Assessing the quality of modelled 3D protein structures using the ModFOLD server

Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.

Diversity of condensed tannin structures affects rumen in vitro methane production in sainfoin (Onobrychis viciifolia) accessions

Sainfoin is a non-bloating temperate forage legume with a moderate-to-high condensed tannin (CT) content. This study investigated whether the diversity of sainfoin accessions in terms of CT structures and contents could be related to rumen in vitro gas and methane (CH4) production and fermentation characteristics. The aim was to identify promising accessions for future investigations. Accessions differed (P < 0·0001) in terms of total gas and CH4 productions. Fermentation kinetics (i.e. parameters describing the shape of the gas production curve and half-time gas production) for CH4 production were influenced by accession (P ≤ 0·038), but not by PEG. Accession, PEG and time affected (P < 0·001) CH4 production, but accession and PEG interaction showed only a tendency (P = 0·08). Increase in CH4 due to PEG addition was not related to CT content. Further analysis of the relationships among multiple traits (nutritional composition, CT structure and CH4 production) using principal component analysis (PCA) based on optimally weighted variables revealed differences among accessions. The first two principal component axes, PC1 (57·6%) and PC2 (18·4%), explained 76·0% of the total variation among accessions. Loading of biplots derived from both PCAs made it possible to establish a relationship between the ratio of prodelphinidin:procyanidin (PD:PC) tannins and CH4 production in some accessions. The PD:PC ratio seems to be an important source of variation that is negatively related to CH4 production. These results suggested that sainfoin accessions collected from across the world exhibited substantial variation in terms of their effects on rumen in vitro CH4 production, revealing some promising accessions for future investigations.

Magnetic resonant modes in a wireless-powered circuit

A pair of circular loops of the same radius set at a distance form a closed induction circuit. Coupled to a capacitor, these loops form a resonant circuit wherein energy is transported from one to the other. When a current is introduced into one of the loops, it is received by its companion. This is due to the propagation of magnetic waves through the medium, in this instance, atmospheric air of a characteristic impedance.

Structures and relationships: women partners' careers in Germany and the UK

Purpose – This paper aims to highlight differences in women's experiences of advancement to partnership in accountancy firms in Germany and the UK and consider the ways in which such differences may be constituted by the institutional context in which they occurred. Design/methodology/approach – This research is based on 60 semi-structured interviews with women partners in Germany and the UK. Techniques adopted from grounded theory were applied. Research limitations/implications – This qualitative research is context-specific and given its cross-national, interdisciplinary nature is limited to the extent that findings cannot be generalised beyond the studied scope. Practical implications – The study points to cross-national differences in women's career advancement in accountancy firms. The findings support extant research suggesting that structured performance evaluation and hiring systems – while not without flaws – are likely more gender-neutral. In addition, the study highlights the potential of headhunters and recruitment agents as an important tool for women to navigate their way out of career culs-de-sac. Originality/value – This research provides unique insights into women partners' experiences of career advancement and, through its interdisciplinary nature, demonstrates the usefulness of employing institutional frameworks in qualitative in-depth studies of this kind

Molecular archaeology of Flaviviridae untranslated regions: duplicated RNA structures in the replication enhancer of flaviviruses and pestiviruses emerged via convergent evolution.

RNA secondary structures in the 3'untranslated regions (3'UTR) of the viruses of the family Flaviviridae, previously identified as essential (promoters) or beneficial (enhancers) for replication, have been analysed. Duplicated enhancer elements are revealed as a global feature in the evolution of the 3'UTR of distantly related viruses within the genera Flavivirus and Pestivirus. For the flaviviruses, duplicated structures occur in the 3'UTR of all four distantly related ecological virus subgroups (tick-borne, mosquito-borne, no known vector and insect-specific flaviviruses (ISFV). RNA structural differences distinguish tick-borne flaviviruses with discrete pathogenetic characteristics. For Aedes- and Culex-associated ISFV, secondary RNA structures with different conformations display numerous short ssRNA direct repeats, exposed as loops and bulges. Long quadruplicate regions comprise almost the entire 3'UTR of Culex-associated ISFV. Extended duplicated sequence and associated RNA structures were also discovered in the 3'UTR of pestiviruses. In both the Flavivirus and Pestivirus genera, duplicated RNA structures were localized to the enhancer regions of the 3'UTR suggesting an adaptive role predominantly in wild-type viruses. We propose sequence reiteration might act as a scaffold for dimerization of proteins involved in assembly of viral replicase complexes. Numerous nucleotide repeats exposed as loops/bulges might also interfere with host immune responses acting as a molecular sponge to sequester key host proteins or microRNAs.

