Dry biobanking as a conservation tool in the Anthropocene

Species are going extinct at an alarming rate, termed by some as the sixth mass extinction event in the history of Earth. Many are the causes for this but in the end, all converge to one entity – humans. Since we are the cause, we also hold the key to making the change. Any change, however, will take time, and for some species this could be too long. While working on possible solutions, we also have the responsibility to buy time for those species on the verge of extinction. Genome resource banks, in the form of cryobanks, where samples are maintained under liquid nitrogen, are already in existence but they come with a host of drawbacks. Biomimicry – innovation inspired by Nature, has been a huge source for ideas. Searching methods that Nature utilizes to preserve biological systems for extended periods of time, we realize that drying rather than freezing is the method of choice. We thus argue here in favor of preserving at least part of the samples from critically endangered species in dry biobanks, a much safer, cost-effective, biobanking approach

Application of the level set method for the visual representation of continuous cellular automata oriented to anisotropic wet etching

[EN] Atomistic models are a very valuable simulation tool in the field of material science. Among them are the continuous cellular automata (CCA), which can simulate accurately the process of chemical etching used in micro-electro-mechanical-systems (MEMS) micromachining. Due to the CCA intrinsic atomistic nature, simulation results are obtained in the form of a cloud of points, so data visualization has been usually problematic. When using these models as a part of a computer aided design tool, good data visualization is very important. In this paper, a minimum energy model implemented with the level set (LS) method for improving the visual representation of simulated MEMS is presented. Additionally, the sparse field method has been applied to reduce the high computational cost of the original LS. Finally, some reconstructed surfaces with completely different topologies are presented, proving the effectiveness of our implementation and the fact that it is capable of producing any real surface, flat and smooth ones.We thank Miguel Angel Gosalvez for his collaboration in the early stages of this research. This work has been supported by the Spanish FPI-MICINN BES-2011-045940 grant. Also, we acknowledge support by the JAE-Doc grant form the Junta para la Ampliacion de Estudios program co-funded by FSE.Montoliu Álvaro, C.; Ferrando Jódar, N.; Cerdá Boluda, J.; Colom Palero, RJ. (2014). Application of the level set method for the visual representation of continuous cellular automata oriented to anisotropic wet etching. International Journal of Computer Mathematics. 91(1):124-134. https://doi.org/10.1080/00207160.2013.801464S12413491

Chemical Reaction Dynamics at Surfaces

Contains reports on four research projects.Joint Services Electronics Program Contract DAAL03-92-C-000

Evolutionary continuous cellular automaton for the simulation of wet etching of quartz

