The effects of localized damping on structural response

The effect of localized structural damping on the excitability of higher order normal modes of the large space telescope was investigated. A preprocessor computer program was developed to incorporate Voigt structural joint damping models in a NASTRAN finite-element dynamic model. A postprocessor computer program was developed to select critical modes for low-frequency attitude control problems and for higher frequency fine-stabilization problems. The mode selection is accomplished by ranking the flexible modes based on coefficients for rate gyro, position gyro, and optical sensors, and on image-plane motions due to sinusoidal or random power spectral density force and torque inputs

Calibración de sensores de humedad capacitivos usando redes neuronales

X Jornadas de Investigación de la Zona no Saturada del Suelo, Salamanca (España), 2011El estudio de la variabilidad espacial de la humedad del suelo a escala de parcela o cuenca agrícola requiere el uso de redes de sensores de humedad de bajo coste, que suelen mostrar una fiabilidad limitada y requieren de calibraciones específicas, especialmente en suelos con elevados contenidos en arcilla. El presente trabajo pretende plantear una calibración más fiable de sondas de humedad mediante un análisis mixto campo-laboratorio. Para la calibración de campo se dispone de datos gravimétricos; para la calibración en laboratorio se han usado columnas de suelo inalterado que tras ser saturadas fueron desecadas en un entorno controlado mientras se monitorizaba la evolución de su peso y la de su humedad volumétrica, medida con diferentes sondas capacitivas Decagon. Tras obtener curvas de secado y la relación entre la humedad gravimétrica y la volumétrica es posible realizar una calibración mejorada específica para cada tipo de suelo. Las redes neuronales son particularmente útiles para el modelado de procesos físicos y el ajuste de modelos. En este trabajo se propone el empleo de dichas herramientas para obtener calibraciones para las sondas analizadas en el tipo de suelo objeto de estudio. Los resultados muestran que dichas calibraciones permiten mejorar la precisión de las mediciones de humedad realizadas.The study of the spatial variability of soil water content at agricultural plot or catchment scales requires the use of low-cost soil water content sensor networks, which usually show a limited reliability and require specific calibrations, specially for soils with a high clay content. This work proposes a more reliable calibration of soil water content probes with a laboratory analysis. Minimally disturbed soil columns were saturated with water and dried in a controlled environment while monitorizing the evolution of their volumetric soil water content (with different capacitive Decagon Probes) and weights. After obtaining the drying curves and the relation between the volumetric and the measured gravimetric soil water contents it is possible to achieve an improved calibration specific for different kinds of soil. Neural networks are especially interesting for the modeling of physical processes and model adjustment. In this work, these tools were used in order to obtain improved calibrations for the analyzed probes in the studied soil type. Results show that this calibration improves the accuracy and pMinisterio de Ciencia e Innovación AGL2009 C03-03Junta de Andalucía AGR-478

The free energy landscape of retroviral integration

Retroviral integration, the process of covalently inserting viral DNA into the host genome, is a point of no return in the replication cycle. Yet, strand transfer is intrinsically iso-energetic and it is not clear how efficient integration can be achieved. Here we investigate the dynamics of strand transfer and demonstrate that consecutive nucleoprotein intermediates interacting with a supercoiled target are increasingly stable, resulting in a net forward rate. Multivalent target interactions at discrete auxiliary interfaces render target capture irreversible, while allowing dynamic site selection. Active site binding is transient but rapidly results in strand transfer, which in turn rearranges and stabilizes the intasome in an allosteric manner. We find the resulting strand transfer complex to be mechanically stable and extremely long-lived, suggesting that a resolving agent is required in vivo

DNA fluctuations reveal the size and dynamics of topological domains

DNA supercoiling is a key regulatory mechanism that orchestrates DNA readout, recombination, and genome maintenance. DNA-binding proteins often mediate these processes by bringing two distant DNA sites together, thereby inducing (transient) topological domains. In order to understand the dynamics and molecular architecture of protein-induced topological domains in DNA, quantitative and time-resolved approaches are required. Here, we present a methodology to determine the size and dynamics of topological domains in supercoiled DNA in real time and at the single-molecule level. Our approach is based on quantifying the extension fluctuations—in addition to the mean extension—of supercoiled DNA in magnetic tweezers (MT). Using a combination of high-speed MT experiments, Monte Carlo simulations, and analytical theory, we map out the dependence of DNA extension fluctuations as a function of supercoiling density and external force. We find that in the plectonemic regime, the extension variance increases linearly with increasing supercoiling density and show how this enables us to determine the formation and size of topological domains. In addition, we demonstrate how the transient (partial) dissociation of DNA-bridging proteins results in the dynamic sampling of different topological states, which allows us to deduce the torsional stiffness of the plectonemic state and the kinetics of protein-plectoneme interactions. We expect our results to further the understanding and optimization of magnetic tweezer measurements and to enable quantification of the dynamics and reaction pathways of DNA processing enzymes in the context of physiologically relevant forces and supercoiling densities

