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  • 1
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    Characterization and quantification of aquifer heterogeneity using outcrop analogs at the Canadian Forces Base Borden, Ontario, Canada (2015)
    Geological Society of America (GSA)
    Details
    Publication Date: 2015-06-25
    Description: Accurate characterization of internal structures and geometries of aquifers is critical for evaluation of plume migration and dispersion of contaminants. For this reason, high-resolution transport study field sites, such as the Waterloo Groundwater Research Site at the Canadian Forces Base Borden, Ontario, Canada, have been established. However, geological characterization at this site is based primarily on cores and shallow geophysical data. Outcrop analog studies offer detailed horizontal data that can help to build quantified models of aquifer heterogeneity. We used a combination of ground-based light detection and ranging (LiDAR) and high-resolution photographs at a sand quarry cut into Borden aquifer sediment to evaluate and quantify the distribution of lithofacies and hydrofacies that control flow properties in the Borden aquifer. We exposed sixteen ~20 m x 1.5 m outcrops, LiDAR surveyed, photographed, and field mapped lithofacies at each exposure, and segmented the lithofacies from photographs to produce maps of facies distributions. We grouped different lithofacies into hydrofacies based on overall facies geometry and estimated hydraulic properties. We used LiDAR scans and the segmented facies maps to produce a digital outcrop model (DOM) of the site. The resultant DOM combines lithofacies and hydrofacies derived from field observations with high-resolution (5 mm) LiDAR data to reconstruct hydrofacies distributions in a three-dimensional (3-D) geomodel. The DOM offers a relatively complete horizontal correlation structure that was used in transition probability geostatistical modeling to create realizations of hydrofacies distributions in the aquifer at the study site.
    Print ISSN: 0016-7606
    Electronic ISSN: 1943-2674
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 2
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    Tracking of Airborne Radionuclides from the Damaged Fukushima Dai-Ichi Nuclear Reactors by European Networks (2011)
    O. Masson, A. Baeza, J. Bieringer, K. Brudecki, S. Bucci, M. Cappai, F.P. Carvalho, O. Connan, C. Cosma, A. Dalheimer, D. Didier, G. Depuydt, L.E. De Geer, A. De Vismes, L. Gini, F. Groppi, K. Gudnason, R. Gurriaran, D. Hainz, Ó. Halldórsson, D. Hammond, O. Hanley, K. Holeý, Zs. Homoki, A. Ioannidou, K. Isajenko, M. Jankovic, C. Katzlberger, M. Kettunen, R. Kierepko, R. Kontro, P.J.M. Kwakman, M. Lecomte, L. Leon Vintro, A.-P. Leppänen, B. Lind, G. Lujaniene, P. Mc Ginnity, C. Mc Mahon, H. Malá, S. Manenti, M. Manolopoulou, A. Mattila, A. Mauring, J.W. Mietelski, B. Møller, S.P. Nielsen, J. Nikolic, R.M.W. Overwater, S. E. Pálsson, C. Papastefanou, I. Penev, M.K. Pham, P.P. Povinec, H. Ramebäck, M.C. Reis, W. Ringer, A. Rodriguez, P. Rulík, P.R.J. Saey, V. Samsonov, C. Schlosser, G. Sgorbati, B. V. Silobritiene, C. Söderström, R. Sogni, L. Solier, M. Sonck, G. Steinhauser, T. Steinkopff, P. Steinmann, S. Stoulos, I. Sýkora, D. Todorovic, N. Tooloutalaie, L. Tositti, J. Tschiersch, A. Ugron, E. Vagena, A. Vargas, H. Wershofen and O. Zhukova
    American Chemical Society (ACS)
    Details
    Publication Date: 2011-08-24
    Description: Environmental Science & Technology DOI: 10.1021/es2017158
    Print ISSN: 0013-936X
    Electronic ISSN: 1520-5851
    Topics: Chemistry and Pharmacology , Energy, Environment Protection, Nuclear Power Engineering
    Published by American Chemical Society (ACS)
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  • 3
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    Coordinate regulation of RAG1 and RAG2 by cell type-specific DNA elements 5' of RAG2 (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-08-14