Anisotropic wet chemical etching of quartz is a bulk micromachining process for the fabrication of micro-electro-mechanical systems (MEMS), such as resonators and temperature sensors. Despite the success of the continuous cellular automaton for the simulation of wet etching of silicon, the simulation of the same process for quartz has received little attention-especially from an atomistic perspective-resulting in a lack of accurate modeling tools. This paper analyzes the crystallographic structure of the main surface orientations of quartz and proposes a novel classification of the surface atoms as well as an evolutionary algorithm to determine suitable values for the corresponding atomistic removal rates. Not only does the presented evolutionary continuous cellular automaton reproduce the correct macroscopic etch rate distribution for quartz hemispheres, but it is also capable of performing fast and accurate 3D simulations of MEMS structures. This is shown by several comparisons between simulated and experimental results and, in particular, by a detailed, quantitative comparison for an extensive collection of trench profiles. © 2012 IOP Publishing Ltd.We are grateful to D Cheng and K Sato (Nagoya University, Japan) for providing part of the experimental data. We acknowledge support by the JAE-Doc grant form the Junta para la Ampliacion de Estudios program co-funded by FSE, the Ramon y Cajal Fellowship Program by the Spanish Ministry of Science and Innovation, NANO-IKER Project (IE11-304) from the ETORTEK program by the Basque Government and the Professor Partnership Program by NVIDIA Corporation.Ferrando Jódar, N.; Gosalvez Ayuso, MA.; Colom Palero, RJ. (2012). Evolutionary continuous cellular automaton for the simulation of wet etching of quartz. Journal of Micromechanics and Microengineering. 22(2). https://doi.org/10.1088/0960-1317/22/2/025021S222Hida, H., Shikida, M., Fukuzawa, K., Murakami, S., Sato, K., Asaumi, K., … Sato, K. (2008). Fabrication of a quartz tuning-fork probe with a sharp tip for AFM systems. Sensors and Actuators A: Physical, 148(1), 311-318. doi:10.1016/j.sna.2008.08.021Oh, H., Kim, G., Seo, H., Song, Y., Lee, K., & Yang, S. S. (2010). Fabrication of micro-lens array using quartz wet etching and polymer. Sensors and Actuators A: Physical, 164(1-2), 161-167. doi:10.1016/j.sna.2010.10.003Xing, Y., Gosálvez, M. A., & Sato, K. (2007). Step flow-based cellular automaton for the simulation of anisotropic etching of complex MEMS structures. New Journal of Physics, 9(12), 436-436. doi:10.1088/1367-2630/9/12/436Zhou, Z., Huang, Q., Li, W., & Deng, W. (2007). A cellular automaton-based simulator for silicon anisotropic etching processes considering high index planes. Journal of Micromechanics and Microengineering, 17(4), S38-S49. doi:10.1088/0960-1317/17/4/s03Gosalvez, M. A., Yan Xing, & Sato, K. (2008). Analytical Solution of the Continuous Cellular Automaton for Anisotropic Etching. Journal of Microelectromechanical Systems, 17(2), 410-431. doi:10.1109/jmems.2008.916339Zhou, Z., Huang, Q., & Li, W. (2009). Modeling and Simulations of Anisotropic Etching of Silicon in Alkaline Solutions with Experimental Verification. Journal of The Electrochemical Society, 156(2), F29. doi:10.1149/1.3031485Rangsten, P., Hedlund, C., Katardjiev, I. V., & Bäcklund, Y. (1998). Etch rates of crystallographic planes inZ-cut quartz - experiments and simulation. Journal of Micromechanics and Microengineering, 8(1), 1-6. doi:10.1088/0960-1317/8/1/001Tellier, C. R., & Leblois, T. G. (2000). Micromachining of quartz plates: determination of a database by combined stereographic analysis and 3-D simulation of etching shapes. IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, 47(5), 1204-1216. doi:10.1109/58.869067Hedlund, C., Lindberg, U., Bucht, U., & Soderkvist, J. (1993). Anisotropic etching of Z-cut quartz. Journal of Micromechanics and Microengineering, 3(2), 65-73. doi:10.1088/0960-1317/3/2/006Liang, J., Kohsaka, F., Matsuo, T., & Ueda, T. (2007). Wet Etched High Aspect Ratio Microstructures on Quartz for MEMS Applications. IEEJ Transactions on Sensors and Micromachines, 127(7), 337-342. doi:10.1541/ieejsmas.127.337Gosálvez, M. A., Xing, Y., Sato, K., & Nieminen, R. M. (2009). Discrete and continuous cellular automata for the simulation of propagating surfaces. Sensors and Actuators A: Physical, 155(1), 98-112. doi:10.1016/j.sna.2009.08.012Zhenjun Zhu, & Chang Liu. (2000). Micromachining process simulation using a continuous cellular automata method. Journal of Microelectromechanical Systems, 9(2), 252-261. doi:10.1109/84.846706Gosálvez, M. A., Xing, Y., Sato, K., & Nieminen, R. M. (2008). Atomistic methods for the simulation of evolving surfaces. Journal of Micromechanics and Microengineering, 18(5), 055029. doi:10.1088/0960-1317/18/5/055029Ferrando, N., Gosálvez, M. A., Cerdá, J., Gadea, R., & Sato, K. (2011). Octree-based, GPU implementation of a continuous cellular automaton for the simulation of complex, evolving surfaces. Computer Physics Communications, 182(3), 628-640. doi:10.1016/j.cpc.2010.11.004Mühlenbein, H., & Schlierkamp-Voosen, D. (1993). Predictive Models for the Breeder Genetic Algorithm I. Continuous Parameter Optimization. Evolutionary Computation, 1(1), 25-49. doi:10.1162/evco.1993.1.1.25Kohsaka, F., Liang, J., Matsuo, T., & Ueda, T. (2007). High Sensitive Tilt Sensor for Quartz Micromachining. IEEJ Transactions on Sensors and Micromachines, 127(10), 431-436. doi:10.1541/ieejsmas.127.43

