Brief Note: Cactus Growth Changes as an Effect of Wind in Baja California Sur, México

Author Institution: Centro de Inverstigaciones Biologicas del NoroesteAt Natividad Island, Baja California Sur, Mexico, we sampled a Ferocactus fordii var. grandiflorus population. All 50 individuals recorded in the northeast part of the island exhibited different degrees of prostration, directly related to their size and the direction of prevailing winds. Prostration was always oriented away from the direction of the dominant winds blowing over the island. There are essentially no previous publications of the effects of wind on the cactus growth form

The structure of an endogenous Drosophila centromere reveals the prevalence of tandemly repeated sequences able to form i-motifs

Centromeres are the chromosomal loci at which spindle microtubules attach to mediate chromosome segregation during mitosis and meiosis. In most eukaryotes, centromeres are made up of highly repetitive DNA sequences (satellite DNA) interspersed with middle repetitive DNA sequences (transposable elements). Despite the efforts to establish complete genomic sequences of eukaryotic organisms, the so-called 'finished' genomes are not actually complete because the centromeres have not been assembled due to the intrinsic difficulties in constructing both physical maps and complete sequence assemblies of long stretches of tandemly repetitive DNA. Here we show the first molecular structure of an endogenous Drosophila centromere and the ability of the C-rich dodeca satellite strand to form dimeric i-motifs. The finding of i-motif structures in simple and complex centromeric satellite DNAs leads us to suggest that these centromeric sequences may have been selected not by their primary sequence but by their ability to form noncanonical secondary structures.Peer Reviewe

Los derechos fundamentales de las personas privadas de su libertad en el contexto de la pandemia por la COVID-19 en el establecimiento penitenciario de Arequipa

El objetivo de la investigación es determinar de qué manera el contexto de emergencia sanitaria por la COVID-19 vulnera los Derechos Fundamentales de las personas privadas de su libertad en el Establecimiento Penitenciario de Arequipa, debido a la insuficiente intervención del Estado en el ámbito penitenciario. Materiales y métodos: El enfoque de estudio es mixto con preponderancia cualitativa y de tipo no experimental transversal, ya que se realizó un análisis de los datos recopilados en un determinado periodo de tiempo contrastando el impacto que trajo consigo el contexto de la COVID-19 sobre la población recluida en el Establecimiento Penitenciario de Arequipa. Asimismo, se estudió la normativa de emergencia que se dictó en los primeros meses del estado de emergencia y se analizó la eficiencia de la misma con la colaboración de los expertos en la materia que brindaron sus opiniones a través del cuestionario planteado y fue analizado en conjunto con los datos recabados de la página web del INPE. Población: Esta se encuentra delimitada a los internos del Establecimiento Penitenciario de Arequipa varones, el cual tiene una capacidad de albergue para 667 reclusos, sin embargo, la media de internos durante el periodo estudiado es de 2038 personas privadas de libertad. Instrumentos: Se utilizó un cuestionario virtual, que consistió en responder ocho preguntas, así como, fichas de recolección de datos, para recopilar los datos numéricos que proporciona el INPE a través del Sistema de Información Estadística Penitenciaria. Resultados: Se analizó las respuestas proporcionadas por los especialistas con respecto a la normativa de emergencia dictada durante los primeros meses de la pandemia, como también su propia apreciación sobre la realidad carcelaria durante el estado de emergencia sanitaria, advirtiéndose la existencia de dos posturas claras entre los participantes; asimismo, se analizó los datos estadísticos proporcionados por el SIEP y que fueron recabados a través de las fichas de recolección de datos, para de esta manera acercarnos a la realidad carcelaria basada en los datos numéricos proporcionados por la administración penitenciaria; de esta manera se llegó a la Conclusión de que sí se ha vulnerado ciertos Derechos Fundamentales de los privados de libertad durante la pandemia por la COVID-19 dentro del Establecimiento Penitenciario de Arequipa por la insuficiente intervención del Estado durante la emergencia sanitaria.Campus Arequip

Effect of the anatomical structure, wood properties and machining conditions on surface roughness of wood

The main aim is to test the influence of anatomical structure (grain direction and elements size), wood hardness and machining conditions on wood surface roughness. 180 samples defect-free were obtained from beech, oak and pine and processed with different machining methods (planning, sanding with 60 grit or sanding with 180 grit). Roughness, hardness, and anatomical structure were analysed using international methodologies. An analysis of variance of the data from all the samples with the four factors in the experimental design were performed. Results showed that machining processes and species are the factors that significantly affect surface roughness, as opposed to grain direction (plane of section and stylus-grain angle), which was only shown to be significant in some subgroups. Roughness parameters of samples sanded with 180 grit were lower in contrast to samples planned or sanded with 60 grit. Hardness was found to be the property of the wood that most clearly affects its final roughness, and makes it difficult to achieve better roughness results as the hardness increases

