Spontaneous Embedding of DNA Mismatches Within the RNA:DNA Hybrid of CRISPR-Cas9.

CRISPR-Cas9 is the forefront technology for editing the genome. In this system, the Cas9 protein is programmed with guide RNAs to process DNA sequences that match the guide RNA forming an RNA:DNA hybrid structure. However, the binding of DNA sequences that do not fully match the guide RNA can limit the applicability of CRISPR-Cas9 for genome editing, resulting in the so-called off-target effects. Here, molecular dynamics is used to probe the effect of DNA base pair mismatches within the RNA:DNA hybrid in CRISPR-Cas9. Molecular simulations revealed that the presence of mismatched pairs in the DNA at distal sites with respect to the Protospacer Adjacent Motif (PAM) recognition sequence induces an extended opening of the RNA:DNA hybrid, leading to novel interactions established by the unwound nucleic acids and the protein counterpart. On the contrary, mismatched pairs upstream of the RNA:DNA hybrid are rapidly incorporated within the heteroduplex, with minor effect on the protein-nucleic acid interactions. As a result, mismatched pairs at PAM distal ends interfere with the activation of the catalytic HNH domain, while mismatches fully embedded in the RNA:DNA do not affect the HNH dynamics and enable its activation to cleave the DNA. These findings provide a mechanistic understanding to the intriguing experimental evidence that PAM distal mismatches hamper a proper function of HNH, explaining also why mismatches within the heteroduplex are much more tolerated. This constitutes a step forward in understanding off-target effects in CRISPR-Cas9, which encourages novel structure-based engineering efforts aimed at preventing the onset of off-target effects

A Tool for Integer Homology Computation: Lambda-At Model

In this paper, we formalize the notion of lambda-AT-model (where $\lambda$ is a non-null integer) for a given chain complex, which allows the computation of homological information in the integer domain avoiding using the Smith Normal Form of the boundary matrices. We present an algorithm for computing such a model, obtaining Betti numbers, the prime numbers p involved in the invariant factors of the torsion subgroup of homology, the amount of invariant factors that are a power of p and a set of representative cycles of generators of homology mod p, for each p. Moreover, we establish the minimum valid lambda for such a construction, what cuts down the computational costs related to the torsion subgroup. The tools described here are useful to determine topological information of nD structured objects such as simplicial, cubical or simploidal complexes and are applicable to extract such an information from digital pictures.Comment: Journal Image and Vision Computing, Volume 27 Issue 7, June, 200

An accreted continental terrane in Northwestern Peru

Cet article présente une étude paléomagnétique des échantillons de plusieurs formations du bassin de Lancones (province de Piura). Les auteurs formulent l'hypothèse de l'accrétion d'une terrane sur la marge péruvienne au cours du Néocomien. Un régime de cisaillement aurait également produit des rotations in situ. L'évolution géodynamique du nord du Pérou est donc comparable aux processus observés sur les Andes septentrionales, en Equateu

How to Teach Pre-Service Teachers to Make a Didactic Program? The Collaborative Learning Associated with Mobile Devices

We acknowledge the researchers of the research group AREA (HUM-672), which belongs to the Ministry of Education and Science of the Junta de Andalucía and is registered in the Department of Didactics and School Organization of the Faculty of Education Sciences of the University of Granada.Today, pedagogical proposals are increasingly moving away from purely traditional approaches, with a proliferation of active methodologies in the teaching–learning processes. This research aims to find out the effectiveness of the collaborative method in mobile learning, as opposed to traditional methodology, for university students in the learning of the didactic program. The research methodology is quantitative, applying a quasi-experimental design with a control group and experimental group. The results show that the collaborative learning teaching method associated with mobile learning mainly increases motivation, the relationships between teachers and students, the relationships between students and content, the relationships between students and students, autonomy in learning, pedagogical collaboration between students, problem-solving, and the sense of time in the training process. It is concluded that the collaborative learning method associated with mobile learning is more effective for learning didactic programming than the traditional method

Engaging Northern Indigenous Communities in Biophysical Research: Pitfalls and Successful Approaches

