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  • 1
    Publication Date: 2008-04-25
    Description: Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this lesion in double-stranded DNA (dsDNA), whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587245/" 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/PMC2587245/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Cai-Guang -- Yi, Chengqi -- Duguid, Erica M -- Sullivan, Christopher T -- Jian, Xing -- Rice, Phoebe A -- He, Chuan -- GM071440/GM/NIGMS NIH HHS/ -- R01 GM071440/GM/NIGMS NIH HHS/ -- R01 GM071440-03/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Apr 24;452(7190):961-5. doi: 10.1038/nature06889.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18432238" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/analogs & derivatives/metabolism ; Binding Sites ; Cross-Linking Reagents/chemistry ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Damage ; DNA Repair ; DNA Repair Enzymes/*chemistry/metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Dioxygenases/*chemistry/*metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Humans ; Mixed Function Oxygenases/*chemistry/*metabolism ; Models, Molecular ; Protein Binding ; RNA/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2008-12-05
    Description: Haematopoietic stem cell (HSC) niches, although proposed decades ago, have only recently been identified as separate osteoblastic and vascular microenvironments. Their interrelationships and interactions with HSCs in vivo remain largely unknown. Here we report the use of a newly developed ex vivo real-time imaging technology and immunoassaying to trace the homing of purified green-fluorescent-protein-expressing (GFP(+)) HSCs. We found that transplanted HSCs tended to home to the endosteum (an inner bone surface) in irradiated mice, but were randomly distributed and unstable in non-irradiated mice. Moreover, GFP(+) HSCs were more frequently detected in the trabecular bone area compared with compact bone area, and this was validated by live imaging bioluminescence driven by the stem-cell-leukaemia (Scl) promoter-enhancer. HSCs home to bone marrow through the vascular system. We found that the endosteum is well vascularized and that vasculature is frequently localized near N-cadherin(+) pre-osteoblastic cells, a known niche component. By monitoring individual HSC behaviour using real-time imaging, we found that a portion of the homed HSCs underwent active division in the irradiated mice, coinciding with their expansion as measured by flow assay. Thus, in contrast to central marrow, the endosteum formed a special zone, which normally maintains HSCs but promotes their expansion in response to bone marrow damage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xie, Yucai -- Yin, Tong -- Wiegraebe, Winfried -- He, Xi C -- Miller, Diana -- Stark, Danny -- Perko, Katherine -- Alexander, Richard -- Schwartz, Joel -- Grindley, Justin C -- Park, Jungeun -- Haug, Jeff S -- Wunderlich, Joshua P -- Li, Hua -- Zhang, Simon -- Johnson, Teri -- Feldman, Ricardo A -- Li, Linheng -- England -- Nature. 2009 Jan 1;457(7225):97-101. doi: 10.1038/nature07639. Epub 2008 Dec 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, Missouri 64110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19052548" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD31/analysis ; Blood Vessels/cytology ; Bone Marrow/pathology ; Cadherins/analysis ; Cell Division ; *Cell Movement ; Cell Separation ; Femur/cytology ; Hematopoietic Stem Cells/*cytology ; Immunoassay/*methods ; Immunohistochemistry ; Mice ; Models, Animal ; Osteoblasts/cytology ; Stem Cell Niche/*cytology ; Tibia/cytology
    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: 2008-12-20
    Description: Label-free chemical contrast is highly desirable in biomedical imaging. Spontaneous Raman microscopy provides specific vibrational signatures of chemical bonds, but is often hindered by low sensitivity. Here we report a three-dimensional multiphoton vibrational imaging technique based on stimulated Raman scattering (SRS). The sensitivity of SRS imaging is significantly greater than that of spontaneous Raman microscopy, which is achieved by implementing high-frequency (megahertz) phase-sensitive detection. SRS microscopy has a major advantage over previous coherent Raman techniques in that it offers background-free and readily interpretable chemical contrast. We show a variety of biomedical applications, such as differentiating distributions of omega-3 fatty acids and saturated lipids in living cells, imaging of brain and skin tissues based on intrinsic lipid contrast, and monitoring drug delivery through the epidermis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3576036/" 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/PMC3576036/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Freudiger, Christian W -- Min, Wei -- Saar, Brian G -- Lu, Sijia -- Holtom, Gary R -- He, Chengwei -- Tsai, Jason C -- Kang, Jing X -- Xie, X Sunney -- CA113605/CA/NCI NIH HHS/ -- DP1 OD000277/OD/NIH HHS/ -- DP1 OD000277-05/OD/NIH HHS/ -- R01 CA113605/CA/NCI NIH HHS/ -- R01 CA113605-01A2/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2008 Dec 19;322(5909):1857-61. doi: 10.1126/science.1165758.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19095943" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line, Tumor ; Corpus Callosum/chemistry/cytology ; Dimethyl Sulfoxide/administration & dosage/pharmacokinetics ; Eicosapentaenoic Acid/metabolism ; Epidermis/chemistry/metabolism/ultrastructure ; Humans ; Imaging, Three-Dimensional/*methods ; Lipids/*analysis ; Mice ; Microscopy/*methods ; Neurons/ultrastructure ; Sensitivity and Specificity ; Skin/chemistry/ultrastructure ; *Spectrum Analysis, Raman ; Tretinoin/administration & dosage/pharmacokinetics ; Vitamin A/analysis/chemistry
    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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