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  • 1
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    Nucleotide variation along the Drosophila melanogaster fourth chromosome (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-01-05
    Description: The Drosophila melanogaster fourth chromosome, believed to be nonrecombining and invariable, is a classic example of the effect of natural selection in eliminating genetic variation in linked loci. However, in a chromosome-wide assay of nucleotide variation in natural populations, we have observed a high level of polymorphism in a approximately 200-kilobase region and marked levels of polymorphism in several other fragments interspersed with regions of little variation, suggesting different evolutionary histories in different chromosomal domains. Statistical tests of neutral evolution showed that a few haplotypes predominate in the 200-kilobase polymorphic region. Finally, contrary to the expectation of no recombination, we identified six recombination events within the chromosome. Thus, positive Darwinian selection and recombination have affected the evolution of this chromosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Wen -- Thornton, Kevin -- Berry, Andrew -- Long, Manyuan -- New York, N.Y. -- Science. 2002 Jan 4;295(5552):134-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolution, Committee on Genetics, University of Chicago, 1101 East 57 Street, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11778050" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Pairing ; Chromosome Inversion ; Chromosomes/*genetics ; Drosophila Proteins/genetics ; Drosophila melanogaster/*genetics ; Evolution, Molecular ; *Genes, Insect ; *Genetic Variation ; Haplotypes ; Introns ; Linkage Disequilibrium ; Monte Carlo Method ; Mutation ; Nucleotides/genetics ; *Polymorphism, Genetic ; *Recombination, Genetic ; Selection, Genetic ; Sequence Analysis, DNA ; Trans-Activators/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Mating type switching in yeast controlled by asymmetric localization of ASH1 mRNA (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-18
    Description: Cell divisions that produce progeny differing in their patterns of gene expression are key to the development of multicellular organisms. In the budding yeast Saccharomyces cerevisiae, mother cells but not daughter cells can switch mating type because they selectively express the HO endonuclease gene. This asymmetry is due to the preferential accumulation of an unstable transcriptional repressor protein, Ash1p, in daughter cell nuclei. Here it is shown that ASH1 messenger RNA (mRNA) preferentially accumulates in daughter cells by a process that is dependent on actin and myosin. A cis-acting element in the 3'-untranslated region of ASH1 mRNA is sufficient to localize a chimeric RNA to daughter cells. These results suggest that localization of mRNA may have been an early property of the eukaryotic lineage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Long, R M -- Singer, R H -- Meng, X -- Gonzalez, I -- Nasmyth, K -- Jansen, R P -- 7 F32 HD08088-02/HD/NICHD NIH HHS/ -- GM54887/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jul 18;277(5324):383-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9219698" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/genetics/*physiology ; Cell Cycle ; Cell Nucleus/metabolism ; *DNA-Binding Proteins ; Deoxyribonucleases, Type II Site-Specific/genetics ; Fungal Proteins/genetics ; Genes, Fungal ; Genes, Mating Type, Fungal ; In Situ Hybridization, Fluorescence ; Microtubules/physiology ; Mutation ; *Myosin Heavy Chains ; *Myosin Type V ; Myosins/genetics ; RNA, Fungal/genetics/*metabolism ; RNA, Messenger/genetics/*metabolism ; Repressor Proteins/biosynthesis/*genetics ; Saccharomyces cerevisiae/cytology/genetics/metabolism/*physiology ; *Saccharomyces cerevisiae Proteins ; Transcription Factors/biosynthesis/*genetics ; Transformation, Genetic ; Tropomyosin/genetics/physiology ; Zinc Fingers
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Extensive gene traffic on the mammalian X chromosome (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-24
