Sensitive electrochemical assays of DNA structure

Electrochemical methods have been used to study the structure and function of nucleic acids for more than 50 years. These approaches complement other experimental techniques, which we illustrate by using examples from studies of processes involved in the repair of DNA damage. The excellent sensitivity of the electrochemical approaches makes them good candidates for use as biosensors of a wide range of molecules and biological processes

Mechanistic and Performance Studies on the Ligand Promoted Ullmann Amination Reaction

Over the last two decades many different auxiliary ligand systems have been utilized in the copper-catalyzed Ullmann amination reaction. However, there has been little consensus on the relative merits of the varied ligands and the exact role they might play in the catalytic process. Accordingly, in this work some of the most commonly employed auxiliary ligands have been evaluated for C–N coupling using reaction progress kinetic analysis (RPKA) methodology. The results reveal not only the relative kinetic competencies of the different auxiliary ligands but also their markedly different influences on catalyst degradation rates. For the model Ullmann reaction between piperidine and iodobenzene using the soluble organic base bis(tetra-n-butylphosphonium) malonate (TBPM) at room temperature, N-methylglycine was shown to give the best performance in terms of high catalytic rate of reaction and comparatively low catalyst deactivation rates. Further experimental and rate data indicate a common catalytic cycle for all auxiliary ligands studied, although additional off-cycle processes are observed for some of the ligands (notably phenanthroline). The ability of the auxiliary ligand, base (malonate dianion), and substrate (amine) to all act competitively as ligands for the copper center is also demonstrated. On the basis of these results an improved protocol for room-temperature copper-catalyzed C–N couplings is presented with 27 different examples reported

Mechanistic studies on the copper-catalyzed N-arylation of alkylamines promoted by organic soluble ionic bases

Experimental studies on the mechanism of copper-catalyzed amination of aryl halides have been undertaken for the coupling of piperidine with iodobenzene using a Cu­(I) catalyst and the organic base tetrabutylphosphonium malonate (TBPM). The use of TBPM led to high reactivity and high conversion rates in the coupling reaction, as well as obviating any mass transfer effects. The often commonly employed O,O-chelating ligand 2-acetylcyclohexanone was surprisingly found to have a negligible effect on the reaction rate, and on the basis of NMR, calorimetric, and kinetic modeling studies, the malonate dianion in TBPM is instead postulated to act as an ancillary ligand in this system. Kinetic profiling using reaction progress kinetic analysis (RPKA) methods show the reaction rate to have a dependence on all of the reaction components in the concentration range studied, with first-order kinetics with respect to [amine], [aryl halide], and [Cu]_total. Unexpectedly, negative first-order kinetics in [TBPM] was observed. This negative rate dependence in [TBPM] can be explained by the formation of an off-cycle copper­(I) dimalonate species, which is also argued to undergo disproportionation and is thus responsible for catalyst deactivation. The key role of the amine in minimizing catalyst deactivation is also highlighted by the kinetic studies. An examination of the aryl halide activation mechanism using radical probes was undertaken, which is consistent with an oxidative addition pathway. On the basis of these findings, a more detailed mechanistic cycle for the C–N coupling is proposed, including catalyst deactivation pathways

Elastohydrodynamic Lift at a Soft Wall

We study experimentally the motion of nondeformable microbeads in a linear shear flow close to a wall bearing a thin and soft polymer layer. Combining microfluidics and 3D optical tracking, we demonstrate that the steady-state bead-to-surface distance increases with the flow strength. Moreover, such lift is shown to result from flow-induced deformations of the layer, in quantitative agreement with theoretical predictions from elastohydrodynamics. This study thus provides the first experimental evidence of “soft lubrication” at play at small scale, in a system relevant, for example, to the physics of blood microcirculation

Use of Caval Subtraction 2D Phase-Contrast MR Imaging to Measure Total Liver and Hepatic Arterial Blood Flow: Preclinical Validation and Initial Clinical Translation

