positive role in the initiation of protein synthesis. However, no data for this have previously been presented. Similarly, the manner in which ABC50 binds to ribosomes, the significance of its ABC domains, and other features remained unclear.The two NBDs of ABC proteins are involved in nucleotide binding/hydrolysis and contain a number of conserved features, including the Walker box A and B motifs and the “ABC signature motif” (usually LSGGQ) (5, 6). The NBDs of eukaryotic ABC proteins “dimerize” such that the two ATP-binding/hydrolytic sites involve Walker box A of one NBD and the ABC signature motif of the other.Certain other non-membrane ABC proteins are known to be involved in translation or its control (7). Indeed, three of the eukaryotic ABCF classes contain proteins involved in the control of protein translation. Class I proteins are exemplified by ABC50 (also termed ABCF1). Class III proteins (exemplified by yeast Gcn20p) can interact with the ribosome in an ATP-dependent manner (4). The proteins of Class IVA (elongation factor 3) mediate translation elongation in certain fungi. eEF3 stimulates binding of the eEF1·GTP·aminoacyl-tRNA ternary complex to the ribosomal A site by facilitating the release of the deacylated tRNA from the E site, thus stimulating protein synthesis (8, 9). On the other hand, Class IVB contains proteins thought to be important for the export of mRNAs from the nucleus in yeast (10).The ABCE1 gene product was originally identified for its inhibition of ribonuclease L (11) and is hence also termed RLI1. Yeast Rli1p associates with 40 S ribosomal subunits in vivo and can interact with eIF3 and eIF5 independently of ribosomes (12). The available data indicate that ABCE1 is involved in both ribosome biogenesis and mRNA translation and shuttles between cytoplasm and nucleus, possibly as a nucleocytoplasmic transporter (13–17).Here, we report the first detailed investigation into the function and interactions of ABC50. The data described here identify features of ABC50 that are required for its interaction with ribosomes. Most importantly, we provide the first evidence that ABC50 is required for efficient translation initiation in living cells and show that the requirement for ABC50 differs between cap-dependent and internal ribosome entry segment (IRES)-dependent translation. These and other data indicate that the function of ABC50 is distinct from those of other ABC proteins.     

Cell-specific regulation of Fas exon 6 splicing mediated by Hu antigen R

The differential expression levels of T-cell intracellular antigens (TIA) and Hu antigen R (HuR) are concomitant with a splicing switch in apoptosis receptor Fas in HCT-116 cells. Thus, overexpression and knockdown of HuR led to Fas exon 6 skipping and inclusion, respectively. These results suggest that the TIA and HuR cellular ratio influences cell-type specific Fas exon 6 splicing pattern.     

Entomotoxic action of Sambucus nigra agglutinin i in Acyrthosiphon pisum aphids and Spodoptera exigua caterpillars through caspase‐3‐like‐dependent apoptosis

In this project, the toxicity and mechanism of action of the ricin‐B‐related lectin SNA‐I from elderberry (Sambucus nigra) in the pea aphid (Acyrthosiphon pisum) and the beet armyworm (Spodoptera exigua), two important pest insects in agriculture, were studied. SNA‐I is a chimeric lectin belonging to the class of ribosome‐inactivating proteins and consists of an A‐chain with N‐glycosidase activity and a carbohydrate‐binding B‐chain. Incorporation of 2 mg/ml of SNA‐I in the diet of neonates and adults of A. pisum caused 40–46% mortality within 2 days, while in third instars of S. exigua, the larval biomass was significantly reduced by 12% after feeding for 3 days on a diet containing 5 mg/g of SNA‐I. Interestingly, extracts of the (mid)gut of treated A. pisum and S. exigua demonstrated DNA fragmentation and this was accompanied with an increase in caspase‐3‐like activity. The involvement of cell death or apoptosis in the entomotoxicity of SNA‐I through induction of caspase‐3‐like activity was also confirmed by addition of the permeable caspase‐3 inhibitor III in the diet, leading to a rescue of the treated aphid neonates. Finally, similar to the chimeric lectin SNA‐I, the hololectin SNA‐II, consisting of two carbohydrate‐binding B‐chains caused high mortality to neonate A. pisum aphids with an LC₅₀ of 1.59 mg/ml, suggesting that the entomotoxic action of the lectins under study mainly relies on their carbohydrate‐binding activity. © 2010 Wiley Periodicals, Inc.