    Description: Mammalian sex chromosomes have undergone profound changes since evolving from ancestral autosomes. By examining retroposed genes in the human and mouse genomes, we demonstrate that, during evolution, the mammalian X chromosome has generated and recruited a disproportionately high number of functional retroposed genes, whereas the autosomes experienced lower gene turnover. Most autosomal copies originating from X-linked genes exhibited testis-biased expression. Such export is incompatible with mutational bias and is likely driven by natural selection to attain male germline function. However, the excess recruitment is consistent with a combination of both natural selection and mutational bias.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Emerson, J J -- Kaessmann, Henrik -- Betran, Esther -- Long, Manyuan -- GM-065429-01A1/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 23;303(5657):537-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14739461" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Chromosomes, Human/genetics ; Chromosomes, Human, X/*genetics ; Chromosomes, Mammalian/genetics ; Computational Biology ; Dosage Compensation, Genetic ; Female ; Gene Expression Profiling ; Genes, Duplicate ; Genetic Linkage ; Genome ; Genome, Human ; Humans ; Introns ; Male ; Mice ; Monte Carlo Method ; Mutation ; Oligonucleotide Array Sequence Analysis ; Ovary/metabolism ; Pseudogenes/*genetics ; *Recombination, Genetic ; Retroelements/*genetics ; Selection, Genetic ; Sex Characteristics ; Testis/metabolism ; X Chromosome/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Nodulation signaling in legumes requires NSP2, a member of the GRAS family of transcriptional regulators (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-06-18
    Description: Rhizobial bacteria enter a symbiotic interaction with legumes, activating diverse responses in roots through the lipochito oligosaccharide signaling molecule Nod factor. Here, we show that NSP2 from Medicago truncatula encodes a GRAS protein essential for Nod-factor signaling. NSP2 functions downstream of Nod-factor-induced calcium spiking and a calcium/calmodulin-dependent protein kinase. We show that NSP2-GFP expressed from a constitutive promoter is localized to the endoplasmic reticulum/nuclear envelope and relocalizes to the nucleus after Nod-factor elicitation. This work provides evidence that a GRAS protein transduces calcium signals in plants and provides a possible regulator of Nod-factor-inducible gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kalo, Peter -- Gleason, Cynthia -- Edwards, Anne -- Marsh, John -- Mitra, Raka M -- Hirsch, Sibylle -- Jakab, Julia -- Sims, Sarah -- Long, Sharon R -- Rogers, Jane -- Kiss, Gyorgy B -- Downie, J Allan -- Oldroyd, Giles E D -- New York, N.Y. -- Science. 2005 Jun 17;308(5729):1786-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Disease and Stress Biology and Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15961668" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Calcium/metabolism ; Calcium Signaling ; Calcium-Calmodulin-Dependent Protein Kinases/genetics/metabolism ; Cell Nucleus/metabolism ; Cloning, Molecular ; Gene Expression Regulation, Plant ; Genes, Plant ; Lipopolysaccharides/*metabolism ; Medicago/genetics/*metabolism/*microbiology ; Molecular Sequence Data ; Mutation ; Oligonucleotide Array Sequence Analysis ; Peas/genetics/metabolism ; Plant Proteins/chemistry/genetics/*metabolism ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction ; Sinorhizobium meliloti/*physiology ; Symbiosis ; Transcription Factors/chemistry/genetics/*metabolism ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 5
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    The competitive cost of antibiotic resistance in Mycobacterium tuberculosis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-01
    Description: Mathematical models predict that the future of the multidrug-resistant tuberculosis epidemic will depend on the fitness cost of drug resistance. We show that in laboratory-derived mutants of Mycobacterium tuberculosis, rifampin resistance is universally associated with a competitive fitness cost and that this cost is determined by the specific resistance mutation and strain genetic background. In contrast, we demonstrate that prolonged patient treatment can result in multidrug-resistant strains with no fitness defect and that strains with low- or no-cost resistance mutations are also the most frequent among clinical isolates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gagneux, Sebastien -- Long, Clara Davis -- Small, Peter M -- Van, Tran -- Schoolnik, Gary K -- Bohannan, Brendan J M -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2006 Jun 30;312(5782):1944-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA. sgagneux@systemsbiology.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16809538" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Antibiotics, Antitubercular/*pharmacology/therapeutic use ; Bacterial Proteins/genetics ; DNA-Directed RNA Polymerases/genetics ; *Drug Resistance, Multiple, Bacterial ; Humans ; Models, Biological ; Mutation ; Mutation, Missense ; Mycobacterium tuberculosis/*drug effects/genetics/*growth & development ; Rifampin/*pharmacology/therapeutic use ; Tuberculosis, Multidrug-Resistant/drug therapy/*microbiology
