Self-assembling auto-fluorescent amphiphiles : nano-sized platform technology for multi-purpose cellular targeting

Amphiphilic molecules emerged as versatile building blocks for the generation of nano-sized architectures in water, as they can be programmed to self-assemble into a wide range of different topologies. In this thesis the generation of auto-fluorescent heterovalent nano-sized structures was explored using two types of amphiphilic scaffolds: disc-shaped and linear amphiphiles self-assembling in water into columnar polymers or into amorphous spherical nanoparticles, respectively. Numerous applications for self-assembling nanostructures were reported in literature based on amphiphilic molecules, ranging from imaging to diagnostics, and from drug delivery to tissue engineering. Many of these applications require the capability of the supramolecular system to actively target specific cell surface receptors. This is typically achieved through decoration with bioactive epitopes such as small molecules, peptides, and proteins. As discussed in chapter 1, the bioactive epitopes can either already be part of the monomeric supramolecular building blocks (pre-functionalization) or introduced after self-assembly via covalent attachment to appending reactive groups (post-functionalization). Selective and multivalent binding of disc-shaped amphiphiles to bacterial receptors was previously shown through the introduction of three functional groups at the periphery of the ethylene oxide tails and subsequent functionalization with bioactive ligands. Here, to expand the library of scaffolds, amphiphiles containing either nine amine functionalities or a single amine, azide and propargyl group were synthesized. Their decoration with bioactive ligands such as peptides, carbohydrates, small molecules and fluorescent dyes using both amide coupling and copper-catalyzed azide-alkyne cycloaddition is described in chapter 2. The orthogonality of the copper-catalyzed azide-alkyne cycloaddition allowed the functionalization with unprotected ligands. Whereas the functionalization of discotics with a carbohydrate was quantitative, the coupling of peptides proceeded with at best 40% conversion. This was probably due to steric crowding of peripheral functionalities in the self-assembly inducing solvent, which is required for solubility of unprotected ligands. In contrast, discotics bearing a single amine emerged as a versatile non-sterically hindered scaffold for ligand attachment as they were rapidly and quantitatively functionalized with a range of peptidic- and non-peptidic ligands using both NHS ester and HBTU activation techniques under non-assembling solvent conditions. The ability to fine-tune the density and display of bioactive epitopes and thereby creating more complex dynamic and heterovalent structures without interfering with the self-assembling process is a key prerequisite for the development of a platform technology for targeting. A versatile and non-sterically hindered scaffold for ligand attachment, such as the presented discotic bearing a single amine, might constitute the basis for such a technology. The functionalization of this discotic leads to monovalent ligand functionalized discotics. The display of multiple ligands, which is important for enhanced binding affinities, will be accomplished upon self-assembly into columnar stacks. This so-called multivalency upon self-assembly has been probed with a number of monovalent ligand-functionalized discotics in chapter 3. Enzyme-linked lectin assay revealed a three-fold increase in binding activity compared with the non self-assembling counterpart. The self-assembly into a columnar stack and the accompanied display of multiple ligands was as well confirmed studying the binding of monovalent streptavidin to discotics functionalized with a single biotin using Förster resonance energy transfer and SDS-PAGE. The formation of heterovalent supramolecular polymers through dynamic intermixing of different functionalized building blocks was shown using mixtures of biotin and fluorescein functionalized discotics incubated with streptavidin coated magnetic beads. Thus the self-assembly into supramolecular polymers not only generates a multivalent, but as well a heterovalent system. The possibility to generate heterovalent supramolecular polymers via simple intermixing of discotics has a great potential in view of advanced biological applications, for example in the field of targeted imaging. To gain further inside into the dynamics of this intermixing process, discotics bearing a single O6 benzylguanine moiety were covalently post-functionalized with two