Using electrical and optical tweezers to facilitate studies of molecular motors

Dielectrophoresis was used to stretch and suspend actin filaments across a trench etched between two electrodes patterned on a glass slide. Optical tweezers were used to bring a motor protein-coated bead into close proximity to a pre-selected, suspended actin filament, facilitating the attachment of the myosin-coated bead to the filament. The clearance beneath the filament allowed the bead to move freely along and around its filamentous track, unhindered by solid surfaces. Using defocused images, the three-dimensional position of the bead was tracked as a function of time to obtain its trajectory. Experiments were carried out with myosin V and myosin X. Both motor proteins followed left-handed helical paths with the myosin X motor exhibiting a shorter pitch than the myosin V. The combined use of electrostatic and optical tweezers facilitates the preparation of motility assays with suspended tracks. Variants of this technique will enable higher complexity experiments in vitro to better understand the behavior of motors in cells

The mechanics of short rod-like molecules in tension

The rapid development of single molecule experimental techniques in the last two decades has made it possible to accurately measure the force-extension response as well as the transverse fluctuations of individual rod-like macromolecules. This information is used in conjunction with a statistical mechanical model based on the treatment of the molecule as a fluctuating elastic rod to extract its bending and extension moduli. The models most commonly used to interpret the experimental data assume that the magnitude of the Brownian fluctuations are independent of the length of the macromolecule, an assumption that holds only in the asymptotic limit of infinitely long rods, and is violated in most experiments. As an alternative, we present a theoretical treatment of a finite length, fluctuating rod and determine its mechanical behavior by measuring the transverse Brownian fluctuations under the action of large stretching forces. to validate of our theory, we have applied our methods to an experiment on short actin filaments whose force-extension relation is difficult to measure, but whose transverse deflections can be captured by current microscopy techniques. An important consequence of the short contour lengths is that the boundary conditions applied in the experiment affect the fluctuations and can no longer be neglected as is commonly done when interpreting data from force-extension measurements. Our theoretical methods account for boundary conditions and can therefore be deployed in conjunction with force extension measurements to obtain detailed information about the mechanical response of rod-like macromolecules

The SPARC Toroidal Field Model Coil Program

The SPARC Toroidal Field Model Coil (TFMC) Program was a three-year effort between 2018 and 2021 that developed novel Rare Earth Yttrium Barium Copper Oxide (REBCO) superconductor technologies and then successfully utilized these technologies to design, build, and test a first-in-class, high-field (~20 T), representative-scale (~3 m) superconducting toroidal field coil. With the principal objective of demonstrating mature, large-scale, REBCO magnets, the project was executed jointly by the MIT Plasma Science and Fusion Center (PSFC) and Commonwealth Fusion Systems (CFS). The TFMC achieved its programmatic goal of experimentally demonstrating a large-scale high-field REBCO magnet, achieving 20.1 T peak field-on-conductor with 40.5 kA of terminal current, 815 kN/m of Lorentz loading on the REBCO stacks, and almost 1 GPa of mechanical stress accommodated by the structural case. Fifteen internal demountable pancake-to-pancake joints operated in the 0.5 to 2.0 nOhm range at 20 K and in magnetic fields up to 12 T. The DC and AC electromagnetic performance of the magnet, predicted by new advances in high-fidelity computational models, was confirmed in two test campaigns while the massively parallel, single-pass, pressure-vessel style coolant scheme capable of large heat removal was validated. The REBCO current lead and feeder system was experimentally qualified up to 50 kA, and the crycooler based cryogenic system provided 600 W of cooling power at 20 K with mass flow rates up to 70 g/s at a maximum design pressure of 20 bar-a for the test campaigns. Finally, the feasibility of using passive, self-protection against a quench in a fusion-scale NI TF coil was experimentally assessed with an intentional open-circuit quench at 31.5 kA terminal current.Comment: 17 pages 9 figures, overview paper and the first of a six-part series of papers covering the TFMC Progra

Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins

Statins effectively lower LDL cholesterol levels in large studies and the observed interindividual response variability may be partially explained by genetic variation. Here we perform a pharmacogenetic meta-analysis of genome-wide association studies (GWAS) in studies addressing the LDL cholesterol response to statins, including up to 18,596 statin-treated subjects. We validate the most promising signals in a further 22,318 statin recipients and identify two loci, SORT1/CELSR2/PSRC1 and SLCO1B1, not previously identified in GWAS. Moreover, we confirm the previously described associations with APOE and LPA. Our findings advance the understanding of the pharmacogenetic architecture of statin response

Meta-analysis of genome-wide association studies of HDL cholesterol response to statins