Mechanical unfolding of long human telomeric RNA (TERRA)

[EN] We report the first single molecule investigation of TERRA molecules. By using optical-tweezers and other biophysical techniques, we have found that long RNA constructions of up to 25 GGGUUA repeats form higher order structures comprised of single parallel G-quadruplex blocks, which unfold at lower forces than their DNA counterparts.This work was supported by grants from the Spanish Ministry of Science and Innovation (grants RYC2007-01765 to JRA-G, BFU2011-30295-C02-01 to AV, and CTQ2010-21567-C02-02 to CG). MG was supported by the FPI fellowship BES-2009-027909. RB and EH-G were supported by Comunidad de Madrid, grant CAM-S2009MAT-1507. AV acknowledges an institutional grant from the Fundacion Ramon Areces to the CBMSO. JRA-G wants to thank Prof. J. L. Carrascosa and Prof. J. M. Valpuesta (CNB-CSIC) for their continuous support and encouragement in this research. We also acknowledge the excellent technical assistance of Beatriz de Pablos (CBMSO).Garavís, M.; Bocanegra, R.; Herrero-Galán, E.; González, C.; Villasante, A.; Arias-Gonzalez, JR. (2013). Mechanical unfolding of long human telomeric RNA (TERRA). Chemical Communications. 49(57):6397-6399. https://doi.org/10.1039/c3cc42981dS639763994957De Lange, T. (2005). Shelterin: the protein complex that shapes and safeguards human telomeres. Genes & Development, 19(18), 2100-2110. doi:10.1101/gad.1346005Blackburn, E. H. (1991). Structure and function of telomeres. Nature, 350(6319), 569-573. doi:10.1038/350569a0Biffi, G., Tannahill, D., McCafferty, J., & Balasubramanian, S. (2013). Quantitative visualization of DNA G-quadruplex structures in human cells. Nature Chemistry, 5(3), 182-186. doi:10.1038/nchem.1548Paeschke, K., Simonsson, T., Postberg, J., Rhodes, D., & Lipps, H. J. (2005). Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo. Nature Structural & Molecular Biology, 12(10), 847-854. doi:10.1038/nsmb982Hwang, H., Buncher, N., Opresko, P. L., & Myong, S. (2012). POT1-TPP1 Regulates Telomeric Overhang Structural Dynamics. Structure, 20(11), 1872-1880. doi:10.1016/j.str.2012.08.018Azzalin, C. M., Reichenbach, P., Khoriauli, L., Giulotto, E., & Lingner, J. (2007). Telomeric Repeat Containing RNA and RNA Surveillance Factors at Mammalian Chromosome Ends. Science, 318(5851), 798-801. doi:10.1126/science.1147182Schoeftner, S., & Blasco, M. A. (2007). Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II. Nature Cell Biology, 10(2), 228-236. doi:10.1038/ncb1685Porro, A., Feuerhahn, S., Reichenbach, P., & Lingner, J. (2010). Molecular Dissection of Telomeric Repeat-Containing RNA Biogenesis Unveils the Presence of Distinct and Multiple Regulatory Pathways. Molecular and Cellular Biology, 30(20), 4808-4817. doi:10.1128/mcb.00460-10Deng, Z., Norseen, J., Wiedmer, A., Riethman, H., & Lieberman, P. M. (2009). TERRA RNA Binding to TRF2 Facilitates Heterochromatin Formation and ORC Recruitment at Telomeres. Molecular Cell, 35(4), 403-413. doi:10.1016/j.molcel.2009.06.025De Silanes, I. L., d’ Alcontres, M. S., & Blasco, M. A. (2010). TERRA transcripts are bound by a complex array of RNA-binding proteins. Nature Communications, 1(1). doi:10.1038/ncomms1032Xu, Y., Suzuki, Y., Ito, K., & Komiyama, M. (2010). Telomeric repeat-containing RNA structure in living cells. Proceedings of the National Academy of Sciences, 107(33), 14579-14584. doi:10.1073/pnas.1001177107Martadinata, H., & Phan, A. T. (2009). Structure of Propeller-Type Parallel-Stranded RNA G-Quadruplexes, Formed by Human Telomeric RNA Sequences in K+Solution. Journal of the American Chemical Society, 131(7), 2570-2578. doi:10.1021/ja806592zXu, Y., Kaminaga, K., & Komiyama, M. (2008). G-Quadruplex Formation by Human Telomeric Repeats-Containing RNA in Na+Solution. Journal of the American Chemical Society, 130(33), 11179-11184. doi:10.1021/ja8031532Collie, G. W., Haider, S. M., Neidle, S., & Parkinson, G. N. (2010). A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex. Nucleic Acids Research, 38(16), 