FRET-pairing fluorescent proteins. Firstly, the covalent post-functionalization with proteins, ligands which are incompatible with the pre-functionalization strategy, was confirmed with several analytical techniques such as SDS-PAGE and LC-MS in chapter 4. The covalent protein conjugation at the same time leads to Förster resonance energy transfer from the auto-fluorescent discotic scaffold to the yellow fluorescent protein and allows on-line monitoring of the conjugation. At the same time the protein conjugation does not interfere with the self-assembling process, leading to a multivalent protein display on a supramolecular wire, as visualized via energy transfer from the cyan to the yellow fluorescent protein. Secondly, the system maintains its intermixing dynamics, which allows the formation of hetero-functionalized supramolecular protein-conjugated polymers through exchange of the protein-functionalized discotics over time. The supramolecular wires act as dynamic framework on which the two proteins can assemble and exchange in a dynamic manner, leading to effective protein interactions, as observed by energy transfer. The cellular uptake of amine-decorated discotics and the dependence of cellular uptake on the peripheral amine density were explored in chapter 5. Using the auto-fluorescence of the discotic scaffolds, their internalization was studied using live cell multiphoton fluorescence microscopy Discotics bearing three or nine amine groups at their periphery efficiently translocated through the plasma membrane via endocytosis. Additionally, the knowledge about the formation of intermixed supramolecular polymers obtained in chapter 3 and 4 was applied to generate multi-functional supramolecular polymers consisting of up to three different cell-permeable and non cell-permeable discotic monomers. Through intermixing with cell-permeable discotic monomers in the supramolecular polymer, the cellular uptake of non-cell permeable discotics was induced and each of the components could be individually visualized, demonstrating the potential of dynamic multi-component supramolecular polymers. The functionalization of self-assembling p-conjugated nanoparticles with bioactive epitopes, a prerequisite for applications in targeted multimodal imaging, was investigated in the last chapter. Upon microinjection into water, these linear and auto-fluorescent amphiphiles self-assemble into highly-fluorescent amorphous nanoparticles of 80-100 nm. Azide and mannose groups were introduced at the periphery of the ethylene glycol chains of the amphiphile and did not interfere with the self-assembly process. The binding of mannose functionalized nanoparticles to proteins and bacteria confirmed the accessibility of the introduced ligand. Co-assembly of different amphiphiles enabled the fine-tuning of ligand density, which was confirmed with Förster resonance energy transfer. Additionally, using copper catalyzed azide-alkyne cycloaddition reaction, azide bearing nanoparticles were post-functionalized with different ligands. Successful combination of both functionalization strategies via intermixing of mannose and azide bearing amphiphiles and subsequent copper catalyzed azide-alkyne cycloaddition led to heterovalent nanoparticles. Nano-sized columnar and spherical supramolecular assemblies were functionalized with a wide range of ligands such as carbohydrates, peptides, and proteins using both pre- and post-functionalization strategies. This allowed for expanding the ligand diversity at two independent stages in the fabrication process of these bioactive nano-structures. Supramolecular synthesis enabled the facile generation of complex heterovalent bioactive assemblies; in the case of nanoparticles via co-assembly of different amphiphiles and in the case of discotics via dynamic intermixing of building blocks between the supramolecular stacks. With this knowledge in hand advanced applications of complex multitargeting and multimodal supramolecular nano-sized structures in imaging can be envisioned; carrying for example several targeting ligands as well as an alternative imaging probe. The ability to tune the optical properties in the case of the nanoparticles should additionally enable multi-color imaging. At the same time, the self-assembling nature of these nanoparticles allows the incorporation of hydrophobic (drug) molecules and functionalized lipids, expanding the scope of functionalization strategies and with it of possible applications. The absence of unspecific adsorption of the bare scaffolds of both the disc-shaped and linear amphiphiles proves their broad potential as selective biological targeting tools