Chemical Reaction Dynamics at Surfaces

Contains reports on three research projects.Joint Services Electronics Program Contract DAAL03-92-C-0001National Science Foundation Grant CHE 90-20623U.S. Department of Energy Grant DE-FG02-89-ER1403

Focal Distribution of Hepatitis C Virus RNA in Infected Livers

Background: Hepatitis C virus (HCV) is a plus-strand RNA virus that replicates by amplification of genomic RNA from minus strands leading to accumulation of almost one thousand copies per cell under in vitro cell culture conditions. In contrast, HCV RNA copy numbers in livers of infected patients appear to be much lower, estimated at a few copies per cell. Methodology/Principal Findings: To gain insights into mechanisms that control HCV replication in vivo, we analyzed HCV RNA levels as well as expression of interferon beta (IFNb) and several interferon stimulated genes (ISGs) from whole liver sections and micro-dissected subpopulations of hepatocytes in biopsy samples from 21 HCV-infected patients. The results showed that intrahepatic HCV RNA levels range form less than one copy per hepatocyte to a maximum of about eight. A correlation existed between viral RNA levels and IFNb expression, but not between viral RNA and ISG levels. Also, IFNb expression did not correlate with ISGs levels. Replication of HCV RNA occurred in focal areas in the liver in the presence of a general induction of ISGs. Conclusion/Significance: The low average levels of HCV RNA in biopsy samples can be explained by focal distribution of infected hepatocytes. HCV replication directly induces IFNb, which then activates ISGs. The apparent lack of a correlation between levels of IFNb and ISG expression indicates that control of the innate immune response during HCV infection

RNA-binding properties and membrane insertion of Melon necrotic spot virus (MNSV) double gene block movement proteins

Advances in structural and biochemical properties of carmovirus movement proteins (MPs) have only been obtained in p7 and p9 from Carnation mottle virus (CarMV). Alignment of carmovirus MPs revealed a low conservation of amino acid identity but interestingly, similarity was elevated in regions associated with the functional secondary structure elements reported for CarMV which were conserved in all studied proteins. Nevertheless, some differential features in relation with CarMV MPs were identified in those from Melon necrotic virus (MNSV) (p7A and p7B). p7A was a soluble non-sequence specific RNA-binding protein, but unlike CarMV p7, its central region alone could not account for the RNA-binding properties of the entire protein. In fact, a 22-amino acid synthetic peptide whose sequence corresponds to this central region rendered an apparent dissociation constant (K(d)) significantly higher than that of the corresponding entire protein (9 mM vs. 0.83-25.7 microM). This p7A-derived peptide could be induced to fold into an alpha-helical structure as demonstrated for other carmovirus p7-like proteins. Additionally, in vitro fractionation of p7B transcription/translation mixtures in the presence of ER-derived microsomal membranes strongly suggested that p7B is an integral membrane protein. Both characteristics of these two small MPs forming the double gene block (DGB) of MNSV are discussed in the context of the intra- and intercellular movement of carmovirus

The Relative Importance of Topography and RGD Ligand Density for Endothelial Cell Adhesion