    Description: RAG1 and RAG2 are essential for V(D)J recombination and lymphocyte development. These genes are thought to encode a transposase derived from a mobile genetic element that was inserted into the vertebrate genome 450 million years ago. The regulation of RAG1 and RAG2 was investigated in vivo with bacterial artificial chromosome (BAC) transgenes containing a fluorescent indicator. Coordinate expression of RAG1 and RAG2 in B and T cells was found to be regulated by distinct genetic elements found on the 5' side of the RAG2 gene. This observation suggests a mechanism by which asymmetrically disposed cis DNA elements could influence the expression of the primordial transposon and thereby capture RAGs for vertebrate evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, W -- Misulovin, Z -- Suh, H -- Hardy, R R -- Jankovic, M -- Yannoutsos, N -- Nussenzweig, M C -- GM07739/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Aug 13;285(5430):1080-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Immunology, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10446057" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; B-Lymphocytes/*metabolism ; Bacterial Proteins/genetics ; DNA-Binding Proteins/*genetics ; *Gene Expression Regulation ; Genes, Immunoglobulin ; *Genes, RAG-1 ; Green Fluorescent Proteins ; Luminescent Proteins/genetics ; Mice ; Mice, Transgenic ; Recombinant Fusion Proteins ; Recombination, Genetic ; *Regulatory Sequences, Nucleic Acid ; Sequence Deletion ; T-Lymphocytes/*metabolism ; Transcription, Genetic ; Transgenes ; Transposases/genetics
    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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  • 4
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    PTIP promotes chromatin changes critical for immunoglobulin class switch recombination (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-07-31
    Description: Programmed genetic rearrangements in lymphocytes require transcription at antigen receptor genes to promote accessibility for initiating double-strand break (DSB) formation critical for DNA recombination and repair. Here, we showed that activated B cells deficient in the PTIP component of the MLL3 (mixed-lineage leukemia 3)-MLL4 complex display impaired trimethylation of histone 3 at lysine 4 (H3K4me3) and transcription initiation of downstream switch regions at the immunoglobulin heavy-chain (Igh) locus, leading to defective immunoglobulin class switching. We also showed that PTIP accumulation at DSBs contributes to class switch recombination (CSR) and genome stability independently of Igh switch transcription. These results demonstrate that PTIP promotes specific chromatin changes that control the accessibility of the Igh locus to CSR and suggest a nonredundant role for the MLL3-MLL4 complex in altering antibody effector function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008398/" 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/PMC3008398/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Daniel, Jeremy A -- Santos, Margarida Almeida -- Wang, Zhibin -- Zang, Chongzhi -- Schwab, Kristopher R -- Jankovic, Mila -- Filsuf, Darius -- Chen, Hua-Tang -- Gazumyan, Anna -- Yamane, Arito -- Cho, Young-Wook -- Sun, Hong-Wei -- Ge, Kai -- Peng, Weiqun -- Nussenzweig, Michel C -- Casellas, Rafael -- Dressler, Gregory R -- Zhao, Keji -- Nussenzweig, Andre -- Z01 AR041149-03/Intramural NIH HHS/ -- Z01 AR041149-04/Intramural NIH HHS/ -- Z01 DK047055-01/Intramural NIH HHS/ -- Z01 DK047055-02/Intramural NIH HHS/ -- Z01 DK075003-04/Intramural NIH HHS/ -- Z01 DK075003-05/Intramural NIH HHS/ -- Z99 DK999999/Intramural NIH HHS/ -- ZIA AR041149-05/Intramural NIH HHS/ -- ZIA DK075017-03/Intramural NIH HHS/ -- ZIADK047055-03/DK/NIDDK NIH HHS/ -- ZIADK075003-06/DK/NIDDK NIH HHS/ -- ZIADK075017-01/DK/NIDDK NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Aug 20;329(5994):917-23. doi: 10.1126/science.1187942. Epub 2010 Jul 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Experimental Immunology Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20671152" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibody Specificity/genetics ; Carrier Proteins/genetics/*physiology ; Cytidine Deaminase/metabolism ; Dna ; Histones/metabolism ; Immunoglobulin Class Switching/genetics/*physiology ; Immunoglobulin Switch Region ; Methylation ; Mice ; Nuclear Proteins/genetics/*physiology ; Promoter Regions, Genetic ; Recombination, Genetic ; Transcriptional Activation