    Print ISSN: 0036-8075
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  • 6
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    TOPLESS regulates apical embryonic fate in Arabidopsis (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-06-10
    Description: The embryos of seed plants develop with an apical shoot pole and a basal root pole. In Arabidopsis, the topless-1 (tpl-1) mutation transforms the shoot pole into a second root pole. Here, we show that TPL resembles known transcriptional corepressors and that tpl-1 acts as a dominant negative mutation for multiple TPL-related proteins. Mutations in the putative coactivator HISTONE ACETYLTRANSFERASE GNAT SUPERFAMILY1 suppress the tpl-1 phenotype. Mutations in HISTONE DEACETYLASE19, a putative corepressor, increase the penetrance of tpl-1 and display similar apical defects. These data point to a transcriptional repression mechanism that prevents root formation in the shoot pole during Arabidopsis embryogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Long, Jeff A -- Ohno, Carolyn -- Smith, Zachery R -- Meyerowitz, Elliot M -- GM072764/GM/NIGMS NIH HHS/ -- GM45697/GM/NIGMS NIH HHS/ -- R01 GM072764/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Jun 9;312(5779):1520-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Biology Laboratory, Salk Institute for Biological Sciences, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA. long@salk.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16763149" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Arabidopsis/*embryology/genetics ; Arabidopsis Proteins/genetics/*physiology ; Cell Polarity ; Chromosome Mapping ; Chromosomes, Plant ; Gene Expression Regulation, Plant ; Histone Deacetylases/genetics/physiology ; Mutation ; Plant Roots/embryology ; Plant Shoots/embryology ; Repressor Proteins/genetics/*physiology ; Seeds
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Cell identity mediates the response of Arabidopsis roots to abiotic stress (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-26
    Description: Little is known about the way developmental cues affect how cells interpret their environment. We characterized the transcriptional response to high salinity of different cell layers and developmental stages of the Arabidopsis root and found that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell layers, several of which correspond to observable physiological changes. We showed that known stress pathways primarily control semiubiquitous responses and used mutants that disrupt epidermal patterning to reveal cell-layer-specific and inter-cell-layer effects. By performing a similar analysis using iron deprivation, we identified common cell-type-specific stress responses and revealed the crucial role the environment plays in defining the transcriptional outcome of cell-fate decisions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dinneny, Jose R -- Long, Terri A -- Wang, Jean Y -- Jung, Jee W -- Mace, Daniel -- Pointer, Solomon -- Barron, Christa -- Brady, Siobhan M -- Schiefelbein, John -- Benfey, Philip N -- New York, N.Y. -- Science. 2008 May 16;320(5878):942-5. doi: 10.1126/science.1153795. Epub 2008 Apr 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Duke University, Durham, NC 27708, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18436742" target="_blank"〉PubMed〈/a〉
    Keywords: Abscisic Acid/metabolism ; Algorithms ; Arabidopsis/*cytology/genetics/*physiology ; Arabidopsis Proteins/genetics/metabolism ; Culture Media ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Genes, Plant ; Iron/metabolism ; Mutation ; Plant Epidermis/cytology/genetics/physiology ; Plant Roots/*cytology/genetics/growth & development/*physiology ; Promoter Regions, Genetic ; Response Elements ; *Salinity ; Transcription Factors/metabolism ; Transcription, Genetic
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-06-07
    Description: The role that natural selection plays in governing the locations and early evolution of copy-number mutations remains largely unexplored. We used high-density full-genome tiling arrays to create a fine-scale genomic map of copy-number polymorphisms (CNPs) in Drosophila melanogaster. We inferred a total of 2658 independent CNPs, 56% of which overlap genes. These include CNPs that are likely to be under positive selection, most notably high-frequency duplications encompassing toxin-response genes. The locations and frequencies of CNPs are strongly shaped by purifying selection, with deletions under stronger purifying selection than duplications. Among duplications, those overlapping exons or introns, as well as those falling on the X chromosome, seem to be subject to stronger purifying selection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Emerson, J J -- Cardoso-Moreira, Margarida -- Borevitz, Justin O -- Long, Manyuan -- New York, N.Y. -- Science. 2008 Jun 20;320(5883):1629-31. doi: 10.1126/science.1158078. Epub 2008 Jun 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA. jje@uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18535209" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA/genetics ; DNA, Intergenic ; Drosophila melanogaster/*genetics ; Exons ; Female ; *Gene Dosage ; Gene Duplication ; Gene Frequency ; Genes, Insect ; *Genome, Insect ; Introns ; Male ; Mutation ; Oligonucleotide Array Sequence Analysis ; *Polymorphism, Genetic ; *Selection, Genetic ; Sequence Deletion ; X Chromosome/genetics
