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  • 1
    Publication Date: 2012-02-08
    Description: Promoter-specific transcriptional activators (activators) stimulate transcription through direct interactions with one or more components of the transcription machinery, termed the “target.” The identification of direct in vivo targets of activators has been a major challenge. Previous studies have provided evidence that the Tra1 subunit of the yeast SAGA (Spt-Ada-Gcn5-acetyltransferase) complex is the target of the yeast activator Gal4. However, several other general transcription factors, in particular the mediator complex, have also been implicated as Gal4 targets. Here we perform a large-scale genetic screen to derive and characterize tra1 alleles that are selectively defective for interaction with Gal4 in vivo [Gal4 interaction defective (GID) mutants]. In contrast to WT Tra1, Tra1 GID mutants are not recruited by Gal4 to the promoter and cannot support Gal4-directed transcription, demonstrating the essentiality of the Gal4–Tra1 interaction. In yeast strains expressing a Tra1 GID mutant, binding of Gal4 to the promoter is unexpectedly also diminished, indicating that Gal4 and Tra1 bind cooperatively. Consistent with cooperative binding, we demonstrate that the Gal4–Tra1 interaction occurs predominantly on the promoter and not off DNA. Finally, we show that although Tra1 is targeted by other activators, these interactions are unaffected by GID mutations, revealing an unanticipated specificity of the Gal4–Tra1 interaction.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 2
    Publication Date: 2014-09-03
    Description: X-chromosome inactivation (XCI), the random transcriptional silencing of one X chromosome in somatic cells of female mammals, is a mechanism that ensures equal expression of X-linked genes in both sexes. XCI is initiated in cis by the noncoding Xist RNA, which coats the inactive X chromosome (Xi) from which it...
    Keywords: Inaugural Articles
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 3
    Publication Date: 2011-01-01
    Description: Continental topography is the result of complex interactions among mantle convection, continental dynamics, and climatic and erosional processes. Therefore, topographic evolution of mountain belts and continental interiors reflects directly upon the coupling between mantle and surface processes. It has recently been proposed that the modern topography of western North America is partly controlled by the removal of the subducting Farallon plate and replacement of lithospheric mantle by hot asthenosphere, creating surface uplift of the Colorado Plateau, the southwestern United States, and northern Mexico, while concomitant subsidence characterizes the central United States. How the topography of the Cenozoic North American Cordillera evolved in the past is largely unknown, yet currently debated tectonic models each have a predictable topographic response. Here we examine Cenozoic surface uplift patterns of western North America based on a record of [~]3000 stable isotope proxy data. This data set is consistent with Eocene north to south surface uplift in the Cordillera, culminating in the assembly of an Eocene-Oligocene highland 3-4 km in elevation. The diachronous record of surface uplift and associated magmatism further supports tectonic models calling for the convective removal of mantle lithosphere or removal of the Farallon slab by buckling along an east-west axis. The Eocene-Oligocene development of rainout patterns similar to present-day patterns along the flanks of the Cordilleran orogen is therefore unlikely to be the result of late Mesozoic crustal thickening and associated development of an Andean-style Altiplano.
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
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  • 4
    Publication Date: 2019
    Description: Abstract Constraining time is of critical importance to evaluating the rates and relative contributions of processes driving landscape change in sedimentary basins. The geomorphic character of the field setting guides the application of geochronologic or instrumental tools to this problem, because the viability of methods can be highly influenced by geomorphic attributes. For example, sediment yield and the linked potential for organic preservation may govern the usefulness of radiocarbon dating. Similarly, the rate of sediment transport from source‐to‐sink may determine the maturity and/or light exposure of mineral grains arriving in the delta and thus the feasibility of luminescence dating. Here, we explore the viability and quirks of dating and instrumental methods that have been applied in the Bengal Basin, and review the records that they have yielded. This immense, dynamic, and spatially variable system hosts the world's most inhabited delta. Outlining a framework for successful chronologic applications is thus of value to managing water and sediment resources for humans, here and in other populated deltas worldwide. Our review covers radiocarbon dating, luminescence dating, archaeological records and historical maps, short‐lived radioisotopes, horizon markers and rod surface elevation tables, geodetic observations, and surface instrumentation. Combined, these tools can be used to reconstruct the history of the Bengal Basin from Late Pleistocene to present‐day. The growing variety and scope of Bengal Basin geochronology and instrumentation opens doors for research integrating basin processes across spatial and temporal scales.