Reporting of suspected dog-fighting to the police, RSPCA and equivalents by veterinary professionals in the UK

Dog fighting became unlawful in the UK in 1835, yet it continues today (as reported by the Royal Society for the Prevention of Cruelty to Animals (RSPCA) and Crown Prosecution Service), although with an unknown prevalence. We used an online questionnaire to (1) determine the occurrence of dogs suspected of use in fighting in UK veterinary practices; (2) explore relative reporting of incidents to police, RSPCA or equivalent charity by registered veterinary nurses (RVN) and veterinarians; and (3) determine factors influencing reporting. Emails (n=2493) containing the questionnaire were sent to UK veterinary practices: 423 questionnaires (159 by RVNs, 264 by veterinarians) were completed. One or more cases of dog fighting were suspected by 14.4 per cent of respondents in 2015; 182 cases suspected in total. Proportionately more RVNs suspected dog fighting than veterinarians (P=0.0009). Thirty-two respondents (7.6 per cent, n=422) claimed to have reported suspicions to the police, the RSPCA or equivalent charity previously; 59 respondents (14.2 per cent) had previously chosen not to. Reasons not to report included: uncertainty of illegal activity (81.4 per cent), fear of the client not returning to the practice (35.6 per cent) and concerns regarding client confidentiality (22.0 per cent). Further work is required to address under-reporting of dog fighting by veterinary professionals

#Bieber + #Blast = #BieberBlast: Early Prediction of Popular Hashtag Compounds

Compounding of natural language units is a very common phenomena. In this paper, we show, for the first time, that Twitter hashtags which, could be considered as correlates of such linguistic units, undergo compounding. We identify reasons for this compounding and propose a prediction model that can identify with 77.07% accuracy if a pair of hashtags compounding in the near future (i.e., 2 months after compounding) shall become popular. At longer times T = 6, 10 months the accuracies are 77.52% and 79.13% respectively. This technique has strong implications to trending hashtag recommendation since newly formed hashtag compounds can be recommended early, even before the compounding has taken place. Further, humans can predict compounds with an overall accuracy of only 48.7% (treated as baseline). Notably, while humans can discriminate the relatively easier cases, the automatic framework is successful in classifying the relatively harder cases.Comment: 14 pages, 4 figures, 9 tables, published in CSCW (Computer-Supported Cooperative Work and Social Computing) 2016. in Proceedings of 19th ACM conference on Computer-Supported Cooperative Work and Social Computing (CSCW 2016

Niche as a determinant of word fate in online groups

Patterns of word use both reflect and influence a myriad of human activities and interactions. Like other entities that are reproduced and evolve, words rise or decline depending upon a complex interplay between {their intrinsic properties and the environments in which they function}. Using Internet discussion communities as model systems, we define the concept of a word niche as the relationship between the word and the characteristic features of the environments in which it is used. We develop a method to quantify two important aspects of the size of the word niche: the range of individuals using the word and the range of topics it is used to discuss. Controlling for word frequency, we show that these aspects of the word niche are strong determinants of changes in word frequency. Previous studies have already indicated that word frequency itself is a correlate of word success at historical time scales. Our analysis of changes in word frequencies over time reveals that the relative sizes of word niches are far more important than word frequencies in the dynamics of the entire vocabulary at shorter time scales, as the language adapts to new concepts and social groupings. We also distinguish endogenous versus exogenous factors as additional contributors to the fates of words, and demonstrate the force of this distinction in the rise of novel words. Our results indicate that short-term nonstationarity in word statistics is strongly driven by individual proclivities, including inclinations to provide novel information and to project a distinctive social identity.Comment: Supporting Information is available here: http://www.plosone.org/article/fetchSingleRepresentation.action?uri=info:doi/10.1371/journal.pone.0019009.s00

