Direct Single-Molecule Observation of Mode and Geometry of RecA-Mediated Homology Search

Genomic integrity, when compromised by accrued DNA lesions, is maintained through efficient repair via homologous recombination. For this process the ubiquitous recombinase A (RecA), and its homologues such as the human Rad51, are of central importance, able to align and exchange homologous sequences within single-stranded and double-stranded DNA in order to swap out defective regions. Here, we directly observe the widely debated mechanism of RecA homology searching at a single-molecule level using high-speed atomic force microscopy (HS-AFM) in combination with tailored DNA origami frames to present the reaction targets in a way suitable for AFM-imaging. We show that RecA nucleoprotein filaments move along DNA substrates via short-distance facilitated diffusions, or slides, interspersed with longer-distance random moves, or hops. Importantly, from the specific interaction geometry, we find that the double-stranded substrate DNA resides in the secondary DNA binding-site within the RecA nucleoprotein filament helical groove during the homology search. This work demonstrates that tailored DNA origami, in conjunction with HS-AFM, can be employed to reveal directly conformational and geometrical information on dynamic protein-DNA interactions which was previously inaccessible at an individual single-molecule level

Label-free electrochemical biosensors for clinical diagnostic

We present the development of a high sensitivity, label-free, biosensor platform suitable for multiplexed point-of-care diagnostics. A sensor surface based on a carboxy-terminated oligo ethylene-glycol (OEG) self-assembled monolayer (SAM) was developed and fully characterised. Optimal conditions for antibody immobilisation were found for a buffer pH approximately one unit below the pI of the antibody, which yielded both higher antibody density on the sensor surface as well as higher sensor response to the antigen. At the same time the surface showed good resistance to non-specific adsorption of high concentrations of proteins. A non-faradaic electrochemical impedance spectroscopy biosensor to detect human chorionic gonadotropin (hCG) in full serum was demonstrated as a proof of concept. By using the phase of the impedance at 100 mHz as the sensor response, a linear relationship of the phase shift vs the logarithm of hCG concentration was established between 26 fM and 0.26 nM with a sensitivity of 0.6 degree per decade, which is a significant improvement over current state-of-the-art biosensor systems

Cooperative RecA clustering: the key to efficient homology searching

The mechanism by which pre-synaptic RecA nucleoprotein filaments efficiently locate sequence homology across genomic DNA remains unclear. Here, using atomic force microscopy, we directly investigate the intermediates of the RecA-mediated homologous recombination process and find it to be highly cooperative, involving multiple phases. Initially, the process is dominated by a rapid 'association' phase, where multiple filaments interact on the same dsDNA simultaneously. This cooperative nature is reconciled by the observation of localized dense clusters of pre-synaptic filaments interacting with the observed dsDNA molecules. This confinement of reactive species within the vicinity of the dsDNA, is likely to play an important role in ensuring that a high interaction rate between the nucleoprotein filaments and the dsDNA can be achieved. This is followed by a slower 'resolution' phase, where the synaptic joints either locate sequence homology and progress to a post-synaptic joint, or dissociate from the dsDNA. Surprisingly, the number of simultaneous synaptic joints decreases rapidly after saturation of the dsDNA population, suggesting a reduction in interaction activity of the RecA filaments. We find that the time-scale of this decay is in line with the time-scale of the dispersion of the RecA filament clusters, further emphasising the important role this cooperative phenomena may play in the RecA-facilitated homology search

A planar surface acoustic wave micropump for closed-loop microfluidics

We have designed and characterized a simple Rayleigh-surface acoustic wave-based micropump, integrated directly with a fully enclosed 3D microfluidic system, which improves significantly the pumping efficiency within a coupled fluid whilst maintaining planar integration of the micropump and microfluidics. We achieve this by exploiting the Rayleigh-scattering angle of surface acoustic waves into pressure waves on contact with overlaid fluids, by designing a microfluidic channel aligned almost co-linearly with the launched pressure waves and by minimizing energy losses by reflections from, or absorption within, the channel walls. This allows the microfluidic system to remain fully enclosed—a pre-requisite for point-of-care applications—removing sources of possible contamination, whilst achieving pump efficiencies up to several orders of magnitude higher than previously reported, at low operating powers of 0.5 W

Discovery of novel biomarkers and phenotypes by semantic technologies.

Biomarkers and target-specific phenotypes are important to targeted drug design and individualized medicine, thus constituting an important aspect of modern pharmaceutical research and development. More and more, the discovery of relevant biomarkers is aided by in silico techniques based on applying data mining and computational chemistry on large molecular databases. However, there is an even larger source of valuable information available that can potentially be tapped for such discoveries: repositories constituted by research documents

DNA self-assembly-driven positioning of molecular components on nanopatterned surfaces.