    Print ISSN: 0360-1269
    Electronic ISSN: 1096-9837
    Topics: Geography , Geosciences
    Published by Wiley
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  • 5
    Publication Date: 2014-09-10
    Description: Article Little is known about the genetic basis of convergent evolution in deeply diverged species. Here, the authors show that variation in the WntA gene is associated with parallel wing pattern variation in two butterflies that diverged more than 65 million years ago. Nature Communications doi: 10.1038/ncomms5817 Authors: Jason R. Gallant, Vance E. Imhoff, Arnaud Martin, Wesley K. Savage, Nicola L. Chamberlain, Ben L. Pote, Chelsea Peterson, Gabriella E. Smith, Benjamin Evans, Robert D. Reed, Marcus R. Kronforst, Sean P. Mullen
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 6
    Publication Date: 2014-12-04
    Description: The TRIM37 (also known as MUL) gene is located in the 17q23 chromosomal region, which is amplified in up to approximately 40% of breast cancers. TRIM37 contains a RING finger domain, a hallmark of E3 ubiquitin ligases, but its protein substrate(s) is unknown. Here we report that TRIM37 mono-ubiquitinates histone H2A, a chromatin modification associated with transcriptional repression. We find that in human breast cancer cell lines containing amplified 17q23, TRIM37 is upregulated and, reciprocally, the major H2A ubiquitin ligase RNF2 (also known as RING1B) is downregulated. Genome-wide chromatin immunoprecipitation (ChIP)-chip experiments in 17q23-amplified breast cancer cells identified many genes, including multiple tumour suppressors, whose promoters were bound by TRIM37 and enriched for ubiquitinated H2A. However, unlike RNF2, which is a subunit of polycomb repressive complex 1 (PRC1), we find that TRIM37 associates with polycomb repressive complex 2 (PRC2). TRIM37, PRC2 and PRC1 are co-bound to specific target genes, resulting in their transcriptional silencing. RNA-interference-mediated knockdown of TRIM37 results in loss of ubiquitinated H2A, dissociation of PRC1 and PRC2 from target promoters, and transcriptional reactivation of silenced genes. Knockdown of TRIM37 in human breast cancer cells containing amplified 17q23 substantially decreases tumour growth in mouse xenografts. Conversely, ectopic expression of TRIM37 renders non-transformed cells tumorigenic. Collectively, our results reveal TRIM37 as an oncogenic H2A ubiquitin ligase that is overexpressed in a subset of breast cancers and promotes transformation by facilitating silencing of tumour suppressors and other genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4269325/" 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/PMC4269325/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhatnagar, Sanchita -- Gazin, Claude -- Chamberlain, Lynn -- Ou, Jianhong -- Zhu, Xiaochun -- Tushir, Jogender S -- Virbasius, Ching-Man -- Lin, Ling -- Zhu, Lihua J -- Wajapeyee, Narendra -- Green, Michael R -- R01 GM033977/GM/NIGMS NIH HHS/ -- R01GM033977/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Dec 4;516(7529):116-20. doi: 10.1038/nature13955. Epub 2014 Nov 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA [2] Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. ; CEA/DSV/iRCM/LEFG, Genopole G2, and Universite Paris Diderot, 91057 Evry, France. ; Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. ; Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, USA. ; 1] Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA [2] Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. ; Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25470042" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Breast Neoplasms/*enzymology/*genetics ; Female ; Gene Expression Profiling ; *Gene Expression Regulation, Neoplastic ; Gene Knockdown Techniques ; Gene Silencing ; Heterografts ; Histones/metabolism ; Humans ; MCF-7 Cells ; Mice ; NIH 3T3 Cells ; Nuclear Proteins/*genetics/*metabolism ; Oncogene Proteins/*genetics/metabolism ; Polycomb Repressive Complex 1/*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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  • 7
    Publication Date: 2009-11-07
    Description: Ecological speciation occurs when ecologically based, divergent selection causes the evolution of reproductive isolation. There are many empirical examples of this process; however, there exists a poorly characterized stage during which the traits that distinguish species ecologically and reproductively segregate in a single population. By using a combination of genetic mapping, mate-choice experiments, field observations, and population genetics, we studied a butterfly population with a mimetic wing color polymorphism and found that the butterflies exhibited partial, color-based, assortative mate preference. These traits represent the divergent, ecologically based signal and preference components of sexual isolation that usually distinguish incipient and sibling species. The association between behavior and recognition trait in a single population may enhance the probability of speciation and provides an example of the missing link between an interbreeding population and isolated species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875868/" 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/PMC2875868/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chamberlain, Nicola L -- Hill, Ryan I -- Kapan, Durrell D -- Gilbert, Lawrence E -- Kronforst, Marcus R -- GM068763/GM/NIGMS NIH HHS/ -- P50 GM068763/GM/NIGMS NIH HHS/ -- P50 GM068763-06/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Nov 6;326(5954):847-50. doi: 10.1126/science.1179141.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19892982" target="_blank"〉PubMed〈/a〉
    Keywords: Amplified Fragment Length Polymorphism Analysis ; Animals ; Butterflies/anatomy & histology/*genetics/*physiology ; Color ; Ecosystem ; Female ; Genes, Insect ; Genetic Linkage ; *Genetic Speciation ; Linkage Disequilibrium ; Male ; *Mating Preference, Animal ; Molecular Sequence Data ; Phenotype ; *Pigmentation/genetics ; *Polymorphism, Genetic ; Reproduction ; Selection, Genetic ; Wings, Animal/*anatomy & histology
    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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  • 8
    Publication Date: 2011-08-16
    Description: Supergenes are tight clusters of loci that facilitate the co-segregation of adaptive variation, providing integrated control of complex adaptive phenotypes. Polymorphic supergenes, in which specific combinations of traits are maintained within a single population, were first described for 'pin' and 'thrum' floral types in Primula and Fagopyrum, but classic examples are also found in insect mimicry and snail morphology. Understanding the evolutionary mechanisms that generate these co-adapted gene sets, as well as the mode of limiting the production of unfit recombinant forms, remains a substantial challenge. Here we show that individual wing-pattern morphs in the polymorphic mimetic butterfly Heliconius numata are associated with different genomic rearrangements at the supergene locus P. These rearrangements tighten the genetic linkage between at least two colour-pattern loci that are known to recombine in closely related species, with complete suppression of recombination being observed in experimental crosses across a 400-kilobase interval containing at least 18 genes. In natural populations, notable patterns of linkage disequilibrium (LD) are observed across the entire P region. The resulting divergent haplotype clades and inversion breakpoints are found in complete association with wing-pattern morphs. Our results indicate that allelic combinations at known wing-patterning loci have become locked together in a polymorphic rearrangement at the P locus, forming a supergene that acts as a simple switch between complex adaptive phenotypes found in sympatry. These findings highlight how genomic rearrangements can have a central role in the coexistence of adaptive phenotypes involving several genes acting in concert, by locally limiting recombination and gene flow.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717454/" 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/PMC3717454/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joron, Mathieu -- Frezal, Lise -- Jones, Robert T -- Chamberlain, Nicola L -- Lee, Siu F -- Haag, Christoph R -- Whibley, Annabel -- Becuwe, Michel -- Baxter, Simon W -- Ferguson, Laura -- Wilkinson, Paul A -- Salazar, Camilo -- Davidson, Claire -- Clark, Richard -- Quail, Michael A -- Beasley, Helen -- Glithero, Rebecca -- Lloyd, Christine -- Sims, Sarah -- Jones, Matthew C -- Rogers, Jane -- Jiggins, Chris D -- ffrench-Constant, Richard H -- 079643/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- BB/E008836/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBE0118451/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0900740/Medical Research Council/United Kingdom -- England -- Nature. 