Large-scale biogeography of marine pelagic bacteria and archaea

The dark ocean contains about 70% of the ocean’s microbial cells and 60% of its heterotrophic activity, which is mainly fueled by the flux of organic particles produced in the surface ocean and exported to the bathypelagic ocean (1,000 – 4,000 m depth). The bathypelagic ocean represents a nonhomogeneous environment and contains a variety of particles that are considered as the main supply of organic carbon to this environment. The microorganisms inhabiting this realm play a pivotal regulatory role in the biogeochemical cycles at a planetary scale. Accordingly, the study of these microorganisms is an essential step to decipher the ecological functioning of the deep ocean. Chapters 1 to 3 in this Thesis are dedicated to the description of the prokaryotic community composition in the bathypelagic ocean at a global scale through the sequencing of ribosomal DNA and RNA fragments using data collected during the Malaspina 2010 expedition. Chapter 1 identifies the dominant prokaryotes in the deep ocean and reveals a high proportion (~50%) of previously undescribed prokaryotes. The water masses and the structure of the deep ocean’s floor, organized into basins, are identified as the main drivers of their biogeography. Chapter 2 addresses the differences between free-living and particle-attached bathypelagic prokaryotic communities. This is shown to be a phylogenetically conserved trait, indicating that the bathypelagic particles and the water surrounding them constitute two distinct niches and that transitions from one to the other have been rare at an evolutionary timescale. Finally, in Chapter 3 we identify a linear relationship between the 16S RNA/DNA ratio and particle attachment preference, suggesting a global relationship between the prokaryote’s preference for a particle-attached lifestyle and their growth rate. While the deep ocean is a highly unexplored environment, a more complete knowledge exists for the epipelagic ocean (0 – 200 m depth). Steep gradients of light intensity and quality, temperature and nutrient availability characterize the oceans and impact on the distribution of species. However, different processes, such as the sinking of particles and the vertical movement of water masses, have been described as mechanisms capable of connecting the surface and deep layers of the ocean. These same processes could transport entire prokaryotic communities, a process theoretically proposed but never tested. In Chapter 4 we develop a tool (mtagger) for the extraction of short 16S ribosomal reads from metagenomes to describe the taxonomical composition of microbial communities. We propose and evaluate technical improvements compared to previous versions as a benchmark for its use in the last chapter. Chapter 5 is dedicated to the development of a modeling tool (disperflux) for the analysis of prokaryotic communities’ connectivity using data collected during the Tara Oceans expedition. We observe and describe a fast-decay relationship between community similarity and depth, which is consistently fitted by a power-law across the whole dataset, with the exception of 5 stations that are compatible with events of whole community export from the photic ocean to the mesopelagic. In summary, this Thesis significantly contributes to the knowledge on the ecological functioning of marine prokaryotes by describing the structure of prokaryotic communities along the bathypelagic realm and the vertical gradient of the ocean and by the development of original methodological tools that may be applied to a variety of environments.El océano profundo contiene el 70% de las células microbianas del océano las cuales suponen el 60% de la actividad heterotrófica. Dicha actividad biológica está mantenida por un flujo de partículas orgánicas producidas en el océano superficial y exportadas al océano batipelágico (1,000 - 4,000 m de profundidad). Éste no es, por tanto, un ambiente homogéneo, sino que contiene una variedad de partículas consideradas el aporte dominante de carbono orgánico. Los microorganismos de este ambiente tienen, por tanto, un papel regulatorio central en los ciclos biogeoquímicos planetarios. Consecuentemente, el estudio de estos microorganismos supone un paso esencial para descifrar el funcionamiento ecológico del océano profundo. Los Capítulos 1 a 3 de esta Tesis están dedicados a la descripción a nivel global de la composición de las comunidades de procariotas en el océano batipelágico mediante la secuenciación de fragmentos del ADN y ARN ribosomal. En el Capítulo 1 se identifican los procariotas dominantes en el océano profundo y se revela la existencia de una alta proporción (~50%) de procariotas previamente no descritos. Se reconocen además las masas de agua y la orografía del fondo oceánico, organizado en cuencas, como factores claves en su biogeografía. En el Capítulo 2 se estudian las diferencias entre las comunidades de procariotas de vida libre y aquellos adheridos a partículas. Este rasgo se demuestra estar conservado filogenéticamente, indicando que las partículas del batipelágico y el agua que las rodea constituyen dos nichos claramente diferenciados y que las transiciones entre uno y otro por parte de los procariotas han sido eventos poco frecuentes a escalas evolutivas. Finalmente se identifica en el Capítulo 3 una relación lineal entre el cociente de 16S ARN/ADN ribosomal y la preferencia a un modo de vida adherido a partículas, lo que sugiere una relación a nivel global entre la adherencia a partículas y su tasa de crecimiento. Mientras el océano profundo es un ambiente ampliamente inexplorado, existe un mayor conocimiento del océano superficial o epipelágico (0 - 200 m de profundidad). Gradientes intensos en la cantidad y calidad de la luz, temperatura y concentración de nutrientes caracterizan a los océanos e influyen en la distribución vertical de las especies. Sin embargo, diferentes procesos, tales como la deposición de partículas o los movimientos verticales de masas de agua, se han descrito como mecanismos capaces de conectar las capas superficiales y profundas del océano. Estos mismos procesos podrían teóricamente exportar comunidades enteras de microorganismos, un proceso teóricamente propuesto pero no evaluado hasta la fecha. En el Capítulo 4 se desarrolla una herramienta informática (mtagger) para la utilización de fragmentos del gen 16S ribosomal extraídos de metagenomas y su utilización para la descripción taxonómica de comunidades de procariotas. En este capítulo se proponen y evalúan mejoras respecto a versiones anteriormente utilizadas, como paso previo a su uso en el último capítulo. El Capítulo 5 está dedicado al desarrollo de un modelo matemático (disperflux) para la descripción de la conectividad vertical entre comunidades de procariotas. Se observa y describe una disminución abrupta de la similitud de las comunidades de procariotas con la profundidad. Esta relación se ajusta a una ecuación potencial que resulta consistente a lo largo de todo el océano, a excepción de 5 localizaciones, que se demuestran compatibles con eventos de exportación masiva de comunidades desde la superficie al océano profundo. En resumen, esta tesis ha contribuido significativamente al conocimiento del funcionamiento ecológico de los procariotas marinos mediante la descripción a nivel global de estas comunidades en el océano profundo y en el gradiente vertical así como mediante el desarrollo de herramientas metodológicas novedosas aplicables a una amplia variedad de entornosPostprint (published version

