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  • 1
    Publication Date: 2016-03-26
    Description: : Breast cancer is one of the most frequent cancers among women. Extensive studies into the molecular heterogeneity of breast cancer have produced a plethora of molecular subtype classification and prognosis prediction algorithms, as well as numerous gene expression signatures. However, reimplementation of these algorithms is a tedious but important task to enable comparison of existing signatures and classification models between each other and with new models. Here, we present the genefu R/Bioconductor package, a multi-tiered compendium of bioinformatics algorithms and gene signatures for molecular subtyping and prognostication in breast cancer. Availability and implementation: The genefu package is available from Bioconductor. http://www.bioconductor.org/packages/devel/bioc/html/genefu.html . Source code is also available on Github https://github.com/bhklab/genefu . Contact: bhaibeka@uhnresearch.ca Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    Publication Date: 2008-01-25
    Description: Cell elongation during seedling development is antagonistically regulated by light and gibberellins (GAs). Light induces photomorphogenesis, leading to inhibition of hypocotyl growth, whereas GAs promote etiolated growth, characterized by increased hypocotyl elongation. The mechanism underlying this antagonistic interaction remains unclear. Here we report on the central role of the Arabidopsis thaliana nuclear transcription factor PIF4 (encoded by PHYTOCHROME INTERACTING FACTOR 4) in the positive control of genes mediating cell elongation and show that this factor is negatively regulated by the light photoreceptor phyB (ref. 4) and by DELLA proteins that have a key repressor function in GA signalling. Our results demonstrate that PIF4 is destabilized by phyB in the light and that DELLAs block PIF4 transcriptional activity by binding the DNA-recognition domain of this factor. We show that GAs abrogate such repression by promoting DELLA destabilization, and therefore cause a concomitant accumulation of free PIF4 in the nucleus. Consistent with this model, intermediate hypocotyl lengths were observed in transgenic plants over-accumulating both DELLAs and PIF4. Destabilization of this factor by phyB, together with its inactivation by DELLAs, constitutes a protein interaction framework that explains how plants integrate both light and GA signals to optimize growth and development in response to changing environments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de Lucas, Miguel -- Daviere, Jean-Michel -- Rodriguez-Falcon, Mariana -- Pontin, Mariela -- Iglesias-Pedraz, Juan Manuel -- Lorrain, Severine -- Fankhauser, Christian -- Blazquez, Miguel Angel -- Titarenko, Elena -- Prat, Salome -- England -- Nature. 2008 Jan 24;451(7177):480-4. doi: 10.1038/nature06520.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnologia-CSIC, Campus Univ. Autonoma de Madrid, Cantoblanco. c/ Darwin 3, 28049 Madrid, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18216857" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/cytology/*drug effects/metabolism/*radiation effects ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Basic Helix-Loop-Helix Transcription Factors/chemistry/genetics/metabolism ; Cell Shape/*drug effects/*radiation effects ; Cell Size/drug effects/radiation effects ; DNA, Plant/metabolism ; Gibberellins/*pharmacology ; Hypocotyl/genetics/growth & development/metabolism ; *Light ; Nuclear Proteins/chemistry/genetics/metabolism ; Phytochrome B/genetics/metabolism ; Plant Leaves/metabolism ; Protein Binding ; Seedlings/metabolism ; Signal Transduction/drug effects ; Tobacco/metabolism ; Triazoles/pharmacology ; Two-Hybrid System Techniques
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2011-09-29