A DFT study of the structures, stabilities and redox behaviour of the major surfaces of magnetite Fe3O4

The renewed interest in magnetite (Fe3O4) as a major phase in different types of catalysts has led us to study the oxidation–reduction behaviour of its most prominent surfaces. We have employed computer modelling techniques based on the density functional theory to calculate the geometries and surface free energies of a number of surfaces at different compositions, including the stoichiometric plane, and those with a deficiency or excess of oxygen atoms. The most stable surfaces are the (001) and (111), leading to a cubic Fe3O4 crystal morphology with truncated corners under equilibrium conditions. The scanning tunnelling microscopy images of the different terminations of the (001) and (111) stoichiometric surfaces were calculated and compared with previous reports. Under reducing conditions, the creation of oxygen vacancies in the surface leads to the formation of reduced Fe species in the surface in the vicinity of the vacant oxygen. The (001) surface is slightly more prone to reduction than the (111), due to the higher stabilisation upon relaxation of the atoms around the oxygen vacancy, but molecular oxygen adsorbs preferentially at the (111) surface. In both oxidized surfaces, the oxygen atoms are located on bridge positions between two surface iron atoms, from which they attract electron density. The oxidised state is thermodynamically favourable with respect to the stoichiometric surfaces under ambient conditions, although not under the conditions when bulk Fe3O4 is thermodynamically stable with respect to Fe2O3. This finding is important in the interpretation of the catalytic properties of Fe3O4 due to the presence of oxidised species under experimental conditions.

Novel bilayer graphene structures produced by arc-discharge

A new form of carbon is described, which consists of hollow, three-dimensional shells bounded by bilayer graphene. The new carbon is produced very simply, by passing a current through graphite rods in a commercial arc-evaporation unit. Characterisation of the carbon using high resolution transmission electron microscopy is described, and the possible formation mechanism discussed.

Can we have confidence in generic structures?

The system dynamics concept of `generic structure' is dividable into three sub-types. This paper analyses the validity of these three, using both practical and theoretical perspectives. Firstly, a new set of measures is developed for generating validity-`confidence'-amongst a group using generic structures in a practical modelling situation. It is concluded that different confidence criteria are implicitly employed; there is an argument for trading-off model precision and analytical quality for simplicity and ease of use and future research is needed to combine these `process' and `content' aspects of confidence. From a theoretical stance it is shown that with two of the sub-types a scientific notion of confidence is achievable whereas the third (`archetypes') involves merely metaphorical thinking. It is concluded that the theoretical status of archetypes requires further development, whilst ensuring that its benefits are retained.

Low-energy ion outflows from the ionosphere during a major polar cap expansion — evidence for equatorward motion of inverted-V structures

Data from the Dynamics Explorer 1 satellite and the EISCAT and Sondrestrom incoherent scatter radars, have allowed a study of low-energy ion outflows from the ionosphere into the magnetosphere during a rapid expansion of the polar cap. From the combined radar data, a 200kV increase in cross-cap potential is estimated. The upflowing ions show “X” signatures in the pitch angle-time spectrograms in the expanding midnight sector of the auroral oval. These signatures reveal low-energy (below about 60eV), light-ion beams sandwiched between two regions of ion conics and are associated with inverted-V electron precipitation. The lack of mass dispersion of the poleward edge of the event, despite great differences in the times of flight, reflects the equatorward expansion of the acceleration regions at velocities similar to those of the antisunward convection. In addition, a transient burst of upflow of 0+ is observed within the cap, possibly due to enhanced Joule heating during the event.

The importance of loop length on the stability of i-motif structures

Using UV and srCD spectroscopy it is found that loop length within the i-motif structure is important for both thermal and pH stability, but in contrast to previous statements, it is the shorter loops that exhibit the highest stability.

The principles underlying the use of powder diffraction data in solving pharmaceutical crystal structures

Solving pharmaceutical crystal structures from powder diffraction data is discussed in terms of the methodologies that have been applied and the complexity of the structures that have been solved. The principles underlying these methodologies are summarized and representative examples of polymorph, solvate, salt and cocrystal structure solutions are provided, together with examples of some particularly challenging structure determinations.

Simple method for sub-diffraction resolution imaging of cellular structures on standard confocal microscopes by three-photon absorption of quantum dots

This study describes a simple technique that improves a recently developed 3D sub-diffraction imaging method based on three-photon absorption of commercially available quantum dots. The method combines imaging of biological samples via tri-exciton generation in quantum dots with deconvolution and spectral multiplexing, resulting in a novel approach for multi-color imaging of even thick biological samples at a 1.4 to 1.9-fold better spatial resolution. This approach is realized on a conventional confocal microscope equipped with standard continuous-wave lasers. We demonstrate the potential of multi-color tri-exciton imaging of quantum dots combined with deconvolution on viral vesicles in lentivirally transduced cells as well as intermediate filaments in three-dimensional clusters of mouse-derived neural stem cells (neurospheres) and dense microtubuli arrays in myotubes formed by stacks of differentiated C2C12 myoblasts.

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

New insights on the role of paired membrane structures in coronavirus replication

The replication of coronaviruses, as in other positive-strand RNA viruses, is closely tied to the formation of membrane-bound replicative organelles inside infected cells. The proteins responsible for rearranging cellular membranes to form the organelles are conserved not just among the Coronaviridae family members, but across the order Nidovirales. Taken together, these observations suggest that the coronavirus replicative organelle plays an important role in viral replication, perhaps facilitating the production or protection of viral RNA. However, the exact nature of this role, and the specific contexts under which it is important have not been fully elucidated. Here, we collect and interpret the recent experimental evidence about the role and importance of membrane-bound organelles in coronavirus replication.