2011 Aug 14;477(7363):203-6. doi: 10.1038/nature10341.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS UMR 7205, Museum National d'Histoire Naturelle, CP50, 45 Rue Buffon, 75005 Paris, France. joron@mnhn.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21841803" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Butterflies/anatomy & histology/*genetics/physiology ; Chromosome Walking ; Chromosomes, Insect/*genetics ; Gene Rearrangement/*genetics ; Genes, Insect/*genetics ; Genetic Linkage/genetics ; Haplotypes/genetics ; Molecular Mimicry/*genetics/physiology ; Molecular Sequence Data ; Multigene Family/genetics ; Phenotype ; Pigmentation/genetics/physiology ; Polymorphism, Genetic/*genetics ; Wings, Animal/anatomy & histology/metabolism/physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2011-07-23
    Description: Mimicry--whereby warning signals in different species evolve to look similar--has long served as a paradigm of convergent evolution. Little is known, however, about the genes that underlie the evolution of mimetic phenotypes or to what extent the same or different genes drive such convergence. Here, we characterize one of the major genes responsible for mimetic wing pattern evolution in Heliconius butterflies. Mapping, gene expression, and population genetic work all identify a single gene, optix, that controls extreme red wing pattern variation across multiple species of Heliconius. Our results show that the cis-regulatory evolution of a single transcription factor can repeatedly drive the convergent evolution of complex color patterns in distantly related species, thus blurring the distinction between convergence and homology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reed, Robert D -- Papa, Riccardo -- Martin, Arnaud -- Hines, Heather M -- Counterman, Brian A -- Pardo-Diaz, Carolina -- Jiggins, Chris D -- Chamberlain, Nicola L -- Kronforst, Marcus R -- Chen, Rui -- Halder, Georg -- Nijhout, H Frederik -- McMillan, W Owen -- New York, N.Y. -- Science. 2011 Aug 26;333(6046):1137-41. doi: 10.1126/science.1208227. Epub 2011 Jul 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA. rreed@uci.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21778360" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; *Biological Evolution ; Butterflies/anatomy & histology/*genetics/growth & development ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; *Genes, Insect ; Genetic Variation ; Genome, Insect ; Homeodomain Proteins/*genetics ; Insect Proteins/*genetics ; Linkage Disequilibrium ; Molecular Sequence Data ; Moths/genetics ; Phenotype ; Pigmentation/*genetics ; Regulatory Elements, Transcriptional ; Selection, Genetic ; Species Specificity ; Transcription Factors/genetics ; Transcription, Genetic ; Wings, Animal/*anatomy & histology/growth & development
    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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  • 10
    Publication Date: 2015-11-18
    Description: The interval between 1.78 and 1.63 Ga was one of major crustal growth and assembly in southwestern Laurentia. The prevailing view is that the culminating event for this tectonism was the ca. 1.654–1.633 Ga Mazatzal orogeny. We present evidence for a continuum of deformation, magmatism, metamorphism, and new mineral growth from 1.65 to 1.58 Ga from southern Wyoming to Sonora, Mexico. We suggest that the Mazatzal orogeny may have extended in time to ca. 1580 Ma and in space to the Cheyenne belt, southern Wyoming. If our interpretation for an extended Mazatzal orogeny is correct, the duration of the orogeny may have been ~70 m.y., similar to many orogenies in Earth’s history. The ca. 1.6 Ga tectonism appears to represent a shift in tectonic style from that typically associated with the Yavapai (ca. 1.70 Ga) and "classic" Mazatzal (1.65 Ga) orogenies to widespread intracontinental deformation. If correct, a corollary to our interpretation is that newly accreted Paleoproterozoic crust stabilized rapidly and facilitated stress transfer far inboard of any active plate margin.
    Print ISSN: 1941-8264
    Electronic ISSN: 1947-4253
    Topics: Geosciences
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