Hydrodynamic modelling of protein conformation in solution: ELLIPS and HYDRO

The last three decades has seen some important advances in our ability to represent the conformation of proteins in solution on the basis of hydrodynamic measurements. Advances in theoretical modeling capabilities have been matched by commensurate advances in the precision of hydrodynamic measurements. We consider the advances in whole-body (simple ellipsoid-based) modeling—still useful for providing an overall idea of molecular shape, particularly for those systems where only a limited amount of data is available—and outline the ELLIPS suite of algorithms which facilitates the use of this approach. We then focus on bead modeling strategies, particularly the surface or shell–bead approaches and the HYDRO suite of algorithms. We demonstrate how these are providing great insights into complex issues such as the conformation of immunoglobulins and other multi-domain complexes

A glycoconjugate of Haemophilus influenzae Type b capsular polysaccharide with tetanus toxoid protein: hydrodynamic properties mainly influenced by the carbohydrate

Three important physical properties which may affect the performance of glycoconjugate vaccines against serious disease are molar mass (molecular weight), heterogeneity (polydispersity), and conformational flexibility in solution. The dilute solution behaviour of native and activated capsular polyribosylribitol (PRP) polysaccharides extracted from Haemophilus influenzae type b (Hib), and the corresponding glycoconjugate made by conjugating this with the tetanus toxoid (TT) protein have been characterized and compared using a combination of sedimentation equilibrium and sedimentation velocity in the analytical ultracentrifuge with viscometry. The weight average molar mass of the activated material was considerably reduced (Mw ~ 0.24 × 106 g.mol−1) compared to the native (Mw ~ 1.2 × 106 g.mol−1). Conjugation with the TT protein yielded large polydisperse structures (of Mw ~ 7.4 × 106 g.mol−1), but which retained the high degree of flexibility of the native and activated polysaccharide, with frictional ratio, intrinsic viscosity, sedimentation conformation zoning behaviour and persistence length all commensurate with highly flexible coil behaviour and unlike the previously characterised tetanus toxoid protein (slightly extended and hydrodynamically compact structure with an aspect ratio of ~3). This non-protein like behaviour clearly indicates that it is the carbohydrate component which mainly influences the physical behaviour of the glycoconjugate in solution

Solution conformation and flexibility of capsular polysaccharides from Neisseria meningitidis and glycoconjugates with the tetanus toxoid protein

The structural integrity of meningococcal native, micro-fluidized and activated capsular polysaccharides and their glycoconjugates – in the form most relevant to their potential use as vaccines (dilute solution) - have been investigated with respect to their homogeneity, conformation and flexibility. Sedimentation velocity analysis showed that the polysaccharide size distributions were generally bimodal with some evidence for higher molar mass forms at higher concentration. Weight average molar masses Mw where lower for activated polysaccharides. Conjugation with tetanus toxoid protein however greatly increased the molar mass and polydispersity of the final conjugates. Glycoconjugates had an approximately unimodal log-normal but broad and large molar mass profiles, confirmed by sedimentation equilibrium “SEDFIT MSTAR” analysis. Conformation analysis using HYDFIT (which globally combines sedimentation and viscosity data), “Conformation Zoning” and Wales-van Holde approaches showed a high degree of flexibility – at least as great as the unconjugated polysaccharides, and very different from the tetanus toxoid (TT) protein used for the conjugation. As with the recently published finding for Hib-TT complexes, it is the carbohydrate component that dictates the solution behaviour of these glycoconjugates, although the lower intrinsic viscosities suggest some degree of compaction of the carbohydrate chains around the protein

Elastic and anelastic relaxation behaviour of perovskite multiferroics II: PbZr0.53_{0.53}Ti0.47_{0.47}O3_3 (PZT)–PbFe0.5_{0.5}Ta0.5_{0.5}O3_3 (PFT)