Large-scale biogeography of marine pelagic bacteria and archaea

The dark ocean contains about 70% of the ocean’s microbial cells and 60% of its heterotrophic activity, which is mainly fueled by the flux of organic particles produced in the surface ocean and exported to the bathypelagic ocean (1,000 – 4,000 m depth). The bathypelagic ocean represents a nonhomogeneous environment and contains a variety of particles that are considered as the main supply of organic carbon to this environment. The microorganisms inhabiting this realm play a pivotal regulatory role in the biogeochemical cycles at a planetary scale. Accordingly, the study of these microorganisms is an essential step to decipher the ecological functioning of the deep ocean. Chapters 1 to 3 in this Thesis are dedicated to the description of the prokaryotic community composition in the bathypelagic ocean at a global scale through the sequencing of ribosomal DNA and RNA fragments using data collected during the Malaspina 2010 expedition. Chapter 1 identifies the dominant prokaryotes in the deep ocean and reveals a high proportion (~50%) of previously undescribed prokaryotes. The water masses and the structure of the deep ocean’s floor, organized into basins, are identified as the main drivers of their biogeography. Chapter 2 addresses the differences between free-living and particle-attached bathypelagic prokaryotic communities. This is shown to be a phylogenetically conserved trait, indicating that the bathypelagic particles and the water surrounding them constitute two distinct niches and that transitions from one to the other have been rare at an evolutionary timescale. Finally, in Chapter 3 we identify a linear relationship between the 16S RNA/DNA ratio and particle attachment preference, suggesting a global relationship between the prokaryote’s preference for a particle-attached lifestyle and their growth rate. While the deep ocean is a highly unexplored environment, a more complete knowledge exists for the epipelagic ocean (0 – 200 m depth). Steep gradients of light intensity and quality, temperature and nutrient availability characterize the oceans and impact on the distribution of species. However, different processes, such as the sinking of particles and the vertical movement of water masses, have been described as mechanisms capable of connecting the surface and deep layers of the ocean. These same processes could transport entire prokaryotic communities, a process theoretically proposed but never tested. In Chapter 4 we develop a tool (mtagger) for the extraction of short 16S ribosomal reads from metagenomes to describe the taxonomical composition of microbial communities. We propose and evaluate technical improvements compared to previous versions as a benchmark for its use in the last chapter. Chapter 5 is dedicated to the development of a modeling tool (disperflux) for the analysis of prokaryotic communities’ connectivity using data collected during the Tara Oceans expedition. We observe and describe a fast-decay relationship between community similarity and depth, which is consistently fitted by a power-law across the whole dataset, with the exception of 5 stations that are compatible with events of whole community export from the photic ocean to the mesopelagic. In summary, this Thesis significantly contributes to the knowledge on the ecological functioning of marine prokaryotes by describing the structure of prokaryotic communities along the bathypelagic realm and the vertical gradient of the ocean and by the development of original methodological tools that may be applied to a variety of environments.El océano profundo contiene el 70% de las células microbianas del océano las cuales suponen el 60% de la actividad heterotrófica. Dicha actividad biológica está mantenida por un flujo de partículas orgánicas producidas en el océano superficial y exportadas al océano batipelágico (1,000 - 4,000 m de profundidad). Éste no es, por tanto, un ambiente homogéneo, sino que contiene una variedad de partículas consideradas el aporte dominante de carbono orgánico. Los microorganismos de este ambiente tienen, por tanto, un papel regulatorio central en los ciclos biogeoquímicos planetarios. Consecuentemente, el estudio de estos microorganismos supone un paso esencial para descifrar el funcionamiento ecológico del océano profundo. Los Capítulos 1 a 3 de esta Tesis están dedicados a la descripción a nivel global de la composición de las comunidades de procariotas en el océano batipelágico mediante la secuenciación de fragmentos del ADN y ARN ribosomal. En el Capítulo 1 se identifican los procariotas dominantes en el océano profundo y se revela la existencia de una alta proporción (~50%) de procariotas previamente no descritos. Se reconocen además las masas de agua y la orografía del fondo oceánico, organizado en cuencas, como factores claves en su biogeografía. En el Capítulo 2 se estudian las diferencias entre las comunidades de procariotas de vida libre y aquellos adheridos a partículas. Este rasgo se demuestra estar conservado filogenéticamente, indicando que las partículas del batipelágico y el agua que las rodea constituyen dos nichos claramente diferenciados y que las transiciones entre uno y otro por parte de los procariotas han sido eventos poco frecuentes a escalas evolutivas. Finalmente se identifica en el Capítulo 3 una relación lineal entre el cociente de 16S ARN/ADN ribosomal y la preferencia a un modo de vida adherido a partículas, lo que sugiere una relación a nivel global entre la adherencia a partículas y su tasa de crecimiento. Mientras el océano profundo es un ambiente ampliamente inexplorado, existe un mayor conocimiento del océano superficial o epipelágico (0 - 200 m de profundidad). Gradientes intensos en la cantidad y calidad de la luz, temperatura y concentración de nutrientes caracterizan a los océanos e influyen en la distribución vertical de las especies. Sin embargo, diferentes procesos, tales como la deposición de partículas o los movimientos verticales de masas de agua, se han descrito como mecanismos capaces de conectar las capas superficiales y profundas del océano. Estos mismos procesos podrían teóricamente exportar comunidades enteras de microorganismos, un proceso teóricamente propuesto pero no evaluado hasta la fecha. En el Capítulo 4 se desarrolla una herramienta informática (mtagger) para la utilización de fragmentos del gen 16S ribosomal extraídos de metagenomas y su utilización para la descripción taxonómica de comunidades de procariotas. En este capítulo se proponen y evalúan mejoras respecto a versiones anteriormente utilizadas, como paso previo a su uso en el último capítulo. El Capítulo 5 está dedicado al desarrollo de un modelo matemático (disperflux) para la descripción de la conectividad vertical entre comunidades de procariotas. Se observa y describe una disminución abrupta de la similitud de las comunidades de procariotas con la profundidad. Esta relación se ajusta a una ecuación potencial que resulta consistente a lo largo de todo el océano, a excepción de 5 localizaciones, que se demuestran compatibles con eventos de exportación masiva de comunidades desde la superficie al océano profundo. En resumen, esta tesis ha contribuido significativamente al conocimiento del funcionamiento ecológico de los procariotas marinos mediante la descripción a nivel global de estas comunidades en el océano profundo y en el gradiente vertical así como mediante el desarrollo de herramientas metodológicas novedosas aplicables a una amplia variedad de entorno