We present a method for the specific, spatially targeted attachment of DNA molecules to lithographically patterned gold surfaces-demonstrated by bridging DNA strands across nanogap electrode structures. An alkanethiol self-assembled monolayer was employed as a molecular resist, which could be selectively removed via electrochemical desorption, allowing the binding of thiolated DNA anchoring oligonucleotides to each electrode. After introducing a bridging DNA molecule with single-stranded ends complementary to the electrode-tethered anchoring oligonucleotides, the positioning of the DNA molecule across the electrode gap, driven by self-assembly, occurred autonomously. This demonstrates control of molecule positioning with resolution limited only by the underlying patterned structure, does not require any alignment, is carried out entirely under biologically compatible conditions, and is scalable

Rapid cell separation with minimal manipulation for autologous cell therapies

The ability to isolate specific, viable cell populations from mixed ensembles with minimal manipulation and within intra-operative time would provide significant advantages for autologous, cell-based therapies in regenerative medicine. Current cell-enrichment technologies are either slow, lack specificity and/or require labelling. Thus a rapid, label-free separation technology that does not affect cell functionality, viability or phenotype is highly desirable. Here, we demonstrate separation of viable from non-viable human stromal cells using remote dielectrophoresis, in which an electric field is coupled into a microfluidic channel using shear-horizontal surface acoustic waves, producing an array of virtual electrodes within the channel. This allows high-throughput dielectrophoretic cell separation in high conductivity, physiological-like fluids, overcoming the limitations of conventional dielectrophoresis. We demonstrate viable/non-viable separation efficacy of > 98% in pre-purified mesenchymal stromal cells, extracted from human dental pulp, with no adverse effects on cell viability, or on their subsequent osteogenic capabilities

A Systematic Review of the Effect of Therapeutic Drug Monitoring on Patient Health Outcomes during Treatment with Carbapenems

Adjusting dosing regimens based on measurements of carbapenem levels may improve carbapenem exposure in patients. This systematic review aims to describe the effect carbapenem therapeutic drug monitoring (TDM) has on health outcomes, including the emergence of antimicrobial resistance (AMR). Four databases were searched for studies that reported health outcomes following adjustment to dosing regimens, according to measurements of carbapenem concentration. Bias in the studies was assessed with risk of bias analysis tools. Study characteristics and outcomes were tabulated and a narrative synthesis was performed. In total, 2 randomised controlled trials (RCTs), 17 non-randomised studies, and 19 clinical case studies were included. Significant variation in TDM practice was seen; consequently, a meta-analysis was unsuitable. Few studies assessed impacts on AMR. No significant improvement on health outcomes and no detrimental effects of carbapenem TDM were observed. Five cohort studies showed significant associations between achieving target concentrations and clinical success, including suppression of resistance. Studies in this review showed no obvious improvement in clinical outcomes when TDM is implemented. Optimisation and standardisation of carbapenem TDM practice are needed to improve intervention success and enable study synthesis. Further suitably powered studies of standardised TDM are required to assess the impact of TMD on clinical outcomes and AMR

Strong Electron-Phonon Coupling in Superconducting MgB2_2: A Specific Heat Study

We report on measurements of the specific heat of the recently discovered superconductor MgB$_2$ in the temperature range between 3 and 220 K. Based on a modified Debye-Einstein model, we have achieved a rather accurate account of the lattice contribution to the specific heat, which allows us to separate the electronic contribution from the total measured specific heat. From our result for the electronic specific heat, we estimate the electron-phonon coupling constant $\lambda$ to be of the order of 2, significantly enhanced compared to common weak-coupling values $\leq 0.4$. Our data also indicate that the electronic specific heat in the superconducting state of MgB$_2$ can be accounted for by a conventional, s-wave type BCS-model.Comment: 4 pages, 4 figure

A systematic review of the effect of therapeutic drug monitoring on patient health outcomes during treatment with penicillins.

Background Dosing regimens guided by therapeutic drug monitoring (TDM) may be able to improve penicillin exposure in patients, which could result in improved patient health outcomes. Objectives This systematic review aims to describe the impact penicillin TDM has on health outcomes, including antimicrobial resistance (AMR). Methods Studies measuring penicillins in patient samples that adjusted regimens according to the result, and reported health outcomes were selected. Study bias was assessed according to study type. Included study characteristics were tabulated and described by narrative synthesis. Results Three randomized controlled trials (RCTs), 16 cohort studies, and 9 case studies were included. No RCTs showed statistically significant improvements in health outcomes. Five cohort studies showed improvement in at least one health outcome associated with target attainment. However, there was a high risk of bias in all studies for health outcomes. One study assessed the impact of penicillin TDM on AMR and found that improved target attainment was associated with suppression of resistance. No studies found a detrimental effect of penicillin TDM. Conclusions There is little evidence to suggest that TDM improves health outcomes, however neither health outcomes nor impact on AMR were adequately addressed. Variations in TDM implementation meant that a meta-analysis was not suitable. Penicillin TDM needs standardization, however there is currently no clear evidence of optimal conditions. Suitably powered studies are required to resolve the ambiguity surrounding the impact of TDM on clinical outcomes, including AMR. Further, standardized protocols and concentration targets need to be identified for TDM to be implemented successfully