Genome-wide profiling of uncapped mRNA

Gene transcripts are under extensive posttranscriptional regulation, including the regulation of their stability. A major route for mRNA degradation produces uncapped mRNAs, which can be generated by decapping enzymes, endonucleases, and small RNAs. Profiling uncapped mRNA molecules is important for the understanding of the transcriptome, whose composition is determined by a balance between mRNA synthesis and degradation. In this chapter, we describe a method to profile these uncapped mRNAs at the genome scale

Mimicry technology : a versatile tool for small RNA suppression

A decade ago the discovery of the target mimicry regulatory process on the activity of a mature microRNA (miRNA) enabled for the first time the customized attenuation of miRNA activity in plants. That powerful technology was named MIMIC and was based on engineering the IPS1 long noncoding transcript to become complementary to the miRNA under study. In order to avoid IPS1 degradation, the predicted miRNA-mediated cleavage site was interrupted by three additional nucleotides giving rise to the so-called MIMIC decoy. Since then, MIMIC technology has been used in several plant species and in basic and translational research. We here provide a detailed guide to produce custom-designed MIMIC decoys to facilitate the study of sRNA functions in plants

Scattering Amplitudes and Toric Geometry

In this paper we provide a first attempt towards a toric geometric interpretation of scattering amplitudes. In recent investigations it has indeed been proposed that the all-loop integrand of planar N=4 SYM can be represented in terms of well defined finite objects called on-shell diagrams drawn on disks. Furthermore it has been shown that the physical information of on-shell diagrams is encoded in the geometry of auxiliary algebraic varieties called the totally non negative Grassmannians. In this new formulation the infinite dimensional symmetry of the theory is manifest and many results, that are quite tricky to obtain in terms of the standard Lagrangian formulation of the theory, are instead manifest. In this paper, elaborating on previous results, we provide another picture of the scattering amplitudes in terms of toric geometry. In particular we describe in detail the toric varieties associated to an on-shell diagram, how the singularities of the amplitudes are encoded in some subspaces of the toric variety, and how this picture maps onto the Grassmannian description. Eventually we discuss the action of cluster transformations on the toric varieties. The hope is to provide an alternative description of the scattering amplitudes that could contribute in the developing of this very interesting field of research.Comment: 58 pages, 25 figures, typos corrected, a reference added, to be published in JHE

The Dual Effect of Coordinating -NH Groups and Light in the Electrochemical CO2 Reduction with Pyridylamino Co Complexes

CO2 electroreduction could be improved by applying conceptualized strategies to overcome catalytic bottlenecks. In this regard, we report two new cobalt(II) complexes [Co(Py-2(R)N-3)(OTf)](OTf) (Co(R), R=H, Me) based on a new C-2-symmetric pentacoordinate chiral ligand that are active on the electrochemical CO2 reduction to CO. One of the complexes has a N-H group oriented towards the CO2 binding site (Co-H), while the other has a N-Me group with the same orientation (Co-Me), as showed by X-ray diffraction. We have studied the effect of introducing hydrogen bonding sites, i. e. N-H in Co-H, as a strategy to stabilize reaction intermediates. The complex bearing coordinating unprotected N-H group (Co-H) displays catalytic CO2 reduction at the Co-II/I redox potential (-1.9 V vs. Fc, ca. 40 % FYCO) whereas Co-Me shows CO2 reduction at the Co-I/0 redox pair. FTIR-SEC and DFT calculations identified a [Co-I-CO](+) cation as catalytic intermediate. The beneficial effect of the N-H group has been attributed to the stabilization of reaction intermediates or transition states and by the larger electron-donating capacity, thus enhancing the nucleophilic character of the Co-I intermediate. The study also points to the CO dissociation from the Co(I)-CO resting state intermediate as one of the bottlenecks of the catalytic cycle, which can be overcome with light irradiation, resulting in an increase of the total CO production (-1.9 V, 81 % FYCO, 11.2 TONCO) at the Co-II/I redox potential

Use of q-values to Improve a Genetic Algorithm to Identify Robust Gene Signatures

Several approaches have been proposed for the analysis of DNA microarray datasets, focusing on the performance and robustness of the final feature subsets. The novelty of this paper arises in the use of q-values to pre-filter the features of a DNA microarray dataset identifying the most significant ones and including this information into a genetic algorithm for further feature selection. This method is applied to a lung cancer microarray dataset resulting in similar performance rates and greater robustness in terms of selected features (on average a 36.21% of robustness improvement) when compared to results of the standard algorithm

Decoding the CO2 Reduction Mechanism of a Highly Active Organometallic Manganese Electrocatalyst: Direct Observation of a Hydride Intermediate and Its Implications

