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  • 1
    Publication Date: 2014-12-31
    Description: CSB/ERCC6 (Cockayne syndrome B protein/excision repair cross-complementation group 6), a member of a subfamily of SWI2/SNF2 (SWItch/sucrose nonfermentable)-related chromatin remodelers, plays crucial roles in gene expression and the maintenance of genome integrity. Here, we report the mechanism of the autoregulation of Rhp26, which is the homolog of CSB/ERCC6 in Schizosaccharomyces...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 2
    Publication Date: 2012-12-15
    Description: Although biallelic mutations in non-collagen genes account for 〈10% of individuals with osteogenesis imperfecta, the characterization of these genes has identified new pathways and potential interventions that could benefit even those with mutations in type I collagen genes. We identified mutations in FKBP10 , which encodes the 65 kDa prolyl cis–trans isomerase, FKBP65, in 38 members of 21 families with OI. These include 10 families from the Samoan Islands who share a founder mutation. Of the mutations, three are missense; the remainder either introduce premature termination codons or create frameshifts both of which result in mRNA instability. In four families missense mutations result in loss of most of the protein. The clinical effects of these mutations are short stature, a high incidence of joint contractures at birth and progressive scoliosis and fractures, but there is remarkable variability in phenotype even within families. The loss of the activity of FKBP65 has several effects: type I procollagen secretion is slightly delayed, the stabilization of the intact trimer is incomplete and there is diminished hydroxylation of the telopeptide lysyl residues involved in intermolecular cross-link formation in bone. The phenotype overlaps with that seen with mutations in PLOD2 (Bruck syndrome II), which encodes LH2, the enzyme that hydroxylates the telopeptide lysyl residues. These findings define a set of genes, FKBP10 , PLOD2 and SERPINH1 , that act during procollagen maturation to contribute to molecular stability and post-translational modification of type I procollagen, without which bone mass and quality are abnormal and fractures and contractures result.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 3
    Publication Date: 2012-09-22
    Description: Neuroanatomically precise, genome-wide maps of transcript distributions are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. Here we describe the generation and analysis of a transcriptional atlas of the adult human brain, comprising extensive histological analysis and comprehensive microarray profiling of approximately 900 neuroanatomically precise subdivisions in two individuals. Transcriptional regulation varies enormously by anatomical location, with different regions and their constituent cell types displaying robust molecular signatures that are highly conserved between individuals. Analysis of differential gene expression and gene co-expression relationships demonstrates that brain-wide variation strongly reflects the distributions of major cell classes such as neurons, oligodendrocytes, astrocytes and microglia. Local neighbourhood relationships between fine anatomical subdivisions are associated with discrete neuronal subtypes and genes involved with synaptic transmission. The neocortex displays a relatively homogeneous transcriptional pattern, but with distinct features associated selectively with primary sensorimotor cortices and with enriched frontal lobe expression. Notably, the spatial topography of the neocortex is strongly reflected in its molecular topography-the closer two cortical regions, the more similar their transcriptomes. This freely accessible online data resource forms a high-resolution transcriptional baseline for neurogenetic studies of normal and abnormal human brain function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243026/" 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/PMC4243026/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hawrylycz, Michael J -- Lein, Ed S -- Guillozet-Bongaarts, Angela L -- Shen, Elaine H -- Ng, Lydia -- Miller, Jeremy A -- van de Lagemaat, Louie N -- Smith, Kimberly A -- Ebbert, Amanda -- Riley, Zackery L -- Abajian, Chris -- Beckmann, Christian F -- Bernard, Amy -- Bertagnolli, Darren -- Boe, Andrew F -- Cartagena, Preston M -- Chakravarty, M Mallar -- Chapin, Mike -- Chong, Jimmy -- Dalley, Rachel A -- Daly, Barry David -- Dang, Chinh -- Datta, Suvro -- Dee, Nick -- Dolbeare, Tim A -- Faber, Vance -- Feng, David -- Fowler, David R -- Goldy, Jeff -- Gregor, Benjamin W -- Haradon, Zeb -- Haynor, David R -- Hohmann, John G -- Horvath, Steve -- Howard, Robert E -- Jeromin, Andreas -- Jochim, Jayson M -- Kinnunen, Marty -- Lau, Christopher -- Lazarz, Evan T -- Lee, Changkyu -- Lemon, Tracy A -- Li, Ling -- Li, Yang -- Morris, John A -- Overly, Caroline C -- Parker, Patrick D -- Parry, Sheana E -- Reding, Melissa -- Royall, Joshua J -- Schulkin, Jay -- Sequeira, Pedro Adolfo -- Slaughterbeck, Clifford R -- Smith, Simon C -- Sodt, Andy J -- Sunkin, Susan M -- Swanson, Beryl E -- Vawter, Marquis P -- Williams, Derric -- Wohnoutka, Paul -- Zielke, H Ronald -- Geschwind, Daniel H -- Hof, Patrick R -- Smith, Stephen M -- Koch, Christof -- Grant, Seth G N -- Jones, Allan R -- 066717/Wellcome Trust/United Kingdom -- 077155/Wellcome Trust/United Kingdom -- 1C76HF15069-01-00/PHS HHS/ -- 1C76HF19619-01-00/PHS HHS/ -- G0700399/Medical Research Council/United Kingdom -- G0802238/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2012 Sep 20;489(7416):391-9. doi: 10.1038/nature11405.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Allen Institute for Brain Science, Seattle, Washington 98103, USA. mikeh@alleninstitute.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22996553" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; *Anatomy, Artistic ; Animals ; *Atlases as Topic ; Brain/*anatomy & histology/cytology/*metabolism ; Calbindins ; Databases, Genetic ; Dopamine/metabolism ; *Gene Expression Profiling ; Health ; Hippocampus/cytology/metabolism ; Humans ; In Situ Hybridization ; Internet ; Macaca mulatta/anatomy & histology/genetics ; