High yield and high quality DNA from vegetative and sexual tissues of Mexican white pine (Pinus ayacahuite)

Pines are considered to be difficult for DNA extraction. However, from one species to the other there is variation in phenolic profiles and seed size that might affect final DNA yields and quality. Two DNA extraction protocols (CTAB and SDS based) were compared for their ability to produce DNA on leaves, gametophyte and embryo from Pinus ayacahuite, a pine species with a large seed (8 - 18 mm). The DNA obtained from both procedures was quantified and tested by PCR. The CTAB protocol provided higher DNA yields from vegetative tissue and embryo than the SDS method. Embryos (2n) and gametophytes (n) proved to be very good sources of DNA and the DNA isolated was suitable for PCR-RAPD and SSRmarkers. This paper reports the results and describes the modified CTAB protocol

Histogram Reweighting Method for Dynamic Properties

The histogram reweighting technique, widely used to analyze Monte Carlo data, is shown to be applicable to dynamic properties obtained from Molecular Dynamics simulations. The theory presented here is based on the fact that the correlation functions in systems in thermodynamic equilibrium are averages over initial conditions of functions of the trajectory of the system in phase-space, the latter depending on the volume, the total number of particles and the classical Hamiltonian. Thus, the well-known histogram reweighting method can almost straightforwardly be applied to reconstruct the probability distribution of initial states at different thermodynamic conditions, without extra computational effort. Correlation functions and transport coefficients are obtained with this method from few simulation data sets.Comment: 4 pages, 3 figure

Experimental evidence of solitary wave interaction in Hertzian chains

We study experimentally the interaction between two solitary waves that approach one to another in a linear chain of spheres interacting via the Hertz potential. When these counter propagating waves collide, they cross each other and a phase shift respect to the noninteracting waves is introduced, as a result of the nonlinear interaction potential. This observation is well reproduced by our numerical simulations and it is shown to be independent of viscoelastic dissipation at the beads contact. In addition, when the collision of equal amplitude and synchronized counter propagating waves takes place, we observe that two secondary solitary waves emerge from the interacting region. The amplitude of secondary solitary waves is proportional to the amplitude of incident waves. However, secondary solitary waves are stronger when the collision occurs at the middle contact in chains with even number of beads. Although numerical simulations correctly predict the existence of these waves, experiments show that their respective amplitude are significantly larger than predicted. We attribute this discrepancy to the rolling friction at the beads contacts during solitary wave propagation

Global Attractors for an Extensible Thermoelastic Beam System

This work is focused on the dissipative system describing the dynamics of an extensible thermoelastic beam, where the dissipation is entirely contributed by the second equation ruling the evolution of the temperature. Under natural boundary conditions, we prove the existence of bounded absorbing sets. When both the external body force and the heat source are time-independent, the related semigroup of solutions is shown to possess the global attractor of optimal regularity for all values of the external axial load. The same result holds true when the rotational inertia is taken into consideration. In both cases, the solutions on the attractor are strong solutions.Comment: 21 pages, no figur

Cell dynamics simulations of sphere-forming diblock copolymers in thin films on chemically patterned substrates

The morphology of sphere-forming block copolymers assembled in thin films on patterned surfaces is theoretically analyzed. The patterns on the lower surface are alternating bands of a given width distinctively attracting or repelling a given block. We find that long- range order can be achieved, and it depends on the commensurability of the characteristic length of the block domains with both band periodicity and slit thickness. The comparison of the simulation results with experimental data shows a very good agreement. Furthermore, we show that the proper selection of the band periodicity and, consequently, of the film thickness permits the system to switch from hexagonal packing to body-centered orthohedra. Therefore, we show that it exists a way to control the formation of long-range ordered structures of different types in this kind of system

Universal imprinting of chirality with chiral light by employing plasmonic metastructures

Chirality, either of light or matter, has proved to be very practical in biosensing and nanophotonics. However, the fundamental understanding of its temporal dynamics still needs to be discovered. A realistic setup for this are the so-called metastructures, since they are optically active and are built massively, hence rendering an immediate potential candidate. Here we propose and study the electromagnetic-optical mechanism leading to chiral optical imprinting on metastructures. Induced photothermal responses create anisotropic permittivity modulations, different for left or right circularly polarized light, leading to temporal-dependent chiral imprinting of hot-spots, namely imprinting of chirality. The above effect has not been observed yet, but it is within reach of modern experimental approaches. The proposed nonlinear chiroptical effect is general and should appear in any anisotropic material; however, we need to design a particular geometry for this effect to be strong. These new chiral time-dependent metastructures may lead to a plethora of applications.Comment: Main (29 pages, 6 figures) and supplemental (46 pages, 35 figures

Tissue inhibitor of metalloproteinase-1 (TIMP-1) regulates mesenchymal stem cells through let-7f microRNA and Wnt/β-catenin signaling

Tissue inhibitor of metalloproteinases 1 (TIMP-1) is a matrix metalloproteinase (MMP)-independent regulator of growth and apoptosis in various cell types. The receptors and signaling pathways that are involved in the growth factor activities of TIMP-1, however, remain controversial. RNA interference of TIMP-1 has revealed that endogenous TIMP-1 suppresses the proliferation, metabolic activity, and osteogenic differentiation capacity of human mesenchymal stem cells (hMSCs). The knockdown of TIMP-1 in hMSCs activated the Wnt/β-catenin signaling pathway as indicated by the increased stability and nuclear localization of β-catenin in TIMP-1–deficient hMSCs. Moreover, TIMP-1 knockdown cells exhibited enhanced β-catenin transcriptional activity, determined by Wnt/β-catenin target gene expression analysis and a luciferase-based β-catenin– activated reporter assay. An analysis of a mutant form of TIMP-1 that cannot inhibit MMP indicated that the effect of TIMP-1 on β-catenin signaling is MMP independent. Furthermore, the binding of CD63 to TIMP-1 on the surface of hMSCs is essential for the TIMP-1–mediated effects on Wnt/β-catenin signaling. An array analysis of microRNAs (miRNAs) and transfection studies with specific miRNA inhibitors and mimics showed that let-7f miRNA is crucial for the regulation of β-catenin activity and osteogenic differentiation by TIMP-1. Let-7f was up-regulated in TIMP-1–depleted hMSCs and demonstrably reduced axin 2, an antagonist of β-catenin stability. Our results demonstrate that TIMP-1 is a direct regulator of hMSC functions and reveal a regulatory network in which let-7f modulates Wnt/β-catenin activity

The ESCRT-III machinery participates in the production of extracellular vesicles and protein export during Plasmodium falciparum infection

Malaria is a disease caused by Plasmodium parasites that is still a leading cause of death in many low-income countries, and for which currently available therapeutic strategies are not succeeding in its control, let alone eradication. An interesting feature observed after Plasmodium invasion is the increase of extracellular vesicles (EVs) generated by parasitized red blood cells (pRBCs), which lack a vesicular trafficking that would explain EV production. Here, by combining different approaches, we demonstrated the participation of the endosomal sorting complex required for transport (ESCRT) machinery from Plasmodium falciparum in the production of EVs in pRBCs. Moreover, we were able to detect ESCRT-III proteins adjacent to the membrane of the host and in EVs purified from a pRBC culture, which shows the export of these proteins and their participation in EV production. Finally, the disruption of an ESCRT-III associated gene, Pfvps60, led to a significant reduction in the amount of EVs. Altogether, these results confirm ESCRT-III participation in EV production and provide novel information on the P. falciparum protein export mechanisms, which can be used for the development of new therapeutic strategies against malaria, based on the disruption of EV formation and trafficking