5569-5580. doi:10.1093/nar/gkq259Collie, G. W., Parkinson, G. N., Neidle, S., Rosu, F., De Pauw, E., & Gabelica, V. (2010). Electrospray Mass Spectrometry of Telomeric RNA (TERRA) Reveals the Formation of Stable Multimeric G-Quadruplex Structures. Journal of the American Chemical Society, 132(27), 9328-9334. doi:10.1021/ja100345zMartadinata, H., Heddi, B., Lim, K. W., & Phan, A. T. (2011). Structure of Long Human Telomeric RNA (TERRA): G-Quadruplexes Formed by Four and Eight UUAGGG Repeats Are Stable Building Blocks. Biochemistry, 50(29), 6455-6461. doi:10.1021/bi200569fArora, A., & Maiti, S. (2009). Differential Biophysical Behavior of Human Telomeric RNA and DNA Quadruplex. The Journal of Physical Chemistry B, 113(30), 10515-10520. doi:10.1021/jp810638nJoachimi, A., Benz, A., & Hartig, J. S. (2009). A comparison of DNA and RNA quadruplex structures and stabilities. Bioorganic & Medicinal Chemistry, 17(19), 6811-6815. doi:10.1016/j.bmc.2009.08.043Qi, J., & Shafer, R. H. (2007). Human Telomere Quadruplex:  Refolding and Selection of Individual Conformers via RNA/DNA Chimeric Editing†. Biochemistry, 46(25), 7599-7606. doi:10.1021/bi602392uRandall, A., & Griffith, J. D. (2009). Structure of Long Telomeric RNA Transcripts. Journal of Biological Chemistry, 284(21), 13980-13986. doi:10.1074/jbc.m900631200Kumari, S., Bugaut, A., & Balasubramanian, S. (2008). Position and Stability Are Determining Factors for Translation Repression by an RNA G-Quadruplex-Forming Sequence within the 5′ UTR of theNRASProto-oncogene†. Biochemistry, 47(48), 12664-12669. doi:10.1021/bi8010797McKenna, S. A., Kim, I., Puglisi, E. V., Lindhout, D. A., Aitken, C. E., Marshall, R. A., & Puglisi, J. D. (2007). Purification and characterization of transcribed RNAs using gel filtration chromatography. Nature Protocols, 2(12), 3270-3277. doi:10.1038/nprot.2007.480Parkinson, G. N., Lee, M. P. H., & Neidle, S. (2002). Crystal structure of parallel quadruplexes from human telomeric DNA. Nature, 417(6891), 876-880. doi:10.1038/nature755Herrero-Galán, E., Fuentes-Perez, M. E., Carrasco, C., Valpuesta, J. M., Carrascosa, J. L., Moreno-Herrero, F., & Arias-Gonzalez, J. R. (2012). Mechanical Identities of RNA and DNA Double Helices Unveiled at the Single-Molecule Level. Journal of the American Chemical Society, 135(1), 122-131. doi:10.1021/ja3054755Bustamante, C., Bryant, Z., & Smith, S. B. (2003). Ten years of tension: single-molecule DNA mechanics. Nature, 421(6921), 423-427. doi:10.1038/nature01405Yu, Z., Schonhoft, J. D., Dhakal, S., Bajracharya, R., Hegde, R., Basu, S., & Mao, H. (2009). ILPR G-Quadruplexes Formed in Seconds Demonstrate High Mechanical Stabilities. Journal of the American Chemical Society, 131(5), 1876-1882. doi:10.1021/ja806782sKoirala, D., Dhakal, S., Ashbridge, B., Sannohe, Y., Rodriguez, R., Sugiyama, H., … Mao, H. (2011). A single-molecule platform for investigation of interactions between G-quadruplexes and small-molecule ligands. Nature Chemistry, 3(10), 782-787. doi:10.1038/nchem.1126Dhakal, S., Cui, Y., Koirala, D., Ghimire, C., Kushwaha, S., Yu, Z., … Mao, H. (2013). Structural and mechanical properties of individual human telomeric G-quadruplexes in molecularly crowded solutions. Nucleic Acids Research, 41(6), 3915-3923. doi:10.1093/nar/gkt038De Messieres, M., Chang, J.-C., Brawn-Cinani, B., & La Porta, A. (2012). Single-Molecule Study ofG-Quadruplex Disruption Using Dynamic Force Spectroscopy. Physical Review Letters, 109(5). doi:10.1103/physrevlett.109.058101Schonhoft, J. D., Bajracharya, R., Dhakal, S., Yu, Z., Mao, H., & Basu, S. (2009). Direct experimental evidence for quadruplex–quadruplex interaction within the human ILPR. Nucleic Acids Research, 37(10), 3310-3320. doi:10.1093/nar/gkp181Carrion-Vazquez, M., Oberhauser, A. F., Fowler, S. B., Marszalek, P. E., Broedel, S. E., Clarke, J., & Fernandez, J. M. (1999). Mechanical and chemical unfolding of a single protein: A comparison. Proceedings of the National Academy of Sciences, 96(7), 3694-3699. doi:10.1073/pnas.96.7.369

