Atomic and Electronic Structure of the BaTiO\u3csub\u3e3\u3c/sub\u3e(001) (√5×√5)\u3cem\u3eR\u3c/em\u3e26.6° Surface Reconstruction

This contribution presents a study of the atomic and electronic structure of the (√5×√5)R26.6° surface reconstruction on BaTiO3 (001) formed by annealing in ultrahigh vacuum at 1300 K. Through density functional theory calculations in concert with thermodynamic analysis, we assess the stability of several BaTiO3 surface reconstructions and construct a phase diagram as a function of the chemical potential of the constituent elements. Using both experimental scanning tunneling microscopy (STM) and scanning tunneling spectroscopy measurements, we were able to further narrow down the candidate structures, and conclude that the surface is either TiO2-Ti3/5, TiO2-Ti4/5, or some combination, where Ti adatoms occupy hollow sites of the TiO2 surface. Density functional theory indicates that the defect states close to the valence band are from Ti adatom 3d orbitals (≈1.4  eV below the conduction band edge) in agreement with scanning tunneling spectroscopy measurements showing defect states 1.56±0.11  eV below the conduction band minimum (1.03±0.09  eV below the Fermi level). STM measurements show electronic contrast between empty and filled states’ images. The calculated local density of states at the surface shows that Ti 3d states below and above the Fermi level explain the difference in electronic contrast in the experimental STM images by the presence of electronically distinctive arrangements of Ti adatoms. This work provides an interesting contrast with the related oxide SrTiO3, for which the (001) surface (√5×√5)R26.6° reconstruction is reported to be the TiO2 surface with Sr adatoms

Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments

In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We present a new technique for characterizing the kinetics of loop formation in vitro, as observed using the tethered particle method, and apply it to experimental data on looping induced by lambda repressor. Our method uses a modified (diffusive) hidden Markov analysis that directly incorporates the Brownian motion of the observed tethered bead. We compare looping lifetimes found with our method (which we find are consistent over a range of sampling frequencies) to those obtained via the traditional threshold-crossing analysis (which can vary depending on how the raw data are filtered in the time domain). Our method does not involve any time filtering and can detect sudden changes in looping behavior. For example, we show how our method can identify transitions between long-lived, kinetically distinct states that would otherwise be difficult to discern

Differential Impact of Blood Pressure Control Targets on Epicardial Coronary Flow After Transcatheter Aortic Valve Replacement

Background: The cause for the association between increased cardiovascular mortality rates and lower blood pressure (BP) after aortic valve replacement (AVR) is unclear. This study aims to assess how the epicardial coronary flow (ECF) after AVR varies as BP levels are changed in the presence of a right coronary lesion. Methods: The hemodynamics of a 3D printed aortic root model with a SAPIEN 3 26 deployed were evaluated in an in vitro left heart simulator under a range of varying systolic blood pressure (SBP) and diastolic blood pressure (DBP). ECF and the flow ratio index were calculated. Flow index value 0.9 for SBP ≥130 mmHg. However, at an SBP of 120 mmHg, the flow ratio was 0.63 (p ≤ 0.0055). With decreasing DBP, no BP condition yielded a flow ratio index that was less than 0.91. Conclusions: Reducing BP to the current recommended levels assigned for the general population after AVR in the presence of coronary artery disease may require reconsideration of levels and treatment priority. Additional studies are needed to fully understand the changes in ECF dynamics after AVR in the presence and absence of coronary artery disease

High accuracy FIONA–AFM hybrid imaging

Multi-protein complexes are ubiquitous and play essential roles in many biological mechanisms. Single molecule imaging techniques such as electron microscopy (EM) and atomic force microscopy (AFM) are powerful methods for characterizing the structural properties of multi-protein and multi-protein–DNA complexes. However, a significant limitation to these techniques is the ability to distinguish different proteins from one another. Here, we combine high resolution fluorescence microscopy and AFM (FIONA–AFM) to allow the identification of different proteins in such complexes. Using quantum dots as fiducial markers in addition to fluorescently labeled proteins, we are able to align fluorescence and AFM information to ≥8 nm accuracy. This accuracy is sufficient to identify individual fluorescently labeled proteins in most multi-protein complexes. We investigate the limitations of localization precision and accuracy in fluorescence and AFM images separately and their effects on the overall registration accuracy of FIONA–AFM hybrid images. This combination of the two orthogonal techniques (FIONA and AFM) opens a wide spectrum of possible applications to the study of protein interactions, because AFM can yield high resolution (5–10 nm) information about the conformational properties of multi-protein complexes and the fluorescence can indicate spatial relationships of the proteins in the complexes

Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy

Atomic force microscopy (AFM) has been used to image, at single molecule resolution, transcription events by Escherichia coli RNA polymerase (RNAP) on a linear DNA template with two convergently aligned λ(pr) promoters. For the first time experimentally, the outcome of collision events during convergent transcription by two identical RNAP has been studied. Measurement of the positions of the RNAP on the DNA, allows distinction of open promoter complexes (OPCs) and elongating complexes (EC) and collided complexes (CC). This discontinuous time-course enables subsequent analysis of collision events where both RNAP remain bound on the DNA. After collision, the elongating RNAP has caused the other (usually stalled) RNAP to back-track along the template. The final positions of the two RNAP indicate that these are collisions between an EC and a stalled EC (SEC) or OPC (previously referred to as sitting-ducks). Interestingly, the distances between the two RNAP show that they are not always at closest approach after ‘collision’ has caused their arrest

DNA bending and unbending by MutS govern mismatch recognition and specificity

DNA mismatch repair is central to the maintenance of genomic stability. It is initiated by the recognition of base–base mismatches and insertion/deletion loops by the family of MutS proteins. Subsequently, ATP induces a unique conformational change in the MutS–mismatch complex but not in the MutS–homoduplex complex that sets off the cascade of events that leads to repair. To gain insight into the mechanism by which MutS discriminates between mismatch and homoduplex DNA, we have examined the conformations of specific and nonspecific MutS–DNA complexes by using atomic force microscopy. Interestingly, MutS–DNA complexes exhibit a single population of conformations, in which the DNA is bent at homoduplex sites, but two populations of conformations, bent and unbent, at mismatch sites. These results suggest that the specific recognition complex is one in which the DNA is unbent. Combining our results with existing biochemical and crystallographic data leads us to propose that MutS: (i) binds to DNA nonspecifically and bends it in search of a mismatch; (ii) on specific recognition of a mismatch, undergoes a conformational change to an initial recognition complex in which the DNA is kinked, with interactions similar to those in the published crystal structures; and (iii) finally undergoes a further conformational change to the ultimate recognition complex in which the DNA is unbent. Our results provide a structural explanation for the long-standing question of how MutS achieves mismatch repair specificity

Regionalizing the infrastructure turn : a research agenda

An interdisciplinary ‘infrastructure turn’ has emerged over the past 20 years that disputes the concept of urban infrastructure as a staid or neutral set of physical artefacts. Responding to the increased conceptual, geographical and political importance of infrastructure – and endemic issues of access, expertise and governance that the varied provision of infrastructures can cause – this intervention asserts the significance of applying a regional perspective to the infrastructure turn. This paper forwards a critical research agenda for the study of ‘infrastructural regionalisms’ to interrogate: (1) how we study and produce knowledge about infrastructure; (2) how infrastructure is governed across or constrained by jurisdictional boundaries; (3) who drives the construction of regional infrastructural imaginaries; and (4) how individuals and communities differentially experience regional space through infrastructure. Analysing regions through infrastructure provides a novel perspective on the regional question and consequently offers a framework to understand better the implications of the current infrastructure moment for regional spaces worldwide

Tuning the translational freedom of DNA for high speed AFM

Direct observation is arguably the preferred way to investigate the interactions between two molecular complexes. With the development of high speed atomic force microscopy it is becoming possible to observe directly DNA protein interactions with relevant spatial and temporal resolutions. These interactions are of central importance to biology, bio-nanotechnology but also functional biologically inspired materials. Critically, sample preparation plays a central role in all microscopy studies and minimal perturbation of the sample is desired. Here, we demonstrate the ability to tune the interactions of DNA molecules with the surface such that an association strong enough to enable high resolution AFM imaging while providing sufficient translational freedom to allow the relevant protein DNA interactions to take place, can be maintained. Furthermore, we describe a quantitative method for measuring the DNA mobility, which also allows the dissection of the different contributions to the overall movement of the DNA molecules. We find that for weak surface association, a significant contribution to the movement arises from the interaction of the AFM tip with the DNA. In combination, these methods enable the tuning of the surface translational freedom of DNA molecules to allow the direct study of a wide range of nucleo-protein interactions by high speed atomic force microscopy