Extracellular Vesicles from Mesenchymal Stem Cells as Novel Treatments for Musculoskeletal Diseases

[EN] Mesenchymal stem/stromal cells (MSCs) represent a promising therapy for musculoskeletal diseases. There is compelling evidence indicating that MSC effects are mainly mediated by paracrine mechanisms and in particular by the secretion of extracellular vesicles (EVs). Many studies have thus suggested that EVs may be an alternative to cell therapy with MSCs in tissue repair. In this review, we summarize the current understanding of MSC EVs actions in preclinical studies of (1) immune regulation and rheumatoid arthritis, (2) bone repair and bone diseases, (3) cartilage repair and osteoarthritis, (4) intervertebral disk degeneration and (5) skeletal muscle and tendon repair. We also discuss the mechanisms underlying these actions and the perspectives of MSC EVs-based strategies for future treatments of musculoskeletal disorders.This work has been funded by grant SAF2017-85806-R (Ministerio de Ciencia, Innovación y Universidades, Spain, FEDER.Alcaraz Tormo, MJ.; Compañ, Á.; Guillem Salazar, MI. (2019). Extracellular Vesicles from Mesenchymal Stem Cells as Novel Treatments for Musculoskeletal Diseases. Cells. 9(1):1-21. https://doi.org/10.3390/cells9010098S12191Musculoskeletal Conditions https://www.who. int/news-room/fact-sheets/detail/musculoskeletal-conditionsHofer, H. R., & Tuan, R. S. (2016). Secreted trophic factors of mesenchymal stem cells support neurovascular and musculoskeletal therapies. Stem Cell Research & Therapy, 7(1). doi:10.1186/s13287-016-0394-0Wang, L., Wang, L., Cong, X., Liu, G., Zhou, J., Bai, B., … Liu, Y. (2013). Human Umbilical Cord Mesenchymal Stem Cell Therapy for Patients with Active Rheumatoid Arthritis: Safety and Efficacy. Stem Cells and Development, 22(24), 3192-3202. doi:10.1089/scd.2013.0023Franceschetti, T., & De Bari, C. (2017). The potential role of adult stem cells in the management of the rheumatic diseases. Therapeutic Advances in Musculoskeletal Disease, 9(7), 165-179. doi:10.1177/1759720x17704639Freitag, J., Bates, D., Boyd, R., Shah, K., Barnard, A., Huguenin, L., & Tenen, A. (2016). Mesenchymal stem cell therapy in the treatment of osteoarthritis: reparative pathways, safety and efficacy – a review. BMC Musculoskeletal Disorders, 17(1). doi:10.1186/s12891-016-1085-9Vega, A., Martín-Ferrero, M. A., Del Canto, F., Alberca, M., García, V., Munar, A., … García-Sancho, J. (2015). Treatment of Knee Osteoarthritis With Allogeneic Bone Marrow Mesenchymal Stem Cells. Transplantation, 99(8), 1681-1690. doi:10.1097/tp.0000000000000678Cui, G.-H., Wang, Y. Y., Li, C.-J., Shi, C.-H., & Wang, W.-S. (2016). Efficacy of mesenchymal stem cells in treating patients with osteoarthritis of the knee: A meta-analysis. Experimental and Therapeutic Medicine, 12(5), 3390-3400. doi:10.3892/etm.2016.3791Iaquinta, M. R., Mazzoni, E., Bononi, I., Rotondo, J. C., Mazziotta, C., Montesi, M., … Martini, F. (2019). Adult Stem Cells for Bone Regeneration and Repair. Frontiers in Cell and Developmental Biology, 7. doi:10.3389/fcell.2019.00268Marolt Presen, D., Traweger, A., Gimona, M., & Redl, H. (2019). Mesenchymal Stromal Cell-Based Bone Regeneration Therapies: From Cell Transplantation and Tissue Engineering to Therapeutic Secretomes and Extracellular Vesicles. Frontiers in Bioengineering and Biotechnology, 7. doi:10.3389/fbioe.2019.00352Jo, C. H., Chai, J. W., Jeong, E. C., Oh, S., & Yoon, K. S. (2020). Intratendinous Injection of Mesenchymal Stem Cells for the Treatment of Rotator Cuff Disease: A 2-Year Follow-Up Study. Arthroscopy: The Journal of Arthroscopic & Related Surgery, 36(4), 971-980. doi:10.1016/j.arthro.2019.11.120Klimczak, A., Kozlowska, U., & Kurpisz, M. (2018). Muscle Stem/Progenitor Cells and Mesenchymal Stem Cells of Bone Marrow Origin for Skeletal Muscle Regeneration in Muscular Dystrophies. Archivum Immunologiae et Therapiae Experimentalis, 66(5), 341-354. doi:10.1007/s00005-018-0509-7Ferreira, J. R., Teixeira, G. Q., Santos, S. G., Barbosa, M. A., Almeida-Porada, G., & Gonçalves, R. M. (2018). Mesenchymal Stromal Cell Secretome: Influencing Therapeutic Potential by Cellular Pre-conditioning. Frontiers in Immunology, 9. doi:10.3389/fimmu.2018.02837Aggarwal, S., & Pittenger, M. F. (2005). Human mesenchymal stem cells modulate allogeneic