Elastic and anelastic properties of ceramic samples of multiferroic perovskites with nominal compositions across the binary join PbZr$_{0.53}$Ti$_{0.47}$O$_3$–PbFe$_{0.5}$Ta$_{0.5}$O$_3$ (PZT–PFT) have been assembled to create a binary phase diagram and to address the role of strain relaxation associated with their phase transitions. Structural relationships are similar to those observed previously for PbZr$_{0.53}$Ti$_{0.47}$O$_3$–PbFe$_{0.5}$Nb$_{0.5}$O$_3$ (PZT–PFN), but the magnitude of the tetragonal shear strain associated with the ferroelectric order parameter appears to be much smaller. This leads to relaxor character for the development of ferroelectric properties in the end member PbFe$_{0.5}$Ta$_{0.5}$O$_3$. As for PZT–PFN, there appear to be two discrete instabilities rather than simply a reorientation of the electric dipole in the transition sequence cubic–tetragonal–monoclinic, and the second transition has characteristics typical of an improper ferroelastic. At intermediate compositions, the ferroelastic microstructure has strain heterogeneities on a mesoscopic length scale and, probably, also on a microscopic scale. This results in a wide anelastic freezing interval for strain-related defects rather than the freezing of discrete twin walls that would occur in a conventional ferroelastic material. In PFT, however, the acoustic loss behaviour more nearly resembles that due to freezing of conventional ferroelastic twin walls. Precursor softening of the shear modulus in both PFT and PFN does not fit with a Vogel–Fulcher description, but in PFT there is a temperature interval where the softening conforms to a power law suggestive of the role of fluctuations of the order parameter with dispersion along one branch of the Brillouin zone. Magnetic ordering appears to be coupled only weakly with a volume strain and not with shear strain but, as with multiferroic PZT–PFN perovskites, takes place within crystals which have significant strain heterogeneities on different length scales.RUS facilities in Cambridge were established with funding from the Natural Environment Research Council (Grants NE/B505738/1, NE/F017081/1). The present work was supported by Grant No. EP/ I036079/1 from the Engineering and Physical Sciences Research Council. We thank Dr. Sam Crossley for his assistance with dielectric analysis and the use of his software to run those measurements. JAS gratefully acknowledges the hospitality of the Max Planck Institute for Chemical Physics of Solids. The Nanopaleomagnetism lab has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007– 2013)/ERC Grant Agreement 320750. SED and HS acknowledge support from the Winton Programme for the physics of sustainability. HS also acknowledges support from the Funai Foundation for Information Technology and the British Council Japan Association. Part of the work was carried out at the University of Puerto Rico, supported by the DOEEBSCoR project DEG02-ER46526

Does Microsoft Academic find early citations?

This is an accepted manuscript of an article published by Springer in Scientometrics on 27/10/2017, available online: https://doi.org/10.1007/s11192-017-2558-9 The accepted version of the publication may differ from the final published version.This article investigates whether Microsoft Academic can use its web search component to identify early citations to recently published articles to help solve the problem of delays in research evaluations caused by the need to wait for citation counts to accrue. The results for 44,398 articles in Nature, Science and seven library and information science journals 1996-2017 show that Microsoft Academic and Scopus citation counts are similar for all years, with no early citation advantage for either. In contrast, Mendeley reader counts are substantially higher for more recent articles. Thus, Microsoft Academic appears to be broadly like Scopus for citation count data, and is apparently not more able to take advantage of online preprints to find early citations

The Association of Anisakiasis in the Ascending Colon with Sigmoid Colon Cancer: CT Colonography Findings

The association of anisakiasis of the colon with colon cancer is rare and difficult to diagnose. Only one case of this type has been reported to date. In this study, we report a case of synchronous colon cancer and colonic anisakiasis. A 50-year-old woman was admitted for abdominal pain, and a volume-rendered surface-shaded image of CT colonography (CTC) revealed a concentric narrowing in the sigmoid colon and a segmental fold thickening in the ascending colon. A total colectomy was performed and the diagnosis of synchronous sigmoid colon cancer and anisakiasis of the ascending colon was confirmed. This case is the first reported visualization of synchronous colon cancer and colonic anisakiasis on a CTC