    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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  • 5
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    Rif1 prevents resection of DNA breaks and promotes immunoglobulin class switching (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-01-12
    Description: DNA double-strand breaks (DSBs) represent a threat to the genome because they can lead to the loss of genetic information and chromosome rearrangements. The DNA repair protein p53 binding protein 1 (53BP1) protects the genome by limiting nucleolytic processing of DSBs by a mechanism that requires its phosphorylation, but whether 53BP1 does so directly is not known. Here, we identify Rap1-interacting factor 1 (Rif1) as an ATM (ataxia-telangiectasia mutated) phosphorylation-dependent interactor of 53BP1 and show that absence of Rif1 results in 5'-3' DNA-end resection in mice. Consistent with enhanced DNA resection, Rif1 deficiency impairs DNA repair in the G(1) and S phases of the cell cycle, interferes with class switch recombination in B lymphocytes, and leads to accumulation of chromosome DSBs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815530/" 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/PMC3815530/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Di Virgilio, Michela -- Callen, Elsa -- Yamane, Arito -- Zhang, Wenzhu -- Jankovic, Mila -- Gitlin, Alexander D -- Feldhahn, Niklas -- Resch, Wolfgang -- Oliveira, Thiago Y -- Chait, Brian T -- Nussenzweig, Andre -- Casellas, Rafael -- Robbiani, Davide F -- Nussenzweig, Michel C -- AI037526/AI/NIAID NIH HHS/ -- GM007739/GM/NIGMS NIH HHS/ -- GM103314/GM/NIGMS NIH HHS/ -- R01 AI037526/AI/NIAID NIH HHS/ -- RR00862/RR/NCRR NIH HHS/ -- RR022220/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 Feb 8;339(6120):711-5. doi: 10.1126/science.1230624. Epub 2013 Jan 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23306439" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ataxia Telangiectasia Mutated Proteins ; B-Lymphocytes/immunology/metabolism ; Cell Cycle Proteins/antagonists & inhibitors/metabolism ; Cells, Cultured ; Chromosomal Proteins, Non-Histone/*metabolism ; DNA/*metabolism ; *DNA Breaks, Double-Stranded ; DNA Repair ; DNA-Binding Proteins/antagonists & inhibitors/*metabolism ; G1 Phase ; G2 Phase ; Genomic Instability ; *Immunoglobulin Class Switching ; Mice ; Phosphorylation ; Protein-Serine-Threonine Kinases/antagonists & inhibitors/metabolism ; S Phase ; Telomere-Binding Proteins/*metabolism ; Tumor Suppressor Proteins/antagonists & inhibitors/metabolism
    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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  • 6
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    DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-02-09
    Description: Recurrent chromosomal translocations underlie both haematopoietic and solid tumours. Their origin has been ascribed to selection of random rearrangements, targeted DNA damage, or frequent nuclear interactions between translocation partners; however, the relative contribution of each of these elements has not been measured directly or on a large scale. Here we examine the role of nuclear architecture and frequency of DNA damage in the genesis of chromosomal translocations by measuring these parameters simultaneously in cultured mouse B lymphocytes. In the absence of recurrent DNA damage, translocations between Igh or Myc and all other genes are directly related to their contact frequency. Conversely, translocations associated with recurrent site-directed DNA damage are proportional to the rate of DNA break formation, as measured by replication protein A accumulation at the site of damage. Thus, non-targeted rearrangements reflect nuclear organization whereas DNA break formation governs the location and frequency of recurrent translocations, including those driving B-cell malignancies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459314/" 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/PMC3459314/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hakim, Ofir -- Resch, Wolfgang -- Yamane, Arito -- Klein, Isaac -- Kieffer-Kwon, Kyong-Rim -- Jankovic, Mila -- Oliveira, Thiago -- Bothmer, Anne -- Voss, Ty C -- Ansarah-Sobrinho, Camilo -- Mathe, Ewy -- Liang, Genqing -- Cobell, Jesse -- Nakahashi, Hirotaka -- Robbiani, Davide F -- Nussenzweig, Andre -- Hager, Gordon L -- Nussenzweig, Michel C -- Casellas, Rafael -- AI037526/AI/NIAID NIH HHS/ -- R01 AI037526/AI/NIAID NIH HHS/ -- Z01 AR041148-03/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Feb 7;484(7392):69-74. doi: 10.1038/nature10909.