immune cell responses. Blood, 105(4), 1815-1822. doi:10.1182/blood-2004-04-1559Ren, G., Zhang, L., Zhao, X., Xu, G., Zhang, Y., Roberts, A. I., … Shi, Y. (2008). Mesenchymal Stem Cell-Mediated Immunosuppression Occurs via Concerted Action of Chemokines and Nitric Oxide. Cell Stem Cell, 2(2), 141-150. doi:10.1016/j.stem.2007.11.014Chabannes, D., Hill, M., Merieau, E., Rossignol, J., Brion, R., Soulillou, J. P., … Cuturi, M. C. (2007). A role for heme oxygenase-1 in the immunosuppressive effect of adult rat and human mesenchymal stem cells. Blood, 110(10), 3691-3694. doi:10.1182/blood-2007-02-075481Bernardo, M. E., & Fibbe, W. E. (2013). Mesenchymal Stromal Cells: Sensors and Switchers of Inflammation. Cell Stem Cell, 13(4), 392-402. doi:10.1016/j.stem.2013.09.006Selmani, Z., Naji, A., Zidi, I., Favier, B., Gaiffe, E., Obert, L., … Deschaseaux, F. (2008). Human Leukocyte Antigen-G5 Secretion by Human Mesenchymal Stem Cells Is Required to Suppress T Lymphocyte and Natural Killer Function and to Induce CD4+CD25highFOXP3+Regulatory T Cells. Stem Cells, 26(1), 212-222. doi:10.1634/stemcells.2007-0554Di Nicola, M., Carlo-Stella, C., Magni, M., Milanesi, M., Longoni, P. D., Matteucci, P., … Gianni, A. M. (2002). Human bone marrow stromal cells suppress T-lymphocyte proliferation induced by cellular or nonspecific mitogenic stimuli. Blood, 99(10), 3838-3843. doi:10.1182/blood.v99.10.3838Gunawardena, T. N. A., Rahman, M. T., Abdullah, B. J. J., & Abu Kasim, N. H. (2019). Conditioned media derived from mesenchymal stem cell cultures: The next generation for regenerative medicine. Journal of Tissue Engineering and Regenerative Medicine, 13(4), 569-586. doi:10.1002/term.2806Arslan, F., Lai, R. C., Smeets, M. B., Akeroyd, L., Choo, A., Aguor, E. N. E., … de Kleijn, D. P. (2013). Mesenchymal stem cell-derived exosomes increase ATP levels, decrease oxidative stress and activate PI3K/Akt pathway to enhance myocardial viability and prevent adverse remodeling after myocardial ischemia/reperfusion injury. Stem Cell Research, 10(3), 301-312. doi:10.1016/j.scr.2013.01.002Tian, T., Wang, Y., Wang, H., Zhu, Z., & Xiao, Z. (2010). Visualizing of the cellular uptake and intracellular trafficking of exosomes by live-cell microscopy. Journal of Cellular Biochemistry, 111(2), 488-496. doi:10.1002/jcb.22733Feng, D., Zhao, W.-L., Ye, Y.-Y., Bai, X.-C., Liu, R.-Q., Chang, L.-F., … Sui, S.-F. (2010). Cellular Internalization of Exosomes Occurs Through Phagocytosis. Traffic, 11(5), 675-687. doi:10.1111/j.1600-0854.2010.01041.xXu, J., Wang, Y., Hsu, C.-Y., Gao, Y., Meyers, C. A., Chang, L., … James, A. W. (2019). Human perivascular stem cell-derived extracellular vesicles mediate bone repair. eLife, 8. doi:10.7554/elife.48191Morrison, T. J., Jackson, M. V., Cunningham, E. K., Kissenpfennig, A., McAuley, D. F., O’Kane, C. M., & Krasnodembskaya, A. D. (2017). Mesenchymal Stromal Cells Modulate Macrophages in Clinically Relevant Lung Injury Models by Extracellular Vesicle Mitochondrial Transfer. American Journal of Respiratory and Critical Care Medicine, 196(10), 1275-1286. doi:10.1164/rccm.201701-0170ocLener, T., Gimona, M., Aigner, L., Börger, V., Buzas, E., Camussi, G., … Portillo, H. A. del. (2015). Applying extracellular vesicles based therapeutics in clinical trials – an ISEV position paper. Journal of Extracellular Vesicles, 4(1), 30087. doi:10.3402/jev.v4.30087Raposo, G., & Stoorvogel, W. (2013). Extracellular vesicles: Exosomes, microvesicles, and friends. Journal of Cell Biology, 200(4), 373-383. doi:10.1083/jcb.201211138Qiu, G., Zheng, G., Ge, M., Wang, J., Huang, R., Shu, Q., & Xu, J. (2018). Mesenchymal stem cell-derived extracellular vesicles affect disease outcomes via transfer of microRNAs. Stem Cell Research & Therapy, 9(1). doi:10.1186/s13287-018-1069-9Van Niel, G., D’Angelo, G., & Raposo, G. (2018). Shedding light on the cell biology of extracellular vesicles. Nature Reviews Molecular Cell Biology, 19(4), 213-228. doi:10.1038/nrm.2017.125Lai, R. C., Tan, S. S., Yeo, R. W. Y., Choo, A. B. H., Reiner, A. T., Su, Y., … Lim, S. K. (2016). MSC secretes at least 3 EV types each with a unique permutation of membrane lipid, protein and RNA. Journal of Extracellular Vesicles, 5(1), 29828. doi:10.3402/jev.v5.29828Théry, C., Witwer, K. W., Aikawa, E., Alcaraz, M. J., Anderson, J. D., Andriantsitohaina, R., … Atkin-Smith, G. K. (2018). Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines. Journal of Extracellular Vesicles, 7(1), 1535750. doi:10.1080/20013078.2018.1535750Tofiño-Vian, M., Guillén, M. I., & Alcaraz, M. J. (2018). Extracellular vesicles: A new therapeutic strategy for joint conditions. Biochemical Pharmacology, 153, 134-146. doi:10.1016/j.bcp.2018.02.004Wong, D. E., Banyard, D. A., Santos, P. J. F., Sayadi, L. R., Evans, G. R. D., & Widgerow, A. D. (2019). Adipose-derived stem cell extracellular vesicles: A systematic review✰. Journal of Plastic, Reconstructive & Aesthetic Surgery, 72(7), 1207-1218. doi:10.1016/j.bjps.2019.03.008Zhou, Y., Xu, H., Xu, W., Wang, B., Wu, H., Tao, Y., … Qian, H. (2013). Exosomes released by human umbilical cord mesenchymal stem cells protect against cisplatin-induced renal oxidative stress and apoptosis in vivo and in vitro. Stem Cell Research & Therapy, 4(2), 34. doi:10.1186/scrt194De Jong, O. G., Van Balkom, B. W. M., Schiffelers, R. M., Bouten, C. V. C., & Verhaar, M. C. (2014). Extracellular Vesicles: Potential Roles in Regenerative Medicine. Frontiers in Immunology, 5. doi:10.3389/fimmu.2014.00608Robbins, P. D., & Morelli, A. E. (2014). Regulation of immune responses by extracellular vesicles. Nature Reviews Immunology, 14(3), 195-208. doi:10.1038/nri3622Burrello, J., Monticone, S., Gai, C., Gomez, Y., Kholia, S., & Camussi, G. (2016). Stem Cell-Derived Extracellular Vesicles and Immune-Modulation. Frontiers in Cell and Developmental Biology, 4. doi:10.3389/fcell.2016.00083Siegel, G., Schäfer, R., & Dazzi, F. (2009). The Immunosuppressive Properties of Mesenchymal Stem Cells. Transplantation, 87(Supplement), S45-S49. doi:10.1097/tp.0b013e3181a285b0Fierabracci, A., Del Fattore, A., Luciano, R., Muraca, M., Teti, A., & Muraca, M. (2015). Recent Advances in Mesenchymal Stem Cell Immunomodulation: The Role of Microvesicles. Cell Transplantation, 24(2), 133-149. doi:10.3727/096368913x675728Mokarizadeh, A., Delirezh, N., Morshedi, A., Mosayebi, G., Farshid, A.-A., & Mardani, K. (2012). Microvesicles derived from mesenchymal stem cells: Potent organelles for induction of tolerogenic signaling. Immunology Letters, 147(1-2), 47-54. doi:10.1016/j.imlet.2012.06.001Conforti, A., Scarsella, M., Starc, N., Giorda, E., Biagini, S., Proia, A., … Bernardo, M. E. (2014). Microvescicles Derived from Mesenchymal Stromal Cells Are Not as Effective as Their Cellular Counterpart in the Ability to Modulate Immune Responses In Vitro. Stem Cells and Development, 23(21), 2591-2599. doi:10.1089/scd.2014.0091Carreras-Planella, L., Monguió-Tortajada, M., Borràs, F. E., & Franquesa, M. (2019). Immunomodulatory Effect of MSC on B Cells Is Independent of Secreted Extracellular Vesicles. Frontiers in Immunology, 10. doi:10.3389/fimmu.2019.01288Chen, W., Huang, Y., Han, J., Yu, L., Li, Y., Lu, Z., … Xiao, Y. (2016). Immunomodulatory effects of mesenchymal stromal cells-derived exosome. Immunologic Research, 64(4), 831-840. doi:10.1007/s12026-016-8798-6Harting, M. T., Srivastava, A. K., Zhaorigetu, S., Bair, H., Prabhakara, K. S., Toledano Furman, N. E., … Olson, S. D. (2017). Inflammation-Stimulated Mesenchymal Stromal Cell-Derived Extracellular Vesicles Attenuate Inflammation. STEM CELLS, 36(1), 79-90. doi:10.1002/stem.2730Reis, M., Mavin, E., Nicholson, L., Green, K., Dickinson, A. M., & Wang, X. (2018). Mesenchymal Stromal Cell-Derived Extracellular Vesicles Attenuate Dendritic Cell Maturation and Function. Frontiers in Immunology, 9. doi:10.3389/fimmu.2018.02538Ji, L., Bao, L., Gu, Z., Zhou, Q., Liang, Y., Zheng, Y., … Feng, X. (2019). Comparison of immunomodulatory properties of exosomes derived from bone marrow mesenchymal stem cells and dental pulp stem cells. Immunologic Research, 67(4-5), 432-442. doi:10.1007/s12026-019-09088-6Blazquez, R., Sanchez-Margallo, F. M., de la Rosa, O., Dalemans, W., Ã lvarez, V., Tarazona, R., & Casado, J. G. (2014). Immunomodulatory Potential of Human Adipose Mesenchymal Stem Cells Derived Exosomes on in vitro Stimulated T Cells. Frontiers in Immunology, 5. doi:10.3389/fimmu.2014.00556Zhang, B., Yin, Y., Lai, R. C., Tan, S. S., Choo, A. B. H., & Lim, S. K. (2014). Mesenchymal Stem Cells Secrete Immunologically Active Exosomes. Stem Cells and Development, 23(11), 