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  • 1
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    PLETHORA gradient formation mechanism separates auxin responses (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-08-27
    Description: During plant growth, dividing cells in meristems must coordinate transitions from division to expansion and differentiation, thus generating three distinct developmental zones: the meristem, elongation zone and differentiation zone. Simultaneously, plants display tropisms, rapid adjustments of their direction of growth to adapt to environmental conditions. It is unclear how stable zonation is maintained during transient adjustments in growth direction. In Arabidopsis roots, many aspects of zonation are controlled by the phytohormone auxin and auxin-induced PLETHORA (PLT) transcription factors, both of which display a graded distribution with a maximum near the root tip. In addition, auxin is also pivotal for tropic responses. Here, using an iterative experimental and computational approach, we show how an interplay between auxin and PLTs controls zonation and gravitropism. We find that the PLT gradient is not a direct, proportionate readout of the auxin gradient. Rather, prolonged high auxin levels generate a narrow PLT transcription domain from which a gradient of PLT protein is subsequently generated through slow growth dilution and cell-to-cell movement. The resulting PLT levels define the location of developmental zones. In addition to slowly promoting PLT transcription, auxin also rapidly influences division, expansion and differentiation rates. We demonstrate how this specific regulatory design in which auxin cooperates with PLTs through different mechanisms and on different timescales enables both the fast tropic environmental responses and stable zonation dynamics necessary for coordinated cell differentiation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4326657/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4326657/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mahonen, Ari Pekka -- ten Tusscher, Kirsten -- Siligato, Riccardo -- Smetana, Ondrej -- Diaz-Trivino, Sara -- Salojarvi, Jarkko -- Wachsman, Guy -- Prasad, Kalika -- Heidstra, Renze -- Scheres, Ben -- 232914/European Research Council/International -- England -- Nature. 2014 Nov 6;515(7525):125-9. doi: 10.1038/nature13663. Epub 2014 Aug 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland [2] Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, the Netherlands [3] Department of Biosciences, University of Helsinki, Helsinki 00014, Finland [4]. ; 1] Theoretical Biology and Bioinformatics, Utrecht University, Utrecht 3584 CH, the Netherlands [2]. ; 1] Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland [2] Department of Biosciences, University of Helsinki, Helsinki 00014, Finland. ; 1] Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, the Netherlands [2] Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, the Netherlands. ; Department of Biosciences, University of Helsinki, Helsinki 00014, Finland. ; Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, the Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25156253" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/cytology/*growth & development/*metabolism ; Arabidopsis Proteins/*metabolism ; Cell Differentiation ; Cell Movement ; Gene Expression Regulation, Plant ; Gravitropism ; Indoleacetic Acids/*metabolism ; Meristem/growth & development/metabolism ; Mitosis ; Plant Roots/cytology/growth & development/metabolism ; Transcription Factors/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Durable coexistence of donor and recipient strains after fecal microbiota transplantation (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-04-30
    Description: Fecal microbiota transplantation (FMT) has shown efficacy in treating recurrent Clostridium difficile infection and is increasingly being applied to other gastrointestinal disorders, yet the fate of native and introduced microbial strains remains largely unknown. To quantify the extent of donor microbiota colonization, we monitored strain populations in fecal samples from a recent FMT study on metabolic syndrome patients using single-nucleotide variants in metagenomes. We found extensive coexistence of donor and recipient strains, persisting 3 months after treatment. Colonization success was greater for conspecific strains than for new species, the latter falling within fluctuation levels observed in healthy individuals over a similar time frame. Furthermore, same-donor recipients displayed varying degrees of microbiota transfer, indicating individual patterns of microbiome resistance and donor-recipient compatibilities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Simone S -- Zhu, Ana -- Benes, Vladimir -- Costea, Paul I -- Hercog, Rajna -- Hildebrand, Falk -- Huerta-Cepas, Jaime -- Nieuwdorp, Max -- Salojarvi, Jarkko -- Voigt, Anita Y -- Zeller, Georg -- Sunagawa, Shinichi -- de Vos, Willem M -- Bork, Peer -- New York, N.Y. -- Science. 2016 Apr 29;352(6285):586-9. doi: 10.1126/science.aad8852.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052 Sydney, Australia. ; Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. ; Genomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. ; Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, Netherlands. Diabetes Center, Vrije University Medical Center, 1018 HV Amsterdam, Netherlands. Wallenberg Laboratory, University of Gothenburg, 41345 Gothenburg, Sweden. ; Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland. Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland. ; Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany. Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany. ; Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. bork@embl.de willem.devos@wur.nl sunagawa@embl.de. ; Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland. Laboratory of Microbiology, Wageningen University, 6703 HB Wageningen, Netherlands. Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, 00014 Helsinki, Finland. bork@embl.de willem.devos@wur.nl sunagawa@embl.de. ; Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany. Max Delbruck Centre for Molecular Medicine, 13125 Berlin, Germany. Department of Bioinformatics, Biocenter, University of Wurzburg, 97074 Wurzburg, Germany. bork@embl.de willem.devos@wur.nl sunagawa@embl.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27126044" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/classification/isolation & purification ; Clostridium Infections/microbiology/*therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Symbiosis ; Tissue Donors ; Transplantation, Homologous
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Targeted retrieval of gene expression measurements using regulatory models (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-08
    Description: Motivation : Large public repositories of gene expression measurements offer the opportunity to position a new experiment into the context of earlier studies. While previous methods rely on experimental annotation or global similarity of expression profiles across genes or gene sets, we compare experiments by measuring similarity based on an unsupervised, data-driven regulatory model around pre-specified genes of interest. Our experiment retrieval approach is novel in two conceptual respects: (i) targetable focus and interpretability: the analysis is targeted at regulatory relationships of genes that are relevant to the analyst or come from prior knowledge; (ii) regulatory model-based similarity measure: related experiments are retrieved based on the strength of inferred regulatory links between genes. Results: We learn a model for the regulation of specific genes from a data repository and exploit it to construct a similarity metric for an information retrieval task. We use the Fisher kernel, a rigorous similarity measure that typically has been applied to use generative models in discriminative classifiers. Results on human and plant microarray collections indicate that our method is able to substantially improve the retrieval of related experiments against standard methods. Furthermore, it allows the user to interpret biological conditions in terms of changes in link activity patterns. Our study of the osmotic stress network for Arabidopsis thaliana shows that the method successfully identifies relevant relationships around given key genes. Availability: The code (R) is available at http://research.ics.tkk.fi/mi/software.shtml . Contact : elisabeth.georgii@aalto.fi ; jarkko.salojarvi@helsinki.fi ; samuel.kaski@hiit.fi Supplementary Information : Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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