The morphology and function of endothelial cells depends on the physical and chemical characteristics of the extracellular environment. Here, we designed silicon surfaces on which topographical features and surface densities of the integrin binding peptide arginine-glycine-aspartic acid (RGD) could be independently controlled. We used these surfaces to investigate the relative importance of the surface chemistry of ligand presentation versus surface topography in endothelial cell adhesion. We compared cell adhesion, spreading and migration on surfaces with nano- to micro-scaled pyramids and average densities of 6×102–6×1011 RGD/mm2. We found that fewer cells adhered onto rough than flat surfaces and that the optimal average RGD density for cell adhesion was 6×105 RGD/mm2 on flat surfaces and substrata with nano-scaled roughness. Only on surfaces with micro-scaled pyramids did the topography hinder cell migration and a lower average RGD density was optimal for adhesion. In contrast, cell spreading was greatest on surfaces with 6×108 RGD/mm2 irrespectively of presence of feature and their size. In summary, our data suggest that the size of pyramids predominately control the number of endothelial cells that adhere to the substratum but the average RGD density governs the degree of cell spreading and length of focal adhesion within adherent cells. The data points towards a two-step model of cell adhesion: the initial contact of cells with a substratum may be guided by the topography while the engagement of cell surface receptors is predominately controlled by the surface chemistry

Male oxidative stress infertility (MOSI): proposed terminology and clinical practice guidelines for management of idiopathic male infertility

Despite advances in the field of male reproductive health, idiopathic male infertility, in which a man has altered semen characteristics without an identifiable cause and there is no female factor infertility, remains a challenging condition to diagnose and manage. Increasing evidence suggests that oxidative stress (OS) plays an independent role in the etiology of male infertility, with 30% to 80% of infertile men having elevated seminal reactive oxygen species levels. OS can negatively affect fertility via a number of pathways, including interference with capacitation and possible damage to sperm membrane and DNA, which may impair the sperm's potential to fertilize an egg and develop into a healthy embryo. Adequate evaluation of male reproductive potential should therefore include an assessment of sperm OS. We propose the term Male Oxidative Stress Infertility, or MOSI, as a novel descriptor for infertile men with abnormal semen characteristics and OS, including many patients who were previously classified as having idiopathic male infertility. Oxidation-reduction potential (ORP) can be a useful clinical biomarker for the classification of MOSI, as it takes into account the levels of both oxidants and reductants (antioxidants). Current treatment protocols for OS, including the use of antioxidants, are not evidence-based and have the potential for complications and increased healthcare-related expenditures. Utilizing an easy, reproducible, and cost-effective test to measure ORP may provide a more targeted, reliable approach for administering antioxidant therapy while minimizing the risk of antioxidant overdose. With the increasing awareness and understanding of MOSI as a distinct male infertility diagnosis, future research endeavors can facilitate the development of evidence-based treatments that target its underlying cause

Male Oxidative Stress Infertility (MOSI):proposed terminology and clinical practice guidelines for management of idiopathic male infertility

Despite advances in the field of male reproductive health, idiopathic male infertility, in which a man has altered semen characteristics without an identifiable cause and there is no female factor infertility, remains a challenging condition to diagnose and manage. Increasing evidence suggests that oxidative stress (OS) plays an independent role in the etiology of male infertility, with 30% to 80% of infertile men having elevated seminal reactive oxygen species levels. OS can negatively affect fertility via a number of pathways, including interference with capacitation and possible damage to sperm membrane and DNA, which may impair the sperm's potential to fertilize an egg and develop into a healthy embryo. Adequate evaluation of male reproductive potential should therefore include an assessment of sperm OS. We propose the term Male Oxidative Stress Infertility, or MOSI, as a novel descriptor for infertile men with abnormal semen characteristics and OS, including many patients who were previously classified as having idiopathic male infertility. Oxidation-reduction potential (ORP) can be a useful clinical biomarker for the classification of MOSI, as it takes into account the levels of both oxidants and reductants (antioxidants). Current treatment protocols for OS, including the use of antioxidants, are not evidence-based and have the potential for complications and increased healthcare-related expenditures. Utilizing an easy, reproducible, and cost-effective test to measure ORP may provide a more targeted, reliable approach for administering antioxidant therapy while minimizing the risk of antioxidant overdose. With the increasing awareness and understanding of MOSI as a distinct male infertility diagnosis, future research endeavors can facilitate the development of evidence-based treatments that target its underlying cause