1233-1244. doi:10.1089/scd.2013.0479Zhang, B., Yeo, R. W. Y., Lai, R. C., Sim, E. W. K., Chin, K. C., & Lim, S. K. (2018). Mesenchymal stromal cell exosome–enhanced regulatory T-cell production through an antigen-presenting cell–mediated pathway. Cytotherapy, 20(5), 687-696. doi:10.1016/j.jcyt.2018.02.372TOH, W. S., ZHANG, B., LAI, R. C., & LIM, S. K. (2018). Immune regulatory targets of mesenchymal stromal cell exosomes/small extracellular vesicles in tissue regeneration. Cytotherapy, 20(12), 1419-1426. doi:10.1016/j.jcyt.2018.09.008Budoni, M., Fierabracci, A., Luciano, R., Petrini, S., Di Ciommo, V., & Muraca, M. (2013). The Immunosuppressive Effect of Mesenchymal Stromal Cells on B Lymphocytes is Mediated by Membrane Vesicles. Cell Transplantation, 22(2), 369-379. doi:10.3727/096368911x582769bDi Trapani, M., Bassi, G., Midolo, M., Gatti, A., Takam Kamga, P., Cassaro, A., … Krampera, M. (2016). Differential and transferable modulatory effects of mesenchymal stromal cell-derived extracellular vesicles on T, B and NK cell functions. Scientific Reports, 6(1). doi:10.1038/srep24120Henao Agudelo, J. S., Braga, T. T., Amano, M. T., Cenedeze, M. A., Cavinato, R. A., Peixoto-Santos, A. R., … Camara, N. O. S. (2017). Mesenchymal Stromal Cell-Derived Microvesicles Regulate an Internal Pro-Inflammatory Program in Activated Macrophages. Frontiers in Immunology, 8. doi:10.3389/fimmu.2017.00881Lo Sicco, C., Reverberi, D., Balbi, C., Ulivi, V., Principi, E., Pascucci, L., … Tasso, R. (2017). Mesenchymal Stem Cell-Derived Extracellular Vesicles as Mediators of Anti-Inflammatory Effects: Endorsement of Macrophage Polarization. STEM CELLS Translational Medicine, 6(3), 1018-1028. doi:10.1002/sctm.16-0363Ti, D., Hao, H., Tong, C., Liu, J., Dong, L., Zheng, J., … Han, W. (2015). LPS-preconditioned mesenchymal stromal cells modify macrophage polarization for resolution of chronic inflammation via exosome-shuttled let-7b. Journal of Translational Medicine, 13(1). doi:10.1186/s12967-015-0642-6Firestein, G. S. (2003). Evolving concepts of rheumatoid arthritis. Nature, 423(6937), 356-361. doi:10.1038/nature01661Goronzy, J. J., & Weyand, C. M. (2009). Developments in the scientific understanding of rheumatoid arthritis. Arthritis Research & Therapy, 11(5), 249. doi:10.1186/ar2758Casado, J. G., Blázquez, R., Vela, F. J., Álvarez, V., Tarazona, R., & Sánchez-Margallo, F. M. (2017). Mesenchymal Stem Cell-Derived Exosomes: Immunomodulatory Evaluation in an Antigen-Induced Synovitis Porcine Model. Frontiers in Veterinary Science, 4. doi:10.3389/fvets.2017.00039Cosenza, S., Toupet, K., Maumus, M., Luz-Crawford, P., Blanc-Brude, O., Jorgensen, C., & Noël, D. (2018). Mesenchymal stem cells-derived exosomes are more immunosuppressive than microparticles in inflammatory arthritis. Theranostics, 8(5), 1399-1410. doi:10.7150/thno.21072Yang, Y., Hutchinson, P., & Morand, E. F. (1999). Inhibitory effect of annexin I on synovial inflammation in rat adjuvant arthritis. Arthritis & Rheumatism, 42(7), 1538-1544. doi:10.1002/1529-0131(199907)42:73.0.co;2-3Headland, S. E., Jones, H. R., Norling, L. V., Kim, A., Souza, P. R., Corsiero, E., … Perretti, M. (2015). Neutrophil-derived microvesicles enter cartilage and protect the joint in inflammatory arthritis. Science Translational Medicine, 7(315), 315ra190-315ra190. doi:10.1126/scitranslmed.aac5608Tofiño-Vian, M., Guillén, M. I., Pérez del Caz, M. D., Silvestre, A., & Alcaraz, M. J. (2018). Microvesicles from Human Adipose Tissue-Derived Mesenchymal Stem Cells as a New Protective Strategy in Osteoarthritic Chondrocytes. Cellular Physiology and Biochemistry, 47(1), 11-25. doi:10.1159/000489739Ando, Y., Matsubara, K., Ishikawa, J., Fujio, M., Shohara, R., Hibi, H., … Yamamoto, A. (2014). Stem cell-conditioned medium accelerates distraction osteogenesis through multiple regenerative mechanisms. Bone, 61, 82-90. doi:10.1016/j.bone.2013.12.029Lu, Z., Chen, Y., Dunstan, C., Roohani-Esfahani, S., & Zreiqat, H. (2017). Priming Adipose Stem Cells with Tumor Necrosis Factor-Alpha Preconditioning Potentiates Their Exosome Efficacy for Bone Regeneration. Tissue Engineering Part A, 23(21-22), 1212-1220. doi:10.1089/ten.tea.2016.0548Qin, Y., Wang, L., Gao, Z., Chen, G., & Zhang, C. (2016). Bone marrow stromal/stem cell-derived extracellular vesicles regulate osteoblast activity and differentiation in vitro and promote bone regeneration in vivo. Scientific Reports, 6(1). doi:10.1038/srep21961Wang, X., Omar, O., Vazirisani, F., Thomsen, P., & Ekström, K. (2018). Mesenchymal stem cell-derived exosomes have altered microRNA profiles and induce osteogenic differentiation depending on the stage of differentiation. PLOS ONE, 13(2), e0193059. doi:10.1371/journal.pone.0193059Shirley, D., Marsh, D., Jordan, G., McQuaid, S., & Li, G. (2005). Systemic recruitment of osteoblastic cells in fracture healing. Journal of Orthopaedic Research, 23(5), 1013-1021. doi:10.1016/j.orthres.2005.01.013Lee, D. Y., Cho, T.