Relations among higher Whitehead maps

We define generalised higher Whitehead maps between polyhedral products. By investigating the interplay between the homotopy-theoretic properties of polyhedral products and the combinatorial properties of simplicial complexes, we describe new families of relations among these maps, while recovering and generalising known identities among Whitehead products.Comment: 44 page

Unravelling the photoprotection properties of mycosporine amino acid motifs

Photoprotection from harmful ultraviolet (UV) radiation exposure is a key problem in modern society. Mycosporine like amino acids found in fungi, cyanobacteria, macroalgae, phytoplankton and humans, are already presenting a promising form of natural photoprotection in sunscreen formulations. Using time-resolved transient electronic absorption spectroscopy and guided by complementary ab initio calculations, we help to unravel how the core structures of these molecules perform under UV irradiation. Through such detailed insight into the relaxation mechanisms of these ubiquitous molecules, we hope to inspire new thinking in developing next generation sun protecting molecules

Mapping local structural perturbations in the native state of stefin B (cystatin B) under amyloid forming conditions

Unlike a number of amyloid-forming proteins, stefins, and in particular stefin B (cystatin B) form amyloids under conditions where the native state predominates. In order to trigger oligomerization processes, the stability of the protein needs to be compromised, favoring structural re-arrangement however, accelerating fibril formation is not a simple function of protein stability. We report here on how optimal conditions for amyloid formation lead to the destabilization of dimeric and tetrameric states of the protein in favor of the monomer. Small, highly localized structural changes can be mapped out that allow us to visualize directly areas of the protein which eventually become responsible for triggering amyloid formation. These regions of the protein overlap with the Cu (II)-binding sites which we identify here for the first time. We hypothesize that in vivo modulators of amyloid formation may act similarly to painstakingly optimized solvent conditions developed in vitro. We discuss these data in the light of current structural models of stefin B amyloid fibrils based on H-exchange data, where the detachment of the helical part and the extension of loops were observed

Rationale and study design of the MINERVA study: Multicentre Investigation of Novel Electrocardiogram Risk markers in Ventricular Arrhythmia prediction-UK multicentre collaboration

Introduction The purpose of this study is to assess the ability of two new ECG markers (Regional Repolarisation Instability Index (R2I2) and Peak Electrical Restitution Slope) to predict sudden cardiac death (SCD) or ventricular arrhythmia (VA) events in patients with ischaemic cardiomyopathy undergoing implantation of an implantable cardioverter defibrillator for primary prevention indication. Methods and analysis Multicentre Investigation of Novel Electrocardiogram Risk markers in Ventricular Arrhythmia prediction is a prospective, open label, single blinded, multicentre observational study to establish the efficacy of two ECG biomarkers in predicting VA risk. 440 participants with ischaemic cardiomyopathy undergoing routine first time implantable cardioverter-defibrillator (ICD) implantation for primary prevention indication are currently being recruited. An electrophysiological (EP) study is performed using a non-invasive programmed electrical stimulation protocol via the implanted device. All participants will undergo the EP study hence no randomisation is required. Participants will be followed up over a minimum of 18 months and up to 3 years. The first patient was recruited in August 2016 and the study will be completed at the final participant follow-up visit. The primary endpoint is ventricular fibrillation or sustained ventricular tachycardia >200 beats/min as recorded by the ICD. The secondary endpoint is SCD. Analysis of the ECG data obtained during the EP study will be performed by the core lab where blinding of patient health status and endpoints will be maintained. Ethics and dissemination Ethical approval has been granted by Research Ethics Committees Northern Ireland (reference no. 16/NI/0069). The results will inform the design of a definitive Randomised Controlled Trial (RCT). Dissemination will include peer reviewed journal articles reporting the qualitative and quantitative results, as well as presentations at conferences and lay summaries

Communication breakdown : dissecting the COM interfaces between the subunits of nonribosomal peptide synthetases