    Description: Seasonal fluctuations in day length regulate important aspects of plant development such as the flowering transition or, in potato (Solanum tuberosum), the formation of tubers. Day length is sensed by the leaves, which produce a mobile signal transported to the shoot apex or underground stems to induce a flowering transition or, respectively, a tuberization transition. Work in Arabidopsis, tomato and rice (Oryza sativa) identified the mobile FLOWERING LOCUS T (FT) protein as a main component of the long-range 'florigen', or flowering hormone, signal. Here we show that expression of the Hd3a gene, the FT orthologue in rice, induces strict short-day potato types to tuberize in long days. Tuber induction is graft transmissible and the Hd3a-GFP protein is detected in the stolons of grafted plants, transport of the fusion protein thus correlating with tuber formation. We provide evidence showing that the potato floral and tuberization transitions are controlled by two different FT-like paralogues (StSP3D and StSP6A) that respond to independent environmental cues, and show that an autorelay mechanism involving CONSTANS modulates expression of the tuberization-control StSP6A gene.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Navarro, Cristina -- Abelenda, Jose A -- Cruz-Oro, Eduard -- Cuellar, Carlos A -- Tamaki, Shojiro -- Silva, Javier -- Shimamoto, Ko -- Prat, Salome -- England -- Nature. 2011 Sep 25;478(7367):119-22. doi: 10.1038/nature10431.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Madrid, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21947007" target="_blank"〉PubMed〈/a〉
    Keywords: Environment ; Flowers/genetics/growth & development/*physiology/radiation effects ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Light ; Phenotype ; Plant Leaves/metabolism/radiation effects ; Plant Proteins/genetics/*metabolism ; Plant Tubers/genetics/*growth & development/metabolism/radiation effects ; Plants, Genetically Modified ; Recombinant Fusion Proteins/genetics/metabolism ; Seasons ; Solanum tuberosum/*anatomy & histology/genetics/growth & development/*physiology ; Time Factors ; Transcription Factors/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2013-03-08
    Description: Potato (Solanum tuberosum L.) originates from the Andes and evolved short-day-dependent tuber formation as a vegetative propagation strategy. Here we describe the identification of a central regulator underlying a major-effect quantitative trait locus for plant maturity and initiation of tuber development. We show that this gene belongs to the family of DOF (DNA-binding with one finger) transcription factors and regulates tuberization and plant life cycle length, by acting as a mediator between the circadian clock and the StSP6A mobile tuberization signal. We also show that natural allelic variants evade post-translational light regulation, allowing cultivation outside the geographical centre of origin of potato. Potato is a member of the Solanaceae family and is one of the world's most important food crops. This annual plant originates from the Andean regions of South America. Potato develops tubers from underground stems called stolons. Its equatorial origin makes potato essentially short-day dependent for tuberization and potato will not make tubers in the long-day conditions of spring and summer in the northern latitudes. When introduced in temperate zones, wild material will form tubers in the course of the autumnal shortening of day-length. Thus, one of the first selected traits in potato leading to a European potato type is likely to have been long-day acclimation for tuberization. Potato breeders can exploit the naturally occurring variation in tuberization onset and life cycle length, allowing varietal breeding for different latitudes, harvest times and markets.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kloosterman, Bjorn -- Abelenda, Jose A -- Gomez, Maria del Mar Carretero -- Oortwijn, Marian -- de Boer, Jan M -- Kowitwanich, Krissana -- Horvath, Beatrix M -- van Eck, Herman J -- Smaczniak, Cezary -- Prat, Salome -- Visser, Richard G F -- Bachem, Christian W B -- England -- Nature. 2013 Mar 14;495(7440):246-50. doi: 10.1038/nature11912. Epub 2013 Mar 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, PO Box 386, 6700 AJ Wageningen, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23467094" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization ; *Agriculture ; *Alleles ; Arabidopsis ; Chromosomes, Plant/genetics ; Circadian Clocks/physiology/radiation effects ; Crops, Agricultural/genetics/growth & development/radiation effects ; Europe ; Flowers/genetics/growth & development ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genetic Variation/*genetics ; Light ; Molecular Sequence Data ; Plant Leaves/metabolism/radiation effects ; Plant Proteins/genetics/metabolism ; Plant Tubers/genetics/growth & development/radiation effects ; Solanum tuberosum/*genetics/*growth & development/radiation effects ; South America ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2015-05-23