Guidelines and best practices to engage Indigenous people in Arctic regions in biophysical research have emerged since the 1990s. Despite these guidelines, mainstream scientists still struggle to create effective working relationships with Indigenous people and engage them in their research. We encountered this issue when we visited three communities on Alaska’s west coast to study impactful weather events and the formation of “slush ice berms,” which can protect towns from storm surges. As we worked to build relationships with residents of the towns, we found the existing guidelines are often helpful for telling us what to do—for example, they emphasize the importance of face-to-face communication—but researchers also need to think about how to do it (skills) and how to be (personal attributes). To demonstrate to Indigenous people that we value and respect their culture, researchers could learn to use language that is understandable and that reflects a collaborative rather than a top-down approach. We should be ready to adjust our schedules and to help the community we are visiting, rather than simply focusing on our own needs. We might look for benefits for the community and ensure residents understand and are satisfied with the research we are doing. Some of the necessary attributes we identified are curiosity, honesty, interpersonal awareness, empathy, flexibility, and openness. Although the skills and attributes presented here are useful to bridge the gap between cultures, we caution that there is no specific formula that can guarantee success.Des lignes directrices et des pratiques exemplaires visant à faire participer les peuples autochtones des régions arctiques à la recherche biophysique sont publiées depuis les années 1990. Malgré ces lignes directrices, les scientifiques généraux ont toujours de la difficulté à créer des relations de travail efficaces avec les peuples autochtones et à les faire participer à leurs recherches. Nous avons fait face à cet enjeu quand nous avons visité trois collectivités de la côte ouest de l’Alaska pour étudier les événements climatiques percutants et la formation de « bermes de bouillie de glace » susceptibles de protéger les localités des ondes de tempête. Quand nous avons essayé de nouer des liens avec les résidents des diverses localités, nous avons constaté que les lignes directrices actuelles sont souvent utiles pour nous indiquer quoi faire (par exemple, elles mettent l’accent sur l’importance des communications face à face), mais les chercheurs doivent aussi penser à comment le faire (les compétences) et à comment se présenter (attributs personnels). Pour prouver aux Autochtones qu’ils valorisent et respectent leur culture, les chercheurs pourraient apprendre à employer du vocabulaire qui est compréhensible et qui tient compte d’une démarche de collaboration au lieu d’une démarche hiérarchique du sommet à la base. Il faudrait que nous soyons prêts à adapter nos emplois du temps et à aider la collectivité que nous visitons au lieu de nous concentrer seulement sur nos propres besoins. Il faudrait aussi considérer les avantages pour la collectivité et nous assurer que les résidents comprennent la recherche que nous faisons et soient satisfaits. Parmi les attributs nécessaires pour ces travaux de recherche, notons la curiosité, l’honnêteté, la sensibilisation aux besoins d’autrui, l’empathie, la flexibilité et l’ouverture d’esprit. Même si les compétences et les attributs dont il est question ici aident à combler l’écart entre les cultures, nous tenons à souligner qu’aucune formule particulière ne garantit le succès

Chain Homotopies for Object Topological Representations

This paper presents a set of tools to compute topological information of simplicial complexes, tools that are applicable to extract topological information from digital pictures. A simplicial complex is encoded in a (non-unique) algebraic-topological format called AM-model. An AM-model for a given object K is determined by a concrete chain homotopy and it provides, in particular, integer (co)homology generators of K and representative (co)cycles of these generators. An algorithm for computing an AM-model and the cohomological invariant HB1 (derived from the rank of the cohomology ring) with integer coefficients for a finite simplicial complex in any dimension is designed here. A concept of generators which are "nicely" representative cycles is also presented. Moreover, we extend the definition of AM-models to 3D binary digital images and we design algorithms to update the AM-model information after voxel set operations (union, intersection, difference and inverse)

Portable low-power electronic interface for explosive detection using microcantilevers

Microcantilevers have been recently revealed as a highly effective technique for gas detection at trace level when acting as chemical sensors. However, an important milestone still remains to achieve a full-scale development in commercial applications: the cumbersome systems traditionally used to read-out its responses. To accomplish this, a portable low-power electronic interface, based on an analog lock-in amplifier processing square signals, which is fully capable of creating the excitation signal as well as obtaining the response values from resonating microcantilevers functionalized with zeolite based coatings has been herein attempted. The so obtained read-out results are in good agreement with the commercial lock-in amplifier's measurements, demonstrating the accuracy and reliability of the electronic interface. Finally, its performance has been validated for 2-nitrotoluene (o-MNT) detection at ppm V level, as an example of an explosive-related molecule, with BEA zeolite coated microcantilevers. Theoretical limit of detection (LOD) values below 100 ppb have been obtained for Co exchanged BEA modified sensors