Pràctiques de laboratori de Genètica: Grau en Biotecnologia

Es realitzaran dues pràctiques, una sobre la "Segregació de caràcters", en què es farà ús de la Drosophila melanogaster com a organisme experimental, i una altra sobre "Cromosomes politènics", en què es farà ús de la Drosophila subobscura. Ambdues pràctiques estaran imbricades en el temps per optimitzar les sessions de laboratori

Prácticas de laboratorio de Genética: Grado en Biotecnología

Se realizarán dos prácticas, una sobre la "Segregación de Caracteres" utilizando Drosophila melanogaster como organismo experimental, y otra sobre "Cromosomas Politénicos" utilizando Drosophila subobscura. Ambas prácticas estarán imbricadas en el tiempo para optimizar las sesiones de laboratorio

A free-energy stable nodal discontinuous Galerkin approximation with summation-by-parts property for the Cahn-Hilliard equation

We present a nodal Discontinuous Galerkin (DG) scheme for the Cahn-Hilliard equation that satisfies the summation-by-parts simultaneous-approximation-term (SBP-SAT) property. The latter permits us to show that the discrete free-energy is bounded, and as a result, the scheme is provably stable. The scheme and the stability proof are presented for general curvilinear three-dimensional hexahedral meshes. We use the Bassi-Rebay 1 (BR1) scheme to compute interface fluxes, and an IMplicit-EXplicit (IMEX) scheme to integrate in time. Lastly, we test the theoretical findings numerically and present examples for two and three-dimensional problems

An entropy stable spectral vanishing viscosity for discontinuous Galerkin schemes: application to shock capturing and LES models

We present a stable spectral vanishing viscosity for discontinuous Galerkin schemes, with applications to turbulent and supersonic flows. The idea behind the SVV is to spatially filter the dissipative fluxes, such that it concentrates in higher wavenumbers, where the flow is typically under-resolved, leaving low wavenumbers dissipation-free. Moreover, we derive a stable approximation of the Guermond-Popov fluxes with the Bassi-Rebay 1 scheme, used to introduce density regularization in shock capturing simulations. This filtering uses a Cholesky decomposition of the fluxes that ensures the entropy stability of the scheme, which also includes a stable approximation of boundary conditions for adiabatic walls. For turbulent flows, we test the method with the three-dimensional Taylor-Green vortex and show that energy is correctly dissipated, and the scheme is stable when a kinetic energy preserving split-form is used in combination with a low dissipation Riemann solver. Finally, we test the shock capturing capabilities of our method with the Shu-Osher and the supersonic forward facing step cases, obtaining good results without spurious oscillations even with coarse meshes

Bacillus thuringiensis Toxins: Functional Characterization and Mechanism of Action

Bacillus thuringiensis (Bt)-based products are the most successful microbial insecticides to date. This entomopathogenic bacterium produces different kinds of proteins whose specific toxicity has been shown against a wide range of insect orders, nematodes, mites, protozoa, and human cancer cells. Some of these proteins are accumulated in parasporal crystals during the sporulation phase (Cry and Cyt proteins), whereas other proteins are secreted in the vegetative phase of growth (Vip and Sip toxins). Currently, insecticidal proteins belonging to different groups (Cry and Vip3 proteins) are widely used to control insect pests and vectors both in formulated sprays and in transgenic crops (the so-called Bt crops). Despite the extensive use of these proteins in insect pest control, especially Cry and Vip3, their mode of action is not completely understood

A Genomic and Proteomic Approach to Identify and Quantify the Expressed Bacillus thuringiensis Proteins in the Supernatant and Parasporal Crystal

The combined analysis of genomic and proteomic data allowed us to determine which cry and vip genes are present in a Bacillus thuringiensis (Bt) isolate and which ones are being expressed. Nine Bt isolates were selected from Spanish collections of Bt based on their vip1 and vip2 gene content. As a first step, nine isolates were analyzed by PCR to select those Bt isolates that contained genes with the lowest similarity to already described vip1 and vip2 genes (isolates E-SE10.2 and O-V84.2). Two selected isolates were subjected to a combined genomic and proteomic analysis. The results showed that the Bt isolate E-SE10.2 codifies for two new vegetative proteins, Vip2Ac-like_1 and Sip1Aa-like_1, that do not show expression differences at 24 h vs. 48 h and are expressed in a low amount. The Bt isolate O-V84.2 codifies for three new vegetative proteins, Vip4Aa-like_1, Vip4Aa-like_2, and Vip2Ac-like_2, that are marginally expressed. The Vip4Aa-like_1 protein was two-fold more abundant at 24 h vs. 48 h, while the Vip4Aa-like_2 was detected only at 24 h. For Vip2Ac-like_2, no differences in expression were found at 24 h vs. 48 h. Moreover, the parasporal crystal of the E-SE10.2 isolate contains a single type of crystal protein, Cry23Aa-like, while the parasporal crystal from O-V84.2 contains three kinds of crystal proteins: 7.0-9.8% weight of Cry45Aa-like proteins, 35-37% weight of Cry32-like proteins and 2.8-4.3% weight of Cry73-like protein

Entropy-stable discontinuous Galerkin approximation with summation-by-parts property for the incompressible Navier-Stokes equations with variable density and artificial compressibility

We present a provably stable discontinuous Galerkin spectral element method for the incompressible Navier-Stokes equations with artificial compressibility and variable density. Stability proofs, which include boundary conditions, that follow a continuous entropy analysis are provided. We define a mathematical entropy function that combines the traditional kinetic energy and an additional energy term for the artificial compressiblity, and derive its associated entropy conservation law. The latter allows us to construct a provably stable split-form nodal Discontinuous Galerkin (DG) approximation that satisfies the summation-by-parts simultaneous-approximation-term (SBP-SAT) property. The scheme and the stability proof are presented for general curvilinear three-dimensional hexahedral meshes. We use the exact Riemann solver and the Bassi-Rebay 1 (BR1) scheme at the inter-element boundaries for inviscid and viscous fluxes respectively, and an explicit low storage Runge-Kutta RK3 scheme to integrate in time. We assess the accuracy and robustness of the method by solving the Kovasznay flow, the inviscid Taylor-Green vortex, and the Rayleigh-Taylor instability

Specific binding of Bacillus thuringiensis Cry2A insecticidal proteins to a common site in the midgut of Helicoverpa species

For a long time, it has been assumed that the mode of action of Cry2A toxins was unique and different from that of other three-domain Cry toxins due to their apparent nonspecific and unsaturable binding to an unlimited number of receptors. However, based on the homology of the tertiary structure among three-domain Cry toxins, similar modes of action for all of them are expected. To confirm this hypothesis, binding assays were carried out with 125 I-labeled Cry2Ab. Saturation assays showed that Cry2Ab binds in a specific and saturable manner to brush border membrane vesicles (BBMVs) of Helicoverpa armigera. Homologous-competition assays with 125 I-Cry2Ab demonstrated that this toxin binds with high affinity to binding sites in H. armigera and Helicoverpa zea midgut. Heterologous-competition assays showed a common binding site for three toxins belonging to the Cry2A family (Cry2Aa, Cry2Ab, and Cry2Ae), which is not shared by Cry1Ac. Estimation of Kd (dissociation constant) values revealed that Cry2Ab had around 35-fold less affinity than Cry1Ac for BBMV binding sites in both insect species. Only minor differences were found regarding Rt (concentration of binding sites) values. This study questions previous interpretations from other authors performing binding assays with Cry2A toxins and establishes the basis for the mode of action of Cry2A toxins