Purpose To validate caval subtraction two-dimensional (2D) phase-contrast magnetic resonance (MR) imaging measurements of total liver blood flow (TLBF) and hepatic arterial fraction in an animal model and evaluate consistency and reproducibility in humans. Materials and Methods Approval from the institutional ethical committee for animal care and research ethics was obtained. Fifteen Sprague-Dawley rats underwent 2D phase-contrast MR imaging of the portal vein (PV) and infrahepatic and suprahepatic inferior vena cava (IVC). TLBF and hepatic arterial flow were estimated by subtracting infrahepatic from suprahepatic IVC flow and PV flow from estimated TLBF, respectively. Direct PV transit-time ultrasonography (US) and fluorescent microsphere measurements of hepatic arterial fraction were the standards of reference. Thereafter, consistency of caval subtraction phase-contrast MR imaging-derived TLBF and hepatic arterial flow was assessed in 13 volunteers (mean age, 28.3 years ± 1.4) against directly measured phase-contrast MR imaging PV and proper hepatic arterial inflow; reproducibility was measured after 7 days. Bland-Altman analysis of agreement and coefficient of variation comparisons were undertaken. Results There was good agreement between PV flow measured with phase-contrast MR imaging and that measured with transit-time US (mean difference, -3.5 mL/min/100 g; 95% limits of agreement [LOA], ±61.3 mL/min/100 g). Hepatic arterial fraction obtained with caval subtraction agreed well with those with fluorescent microspheres (mean difference, 4.2%; 95% LOA, ±20.5%). Good consistency was demonstrated between TLBF in humans measured with caval subtraction and direct inflow phase-contrast MR imaging (mean difference, -1.3 mL/min/100 g; 95% LOA, ±23.1 mL/min/100 g). TLBF reproducibility at 7 days was similar between the two methods (95% LOA, ±31.6 mL/min/100 g vs ±29.6 mL/min/100 g). Conclusion Caval subtraction phase-contrast MR imaging is a simple and clinically viable method for measuring TLBF and hepatic arterial flow. Online supplemental material is available for this article

Resummation of transverse energy in vector boson and Higgs boson production at hadron colliders

We compute the resummed hadronic transverse energy (E_T) distribution due to initial-state QCD radiation in vector boson and Higgs boson production at hadron colliders. The resummed exponent, parton distributions and coefficient functions are treated consistently to next-to-leading order. The results are matched to fixed-order calculations at large E_T and compared with parton-shower Monte Carlo predictions at Tevatron and LHC energies.Comment: 24 pages, 15 figure

Mobility as a service : defining a transport utopia

Having been widely acknowledged as enabling access to education, employment, leisure and social activities, transport choices are also the cause of many challenges cities face. Recognising that change is needed, planners and policymakers are considering alternative methods of planning and delivering transport. Mobility as a Service (or MaaS) is one such idea that has gained traction with academics and professionals alike. Hailed as the answer to integrating complex transport systems, MaaS has yet to be implemented at scale in urban transport systems due in part to the lack of an agreed conceptual definition, the top-down approach to implementing what is meant to be a more personalised method of accessing transport, and the lack of local promoters (in comparison to global corporations and lobbyists). This article reflects on the current barriers to defining MaaS, considers how a novel public engagement approach could be used to create local definitions that support citizen engagement, and suggests a route forward for future research

An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments

Cell-cell and cell-glycocalyx interactions under flow are important for the behaviour of circulating cells in blood and lymphatic vessels. However, such interactions are not well understood due in part to a lack of tools to study them in defined environments. Here, we develop a versatile in vitro platform for the study of cell-glycocalyx interactions in well-defined physical and chemical settings under flow. Our approach is demonstrated with the interaction between hyaluronan (HA, a key component of the endothelial glycocalyx) and its cell receptor CD44. We generate HA brushes in situ within a microfluidic device, and demonstrate the tuning of their physical (thickness and softness) and chemical (density of CD44 binding sites) properties using characterisation with reflection interference contrast microscopy (RICM) and application of polymer theory. We highlight the interactions of HA brushes with CD44-displaying beads and cells under flow. Observations of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories to be generated, and revealed interactions in the form of stop and go phases with reduced rolling velocity and reduced distance between the bead and the HA brush, compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+ AKR1 T-lymphocytes revealed complementary information about the dynamics of cell rolling and cell morphology, and highlighted the formation of tethers and slings, as they interacted with a HA brush under flow. This platform can readily incorporate more complex models of the glycocalyx, and should permit the study of how mechanical and biochemical factors are orchestrated to enable highly selective blood cell-vessel wall interactions under flow