-J., Kim, J. A., Lee, H. R., Yoo, W. J., Chung, C. Y., & Choi, I. H. (2008). Mobilization of endothelial progenitor cells in fracture healing and distraction osteogenesis. Bone, 42(5), 932-941. doi:10.1016/j.bone.2008.01.007Furuta, T., Miyaki, S., Ishitobi, H., Ogura, T., Kato, Y., Kamei, N., … Ochi, M. (2016). Mesenchymal Stem Cell-Derived Exosomes Promote Fracture Healing in a Mouse Model. STEM CELLS Translational Medicine, 5(12), 1620-1630. doi:10.5966/sctm.2015-0285Li, W., Liu, Y., Zhang, P., Tang, Y., Zhou, M., Jiang, W., … Zhou, Y. (2018). Tissue-Engineered Bone Immobilized with Human Adipose Stem Cells-Derived Exosomes Promotes Bone Regeneration. ACS Applied Materials & Interfaces, 10(6), 5240-5254. doi:10.1021/acsami.7b17620Hirschi, K. K., Li, S., & Roy, K. (2014). Induced Pluripotent Stem Cells for Regenerative Medicine. Annual Review of Biomedical Engineering, 16(1), 277-294. doi:10.1146/annurev-bioeng-071813-105108Sabapathy, V., & Kumar, S. (2016). hi PSC ‐derived iMSC s: NextGen MSC s as an advanced therapeutically active cell resource for regenerative medicine. Journal of Cellular and Molecular Medicine, 20(8), 1571-1588. doi:10.1111/jcmm.12839Zhang, J., Liu, X., Li, H., Chen, C., Hu, B., Niu, X., … Wang, Y. (2016). Exosomes/tricalcium phosphate combination scaffolds can enhance bone regeneration by activating the PI3K/Akt signaling pathway. Stem Cell Research & Therapy, 7(1). doi:10.1186/s13287-016-0391-3Narayanan, R., Huang, C.-C., & Ravindran, S. (2016). Hijacking the Cellular Mail: Exosome Mediated Differentiation of Mesenchymal Stem Cells. Stem Cells International, 2016, 1-11. doi:10.1155/2016/3808674Zhu, Y., Jia, Y., Wang, Y., Xu, J., & Chai, Y. (2019). Impaired Bone Regenerative Effect of Exosomes Derived from Bone Marrow Mesenchymal Stem Cells in Type 1 Diabetes. STEM CELLS Translational Medicine, 8(6), 593-605. doi:10.1002/sctm.18-0199Ferreira, E., & Porter, R. M. (2018). Harnessing extracellular vesicles to direct endochondral repair of large bone defects. Bone & Joint Research, 7(4), 263-273. doi:10.1302/2046-3758.74.bjr-2018-0006Moya, A., Paquet, J., Deschepper, M., Larochette, N., Oudina, K., Denoeud, C., … Petite, H. (2018). Human Mesenchymal Stem Cell Failure to Adapt to Glucose Shortage and Rapidly Use Intracellular Energy Reserves Through Glycolysis Explains Poor Cell Survival After Implantation. STEM CELLS, 36(3), 363-376. doi:10.1002/stem.2763Moya, A., Larochette, N., Paquet, J., Deschepper, M., Bensidhoum, M., Izzo, V., … Logeart-Avramoglou, D. (2016). Quiescence Preconditioned Human Multipotent Stromal Cells Adopt a Metabolic Profile Favorable for Enhanced Survival under Ischemia. STEM CELLS, 35(1), 181-196. doi:10.1002/stem.2493Potier, E., Ferreira, E., Andriamanalijaona, R., Pujol, J.-P., Oudina, K., Logeart-Avramoglou, D., & Petite, H. (2007). Hypoxia affects mesenchymal stromal cell osteogenic differentiation and angiogenic factor expression. Bone, 40(4), 1078-1087. doi:10.1016/j.bone.2006.11.024Jia, Y., Zhu, Y., Qiu, S., Xu, J., & Chai, Y. (2019). Exosomes secreted by endothelial progenitor cells accelerate bone regeneration during distraction osteogenesis by stimulating angiogenesis. Stem Cell Research & Therapy, 10(1). doi:10.1186/s13287-018-1115-7Zhang, Y., Hao, Z., Wang, P., Xia, Y., Wu, J., Xia, D., … Xu, S. (2019). Exosomes from human umbilical cord mesenchymal stem cells enhance fracture healing through HIF‐1α‐mediated promotion of angiogenesis in a rat model of stabilized fracture. Cell Proliferation, 52(2), e12570. doi:10.1111/cpr.12570Qi, X., Zhang, J., Yuan, H., Xu, Z., Li, Q., Niu, X., … Li, X. (2016). Exosomes Secreted by Human-Induced Pluripotent Stem Cell-Derived Mesenchymal Stem Cells Repair Critical-Sized Bone De

