Clase 1 abril (Valeria Souza)
genomica evolutiva 1
20 de marzo: Defining the core Arabidopsis thaliana root microbiome
Lundberg, D. S., Lebeis, S. L., Paredes, S. H., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., et al. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488(7409), 86–90. doi:10.1038/nature11237 Land plants associate with a rootmicrobiota distinct from the com- plexmicrobial community present in surrounding soil. The micro- biota colonizingtherhizosphere (immediately surroundingthe root) and…
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20 de marzo: The oral metagenome in health and disease
Belda-Ferre, P., Alcaraz, L. D., Cabrera-Rubio, R., Romero, H., Simón-Soro, A., Pignatelli, M., & Mira, A. (2011). The oral metagenome in health and disease. The ISME journal, 1(11), 46–56. doi:10.1038/ismej.2011.85 The oral cavity of humans is inhabited by hundreds of bacterial species and some of them have a key role in the development of oral…
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20 de marzo: A framework for human microbiome research.
Human, T., & Project, M. (2012). A framework for human microbiome research. Nature, 486(7402), 215–21. doi:10.1038/nature11209 A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to…
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20 de marzo: Temporal dynamics of the human vaginal microbiota
Gajer, P., Brotman, R. M., Bai, G., Sakamoto, J., Schütte, U. M. E., Zhong, X., Koenig, S. S. K., et al. (2012). Temporal dynamics of the human vaginal microbiota. Science translational medicine, 4(132), 132ra52. doi:10.1126/scitranslmed.3003605 Elucidating the factors that impinge on the stability of bacterial communities in the vagina may help in predicting the risk…
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11 de marzo: The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0050077 Abstract: The world’s oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected…
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27 de febrero: Reference databases for taxonomic assignment in metagenomics.
Santamaria, M., Fosso, B., Consiglio, A., De Caro, G., Grillo, G., Licciulli, F., Liuni, S., et al. (2012). Reference databases for taxonomic assignment in metagenomics. Briefings in bioinformatics, 13(6), 682–695. doi:10.1093/bib/bbs036 Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus…
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27 de febrero, ejemplo de microbioma: Microbiome of the upper troposphere Species composition and prevalence effects of tropical storms and atmospheric implications.
DeLeon-Rodriguez, N., Lathem, T. L., Rodriguez-r, L. M., Barazesh, J. M., Anderson, B. E., Beyersdorf, A. J., Ziemba, L. D., et al. (2013). Microbiome of the upper troposphere Species composition and prevalence effects of tropical storms and atmospheric implications. PNAS, 1212089110–. doi:10.1073/pnas.1212089110 The composition and prevalence of microorganisms in the middle-to-upper troposphere (8-15 km altitude)…
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27 de febrero: Genoma de ejemplo: Bacterial growth at −15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1
Mykytczuk, N. C., Foote, S. J., Omelon, C. R., Southam, G., Greer, C. W., & Whyte, L. G. (2013). Bacterial growth at −15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1. The ISME Journal, 1–16. doi:10.1038/ismej.2013.8 Planococcus halocryophilus strain Or1, isolated from high Arctic permafrost, grows and divides at ~15 °C, the lowest…
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25 de febrero: The metagenomics RAST server
Meyer, F., Paarmann, D., D’Souza, M., Olson, R., Glass, E. M., Kubal, M., Paczian, T., et al. (2008).The metagenomics RAST server a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC bioinformatics, 9, 386. doi:10.1186/1471-2105-9-386 BACKGROUND: Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the…
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25 de febrero: Current opportunities and challenges in microbial metagenome analysis–a bioinformatic perspective
Teeling, H., & Glöckner, F. O. (2012). Current opportunities and challenges in microbial metagenome analysis–a bioinformatic perspective. Briefings in bioinformatics, 13(6), 728–742. doi:10.1093/bib/bbs039 Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable. Continual progress in next-generation sequencing allows for generating increasingly large…
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25 de febrero: Bioinformatic approaches for functional annotation and pathway inference in metagenomics
De Filippo, C., Ramazzotti, M., Fontana, P., & Cavalieri, D. (2012). Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. Briefings in Bioinformatics, 13(6), 696–710. doi:10.1093/bib/bbs070 Metagenomic approaches are increasingly recognized as a baseline for understanding the ecology and evolution of microbial ecosystems.The development ofmethods for pathway inference frommetagenomics data is of paramount…
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20 de Febrero: High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity.
Loman, N. J., Constantinidou, C., Chan, J. Z. M., Halachev, M., Sergeant, M., Penn, C. W., Robinson, E. R., et al. (2012). High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nature reviews. Microbiology, 10(9), 599–606. doi:10.1038/nrmicro2850 Here, we take a snapshot of the high-throughput sequencing platforms, together with the relevant analytical…
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