A detailed mechanistic study of the electrochemical CO2 reduction catalyzed by the fac-[Mn-I(CO)(3)(bis-(NHC)-N-Me)MeCN](+) complex (1-MeCN+ ) is reported herein by combining in situFTIR spectroelectrochemistry(SEC), synthesis and characterization of catalytic intermediates,and DFT calculations. Under low proton concentrations, 1-MeCN+ efficiently catalyzes CO2 electroreductionwith long catalyst durability and selectivity toward CO (ca. 100%). The [Mn-I(CO)(3)(bis-(NHC)-N-Me)](-) anion (1(-) ) and the tetracarbonyl [Mn-I(CO)(4)(bis-(NHC)-N-Me)](+) complex (1-CO+ )are key intermediates of the catalytic CO2-to-CO mechanismdue to their impact on the selectivity and the reaction rate, respectively.Increasing the proton concentration increases formate production (upto 15% FE), although CO remains the major product. The origin of formateis ascribed to the competitive protonation of 1(-) to form a Mn(I) hydride (1-H), detected by SECin the absence of CO2. 1-H was also synthesizedand thoroughly characterized, including by X-ray diffraction analysis.Stoichiometric reactivity studies of 1-H with CO2 and labeled (CO2)-C-13 indicate a fast formationof the corresponding neutral Mn(I) formate species (1-OCOH) at room temperature. DFT modeling confirms the intrinsic capabilityof 1-H to undergo hydride transfer to CO2 dueto the strong & sigma;-donor properties of the bis-(Me)NHCmoiety. However, the large potential required for the HCOO- release from 1-OCOH limits the overall catalytic CO2-to-HCOO- cycle. Moreover, the experimentallyobserved preferential selectivity for CO over formate is dictatedby the shallow kinetic barrier for CO2 binding to 1(-) compared to the Mn-H bond formation.The detailed mechanistic study highlights the reduction potential,pK (a), and hydricity of the metal hydrideintermediate as crucial factors affecting the CO2RR selectivityin molecular systems

Heavy Squarks at the LHC

The LHC, with its seven-fold increase in energy over the Tevatron, is capable of probing regions of SUSY parameter space exhibiting qualitatively new collider phenomenology. Here we investigate one such region in which first generation squarks are very heavy compared to the other superpartners. We find that the production of these squarks, which is dominantly associative, only becomes rate-limited at mSquark > 4(5) TeV for L~10(100) fb-1. However, discovery of this scenario is complicated because heavy squarks decay primarily into a jet and boosted gluino, yielding a dijet-like topology with missing energy (MET) pointing along the direction of the second hardest jet. The result is that many signal events are removed by standard jet/MET anti-alignment cuts designed to guard against jet mismeasurement errors. We suggest replacing these anti-alignment cuts with a measurement of jet substructure that can significantly extend the reach of this channel while still removing much of the background. We study a selection of benchmark points in detail, demonstrating that mSquark= 4(5) TeV first generation squarks can be discovered at the LHC with L~10(100)fb-1

PROTOCOLO DE USO Y MANTENIMIENTO DEL RESERVORIO VENOSO SUBCUTÁNEO

Objetive: To establish a standardized care plan for carrier patients of venous reservoir in primary care. Material and Method: A revision of articles related to subcutaneous venous reservoir use and management was carried out in various data base. The articles were revised two at a time and classified by affinity and technical scientific quality. Later on, the authors, by consent, determine a standardized care plan for this kind of patients, as well as a connection of the plan to the different work lines (assistance process, health programs, shared performance guide and protocols) existing in the Public Health System of Andalucia, Spain (SSPA). Results: Once the theory phase of making the care plan was completed, the same one was carried out with the related cases in one of the health basic areas. Its adequacy and acceptance by professionals and patients was evaluated. At present, the mentioned plan it has been sent to the care board for its assessment, if necessary, to the rest of basic areas of the health district. Conclusions: In accordance with the results we have found in readings, determining standardized care plans is an excellent tool in care: It facilitates the decision making, decreases the variability, and improves the registry and the professional and users satisfaction.Objetivos: Establecer un plan de cuidados estandarizado para los pacientes portadores de reservorio venoso en atención primaria. Material y método: Se realizó una revisión de la literatura de artículos relacionados con uso y manejo del reservorio venoso subcutáneo en distintas bases de datos. Los artículos fueron revisados por pares y filtrados por afinidad y calidad científico técnica. Posteriormente los autores, mediante técnicas de consenso, determinaron el plan de cuidados estandarizado para este tipo de pacientes así como la conexión de éste con las diferentes líneas de trabajo (procesos asistenciales, programas de salud, guías de actuación compartida y protocolos) existentes en el sistema sanitario público andaluz (SSPA). Resultados: Concluida la fase teórica de elaboración del plan de cuidados, se pilotó el mismo con los casos incidentes en una de las zonas básicas de salud, viendo su adecuación y aceptación por profesionales y pacientes. En la actualidad dicho plan se ha remitido a la dirección de cuidados para su valoración y difusión, si procede, al resto de zonas básicas del distrito sanitario Conclusiones: En concordancia con los resultados encontrados en la literatura, la determinación de planes de cuidados estandarizados constituye una herramienta de excelencia en los cuidados que: facilita la toma de decisiones, disminuye la variabilidad, mejora el registro y la satisfacción de profesionales y usuarios