Evolutionary trends in RNA base selectivity within the RNase A superfamily

Altres ajuts: Fundació La Marató de TV3 (Marató 20180310)There is a growing interest in the pharmaceutical industry to design novel tailored drugs for RNA targeting. The vertebrate-specific RNase A superfamily is nowadays one of the best characterized family of enzymes and comprises proteins involved in host defense with specific cytotoxic and immune-modulatory properties. We observe within the family a structural variability at the substrate-binding site associated to a diversification of biological properties. In this work, we have analyzed the enzyme specificity at the secondary base binding site. Towards this end, we have performed a kinetic characterization of the canonical RNase types together with a molecular dynamic simulation of selected representative family members. The RNases' catalytic activity and binding interactions have been compared using UpA, UpG and UpI dinucleotides. Our results highlight an evolutionary trend from lower to higher order vertebrates towards an enhanced discrimination power of selectivity for adenine respect to guanine at the secondary base binding site (B2). Interestingly, the shift from guanine to adenine preference is achieved in all the studied family members by equivalent residues through distinct interaction modes. We can identify specific polar and charged side chains that selectively interact with donor or acceptor purine groups. Overall, we observe selective bidentate polar and electrostatic interactions: Asn to N1/N6 and N6/N7 adenine groups in mammals versus Glu/Asp and Arg to N1/N2, N1/O6 and O6/N7 guanine groups in non-mammals. In addition, kinetic and molecular dynamics comparative results on UpG versus UpI emphasize the main contribution of Glu/Asp interactions to N1/N2 group for guanine selectivity in lower order vertebrates. A close inspection at the B2 binding pocket also highlights the principal contribution of the protein β6 and L4 loop regions. Significant differences in the orientation and extension of the L4 loop could explain how the same residues can participate in alternative binding modes. The analysis suggests that within the RNase A superfamily an evolution pressure has taken place at the B2 secondary binding site to provide novel substrate-recognition patterns. We are confident that a better knowledge of the enzymes' nucleotide recognition pattern would contribute to identify their physiological substrate and eventually design applied therapies to modulate their biological functions

Hypergravity induces changes in physiology, gene expression and epigenetics in zebrafish

All living organisms that inhabit Earth have evolved under a common value of gravity, which amounts to an acceleration of 9.81 m/s2 at mean sea level. Changes on it could cause important alterations that affect vital biological functions. The crescent interest in spatial exploration has opened the question of how exactly these changes in gravity would affect Earth life forms on space environments. This work is the result of a collaborative co-supervision of a master thesis between experts in the area of space sciences and biology, and it can serve as a case study for training experts in such interdisciplinary environments. In particular, we focus on the effect of gravity as a pressure factor in the development of zebrafish (Danio rerio) in the larval stage as a model organism using up-to-date (genomic and epigenetic) techniques. Given the high cost of any experiment in true low gravity (which would require a space launch), we performed an initial experiment in hypergravity to develop the methodologies and identify good (epi)genetic markers of the effect of gravity in our model organism. Previous studies in zebrafish have shown how alteration in gravity effects the development and the gene expression of important regulatory genes. For this study, we firstly customized a small laboratory scale centrifuge to study changes in fish physiology together with changes at molecular levels. We exposed zebrafish larvae from 0 to 6 days post fertilization to the simulated hypergravity (SHG) (100 rpm 3g). After 6 days of hypergravity exposition the larvae showed changes in their swimming and flotation patterns, and presented corporal alterations. Then, we assessed gene expression of genes implicated in important biological processes, (e.g., epigenetics), and an upregulation were observed when compared to the control. Taken together, these preliminary findings show how gravity alterations could affect some basic biological responses, and illustrate the potential of developing new science cases to be developed by students at postgraduate level (MSc and beyond) in a multidisciplinary environmen

Dataciones radiocarbónicas de la Cova de la Sarsa (Bocairent, València)

La revisión de los materiales arqueológicos recuperados en la Cova de la Sarsa nos ha llevado a establecer una serie de propuestas sobre sus diferentes ocupaciones y su funcionalidad. En relación con estos estudios se han seleccionado una serie de muestras para su datación por radiocarbono. Presentamos los resultados de dichas dataciones. La revisió dels materials arqueològics recuperats en la Cova de la Sarsa ens ha portat a establir una série de propostes sobre les seues diferents ocupacions i la seua funcionalitat. En relació amb aquests estudis s"han seleccionat una série de mostres per a la seua datació per radiocarbon. Presentem els resultats de les dites datacions. The revision of the archaeological materials recovered from Cova de la Sarsa has enabled us to put forward several proposals regarding the site"s occupation and functionality. In order to better assess these materials, eight bone samples have been chosen for radiocarbon dating. In this paper we present and discuss these results

Dataciones radiocarbónicas de la Cova de la Sarsa (Bocairent, València)

La revisión de los materiales arqueológicos recuperados en la Cova de la Sarsa nos ha llevado a establecer una serie de propuestas sobre sus diferente

Epigenetic and physiological alterations in zebrafish subjected to hypergravity [Dataset]

1 dataset, 16 videosVideos exhibiting every morphological characteristic observed in both the control and hypergravity groups of zebrafish larvaWith the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Characteristic, Abbreviation, Number of the video file control group, Number of the video file hypergravity group / Position, Movement frequency, Swimming behaviorPeer reviewe

Large-scale ocean connectivity and planktonic body size

Villarino, Ernesto ... et al.-- 13 pages, 5 figures, 5 tables, supplementary material https://dx.doi.org/10.1038/s41467-017-02535-8Global patterns of planktonic diversity are mainly determined by the dispersal of propagules with ocean currents. However, the role that abundance and body size play in determining spatial patterns of diversity remains unclear. Here we analyse spatial community structure - β-diversity - for several planktonic and nektonic organisms from prokaryotes to small mesopelagic fishes collected during the Malaspina 2010 Expedition. β-diversity was compared to surface ocean transit times derived from a global circulation model, revealing a significant negative relationship that is stronger than environmental differences. Estimated dispersal scales for different groups show a negative correlation with body size, where less abundant large-bodied communities have significantly shorter dispersal scales and larger species spatial turnover rates than more abundant small-bodied plankton. Our results confirm that the dispersal scale of planktonic and micro-nektonic organisms is determined by local abundance, which scales with body size, ultimately setting global spatial patterns of diversityThis research was funded by the project Malaspina 2010 Circumnavigation Expedition (Consolider-Ingenio 2010, CSD2008-00077) and cofounded by the Basque Government (Department Deputy of Agriculture, Fishing and Food Policy). [...] E.V. was supported by a PhD Scholarship granted by the Iñaki Goenaga−Technology Centres FoundationPeer Reviewe

Standardizing admission and discharge processes to improve patient flow: A cross sectional study

Abstract Background: The aim of this study was to evaluate how hospital capacity was managed focusing on standardizing the admission and discharge processes