SinEx DB: a database for single exon coding sequences in mammalian genomes

Indexación: Web of Science.Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.https://academic.oup.com/database/article-lookup/doi/10.1093/database/baw09

The origin of the Acheulean: the 1.7 million-year-old site of FLK West, Olduvai Gorge (Tanzania)

The appearance of the Acheulean is one of the hallmarks of human evolution. It represents the emergence of a complex behavior, expressed in the recurrent manufacture of large-sized tools, with standardized forms, implying more advance forethought and planning by hominins than those required by the precedent Oldowan technology. The earliest known evidence of this technology dates back to c. 1.7 Ma. and is limited to two sites (Kokiselei [Kenya] and Konso [Ethiopia]), both of which lack fauna. The functionality of these earliest Acheulean assemblages remains unknown. Here we present the discovery of another early Acheulean site also dating to c. 1.7 Ma from Olduvai Gorge. This site provides evidence of the earliest steps in developing the Acheulean technology and is the oldest Acheulean site in which stone tools occur spatially and functionally associated with the exploitation of fauna. Simple and elaborate large-cutting tools (LCT) and handaxes co-exist at FLK West, showing that complex cognition was present from the earliest stages of the Acheulean. Here we provide a detailed technological study and evidence of the use of these tools on the butchery and consumption of fauna, probably by early Homo erectus sensu lato

Digital-Analog Quantum Simulations Using The Cross-Resonance Effect

Digital-analog quantum computation aims to reduce the currently infeasible resource requirements needed for near-term quantum information processing by replacing sequences of one- and two-qubit gates with a unitary transformation generated by the systems' underlying Hamiltonian. Inspired by this paradigm, we consider superconducting architectures and extend the cross-resonance effect, up to first order in perturbation theory, from a two-qubit interaction to an analog Hamiltonian acting on 1D chains and 2D square lattices which, in an appropriate reference frame, results in a purely two-local Hamiltonian. By augmenting the analog Hamiltonian dynamics with single-qubit gates we show how one may generate a larger variety of distinct analog Hamiltonians. We then synthesize unitary sequences, in which we toggle between the various analog Hamiltonians as needed, simulating the dynamics of Ising, $XY$, and Heisenberg spin models. Our dynamics simulations are Trotter error-free for the Ising and $XY$ models in 1D. We also show that the Trotter errors for 2D $XY$ and 1D Heisenberg chains are reduced, with respect to a digital decomposition, by a constant factor. In order to realize these important near-term speedups, we discuss the practical considerations needed to accurately characterize and calibrate our analog Hamiltonians for use in quantum simulations. We conclude with a discussion of how the Hamiltonian toggling techniques could be extended to derive new analog Hamiltonians which may be of use in more complex digital-analog quantum simulations for various models of interacting spins

Perturbative expansions from Monte Carlo simulations at weak coupling: Wilson loops and the static-quark self-energy

Perturbative coefficients for Wilson loops and the static-quark self-energy are extracted from Monte Carlo simulations at weak coupling. The lattice volumes and couplings are chosen to ensure that the lattice momenta are all perturbative. Twisted boundary conditions are used to eliminate the effects of lattice zero modes and to suppress nonperturbative finite-volume effects due to Z(3) phases. Simulations of the Wilson gluon action are done with both periodic and twisted boundary conditions, and over a wide range of lattice volumes (from $3^4$ to $16^4$) and couplings (from $\beta \approx 9$ to $\beta \approx 60$). A high precision comparison is made between the simulation data and results from finite-volume lattice perturbation theory. The Monte Carlo results are shown to be in excellent agreement with perturbation theory through second order. New results for third-order coefficients for a number of Wilson loops and the static-quark self-energy are reported.Comment: 36 pages, 15 figures, REVTEX documen

Laboratory and field evaluation of acetic acid-based lures for male Asian citrus psyllid, Diaphorina citri.

The Asian citrus psyllid (ACP) is a vector of a pathogen associated with greening and thus a major problem in citriculture worldwide. Lures are much needed for improving ACP trapping systems for monitoring populations and surveillance. Previously, we have identified acetic acid as a putative sex pheromone and measured formic acid- and propionic acid-elicited robust electroantennographic responses. We have now thoroughly examined in indoor behavioral assays (4-way olfactometer) and field tests the feasibility of these three semiochemicals as potential lures for trapping ACP. Formic acid, acetic acid, and propionic acid at appropriate doses are male-specific attractants and suitable lures for ACP traps, but they do not act synergistically. An acetic acid-based homemade lure, prepared by impregnating the attractant in a polymer, was active for a day. A newly developed slow-release formulation had equal performance but lasted longer, thus leading to an important improvement in ACP trap capture at low population densities

Al2O3-3YTZP-Graphene multilayers produced by tape casting and spark plasma sintering

