The recombinase protein is a torque sensitive molecular switch

How a nano-searcher finds its nano-target is a general problem in non-equilibrium statistical physics. It becomes vital when the searcher is a damaged DNA fragment trying to find its counterpart on the intact homologous chromosome. If the two copies are paired, that intact homologous sequence serves as a template to reconstitute the damaged DNA sequence, enabling the cell to survive without genetic mutations. To succeed, the search must stop only when the perfect homology is found. The biological process that ensures such a genomic integrity is called Homologous Recombination and is promoted by the Recombinase proteins. In this article, we use torque-sensitive magnetic tweezers to measure the free-energy landscape of the human Recombinase hRad51 protein assembled a DNA fragment. Based on our measurements we model the hRad51/DNA complex as an out-of-equilibrium two-state system and provide a thermodynamical description of Homologous Recombination. With this dynamical two-state model, we suggest a mechanism by which the recombinase proteins discriminate between homologous and a non-homologous sequences

Le juge administratif dans l'analyse juridique des politiques publiques

Aquesta ponència forma part del Workshop internacional de doctorands organitzat pel Programa de Doctorat en Dret de la UAB i la Facultat de Dret de la UAB, amb el suport de l'École Européenne de Droit de l'Université Toulouse Capitol

Event reconstruction for KM3NeT/ORCA using convolutional neural networks

The KM3NeT research infrastructure is currently under construction at two locations in the Mediterranean Sea. The KM3NeT/ORCA water-Cherenkov neutrino detector off the French coast will instrument several megatons of seawater with photosensors. Its main objective is the determination of the neutrino mass ordering. This work aims at demonstrating the general applicability of deep convolutional neural networks to neutrino telescopes, using simulated datasets for the KM3NeT/ORCA detector as an example. To this end, the networks are employed to achieve reconstruction and classification tasks that constitute an alternative to the analysis pipeline presented for KM3NeT/ORCA in the KM3NeT Letter of Intent. They are used to infer event reconstruction estimates for the energy, the direction, and the interaction point of incident neutrinos. The spatial distribution of Cherenkov light generated by charged particles induced in neutrino interactions is classified as shower- or track-like, and the main background processes associated with the detection of atmospheric neutrinos are recognized. Performance comparisons to machine-learning classification and maximum-likelihood reconstruction algorithms previously developed for KM3NeT/ORCA are provided. It is shown that this application of deep convolutional neural networks to simulated datasets for a large-volume neutrino telescope yields competitive reconstruction results and performance improvements with respect to classical approaches

Event reconstruction for KM3NeT/ORCA using convolutional neural networks

The KM3NeT research infrastructure is currently under construction at two locations in the Mediterranean Sea. The KM3NeT/ORCA water-Cherenkov neutrino de tector off the French coast will instrument several megatons of seawater with photosensors. Its main objective is the determination of the neutrino mass ordering. This work aims at demonstrating the general applicability of deep convolutional neural networks to neutrino telescopes, using simulated datasets for the KM3NeT/ORCA detector as an example. To this end, the networks are employed to achieve reconstruction and classification tasks that constitute an alternative to the analysis pipeline presented for KM3NeT/ORCA in the KM3NeT Letter of Intent. They are used to infer event reconstruction estimates for the energy, the direction, and the interaction point of incident neutrinos. The spatial distribution of Cherenkov light generated by charged particles induced in neutrino interactions is classified as shower-or track-like, and the main background processes associated with the detection of atmospheric neutrinos are recognized. Performance comparisons to machine-learning classification and maximum-likelihood reconstruction algorithms previously developed for KM3NeT/ORCA are provided. It is shown that this application of deep convolutional neural networks to simulated datasets for a large-volume neutrino telescope yields competitive reconstruction results and performance improvements with respect to classical approaches

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta

Integration of microfluidics and multimodal optics for translational bioanalytics