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22314321" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; B-Lymphocytes/cytology/*metabolism/*pathology ; Cell Nucleus/genetics/metabolism ; Cells, Cultured ; Chromosome Positioning ; Chromosomes, Mammalian/genetics/metabolism ; Cytidine Deaminase/deficiency/genetics/metabolism ; DNA Breaks, Double-Stranded ; DNA Damage/*genetics ; Genes, myc/genetics ; Genome/genetics ; Immunoglobulin Heavy Chains/genetics ; Mice ; Replication Protein A/metabolism ; Translocation, Genetic/*genetics
    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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  • 7
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    T follicular helper cell dynamics in germinal centers (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-07-28
    Description: T follicular helper (T(FH)) cells are a specialized subset of effector T cells that provide help to and thereby select high-affinity B cells in germinal centers (GCs). To examine the dynamic behavior of T(FH) cells in GCs in mice, we used two-photon microscopy in combination with a photoactivatable fluorescent reporter. Unlike GC B cells, which are clonally restricted, T(FH) cells distributed among all GCs in lymph nodes and continually emigrated into the follicle and neighboring GCs. Moreover, newly activated T(FH) cells invaded preexisting GCs, where they contributed to B cell selection and plasmablast differentiation. Our data suggest that the dynamic exchange of T(FH) cells between GCs ensures maximal diversification of T cell help and that their ability to enter ongoing GCs accommodates antigenic variation during the immune response.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941467/" 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/PMC3941467/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shulman, Ziv -- Gitlin, Alexander D -- Targ, Sasha -- Jankovic, Mila -- Pasqual, Giulia -- Nussenzweig, Michel C -- Victora, Gabriel D -- 5DP5OD012146-02/OD/NIH HHS/ -- AI037526-19/AI/NIAID NIH HHS/ -- AI072529-06/AI/NIAID NIH HHS/ -- AI100663-01/AI/NIAID NIH HHS/ -- DP5 OD012146/OD/NIH HHS/ -- R01 AI037526/AI/NIAID NIH HHS/ -- R01 AI072529/AI/NIAID NIH HHS/ -- R37 AI037526/AI/NIAID NIH HHS/ -- T32GM07739/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Aug 9;341(6146):673-7. doi: 10.1126/science.1241680. Epub 2013 Jul 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23887872" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigenic Variation ; B-Lymphocytes/cytology/*immunology ; Clone Cells ; Germinal Center/cytology/*immunology ; Mice ; T-Lymphocytes, Helper-Inducer/cytology/*immunology
    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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  • 8
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    Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences (2013)
    Oxford University Press
    Details
    Publication Date: 2013-05-23
    Description: Contact: vladimir.bajic@kaust.edu.sa 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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  • 9
    Electronic Resource
    Electronic Resource
    Studies on the midgut amylase activity of Tenebrio molitor L. larvae
    Amsterdam : Elsevier
    Journal of Insect Physiology 7 (1961), S. 100-108 
    Details
    ISSN: 0022-1910
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/0022-1910(61)90048-8
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  • 10
    Electronic Resource
    Electronic Resource
    Nucleotide Sequence of the Escherichia coli K12 Histidine Operon Revisited
    Amsterdam : Elsevier
    Journal of Molecular Biology 239 (1994), S. 433-435 
    Details
    ISSN: 0022-2836
    Keywords: Escherichia coli K-12; histidine operon; nucleotide sequence;
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1006/jmbi.1994.1384
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