Working Group on Social Indicators (WGSOCIAL; outputs from 2023 meeting)

The Working Group on Social Indicators seeks to improve the integration of social sciences in ICES Ecosystem Overviews and Integrated Ecosystem Assessments through the development of culturally relevant social indicators. To advance progress on this, WGSOCIAL has broadly discussed the context of the social di-mension of fishing. This has led to coordination with other working groups within ICES and outside ICES with the Scientific, Technical and Economic Committee for Fisheries Expert Working Group Social and with the Regional Coordination Group on Economics Issues. WGSOCIAL develops methods for qualitative and quantitative approaches. It has also continued providing input to the updating of ecosystem overviews finalizing those of the Celtic Seas and North Sea. WGSOCIAL has advanced work on the definition and context of trade-offs and trade-off analy sis in the social context of fisheries. To assess social and cultural significance of commercial fishing, WGSOCIAL members have advanced case studies in a number of ICES Member Countries: two regions in Spain, Portugal, the Netherlands, Sweden and Norway. Each case study tackles a different approach with a different context. In addition, WGSOCIAL has advanced work on the topic of what a fishing community is and how the definition can change in different contexts. Lastly, WGSOCIAL has developed a database of social and economic indicators for evaluating fisheries management and identified a comprehensive list of categories and sub-categories of social and economic indicators that could be used to structure the selection of social indicators that inform fisheries managers. As a nest step, WGSOCIAL will identify key social indicators and data gaps for selected ICES Member Countries with recommendations for approaches to close the gaps. To support integrated socio-ecological evaluations in ecosystem-based management, WGSOCIAL has contributed to the development of work on the impacts of wind farms on com-mercial fishing activities. This work will continue in collaboration with WGECON, with whom several parallel terms of reference (ToRs) are shared. WGSOCIAL decided to transfer to the new ICES Human Dimension Steering Group.info:eu-repo/semantics/publishedVersio

On the origin of the eukaryotic chromosome: the role of noncanonical DNA structures in telomere evolution.

The transition of an ancestral circular genome to multiple linear chromosomes was crucial for eukaryogenesis because it allowed rapid adaptive evolution through aneuploidy. Here, we propose that the ends of nascent linear chromosomes should have had a dual function in chromosome end protection (capping) and chromosome segregation to give rise to the >proto-telomeres.> Later on, proper centromeres evolved at subtelomeric regions. We also propose that both noncanonical structures based on guanine-guanine interactions and the end-protection proteins recruited by the emergent telomeric heterochromatin have been required for telomere maintenance through evolution. We further suggest that the origin of Drosophila telomeres may be reminiscent of how the first telomeres arose.Ministerio de Ciencia e Innovación; Ministerio de Economía y Competitividad; Fundación Ramón ArecesPeer Reviewe

Papel de las proteinas asociadas a los microtubulos, MAP1 y MAP2, en el ensamblaje y función del microtubulo

Tesis doctoral inédita de la Universidad Autónoma de Madrid, Facultad de Ciencias. Departamento de Biología Molecular, Instituto de Virología y Genética Molecular. Fecha de lectura: 02-07-1981Bibliog.: h. [87-100

The Release 6 reference sequence of the Drosophila melanogaster genome

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.This work was supported by NIH grants P50 HG00750 (G.M.R.), R01 HG00747 (G.H.K.), and R01 HG002673 (S.E.C.) and performed under U.S. Department of Energy Contracts DE-AC0376SF00098 and DE-AC02-05CH11231, University of California. I.F.Z. was supported by grant 13-04-40137 from the Russian Federation; E.N.A. was supported by grant 12-04-00874-a from the Russian Federation; P.D. was supported by a grant from the Instituto Pasteur-Fondazione Cenci Bolognetti; A.V. was supported by Ministerio de Economía y Competitividad grant BFU2011-30295-C02-01; and A.B.C. was supported by NIH grant R01 GM064590 and grants from Fundaçao de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ) and the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).Peer Reviewe