Assessment of protein assembly prediction in CASP13

We present the assembly category assessment in the 13th edition of the CASP community-wide experiment. For the second time, protein assemblies constitute an independent assessment category. Compared to the last edition we see a clear uptake in participation, more oligomeric targets released, and consistent, albeit modest, improvement of the predictions quality. Looking at the tertiary structure predictions, we observe that ignoring the oligomeric state of the targets hinders modeling success. We also note that some contact prediction groups successfully predicted homomeric interfacial contacts, though it appears that these predictions were not used for assembly modeling. Homology modeling with sizeable human intervention appears to form the basis of the assembly prediction techniques in this round of CASP. Future developments should see more integrated approaches where subunits are modeled in the context of the assemblies they form.     

Evolution of the visual sensory system in cichlid fishes from crater lake Barombi Mbo in Cameroon

In deep‐water animals, the visual sensory system is often challenged by the dim‐light environment. Here, we focus on the molecular mechanisms involved in rapid deep‐water adaptations. We examined visual system evolution in a small‐scale yet phenotypically and ecologically diverse adaptive radiation, the species flock of cichlid fishes in deep crater lake Barombi Mbo in Cameroon, West Africa. We show that rapid adaptations of the visual system to the novel deep‐water habitat primarily occurred at the level of gene expression changes rather than through nucleotide mutations, which is compatible with the young age of the radiation. Based on retinal bulk RNA sequencing of all eleven species, we found that the opsin gene expression pattern was substantially different for the deep‐water species. The nine shallow‐water species feature an opsin palette dominated by the red‐sensitive (LWS) opsin, whereas the two unrelated deep‐water species lack expression of LWS and the violet‐sensitive (SWS2B) opsin, thereby shifting the cone sensitivity to the centre of the light spectrum. Deep‐water species further predominantly express the green‐sensitive RH2Aα over RH2Aβ. We identified one amino acid substitution in the RH2Aα opsin specific to the deep‐water species. We finally performed a comparative gene expression analysis in retinal tissue of deep‐ vs. shallow‐water species. We thus identified 46 differentially expressed genes, many of which are associated with functions in vision, hypoxia management or circadian clock regulation, with some of them being associated with human eye diseases.     

An efficient method for the detection and elimination of systematic error in high-throughput screening

MOTIVATION: High-throughput screening (HTS) is an early-stage process in drug discovery which allows thousands of chemical compounds to be tested in a single study. We report a method for correcting HTS data prior to the hit selection process (i.e. selection of active compounds). The proposed correction minimizes the impact of systematic errors which may affect the hit selection in HTS. The introduced method, called a well correction, proceeds by correcting the distribution of measurements within wells of a given HTS assay. We use simulated and experimental data to illustrate the advantages of the new method compared to other widely-used methods of data correction and hit selection in HTS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

High-fat feeding does not induce an autophagic or apoptotic phenotype in female rat skeletal muscle

Apoptosis and autophagy are critical in normal skeletal muscle homeostasis; however, dysregulation can lead to muscle atrophy and dysfunction. Lipotoxicity and/or lipid accumulation may promote apoptosis, as well as directly or indirectly influence autophagic signaling. Therefore, the purpose of this study was to examine the effect of a 16-week high-fat diet on morphological, apoptotic, and autophagic indices in oxidative and glycolytic skeletal muscle of female rats. High-fat feeding resulted in increased fat pad mass, altered glucose tolerance, and lower muscle pAKT levels, as well as lipid accumulation and reactive oxygen species generation in soleus muscle; however, muscle weights, fiber type-specific cross-sectional area, and fiber type distribution were not affected. Moreover, DNA fragmentation and LC3 lipidation as well as several apoptotic (ARC, Bax, Bid, tBid, Hsp70, pBcl-2) and autophagic (ATG7, ATG4B, Beclin 1, BNIP3, p70 s6k, cathepsin activity) indices were not altered in soleus or plantaris following high-fat diet. Interestingly, soleus muscle displayed small increases in caspase-3, caspase-8, and caspase-9 activity, as well as higher ATG12-5 and p62 protein, while both soleus and plantaris muscle showed dramatically reduced Bcl-2 and X-linked inhibitor of apoptosis protein (XIAP) levels. In conclusion, this work demonstrates that 16 weeks of high-fat feeding does not affect tissue morphology or induce a global autophagic or apoptotic phenotype in skeletal muscle of female rats. However, high-fat feeding selectively influenced a number of apoptotic and autophagic indices which could have implications during periods of enhanced muscle stress.     

The Arabidopsis ascorbate peroxidase 3 is a peroxisomal membrane-bound antioxidant enzyme and is dispensable for Arabidopsis growth and development

Ascorbate peroxidase (APX) exists as several isoforms that are found in various compartments in plant cells. The cytosolic and chloroplast APXs appear to play important roles in antioxidation metabolism in plant cells, yet the function of peroxisomal APX is not well studied. In this study, the localization of a putative peroxisomal membrane-bound ascorbate peroxidase, APX3 from Arabidopsis, was confirmed by studying the green fluorescent protein (GFP)-APX3 fusion protein in transgenic plants. GFP-APX3 was found to co-localize with a reporter protein that was targeted to peroxisomes by the peroxisomal targeting signal 1. The function of APX3 in Arabidopsis was investigated by analysing an APX3 knockout mutant under normal and several stress conditions. It was found that loss of function in APX3 does not affect Arabidopsis growth and development, suggesting that APX3 may not be an important antioxidant enzyme in Arabidopsis, at least under the conditions that were tested, or the function of APX3 could be compensated by other antioxidant enzymes in plant cells.     

