Molecular architecture of Aβ fibrils grown in cerebrospinal fluid solution and in a cell culture model of Aβ plaque formation

OBJECTIVES: The detailed structure of brain-derived Aβ amyloid fibrils is unknown. To approach this issue, we investigate the molecular architecture of Aβ(1-40) fibrils grown in either human cerebrospinal fluid solution, in chemically simple phosphate buffer in vitro or extracted from a cell culture model of Aβ amyloid plaque formation. METHODS: We have used hydrogen-deuterium exchange (HX) combined with nuclear magnetic resonance, transmission electron microscopy, seeding experiments both in vitro and in cell culture as well as several other spectroscopic measurements to compare the morphology and residue-specific conformation of these different Aβ fibrils. RESULTS AND CONCLUSIONS: Our data reveal that, despite considerable variations in morphology, the spectroscopic properties and the pattern of slowly exchanging backbone amides are closely similar in the fibrils investigated. This finding implies that a fundamentally conserved molecular architecture of Aβ peptide fold is common to Aβ fibrils.

Haptics enabled offline AFM image analysis

Current advancements in nanotechnology are dependent on the capabilities that can enable nano-scientists to extend their eyes and hands into the nano-world. For this purpose, a haptics (devices capable of recreating tactile or force sensations) based system for AFM (Atomic Force Microscope) is proposed. The system enables the nano-scientists to touch and feel the sample surfaces, viewed through AFM, in order to provide them with better understanding of the physical properties of the surface, such as roughness, stiffness and shape of molecular architecture. At this stage, the proposed work uses of ine images produced using AFM and perform image analysis to create virtual surfaces suitable for haptics force analysis. The research work is in the process of extension from of ine to online process where interaction will be done directly on the material surface for realistic analysis.

Azobenzene moiety variation directing self-assembly and photoresponsive behavior of azo-surfactants

The effect of varying the position of the azobenzene group within two comparable photoresponsive amphiphiles on their capability to form lyotropic liquid crystals (LLCs) was investigated in detail in this study. Two photoresponsive amphiphiles having comparable structures were designed and synthesized consisting of hydrophilic oligooxyethylene units, a hydrophobic alkyl chain and a light-sensitive azobenzene moiety. When the azobenzene group was located in the middle of the hydrophobic alkyl chain, multiple LLC phases were observed at various water contents in the azo-surfactant–water binary system. In contrast, when the azobenzene group was directly attached to the hydrophilic domain, the azo-surfactant–water binary system exhibited only lamellar phases. The temperature dependence of these self-organised nanostructures was also investigated by the combination of small angle X-ray scattering (SAXS), differential scanning calorimetry (DSC), and rheology. Under alternating UV and visible light irradiation, reversible trans–cis photoisomerization of the azobenzene group occurred efficiently in dilute solution for both azo-surfactants. However, only photoisomerization of the surfactant possessing the azobenzene group localized in the middle of the alkyl chain induced significant changes in the self-assembled structure and its bulk properties. This study demonstrates that self-assembly and photoresponsive behaviour of photosensitive amphiphiles is extremely sensitive to the position of the photoactive moiety within the surfactant molecular architecture.

Architecture of fiber network : from understanding to engineering of molecular gels

A new approach of engineering of molecular gels was established on the basis of a nucleation-initiated network formation mechanism. A variety of gel network structures can be obtained by regulating the starting temperature of the sol−gel transition. This enables us to tune the network from the spherulitic domains pattern to the extensively interconnected fibrillar network. As the consequence of fibrous network structure turning, desirable rheological and other in-use properties of the materials can be obtained accordingly. This approach of micro-/nanostructural fabrication may open up a new route for micro-/nanofunctional materials engineering in general.

Polymer architecture effect on sodium ion transport in PSTFSI-based ionomers: a molecular dynamics study

In this study, we investigated the effect of polymer architecture on the ion dynamics and local structure to understand the factors that might lead to the design of highly conductive and mechanically robust polyelectrolytes. Molecular dynamic simulations were undertaken on the sodium poly[(4-styrenesulfonyl) (trifluoromethanesulfonyl) imide] P(STFSINa) homopolymer and its copolymers with either ether or styrene spacer groups to investigate the spacer length and polarity dependence of Na-ion transport. Using a scaled charge model, we observed a continuous ion aggregate network in the homopolymer, which facilitates the fast ion dynamics despite the rigid polymer matrix. The longest spacer groups disrupt this percolating ionic network differently, with the ether group being more disruptive than the styrene group, and leading to more discrete ionic aggregates. The copolymer with the ether spacer was also found to result in an alternative Na-ion diffusion mechanism.

