Allosterism and signal transfer in DNA

We analysed the basic mechanisms of signal transmission in DNA and the origins of the allostery exhibited by systems such as the ternary complex BAMHI-DNA-GRDBD. We found that perturbation information generated by a primary protein binding event travels as a wave to distant regions of DNA following a hopping mechanism. However, such a structural perturbation is transient and does not lead to permanent changes in the DNA geometry and interaction properties at the secondary binding site. The BAMHI-DNA-GRDBD allosteric mechanism does not occur through any traditional models: direct (protein-protein), indirect (reorganization of the secondary site) readout or solvent-release. On the contrary, it is generated by a subtle and less common entropy-mediated mechanism, which might have an important role to explain other DNA-mediated cooperative effects

Monitoring water parameters using IoT technology

Rivers are one of the most important sources of water for agriculture, industrial use, and other applications. The river systems are particularly exposed to the negative effects of pollution due to their dynamic nature and easy accessibility for waste management. The concept "water quality" refers to the state or condition of a body of water, taking into consideration its chemical, physical, and biological aspects. The importance of measuring the water quality parameters for studying any aquatic system cannot be overstated. Indirectly, increasing the rate of water pollution will affect agriculture, leading to a decrease in the quality and quantity of vegetables and fruits grown. The objective of the article focuses on water quality determined by the analysis of the values of some parameters such as salinity, pH and conductivity. This article is based on the SWAM project’s study, which intends to provide a strong and flexible platform through which humans can discover the reasons their health is affected by low water quality. The parameter monitoring system is based on IoT technology, the data being collected by sensors and then transmitted via an MQTT protocol to a Cloud database where it will be stored and processed. The results obtained from the parameter analysis were optimal, with the data collected not being drastically affected by the external environment. The presented study differs from other research due to the experimental data interpreted in a different way and the monitored parameters, the article being based on the evolution of pH, conductivity and salinity and how these parameters evolve in two weeks

The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA

An accurate understanding of DNA backbone transitions is likely to be the key for elucidating the puzzle of the intricate sequence-dependent mechanical properties that govern most of the biologically relevant functions of the double helix. One factor believed to be important in indirect recognition within protein–DNA complexes is the combined effect of two DNA backbone torsions (ε and ζ) which give rise to the well-known BI/BII conformational equilibrium. In this work we explain the sequence-dependent BII propensity observed in RpY steps (R = purine; Y = pyrimidine) at the tetranucleotide level with the help of a previously undetected C–H···O contact between atoms belonging to adjacent bases. Our results are supported by extensive multimicrosecond molecular dynamics simulations from the Ascona B-DNA Consortium, high-level quantum mechanical calculations, and data mining of the experimental structures deposited in the Protein Data Bank

Parmbsc1: A refined force-field for DNA simulations

We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ∼140 μs) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/

An update on the arrival direction studies made with data from the Pierre Auger Observatory

The search for anisotropies in the arrival directions of ultra-high-energy cosmic rays plays a key role in the efforts to understand their origin. The observed first-harmonic modulation in right ascension above 8EeV, detected by the Pierre Auger Observatory with a current significance of 6.9σ, suggests an extragalactic origin above this energy. Furthermore, there are indications, at the ∼4σ significance level, of anisotropies at intermediate angular scales, which are obtained when comparing the arrival directions against the distribution of potential sources from astrophysical catalogs, in particular that of nearby starburst galaxies, and around the Centaurus region. In this contribution, we present the status of the different searches for anisotropies at small, intermediate and large angular scales. We use the latest available data set, with 19 years of operation that has yielded 135,000km2yrsr of accumulated exposure, covering the sky at declinations from −90∘ to 45∘. At small and intermediate scales, we report updates of the all-sky blind search for localized excesses, the study around the Centaurus region, and the likelihood analysis with catalogs of candidate sources. We have also studied the regions of the sky from which the Telescope Array Collaboration has reported hints of excesses in their data and we find no significant effects in the same directions with a data set of comparable size. At large angular scales, the dipolar and quadrupolar amplitudes in energy bins are updated. We discuss the prospects of these searches, both in regards to increases in statistics and in relation to the future inclusion of event-by-event mass estimators in these analyses through the upgrade of the Observatory, AugerPrime

The performances of the upgraded surface detector stations of AugerPrime

The surface detector of the Pierre Auger Observatory is an array of 1,600 stations using a water Cherenkov detector (WCD) for particle detection. The array is undergoing a major upgrade known as AugerPrime that involves adding scintillator surface detectors (SSDs) and radio antennas to the existing WCDs. Each WCD is also equipped with a smaller photomultiplier tube added to the original ones. As part of the upgrade, underground muon detectors are being installed in an area with a higher density of surface detector stations. AugerPrime required the development of new electronics to process the signals from all the new detectors and handle a higher sampling rate, a more precise GPS receiver, an extended dynamic range, higher processing capacity, and improved monitoring systems and memory. The deployment of the SSDs on top of each surface detector station is currently completed together with the deployment of the new electronics. This contribution will present the first data from the upgraded stations, emphasizing the performances of the SSDs and the new electronics