BACKGROUND: In addition to lowering low density lipoprotein cholesterol (LDL-C), statin therapy also raises high density lipoprotein cholesterol (HDL-C) levels. Inter-individual variation in HDL-C response to statins may be partially explained by genetic variation.METHODS AND RESULTS: We performed a meta-analysis of genome-wide association studies (GWAS) to identify variants with an effect on statin-induced high density lipoprotein cholesterol (HDL-C) changes. The 123 most promising signals with p&lt;1×10(-4) from the 16 769 statin-treated participants in the first analysis stage were followed up in an independent group of 10 951 statin-treated individuals, providing a total sample size of 27 720 individuals. The only associations of genome-wide significance (p&lt;5×10(-8)) were between minor alleles at the CETP locus and greater HDL-C response to statin treatment.CONCLUSIONS: Based on results from this study that included a relatively large sample size, we suggest that CETP may be the only detectable locus with common genetic variants that influence HDL-C response to statins substantially in individuals of European descent. Although CETP is known to be associated with HDL-C, we provide evidence that this pharmacogenetic effect is independent of its association with baseline HDL-C levels.</p

Subsequent Event Risk in Individuals with Established Coronary Heart Disease:Design and Rationale of the GENIUS-CHD Consortium

BACKGROUND: The "GENetIcs of sUbSequent Coronary Heart Disease" (GENIUS-CHD) consortium was established to facilitate discovery and validation of genetic variants and biomarkers for risk of subsequent CHD events, in individuals with established CHD. METHODS: The consortium currently includes 57 studies from 18 countries, recruiting 185,614 participants with either acute coronary syndrome, stable CHD or a mixture of both at baseline. All studies collected biological samples and followed-up study participants prospectively for subsequent events. RESULTS: Enrollment into the individual studies took place between 1985 to present day with duration of follow up ranging from 9 months to 15 years. Within each study, participants with CHD are predominantly of self-reported European descent (38%-100%), mostly male (44%-91%) with mean ages at recruitment ranging from 40 to 75 years. Initial feasibility analyses, using a federated analysis approach, yielded expected associations between age (HR 1.15 95% CI 1.14-1.16) per 5-year increase, male sex (HR 1.17, 95% CI 1.13-1.21) and smoking (HR 1.43, 95% CI 1.35-1.51) with risk of subsequent CHD death or myocardial infarction, and differing associations with other individual and composite cardiovascular endpoints. CONCLUSIONS: GENIUS-CHD is a global collaboration seeking to elucidate genetic and non-genetic determinants of subsequent event risk in individuals with established CHD, in order to improve residual risk prediction and identify novel drug targets for secondary prevention. Initial analyses demonstrate the feasibility and reliability of a federated analysis approach. The consortium now plans to initiate and test novel hypotheses as well as supporting replication and validation analyses for other investigators

Unpacking ecosystem service bundles: towards predictive mapping of synergies and trade-offs between ecosystem services

Multiple ecosystem services (ES) can respond similarly to social and ecological factors to form bundles. Identifying key social-ecological variables and understanding how they co-vary to produce these consistent sets of ES may ultimately allow the prediction and modelling of ES bundles, and thus, help us understand critical synergies and trade-offs across landscapes. Such an understanding is essential for informing better management of multi-functional landscapes and minimising costly trade-offs. However, the relative importance of different social and biophysical drivers of ES bundles in different types of social-ecological systems remains unclear. As such, a bottom-up understanding of the determinants of ES bundles is a critical research gap in ES and sustainability science. Here, we evaluate the current methods used in ES bundle science and synthesize these into four steps that capture the plurality of methods used to examine predictors of ES bundles. We then apply these four steps to a cross-study comparison (North and South French Alps) of relationships between social-ecological variables and ES bundles, as it is widely advocated that cross-study comparisons are necessary for achieving a general understanding of predictors of ES associations. We use the results of this case study to assess the strengths and limitations of current approaches for understanding distributions of ES bundles. We conclude that inconsistency of spatial scale remains the primary barrier for understanding and predicting ES bundles. We suggest a hypothesis-driven approach is required to predict relationships between ES, and we outline the research required for such an understanding to emerge

Debugging Optimized Code: Concepts and Implementation on DIGITAL Alpha Systems

Effective user debugging of optimized code has been a topic of theoretical and practical interest in the software development community for almost two decades, yet today the state of the art is still highly uneven. We present a brief survey of the literature and current practice that leads to the identification of three aspects of debugging optimized code that seem to be critical as well as tractable without extraordinary efforts. These aspects are (1) split lifetime support for variables whose allocation varies within a program combined with definition point reporting for currency determination, (2) stepping and setting breakpoints based on a semantic event characterization of program behavior, and (3) treatment of inlined routine calls in a manner that makes inlining largely transparent. We describe the realization of these capabilities as part of Compaq’s GEM back-end compiler technology and the debugging component of the OpenVMS Alpha operating system