Inhibition of Ice Recrystallization by Nanotube-Forming Cyclic Peptides

While most native ice-binding proteins are rigid, artificial (macro)molecular ice-binders are usually flexible. Realizing a regular array with precisely positioned ice-binding motifs on synthetic proteins, (macro)molecular ice-binders are thus challenging. Here, we exploit the predictable assembly of cyclic peptides into nanotubes as a starting point to prepare large, rigid ice-binders bearing an ice-binding site that is found in hyperactive ice-binding proteins in insects. First, we designed, synthesized, and purified cyclic octapeptide Lys2CP8 bearing a TaT motif to promote ice binding and investigated their solution assembly and activity using circular dichroism (CD) spectroscopy, Fourier-transform infrared (FTIR) spectroscopy, light scattering (LS), cryogenic transmission electron microscopy (cryo-TEM), and ice recrystallization inhibition (IRI) assays. The cyclic peptide Lys2CP8 was synthesized in good yield using Fmoc chemistry and purified by reversed-phase HPLC. Upon dissolution in aqueous solutions, Lys2CP8 was observed to assemble in a pH- and concentration-dependent manner into objects with nanoscopic dimensions. LS revealed the presence of small and large aggregates at pH 3 and 11, held together through a network of intermolecular antiparallel β-sheets as determined by FTIR and CD spectroscopy. Cryo-TEM revealed the presence of one-dimensional objects at pH 3 and 11. These are mostly well-dispersed at pH 3 but appear to bundle at pH 11. Interestingly, the pH-dependent self-assembly behavior translates into a marked pH dependence of IRI activity. Lys2CP8 is IRI-active at pH 3 while inactive at pH 11 hypothetically because the ice-binding sites are inaccessible at pH 11 due to bundling

Improving water productivity in the Australian Grains industry—a nationally coordinated approach

Improving the water-limited yield of dryland crops and farming systems has been an underpinning objective of research within the Australian grains industry since the concept was defined in the 1970s. Recent slowing in productivity growth has stimulated a search for new sources of improvement, but few previous research investments have been targeted on a national scale. In 2008, the Australian grains industry established the 5-year, AU$17.6 million, Water Use Efficiency (WUE) Initiative, which challenged growers and researchers to lift WUE of grain-based production systems by 10%. Sixteen regional grower research teams distributed across southern Australia (300–700 mm annual rainfall) proposed a range of agronomic management strategies to improve water-limited productivity. A coordinating project involving a team of agronomists, plant physiologists, soil scientists and system modellers was funded to provide consistent understanding and benchmarking of water-limited yield, experimental advice and assistance, integrating system science and modelling, and to play an integration and communication role. The 16 diverse regional project activities were organised into four themes related to the type of innovation pursued (integrating break-crops, managing summer fallows, managing in-season water-use, managing variable and constraining soils), and the important interactions between these at the farm-scale were explored and emphasised. At annual meetings, the teams compared the impacts of various management strategies across different regions, and the interactions from management combinations. Simulation studies provided predictions of both a priori outcomes that were tested experimentally and extrapolation of results across sites, seasons and up to the whole-farm scale. We demonstrated experimentally that potential exists to improve water productivity at paddock scale by levels well above the 10% target by better summer weed control (37–140%), inclusion of break crops (16–83%), earlier sowing of appropriate varieties (21–33%) and matching N supply to soil type (91% on deep sands). Capturing synergies from combinations of pre- and in-crop management could increase wheat yield at farm scale by 11–47%, and significant on-farm validation and adoption of some innovations has occurred during the Initiative. An ex post economic analysis of the Initiative estimated a benefit : cost ratio of 3.7 : 1, and an internal return on investment of 18.5%. We briefly review the structure and operation of the initiative and summarise some of the key strategies that emerged to improve WUE at paddock and farm-scale

To what extent does a regional dialect and accent impact on the development of reading and writing skills?

The issue of whether a regional accent and/or dialect impact(s) on the development of literacy skills remains current in the UK. For decades the issue has dogged debate about education outcomes, portable skills and employability. The article summarizes research on the topic using systematic review methodology. A scoping review was undertaken with the research question ‘To what extent does a regional dialect and accent impact on the development of reading and writing skills?’. The review covers research relevant to the teaching of 5-16 year olds in England, but also draws on research within Europe, the USA, Australia and the Caribbean. The results suggest that curricula have marginalized language variation; that the impact of regional accent and dialect on writing is relatively minor; that young people are adept at style-shifting between standard and non-standard forms; and that inappropriate pedagogical responses to regional variation can have detrimental effects on children’s educational achievement