Nonribosomal peptides are a structurally diverse and bioactive class of natural products constructed by multidomain enzymatic assembly lines known as nonribosomal peptide synthetases (NRPSs). While the core catalytic domains and even entire protein subunits of NRPSs have been structurally elucidated, little biophysical work has been reported on the docking domains that promote interactions—and thus transfer of biosynthetic intermediates—between subunits. In the present study, we closely examine the COM domains that mediate COMmunication between donor epimerization (E) and acceptor condensation (C) domains found at the termini of NRPS subunits. Through a combination of X-ray crystallography, circular dichroism spectroscopy, solution- and solid-state NMR spectroscopy, and molecular dynamics (MD) simulations, we provide direct evidence for an intrinsically disordered donor COM region that folds into a dynamic helical motif upon binding to a suitable acceptor. Furthermore, our NMR titration and carbene footprinting experiments illuminate the residues involved at the COM interaction interface, and our MD simulations demonstrate folding consistent with experimental data. Although our results lend credence to the previously proposed helix-hand mode of interaction, they also underscore the importance of viewing COM interfaces as dynamic ensembles rather than single rigid structures and suggest that engineering experiments should account for the interactions which transiently guide folding in addition to those which stabilize the final complex. Through activity assays and affinity measurements, we further substantiate the role of the donor COM region in binding the acceptor C domain and implicate this short motif as readily transposable for noncognate domain crosstalk. Finally, our bioinformatics analyses show that COM domains are widespread in natural product pathways and function at interfaces beyond the canonical type described above, setting a high priority for thorough characterization of these docking domains. Our findings lay the groundwork for future attempts to rationally engineer NRPS domain–domain interactions with the ultimate goal of generating bioactive molecules

Ultrafast optoelectronic processes in 1D radial van der Waals heterostructures : carbon, boron nitride, and MoS 2 nanotubes with coexisting excitons and highly mobile charges

Heterostructures built from 2D, atomically thin crystals are bound by the van der Waals force and exhibit unique optoelectronic properties. Here, we report the structure, composition and optoelectronic properties of 1D van der Waals heterostructures comprising carbon nanotubes wrapped by atomically thin nanotubes of boron nitride and molybdenum disulfide (MoS2). The high quality of the composite was directly made evident on the atomic scale by transmission electron microscopy, and on the macroscopic scale by a study of the heterostructure’s equilibrium and ultrafast optoelectronics. Ultrafast pump−probe spectroscopy across the visible and terahertz frequency ranges identified that, in the MoS 2 nanotubes, excitons coexisted with a prominent population of free charges. The electron mobility was comparable to that found in high-quality atomically thin crystals. The high mobility of the MoS2 nanotubes highlights the potential of 1D van der Waals heterostructures for nanoscale optoelectronic devices

The homotopy theory of polyhedral products

Polyhedral products are topological spaces which unify and generalise many fundamental constructions. Their study is of significant interest in homotopy theory, where they underpin the combinatorics inherent in a broad variety of key objects, such as the join product, the Cartesian product, the smash product, and the Whitehead filtration. More broadly, polyhedral products are of interest in fields including algebraic geometry, geometric group theory, number theory, and representation theory, where they enable the study of familiar objects through underlying combinatorial structures.In this thesis, we study homotopy-theoretic properties of polyhedral products. Our results lie within two major areas. The first of these is the study of duality. Duality phenomena are exhibited by fundamental objects across mathematics, such as manifolds in topology, generalised homology spheres in combinatorics, and Gorenstein rings in commutative algebra. Through a study of polyhedral products known as moment-angle complexes, we equivocate homotopy-theoretic, combinatorial, and algebraic dualities. We show that this equivocation has both algebraic and homotopy-theoretic applications, to the study of moment-angle complexes and to broader families of polyhedral products.The second area in which our results lie is the study of homotopy classes of maps. Generalising known results, we show that a new family of relations is satisfied by certain homotopy classes of maps of polyhedral products. This brings new insight into the rich algebraic structures behind sets of homotopy classes of maps, and as an application we show that this work enables us to analyse the algebraic structure of the homotopy groups of odd spheres from an entirely new angle

Duality in toric topology

We characterise integral Poincaré duality moment-angle complexes ZK in combinatorial terms of the Alexander duality of the simplicial complex K and consequently in algebraic terms of the Gorenstein duality of the Stanley-Reisner ring ℤ[K]. We extend Poincaré duality results to certain polyhedral products using polyhedral join products of simplicial complexes.</p

Three-dimensional domain swapping in the folded and molten-globule states of cystatins, an amyloid-forming structural superfamily

Cystatins, an amyloid-forming structural superfamily, form highly stable, domain-swapped dimers at physiological protein concentrations. In chicken cystatin, the active monomer is a kinetic trap en route to dimerization, and any changes in solution conditions or mutations that destabilize the folded state shorten the lifetime of the monomeric form. In such circumstances, amyloidogenesis will start from conditions where a domain-swapped dimer is the most prevalent species. Domain swapping occurs by a rearrangement of loop I, generating the new intermonomer interface between strands 2 and 3. The transition state for dimerization has a high level of hydrophobic group exposure, indicating that gross conformational perturbation is required for domain swapping to occur. Dimerization also occurs when chicken cystatin is in its reduced, molten-globule state, implying that the organization of secondary structure in this state mirrors that in the folded state and that domain swapping is not limited to the folded states of proteins. Although the interface between cystatin-fold units is poorly defined for cystatin A, the dimers are the appropriate size to account for the electron-dense regions in amyloid protofilaments