    Print ISSN: 0036-8075
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  • 9
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    TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogenesis (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-02-09
    Description: The transcriptional response to auxin is critical for root and vascular development during Arabidopsis embryogenesis. Auxin induces the degradation of AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors, freeing their binding partners, the AUXIN RESPONSE FACTOR (ARF) proteins, which can activate transcription of auxin response genes. We show that TOPLESS (TPL) can physically interact with IAA12/BODENLOS (IAA12/BDL) through an ETHYLENE RESPONSE FACTOR (ERF)-associated amphiphilic repression (EAR) motif. TPL can repress transcription in vivo and is required for IAA12/BDL repressive activity. In addition, tpl-1 can suppress the patterning defects of the bdl-1 mutant. Direct interaction between TPL and ARF5/MONOPTEROS, which is regulated by IAA12/BDL, results in a loss-of-function arf5/mp phenotype. These observations show that TPL is a transcriptional co-repressor and further our understanding of how auxin regulates transcription during plant development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Szemenyei, Heidi -- Hannon, Mike -- Long, Jeff A -- GM072764/GM/NIGMS NIH HHS/ -- R01 GM072764/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Mar 7;319(5868):1384-6. doi: 10.1126/science.1151461. Epub 2008 Feb 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18258861" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Arabidopsis/embryology/*genetics/metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; DNA-Binding Proteins/metabolism ; *Gene Expression Regulation, Plant ; Indoleacetic Acids/*metabolism ; Models, Genetic ; Mutation ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Repressor Proteins/chemistry/genetics/*metabolism ; Seedlings/embryology/metabolism ; Seeds/embryology/metabolism ; Transcription Factors/metabolism ; *Transcription, Genetic ; Two-Hybrid System Techniques
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    A nodule-specific protein secretory pathway required for nitrogen-fixing symbiosis (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-02-27
    Description: The nitrogen-fixing symbiosis between Sinorhizobium meliloti and its leguminous host plant Medicago truncatula occurs in a specialized root organ called the nodule. Bacteria that are released into plant cells are surrounded by a unique plant membrane compartment termed a symbiosome. We found that in the symbiosis-defective dnf1 mutant of M. truncatula, bacteroid and symbiosome development are blocked. We identified the DNF1 gene as encoding a subunit of a signal peptidase complex that is highly expressed in nodules. By analyzing data from whole-genome expression analysis, we propose that correct symbiosome development in M. truncatula requires the orderly secretion of protein constituents through coordinated up-regulation of a nodule-specific pathway exemplified by DNF1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Dong -- Griffitts, Joel -- Starker, Colby -- Fedorova, Elena -- Limpens, Erik -- Ivanov, Sergey -- Bisseling, Ton -- Long, Sharon -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Feb 26;327(5969):1126-9. doi: 10.1126/science.1184096.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20185723" target="_blank"〉PubMed〈/a〉
    Keywords: Endoplasmic Reticulum/metabolism ; Gene Expression ; Gene Expression Profiling ; Genes, Plant ; Medicago truncatula/genetics/*metabolism/*microbiology ; Membrane Proteins/genetics/*metabolism ; Mutation ; *Nitrogen Fixation ; Plant Proteins/genetics/metabolism ; Plants, Genetically Modified ; Protein Subunits/genetics/metabolism ; Root Nodules, Plant/metabolism/*microbiology ; *Secretory Pathway ; Serine Endopeptidases/genetics/*metabolism ; Sinorhizobium meliloti/*physiology ; *Symbiosis
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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