    Description: Human evolutionary scholars have long supposed that the earliest stone tools were made by the genus Homo and that this technological development was directly linked to climate change and the spread of savannah grasslands. New fieldwork in West Turkana, Kenya, has identified evidence of much earlier hominin technological behaviour. We report the discovery of Lomekwi 3, a 3.3-million-year-old archaeological site where in situ stone artefacts occur in spatiotemporal association with Pliocene hominin fossils in a wooded palaeoenvironment. The Lomekwi 3 knappers, with a developing understanding of stone's fracture properties, combined core reduction with battering activities. Given the implications of the Lomekwi 3 assemblage for models aiming to converge environmental change, hominin evolution and technological origins, we propose for it the name 'Lomekwian', which predates the Oldowan by 700,000 years and marks a new beginning to the known archaeological record.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harmand, Sonia -- Lewis, Jason E -- Feibel, Craig S -- Lepre, Christopher J -- Prat, Sandrine -- Lenoble, Arnaud -- Boes, Xavier -- Quinn, Rhonda L -- Brenet, Michel -- Arroyo, Adrian -- Taylor, Nicholas -- Clement, Sophie -- Daver, Guillaume -- Brugal, Jean-Philip -- Leakey, Louise -- Mortlock, Richard A -- Wright, James D -- Lokorodi, Sammy -- Kirwa, Christopher -- Kent, Dennis V -- Roche, Helene -- England -- Nature. 2015 May 21;521(7552):310-5. doi: 10.1038/nature14464.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Turkana Basin Institute, Stony Brook University, Stony Brook, New York 11794-4364, USA [2] CNRS, UMR 7055, Prehistoire et Technologie, Universite Paris Ouest Nanterre La Defense, 21 allee de l'Universite, 92023 Nanterre Cedex, France [3] West Turkana Archaeological Project, P.O. Box 40658-00100, Ngara Rd, Nairobi, Kenya. ; 1] Turkana Basin Institute, Stony Brook University, Stony Brook, New York 11794-4364, USA [2] West Turkana Archaeological Project, P.O. Box 40658-00100, Ngara Rd, Nairobi, Kenya [3] Department of Anthropology and Center for Human Evolutionary Studies, Rutgers University, New Brunswick, New Jersey 08901, USA. ; 1] West Turkana Archaeological Project, P.O. Box 40658-00100, Ngara Rd, Nairobi, Kenya [2] Department of Anthropology and Center for Human Evolutionary Studies, Rutgers University, New Brunswick, New Jersey 08901, USA [3] Department of Earth and Planetary Sciences, Rutgers University, Piscataway, New Jersey 08854, USA. ; 1] West Turkana Archaeological Project, P.O. Box 40658-00100, Ngara Rd, Nairobi, Kenya [2] Department of Earth and Planetary Sciences, Rutgers University, Piscataway, New Jersey 08854, USA [3] Lamont-Doherty Earth Observatory of Columbia University, Palisades, New York 10964, USA. ; 1] West Turkana Archaeological Project, P.O. Box 40658-00100, Ngara Rd, Nairobi, Kenya [2] CNRS, UPR 2147, Dynamique de l'Evolution Humaine, 44 rue de l'Amiral Mouchez, 75014 Paris, France. ; 1] West Turkana Archaeological Project, P.O. Box 40658-00100, Ngara Rd, Nairobi, Kenya [2] CNRS, UMR 5199 PACEA, Universite de Bordeaux, 33615 Pessac, France. ; 1] West Turkana Archaeological Project, P.O. Box 40658-00100, Ngara Rd, Nairobi, Kenya [2] Department of Earth and Planetary Sciences, Rutgers University, Piscataway, New Jersey 08854, USA [3] Department of Sociology, Anthropology and Social Work, Seton Hall University, South Orange, New Jersey 07079, USA. ; 1] CNRS, UMR 5199 PACEA, Universite de Bordeaux, 33615 Pessac, France [2] Inrap, Centre Mixte de Recherche Archeologique, Domaine de Campagne, 24620 Campagne, France. ; CNRS, UMR 7055, Prehistoire et Technologie, Universite Paris Ouest Nanterre La Defense, 21 allee de l'Universite, 92023 Nanterre Cedex, France. ; 1] CNRS, UMR 7055, Prehistoire et Technologie, Universite Paris Ouest Nanterre La Defense, 21 