Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion.

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.

Hydrogel-based magnetoelectric microenvironments for tissue stimulation.

The development of strategies to mimic the natural environment of tissues with engineered scaffolds remains one of the biggest challenges of tissue engineering. Hydrogels appear as suitable materials for this purpose due to their substantial water content, biocompatibility, and for being able to carry nanomaterials that introduce new functionalities to the hydrogel. The incorporation of magnetically responsive and, in particular, magnetoelectric materials into the hydrogel-based scaffolds are a promising approach for bone tissue engineering applications once it can promote not only tissue regeneration through magnetic to mechanic to electrical conversion/stimuli but also the external control of the scaffold by the application of magnetic fields. This work reports on a new CoFe2O4/ Methacrylated Gellan Gum (GGMA)/poly(vinylidene fluoride) (PVDF) hydrogel-based scaffold with 20 kPa Young's modulus and cell viability superior to 80%. The ≈ 1 µm thick PVDF/CoFe2O4 spheres added to GGMA gel (2 wt.%) exhibit 20 emu.g-1 magnetization saturation, 2.7 kOe magnetic coercivity and ß-phase contents ≈ 78%, leading to a piezoelectric response |d33| of ≈ 22 pC N-1 and a magnetoelectric response of Δ|d33| ≈ 6 pC N-1 at a DC magnetic field of 220 m T, as verified for the CoFe2O4/PVDF spheres with 20 wt.% filler content. Such characteristics allow novel tissue regeneration strategies approaches once CoFe2O4/GGMA/PVDF has a porous 3-D structure, biocompatibility, bioresorbability, and mechanical/electrical dynamic responses that can be triggered by an applied external magnetic field.

Tailored Biodegradable and Electroactive Poly(Hydroxybutyrate-Co-Hydroxyvalerate) Based Morphologies for Tissue Engineering Applications.

Polymer-based piezoelectric biomaterials have already proven their relevance for tissue engineering applications. Furthermore, the morphology of the scaffolds plays also an important role in cell proliferation and differentiation. The present work reports on poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV), a biocompatible, biodegradable, and piezoelectric biopolymer that has been processed in different morphologies, including films, fibers, microspheres, and 3D scaffolds. The corresponding magnetically active PHBV-based composites were also produced. The effect of the morphology on physico-chemical, thermal, magnetic, and mechanical properties of pristine and composite samples was evaluated, as well as their cytotoxicity. It was observed that the morphology does not strongly affect the properties of the pristine samples but the introduction of cobalt ferrites induces changes in the degree of crystallinity that could affect the applicability of prepared biomaterials. Young's modulus is dependent of the morphology and also increases with the addition of cobalt ferrites. Both pristine and PHBV/cobalt ferrite composite samples are not cytotoxic, indicating their suitability for tissue engineering applications.

Catalytic performance of the high and low temperature polymorphs of (C6N2H16)0.5[(VO)(HAsO4)F]: structural, thermal, spectroscopic and magnetic studies.

(C(6)N(2)H(16))(0.5)[(VO)(HAsO(4))F] 1 has been synthesized using mild hydrothermal conditions under autogenous pressure. Above 70 degrees C, this phase has a polymorph with the same chemical composition 2 in which the organic 1,4-diamincyclohexane molecule adopts a different conformation. The crystal structures have been solved from single-crystal X-ray diffraction data. The phases crystallize in the C2/c monoclinic space group with the unit-cell parameters a = 21.065(2) A b = 7.2717(4) A c = 10.396(1) A beta = 104.290(8) degrees for compound 1 and a = 23.025(1) A, b = 7.322(1) A, c = 10.344(1) A and beta = 109.250(6) degrees for compound 2. These phases exhibit a layered inorganic framework, with the template molecule linking the layers via electrostatic interaction and hydrogen bonds. In both phases, the structure is built from secondary building units SBU-4, which are constructed from two [V(2)O(8)F(2)] edge-shared dimeric vanadyl octahedra, connected by the vertices of two hydrogenarsenate (HAsO(4)) tetrahedra. The repetition of this SBU unit gives sheets along the [010] direction. Polymorph 1 exists below 70 degrees C, whereas the limit of thermal stability for 2 is approximately 150 degrees C. Both phases coexist in the temperature range from 80 to -15 degrees C. By means of the DSC technique it has been possible to verify that the temperature of the structural transition is between 70 and 100 degrees C. The diffuse reflectance spectrum of 1 confirms the presence of vanadyl ions, in which the vanadium(IV) cations have a d(1) electronic configuration in a slightly distorted octahedral environment. ESR spectra of both phases are isotropic with mean g values of 1.96 and 1.99 for 1 and 2, respectively. Magnetic measurements for 1 indicate the existence of antiferromagnetic exchange couplings. Both phases are effective and selective catalysts in the oxidation of organic sulfides to sulfoxides and 3,7-dimethylocta-1,6-dien-3-ol.