Controlling the supramolecular architecture of molecular gels with surfactants

Manipulating molecular assembly is significant for achieving materials with desirable performances. In this paper, two nonionic surfactants, Span 20 and Triton X-100, are used to tune the nucleation and fiber growth of a molecular gelator 2,3-di-n-decyloxyanthracene (DDOA). Confocal microscopic images show that Span 20 induces elongation of DDOA spherulites, and promotes fiber side branching. In contrast, Triton X-100 enhances the primary nucleation of DDOA leading to the formation of smaller DDOA spherulites, and promotes fiber tip branching. (1)H NMR investigation demonstrates strong interactions between the hydrophobic tails of the surfactants and the alkyl chains of DDOA molecules.The interactions significantly reduce the diffusion of DDOA molecules. The different effects of the two surfactants could be attributable to their different alkyl hydrophobic tails. The hydrophobic tail of Span 20 is similar to the alkyl chain of DDOA, which could promote the adsorption of Span 20 on the fiber side surface rich in alkyl chains of DDOA.While the benzene ring in the hydrophobic tail of Triton X-100 could facilitate the primary nucleation of DDOA and the adsorpion of Triton X-100 on the fiber tip surface rich in aromatic structure of DDOA. The observations of this work will help the development of a convenient approach to tune the fiber network structure of molecular gels.

Engineering molecular self-assembled fibrillar networks by ultrasound

The architecture of self-organized three-dimensionally interconnected nanocrystal fibrillar networks has been achieved by ultrasound from a solution consisting of separate spherulites. The ultrasound stimulated structural transformation is correlated to the striking ultrasonic effects on turning nongelled solutions or weak gels into strong gels instantly, with enhancement of the storage modulus up to 3 magnitudes and up to 4 times more gelling capability. The basic principle involved in the ultrasound-induced structural transformation is established on the basis of the nucleation-and-growth model of a fiber network formation, and the mechanism of seeding multiplication, aggregation suppressing, and fiber distribution and growth promotion is proposed. This novel technique enables us to produce self-supporting gel functional materials possessing significantly modified macroscopic properties, from materials previously thus far considered to be “useless”, without the use of chemical stimuli. Moreover, it provides a general strategy for the engineering of self-organized fiber network architectures, and we are consequently able to achieve the supramolecular functional materials with controllable macroscopic properties.

An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture

Here we present an improved implementation of the TIGER2 Replica Exchange Molecular Dynamics (REMD) method, using the replica exchange Application Programming Interface (API) found in contemporary versions of the NAMD Molecular Dynamics Package. The implementation takes the form of a TCL script which is used in conjunction with the standard configuration file. This implementation is validated against a previous TIGER2 implementation, as well as data reported for the original TIGER2 simulations. Our implementation is compatible with a range of architectures; crucially it enables the use of this wrapper with the BlueGene/Q architecture, in addition to the x86 architecture. Program summary: Program title: TIGER2-NAMD. Catalogue identifier: AEWC_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEWC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 34151. No. of bytes in distributed program, including test data, etc.: 424217. Distribution format: tar.gz. Programming language: Tcl 8.5. Computer: x86 Clusters, BlueGene/Q, Workstations. Operating system: Linux, IBM Compute Node Kernel. Has the code been vectorised or parallelised?: Yes. MPI Parallelism. Classification: 3. External routines: NAMD 2.9 (http://www.ks.uiuc.edu/Research/namd/). Nature of problem: Replica Exchange Molecular Dynamics. Solution method: Each replica runs through multiple cycles of heating and cooling with exchanges between them being attempted. Running time: Typically 30 mins, up to an hour.