Numerous analytical techniques for life sciences have been at the basis of the improvement of medical diagnostics and treatments. Current challenges in bioanalytics are related to the conception of methods enabling large amount of information to be extracted from biological samples, in order to be translated into concrete solutions for the patient. From this point of view, microfluidics constitutes a key element to automate, accelerate and standardize bioanalytical tests. At the same time, obtaining precise information from the analyte of interest is crucial to specifically address diagnoses and therapies. Since the high flexibility of optical readouts can give access to a multitude of diverse aspects of biological matter in multiplexed fashion, in this thesis we have chosen to integrate microfluidics and multimodal optics to address specific problems in translational bioanalytics: drug screening and tumor diagnostics. In the first part of the work, we approached the problem of drug screening on living organisms, and especially the possibility to provide as much information as possible on potential mechanisms of action and clinical targets. For this, we aimed at developing a method to study the model organism Caenorhabditis elegans, i.e. a small soil worm that is widely used by researchers to study physiopathology at whole-organism scale. In fact, while offering the systemic information that is missing with cellular models, this small organism is much easier to handle and grow in large amounts compared to rodents, for which the costs and the ethical concerns are substantial. Moreover, its large genetic homology with humans supports translational analysis and its genetic manipulation is well mastered to model human diseases. Thus, we developed a microfluidic array to select small separated populations of C. elegans specimens, and combined fluorescence and bright-field imaging along with high-throughput feature recognition and signal detection to identify the mode-of-action of an antibiotic. Also, we demonstrated real-time, very large field-of-view capability on multiplexed motility assays for the assessment of the dose-response relation of an anesthetic. Furthermore, to enable on-site antibiotic testing, we explored a method to empower low-magnification optical systems with dielectric micro- and macro-spheres for the detection of pathogens in liquid media. Such dielectric objects offer potential solutions to increase the resolution and the sensitivity of imaging systems in a cost-effective fashion. We first characterized the parameters that govern the resolution increase in the case of microsphere-assisted incoherent microscopy and demonstrated it by imaging silicon microstructures and fluorescent bacteria. Then, we developed a method to easily fabricate microfluidic chips that integrate custom designs and precise location of highly-diffractive macro-spheres, and used it for on-chip detection of bacteria in a flow. In the second part of the work, we aimed at developing a technique to assess the status of individual tumor and immune cells in the conventional tissue sections used in the clinics. The first step was to combine fluorescence-based image segmentation with automated microfluidics to quantify, at the single-cell level, the overexpression of two proteins used as biomarkers for breast cancer diagnostics. We first assessed our method on biological controls such as breast cancer cell lines, and then combined it with ..

Assessing the Potential Deployment of Biosensors for Point-of-Care Diagnostics in Developing Countries: Technological, Economic and Regulatory Aspects

Infectious diseases and antimicrobial resistance are major burdens in developing countries, where very specific conditions impede the deployment of established medical infrastructures. Since biosensing devices are nowadays very common in developed countries, particularly in the field of diagnostics, they are at a stage of maturity at which other potential outcomes can be explored, especially on their possibilities for multiplexing and automation to reduce the time-to-results. However, the translation is far from being trivial. In order to understand the factors and barriers that can facilitate or hinder the application of biosensors in resource-limited settings, we analyze the context from several angles. First, the technology of the devices themselves has to be rethought to take into account the specific needs and the available means of these countries. For this, we describe the partition of a biosensor into its functional shells, which define the information flow from the analyte to the end-user, and by following this partition we assess the strengths and weaknesses of biosensing devices in view of their specific technological development and challenging deployment in low-resource environments. Then, we discuss the problem of cost reduction by pointing out transversal factors, such as throughput and cost of mistreatment, that need to be re-considered when analyzing the cost-effectiveness of biosensing devices. Beyond the technical landscape, the compliance with regulations is also a major aspect that is described with its link to the validation of the devices and to the acceptance from the local medical personnel. Finally, to learn from a successful case, we analyze a breakthrough inexpensive biosensor that is showing high potential with respect to many of the described aspects. We conclude by mentioning both some transversal benefits of deploying biosensors in developing countries, and the key factors that can drive such applications

Microfluidic device, system and method for the study of organisms

The invention discloses a microfluidic device for the culture, selection and/or analysis of sample organisms such as nematodes, as well as for other biological entities such as for instance animal embryos. The device features reservoirs, culture chambers and smart filtering systems allowing for the selection of specific populations/specimens of sample organisms, thus permitting long-term cultures thereof as well as phenotypic/behavioural analyses. Systems and methods for using the microfluidic device are within the present disclosure as well

Clinical Controversy in Transplantation: Tacrolimus Versus Cyclosporine in Statin Drug Interactions

Objective: To review the available literature that provides evidence for the absence of statin interactions with tacrolimus compared with cyclosporine. Data Sources: A literature search of PubMed was performed (1990 to June 2019) using the following search terms: calcineurin inhibitors, tacrolimus, cyclosporine, statins, atorvastatin, simvastatin, and drug interactions. Clinical practice guidelines, article bibliographies, drug interaction database references, and product monographs were also reviewed. Study Selection and Data Extraction: Relevant English-language studies describing the mechanism of interaction, the magnitude of pharmacokinetic alterations, and safety were evaluated. In vitro data and studies conducted in adult humans were considered. Data Synthesis: Studies demonstrate pharmacokinetic differences between cyclosporine and tacrolimus, particularly with regard to inhibition of 2 hepatic transporters: P-glycoprotein and organic anion transporting polypeptide (OATP). Compared with cyclosporine, tacrolimus does not affect these transporters, does not enhance statin exposure, and does not increase statin-associated safety events. Relevance to Patient Care and Clinical Practice: Clinical practice guidelines allude to the need to reduce statin doses in the setting of tacrolimus. Some providers have adopted this practice, and doing so may prevent transplant recipients from attaining cardiovascular benefit, especially when increased or high-intensity doses are required. The pharmacokinetic differences between tacrolimus and cyclosporine highlight different interaction potential with statins. Conclusions: Clinicians need to be aware that tacrolimus and cyclosporine are not the same with regard to causing drug interactions with statins. Tacrolimus can be used with statins without the need for dose adjustments because of lack of an interaction