Structural and Genetic Basis for the Serological Differentiation of Pasteurella multocida Heddleston Serotypes 2 and 5

Pasteurella multocida is classified into 16 serotypes according to the Heddleston typing scheme. As part of a comprehensive study to define the structural and genetic basis of this scheme, we have determined the structure of the lipopolysaccharide (LPS) produced by P. multocida strains M1404 (B:2) and P1702 (E:5), the type strains for serotypes 2 and 5, respectively. The only difference between the LPS structures made by these two strains was the absence of a phosphoethanolamine (PEtn) moiety at the 3 position of the second heptose (Hep II) in M1404. Analysis of the lpt-3 gene, required for the addition of this PEtn residue, revealed that the gene was intact in P1702 but contained a nonsense mutation in M1404. Expression of an intact copy of lpt-3 in M1404 resulted in the attachment of a PEtn residue to the 3 position of the Hep II residue, generating an LPS structure identical to that produced by P1702. We identified and characterized each of the glycosyltransferase genes required for assembly of the serotype 2 and 5 LPS outer core. Monoclonal antibodies raised against serotype 2 LPS recognized the serotype 2/5-specific outer core LPS structure, but recognition of this structure was inhibited by the PEtn residue on Hep II. These data indicate that the serological classification of strains into Heddleston serotypes 2 and 5 is dependent on the presence or absence of PEtn on Hep II.Pasteurella multocida is a gram-negative pathogen that causes serious diseases in animals and humans. It is the causative agent of fowl cholera (7), hemorrhagic septicemia in cattle (9), atrophic rhinitis in pigs (6), and dog and cat bite infections in humans (28).P. multocida isolates may be grouped serologically based on capsular antigens into five serogroups—A, B, D, E, and F—using a passive hemagglutination test with erythrocytes sensitized with capsular antigen. Structural information is available for the capsular polysaccharides synthesized by serogroups A (hyaluronic acid) (22), D (heparin) (10), and F (chondroitin) (10). The genes involved in biosynthesis of the capsules have been identified for all five serogroups (27), and capsule is a critical virulence factor for serogroups A (8) and B (3).Lipopolysaccharide (LPS) is also an important virulence factor in P. multocida (13) and can be used for the identification of strains, with two main somatic typing systems reported (14, 17). The Namioka system is based on a tube agglutination test and is able to recognize 11 serotypes (17), whereas the Heddleston system uses a gel diffusion precipitation test and can recognize 16 serotypes; the Heddleston system is currently the preferred method (14). Current classification of P. multocida strains combines capsular typing with Heddleston somatic typing. Strains are given a designation in which the first letter indicates the capsular group and the number designates the Heddleston LPS serotype (e.g., A:1 indicates a strain that is capsular group A and LPS serotype 1). LPS produced by each of the 16 Heddleston serotype strains has been examined previously for sugar content and reactivity with LPS antisera (21). The LPS isolated from serotype 2 and 5 strains was virtually identical in sodium dodecyl sulfate-polyacrylamide gel electrophoresis migration profile (19), sugar composition, and serological reactivity with anti-LPS antibodies (21). Interestingly, serotypes 2 and 5 were the only serotypes found to elaborate two isomers of heptose in their LPS, namely l-glycero-d-manno-heptose (ld-Hep) and d-glycero-d-manno-heptose (dd-Hep) (21). The aims of this study were to determine whether the LPS molecules made by these two serotypes were structurally distinct and to compare the LPS structures with those previously determined for P. multocida serotypes 1 and 3 (24-26). Furthermore, we identified the transferase genes responsible for the assembly of the outer core LPS structure in each of these strains and characterized the function of each glycosyltransferase.     

Dimethylaminopyridine derivatives of lupane triterpenoids are potent disruptors of mitochondrial structure and function

Development of mitochondrially-targeted drugs is receiving increasing attention because of the central roles these organelles play in energy production, reactive oxygen generation, and regulation of cell death pathways. Previous studies have demonstrated that both natural and synthetic triterpenoids can disrupt mitochondrial structure and function. In this study, we tested the ability of a number of dimethylaminopyridine (DMAP) derivatives of lupane triterpenoids to target mitochochondria in two human melanoma cell lines and an untransformed normal fibroblast line. These compounds induced a striking fragmentation and depolarization of the mitochondrial network, along with an inhibition of cell proliferation. A range of potencies among these compounds was noted, which was correlated with the number, position, and orientation of the DMAP groups. Overall, the extent of proliferation inhibition mirrored the effectiveness of mitochondrial disruption. Thus, DMAP derivatives of lupane triterpenoids can be potent mitochondrial perturbants that appear to suppress cell growth primarily via their mitochondrial effects.     

A cross-sectional study of biotechnology awareness and teaching in European high schools

Undoubtedly, biotechnology has a tremendous impact on our daily lives. As a result of this and in parallel to the advancement of knowledge in this field of applied research, consumer awareness of the potential benefits and risks of this technology has steadily increased, leading to a thorough investigation of the public perception of biotechnology in the past years. Indeed, it has become clear that it is in the general interest of science and especially of applied research to inform the public of its advances. A promising next step is to strengthen biotechnology communication in scholastic institutions. In this paper, we investigate the perception of biotechnology in a specific target group, namely high-school students in the 16–20-year-old age range. We conducted a questionnaire-based survey on a total of 1410 students in six European countries to investigate students’ perception, concern, scientific knowledge, and awareness. Our data revealed some unexpected patterns of acceptance and concern about biotechnology. Knowledge analysis indicated that pupils lack specific knowledge about biotechnological applications and their interest in biotechnology appeared to be linked to knowledge. Analysis of specific questions about teaching practices at schools suggests that a better targeted choice in media as vehicles for information together with selected speakers could be instrumental in increasing students’ interest in science and more specifically in biotechnology.