This work aims to establish a colloidal route to obtain laminates of alumina zirconia combining layers with and without graphene. Green tapes of alumina, alumina with 5 vol.% of 3Y-TZP and alumina with 5 vol.% of 3Y-TZP and graphene-oxide (2 vol.%) were obtained by aqueous tape casting. It is possible to design materials for different structural applications with a controlled microstructure with a high number of different layers. The tapes were punched into 20-mm discs, joined to form laminates alternating up to 18-layers, and sintered in one-step by spark plasma sintering (SPS) at 1400 degrees C. It has demonstrated that there is a significant graphite diffusion provoked by the required graphite holders into the SPS-furnace. Dense laminates with layer thicknesses similar to 100 mu m and good cohesion between layers were obtained. Nanoindentation results showed that hardness and elastic modulus values were higher than 27 GPa and 300 GPa, respectively, and similar for all layers. Crown Copyright (C) 2014 Published by Elsevier Ltd. All rights reserved.This work has been supported by Spanish Ministry of Economy and Competitiviness (MAT2012-31090). A. S. A. Chinelatto thanks to CAPES - Programa Ciencias sem Fronteiras (Brazil) for the concession of a fellowship for post-doctoral sabbatical grant in ICV-CSIC, Spain. A. Borrell, acknowledges the Spanish Ministry of Science and Innovation for her Juan de la Cierva contract (JCI-2011-10498) and the Generalitat Valenciana by the financial support for the BEST/2012/302 grant. Authors thank to Nanoinnova Technologies (Spain) for supplying the graphene oxide and helpful discussions.Rincón, A.; Moreno, R.; Chinelatto, ASA.; Gutierrez-Gonzalez, CF.; Rayón Encinas, E.; Salvador Moya, MD.; Borrell Tomás, MA. (2014). Al2O3-3YTZP-Graphene multilayers produced by tape casting and spark plasma sintering. Journal of the European Ceramic Society. 34(10):2427-2434. https://doi.org/10.1016/j.jeurceramsoc.2014.02.011S24272434341

Poly (GR) in C9ORF72-related ALS/FTD Compromises Mitochondrial Function and Increases Oxidative Stress and DNA Damage in iPSC- derived Motor Neurons

GGGGCC repeat expansions in C9ORF72 are the most common genetic cause of both ALS and FTD. To uncover underlying pathogenic mechanisms, we found that DNA damage was greater, in an age dependent manner, in motor neurons differentiated from iPSCs of multiple C9ORF72 patients than control neurons. Ectopic expression of the dipeptide repeat (DPR) protein (GR)80 in iPSC-derived control neurons increased DNA damage, suggesting poly(GR) contributes to DNA damage in aged C9ORF72neurons. Oxidative stress was also increased inC9ORF72 neurons in an age-dependent manner. Pharmacological or genetic reduction of oxidative stress partially rescued DNA damage in C9ORF72neurons and control neurons expressing (GR)80 or (GR)80-induced toxicity in flies. Moreover, interactome analysis revealed that (GR)80 preferentially bound to mitochondrial ribosomal proteins and caused mitochondrial dysfunction. Thus, poly(GR) in C9ORF72 neurons compromises mitochondrial function and causes DNA damage in part by increasing oxidative stress, revealing another pathogenic mechanism in C9ORF72-related ALS and FTD

Spatial swarm segregation and reproductive isolation between the molecular forms of Anopheles gambiae

Anopheles gambiae, the major malaria vector in Africa, can be divided into two subgroups based on genetic and ecological criteria. These two subgroups, termed the M and S molecular forms, are believed to be incipient species. Although they display differences in the ecological niches they occupy in the field, they are often sympatric and readily hybridize in the laboratory to produce viable and fertile offspring. Evidence for assortative mating in the field was recently reported, but the underlying mechanisms awaited discovery. We studied swarming behaviour of the molecular forms and investigated the role of swarm segregation in mediating assortative mating. Molecular identification of 1145 males collected from 68 swarms in Donéguébougou, Mali, over 2 years revealed a strict pattern of spatial segregation, resulting in almost exclusively monotypic swarms with respect to molecular form. We found evidence of clustering of swarms composed of individuals of a single molecular form within the village. Tethered M and S females were introduced into natural swarms of the M form to verify the existence of possible mate recognition operating within-swarm. Both M and S females were inseminated regardless of their form under these conditions, suggesting no within-mate recognition. We argue that our results provide evidence that swarm spatial segregation strongly contributes to reproductive isolation between the molecular forms in Mali. However this does not exclude the possibility of additional mate recognition operating across the range distribution of the forms. We discuss the importance of spatial segregation in the context of possible geographic variation in mechanisms of reproductive isolation

Summary report of MINSIS workshop in Madrid

Recent developments on tau detection technologies and the construction of high intensity neutrino beams open the possibility of a high precision search for non-standard {\mu} - {\tau} flavour transition with neutrinos at short distances. The MINSIS - Main Injector Non-Standard Interaction Search- is a proposal under discussion to realize such precision measurement. This document contains the proceedings of the workshop which took place on 10-11 December 2009 in Madrid to discuss both the physics reach as well as the experimental requirements for this proposal.Comment: Proceedings of the MINSIS Workshop, Dec 10-11, 2009 in Madrid. 15 pages late

Breaking tolerance to the natural human liver autoantigen cytochrome P450 2D6 by virus infection

Autoimmune liver diseases, such as autoimmune hepatitis (AIH) and primary biliary cirrhosis, often have severe consequences for the patient. Because of a lack of appropriate animal models, not much is known about their potential viral etiology. Infection by liver-tropic viruses is one possibility for the breakdown of self-tolerance. Therefore, we infected mice with adenovirus Ad5 expressing human cytochrome P450 2D6 (Ad-2D6). Ad-2D6–infected mice developed persistent autoimmune liver disease, apparent by cellular infiltration, hepatic fibrosis, “fused” liver lobules, and necrosis. Similar to type 2 AIH patients, Ad-2D6–infected mice generated type 1 liver kidney microsomal–like antibodies recognizing the immunodominant epitope WDPAQPPRD of cytochrome P450 2D6 (CYP2D6). Interestingly, Ad-2D6–infected wild-type FVB/N mice displayed exacerbated liver damage when compared with transgenic mice expressing the identical human CYP2D6 protein in the liver, indicating the presence of a stronger immunological tolerance in CYP2D6 mice. We demonstrate for the first time that infection with a virus expressing a natural human autoantigen breaks tolerance, resulting in a chronic form of severe, autoimmune liver damage. Our novel model system should be instrumental for studying mechanisms involved in the initiation, propagation, and precipitation of virus-induced autoimmune liver diseases