allee de l'Universite, 92023 Nanterre Cedex, France [2] West Turkana Archaeological Project, P.O. Box 40658-00100, Ngara Rd, Nairobi, Kenya. ; 1] West Turkana Archaeological Project, P.O. Box 40658-00100, Ngara Rd, Nairobi, Kenya [2] Inrap, 34-36 avenue Paul-Vaillant Couturier, 93120 La Courneuve, France. ; IPHEP, Institut de Paleoprimatologie, Paleontologie Humaine: Evolution et Paleoenvironnements, CNRS, UMR 7262, Universite de Poitiers, Bat. B35 - TSA 51106, 6 rue Michel Brunet, 86073 Poitiers Cedex 9, France. ; 1] West Turkana Archaeological Project, P.O. Box 40658-00100, Ngara Rd, Nairobi, Kenya [2] Aix-Marseille Universite, CNRS, MCC, UMR 7269, LAMPEA, 13094 Aix-en-Provence Cedex 2, France. ; Turkana Basin Institute, Stony Brook University, Stony Brook, New York 11794-4364, USA. ; Department of Earth and Planetary Sciences, Rutgers University, Piscataway, New Jersey 08854, USA. ; West Turkana Archaeological Project, P.O. Box 40658-00100, Ngara Rd, Nairobi, Kenya. ; 1] West Turkana Archaeological Project, P.O. Box 40658-00100, Ngara Rd, Nairobi, Kenya [2] National Museums of Kenya, Department of Earth Sciences, Archaeology Section, P.O. Box 40658-00100 Ngara Rd, Nairobi, Kenya. ; 1] Department of Earth and Planetary Sciences, Rutgers University, Piscataway, New Jersey 08854, USA [2] Lamont-Doherty Earth Observatory of Columbia University, Palisades, New York 10964, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25993961" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Archaeology ; Biological Evolution ; Environment ; Fossils ; History, Ancient ; *Hominidae ; Kenya ; Paleontology ; Technology/history ; Time Factors ; *Tool Use Behavior
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2015-11-06
    Description: Juvenile granulosa cell tumors (JGCTs) of the ovary are pediatric neoplasms representing 5% of all granulosa cell tumors (GCTs). Most GCTs are of adult type (AGCTs) and bear a mutation in the FOXL2 gene. The molecular basis of JGCTs is poorly understood, although mutations in the GNAS gene have been reported. We have detected in-frame duplications within the oncogene AKT1 in 〉60% of the JGCTs studied. Here, to evaluate the functional impact of these duplications and the existence of potential co-driver alterations, we have sequenced the transcriptome of four JGCTs and compared them with control transcriptomes. A search for gene variants detected only private alterations probably unrelated with tumorigenesis, suggesting that tandem duplications are the best candidates to underlie tumor formation in the absence of GNAS alterations. We previously showed that the duplications were specific to JGCTs. However, the screening of eight AGCTs samples without FOXL2 mutation showed the existence of an AKT1 duplication in one case, also having a stromal luteoma. The analysis of RNA-Seq data pinpointed a series of differentially expressed genes, involved in cytokine and hormone signaling and cell division-related processes. Further analyses pointed to the existence of a possible dedifferentiation process and suggested that most of the transcriptomic dysregulation might be mediated by a limited set of transcription factors perturbed by AKT1 activation. Finally, we show that commercially available AKT inhibitors can modulate the in vitro activity of various mutated forms. These results shed light on the pathogenesis of JGCTs and provide therapeutic leads for a targeted treatment.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 7
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Gene 52 (1987), S. 41-49 
    ISSN: 0378-1119
    Keywords: Northern analysis ; Recombinant DNA ; glutelin ; hybrid selection ; nucleotide sequencing ; zein
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    FEBS Letters 293 (1991), S. 175-178 
    ISSN: 0014-5793
    Keywords: CaMV 35S promoter ; In vivo binding studies ; Octopine synthase enhancer ; Sterical hindrance
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 0014-5793
    Keywords: Patatin ; Proteinase inhibitor II ; Starch metabolism ; Tuberization
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Protoplasma 26 (1936), S. 113-149 
    ISSN: 1615-6102
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
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