Parametric expressions for the adjusted Hargreaves coefficient in Eastern Spain

The application of simple empirical equations for estimating reference evapotranspiration (ETo) is the only alternative in many cases to robust approaches with high input requirements, especially at the local scale. In particular, temperature-based approaches present a high potential applicability, among others, because temperature might explain a high amount of ETo variability, and also because it can be measured easily and is one of the most available climatic inputs. One of the most well-known temperature-based approaches, the Hargreaves (HG) equation, requires a preliminary local calibration that is usually performed through an adjustment of the HG coefficient (AHC). Nevertheless, these calibrations are sitespecific, and cannot be extrapolated to other locations. So, they become useless in many situations, because they are derived from already available benchmarks based on more robust methods, which will be applied in practice. Therefore, the development of accurate equations for estimating AHC at local scale becomes a relevant task. This paper analyses the performance of calibrated and non-calibrated HG equations at 30 stations in Eastern Spain at daily, weekly, fortnightly and monthly scales. Moreover, multiple linear regression was applied for estimating AHC based on different inputs, and the resulting equations yielded higher performance accuracy than the non-calibrated HG estimates. The approach relying on the ratio mean temperature to temperature range did not provide suitable AHC estimations, and was highly improved by splitting it into two independent predictors. Temperature-based equations were improved by incorporating geographical inputs. Finally, the model relying on temperature and geographic inputs was further improved by incorporating wind speed, even just with simple qualitative information about wind category (e.g. poorly vs. highly windy). The accuracy of the calibrated and non-calibrated HG estimates increased for longer time steps (daily < weekly < fortnightly < monthly), although with a decreasing accuracy improvement rate. The variability of goodness-of-fit between AHC models was translated into lower variability of accuracy between the corresponding HG calibrated ETo estimates, because a single AHC was applied per station. The AHC fluctuations throughout the year suggest the convenience of using monthly or, at least, seasonal models. 2015 Elsevier B.V. All rights reserved.P. Marti acknowledges the financial support of the research grant Juan de la Cierva JCI-2012-13513 (Spanish Ministry of Economy and Competitiveness).Martí Pérez, PC.; Zarzo Castelló, M.; Vanderlinden, K.; Girona, J. (2015). Parametric expressions for the adjusted Hargreaves coefficient in Eastern Spain. Journal of Hydrology. 529(3):1713-1724. https://doi.org/10.1016/j.jhydrol.2015.07.054S17131724529

Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold

SYBR Gold is a commonly used and particularly bright fluorescent DNA stain, however, its chemical structure is unknown and its binding mode to DNA remains controversial. Here, we solve the structure of SYBR Gold by NMR and mass spectrometry to be 2-N-(3-dimethylaminopropyl)-N-propylamino]-4-2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene-1-phenyl-quinolinium and determine its extinction coefficient. We quantitate SYBR Gold binding to DNA using two complementary approaches. First, we use single-molecule magnetic tweezers (MT) to determine the effects of SYBR Gold binding on DNA length and twist. The MT assay reveals systematic lengthening and unwinding of DNA by 19.1° ± 0.7° per molecule upon binding, consistent with intercalation, similar to the related dye SYBR Green I. We complement the MT data with spectroscopic characterization of SYBR Gold. The data are well described by a global binding model for dye concentrations ≤2.5~μM, with parameters that quantitatively agree with the MT results. The fluorescence increases linearly with the number of intercalated SYBR Gold molecules up to dye concentrations of ∼2.5~μM, where quenching and inner filter effects become relevant. In summary, we provide a mechanistic understanding of DNA-SYBR Gold interactions and present practical guidelines for optimal DNA detection and quantitative DNA sensing applications using SYBR Gold

Mechanism of polyubiquitination by human anaphase-promoting complex: RING repurposing for ubiquitin chain assembly.

Polyubiquitination by E2 and E3 enzymes is a predominant mechanism regulating protein function. Some RINGE3s, including anaphase-promoting complex/cyclosome (APC), catalyze polyubiquitination by sequential reactions with two different E2s. An initiating E2 ligates ubiquitin to an E3-bound substrate. Another E2 grows a polyubiquitin chain on the ubiquitin-primed substrate through poorly defined mechanisms. Here we show that human APC's RING domain is repurposed for dual functions in polyubiquitination. The canonical RING surface activates an initiating E2-ubiquitin intermediate for substrate modification. However, APC engages and activates its specialized ubiquitin chain-elongating E2 UBE2S in ways that differ from current paradigms. During chain assembly, a distinct APC11 RING surface helps deliver a substrate-linked ubiquitin to accept another ubiquitin from UBE2S. Our data define mechanisms of APC/UBE2S-mediated polyubiquitination, reveal diverse functions of RING E3s and E2s, and provide a framework for understanding distinctive RING E3 features specifying ubiquitin chain elongation

Tests at 2K of the beta 0.35 spoke cryomodule prototype with the MTCA.4-based Low Level RF system prototype for the MYRRHA R&D

Within the framework of the first phase of MYRRHA (Multi-purpose hYbrid Research Reactor for High-tech Applications) project, called MINERVA, IJCLab was in charge of a fully equipped Spoke cryomodule prototype development, tested at 2K. It integrates two superconducting single spoke cavities, the RF power couplers and the Cold Tuning Systems associated. On the control side, a MTCA.4-based Low Level Radio Frequency (LLRF) system prototype and the Software/EPICS developments has been realized by IJCLab and the SCK CEN in collaboration with the company IOxOS Technologies. The final version of the global system and the results of the tests at 2K will show with some perspectives.Comment: Poster pr\'esent\'e au LLRF Workshop 2023 (LLRF2023, arXiv : 2310.03199

Correction to ‘Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold’

This is a correction to: Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5143–5158, https://doi.org/10.1093/nar/gkab26