Distinct kinetics of molecular gelation in a confined space and its relation to the structure and property of thin gel films

Thin films of molecular gels formed in a confined space have potential applications in transdermal delivery, artificial skin, molecular electronics, etc. The microstructures and properties of thin gel films can be significantly different from those of their bulk counterparts. However, so far a comprehensive understanding of the effects of spatial confinement on the molecular gelation kinetics, fiber network structure and related mechanical properties is still lacking. In this work, using rheological techniques, we investigated the effect of one-dimensional confinement on the formation kinetics of fiber networks in the molecular gelation process. Fractal analyses of the kinetic information in terms of an extended Dickinson model enabled us to describe quantitatively the distinct kinetic signature of molecular gelation. The structural features derived from gelation kinetics support well the fractal patterns of the fiber networks acquired by optical and electron microscopy. With the kinetics-structure correlation, we can gain an in-depth understanding of the confinement-induced differences in the structure and consequently the mechanical properties of a model molecular gelling system. Particularly, the confinement induced structural transition, from a three-dimensional, dense and compact spherulitic network composed of highly branched fibers to a quasi-two-dimensional sparse spherulitic network composed of less branched fibers and entangled fibrils at the boundary areas, renders a gel film to become less stiff but more ductile. Our study suggests here a new strategy of engineering the fiber network microstructure to achieve functional gel films with unusual but useful properties.

Morphological and molecular investigations of the holocephalan elephant fish nephron: the existence of a countercurrent-like configuration and two separate diluting segments in the distal tubule

In marine cartilaginous fish, reabsorption of filtered urea by the kidney is essential for retaining a large amount of urea in their body. However, the mechanism for urea reabsorption is poorly understood due to the complexity of the kidney. To address this problem, we focused on elephant fish (Callorhinchus milii) for which a genome database is available, and conducted molecular mapping of membrane transporters along the different segments of the nephron. Basically, the nephron architecture of elephant fish was similar to that described for elasmobranch nephrons, but some unique features were observed. The late distal tubule (LDT), which corresponded to the fourth loop of the nephron, ran straight near the renal corpuscle, while it was convoluted around the tip of the loop. The ascending and descending limbs of the straight portion were closely apposed to each other and were arranged in a countercurrent fashion. The convoluted portion of LDT was tightly packed and enveloped by the larger convolution of the second loop that originated from the same renal corpuscle. In situ hybridization analysis demonstrated that co-localization of Na(+),K(+),2Cl(-) cotransporter 2 and Na(+)/K(+)-ATPase α1 subunit was observed in the early distal tubule and the posterior part of LDT, indicating the existence of two separate diluting segments. The diluting segments most likely facilitate NaCl absorption and thereby water reabsorption to elevate urea concentration in the filtrate, and subsequently contribute to efficient urea reabsorption in the final segment of the nephron, the collecting tubule, where urea transporter-1 was intensely localized.

Colour polymorphism is likely to be disadvantageous to some populations and species due to genetic architecture and morph interactions

Polymorphism describes two or more distinct, genetically determined, phenotypes that co-occur in the same population, where the rarest morph is maintained at a frequency above the mutation rate (Ford 1945; Huxley 1955). In a recent opinion piece, we explored a new idea regarding the role of genetic architectures and morph interactions in colour polymorphisms and how this can negatively affect population performance (Bolton et al. 2015). In this issue of Molecular Ecology, Forsman (2016) thoroughly discusses the current evidence for polymorphisms enhancing population performance and critiques the validity of the definitions of polymorphism we use in our original paper. We respond by clarifying that the negative consequences of polymorphisms that we discussed are likely to be most pertinent in species that have a particular set of characteristics, such as strong sexual or social interactions between morphs and discrete genetic architectures. Although it was not our intention to redefine polymorphism, we do believe that there should be further discussion about refining or characterizing balanced polymorphisms with respect to the degree of morph sympatry, discreteness of traits and their underlying genetic architecture, and the types of selection that drive and maintain the variation. The latter describes whether polymorphism is primarily maintained by external factors such as predation pressure or internal factors such as interactions with members of the same species. The contribution of Forsman (2016) is useful to this discussion, and we hope that our exchange of opinions will inspire new empirical and theoretical ideas on the origin and maintenance of colour polymorphisms.