Glargine and degludec: solution behaviour of higher dose synthetic insulins

Single, double and triple doses of the synthetic insulins glargine and degludec currently used in patient therapy are characterised using macromolecular hydrodynamic techniques (dynamic light scattering and analytical ultracentrifugation) in an attempt to provide the basis for improved personalised insulin profiling in patients with diabetes. Using dynamic light scattering and sedimentation velocity in the analytical ultracentrifuge glargine was shown to be primarily dimeric under solvent conditions used in current formulations whereas degludec behaved as a dihexamer with evidence of further association of the hexamers (“multi-hexamerisation”). Further analysis by sedimentation equilibrium showed that degludec exhibited reversible interaction between mono- and-di-hexamer forms. Unlike glargine, degludec showed strong thermodynamic non-ideality, but this was suppressed by the addition of salt. With such large injectable doses of synthetic insulins remaining in the physiological system for extended periods of time, in some case 24–40 hours, double and triple dose insulins may impact adversely on personalised insulin profiling in patients with diabetes

Essential Role of TGF-β/Smad Pathway on Statin Dependent Vascular Smooth Muscle Cell Regulation

BACKGROUND: The 3-hydroxy-3-methylglutaryl CoA reductase inhibitors (also called statins) exert proven beneficial effects on cardiovascular diseases. Recent data suggest a protective role for Transforming Growth Factor-beta (TGF-beta) in atherosclerosis by regulating the balance between inflammation and extracellular matrix accumulation. However, there are no studies about the effect of statins on TGF-beta/Smad pathway in atherosclerosis and vascular cells. METHODOLOGY: In cultured vascular smooth muscle cells (VSMCs) statins enhanced Smad pathway activation caused by TGF-beta. In addition, statins upregulated TGF-beta receptor type II (TRII), and increased TGF-beta synthesis and TGF-beta/Smad-dependent actions. In this sense, statins, through Smad activation, render VSMCs more susceptible to TGF-beta induced apoptosis and increased TGF-beta-mediated ECM production. It is well documented that high doses of statins induce apoptosis in cultured VSMC in the presence of serum; however the precise mechanism of this effect remains to be elucidated. We have found that statins-induced apoptosis was mediated by TGF-beta/Smad pathway. Finally, we have described that RhoA inhibition is a common intracellular mechanisms involved in statins effects. The in vivo relevance of these findings was assessed in an experimental model of atherosclerosis in apolipoprotein E deficient mice: Treatment with Atorvastatin increased Smad3 phosphorylation and TRII overexpression, associated to elevated ECM deposition in the VSMCs within atheroma plaques, while apoptosis was not detected. CONCLUSIONS: Statins enhance TGF-beta/Smad pathway, regulating ligand levels, receptor, main signaling pathway and cellular responses of VSMC, including apoptosis and ECM accumulation. Our findings show that TGF-beta/Smad pathway is essential for statins-dependent actions in VSMCs

A xandarellid artiopodan from Morocco – a middle Cambrian link between soft-bodied euarthropod communities in North Africa and South China

NB. A corrigendum [correction] for this article was published online on 09 May 2017; this has been attached to this article as an additional file. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ © The Author(s) 2017. The attached file is the published version of the article

Application of recent advances in hydrodynamic methods for characterising mucins in solution

Mucins are the primary macromolecular component of mucus—nature’s natural lubricant—although they are poorly characterised heterogeneous substances. Recent advances in hydrodynamic methodology now offer the opportunity for gaining a better understanding of their solution properties. In this study a combination of such methods was used to provide increased understanding of a preparation of porcine intestinal mucin (PIM), MUC2 mucin, in terms of both heterogeneity and quantification of conformational flexibility. The new sedimentation equilibrium algorithm SEDFIT-MSTAR is applied to yield a weight average (over the whole distribution) molar mass of 7.1 × 106 g mol−1, in complete agreement with size exclusion chromatography coupled with multi-angle light scattering (SEC-MALS), which yielded a value of 7.2 × 106 g mol−1. Sedimentation velocity profiles show mucin to be very polydisperse, with a broad molar mass distribution obtained using the Extended Fujita algorithm, consistent with the elution profiles from SEC-MALS. On-line differential pressure viscometry coupled to the SEC-MALS was used to obtain the intrinsic viscosity [η] as a function of molar mass. These data combined with sedimentation coefficient data into the global conformation algorithm HYDFIT show that PIM has a flexible linear structure, with persistence length Lp ~10 nm and mass per unit length, ML ~2380 g mol−1 nm−1, consistent with a Wales-van Holde ratio of ~1.2 obtained from the concentration dependence of the sedimentation coefficient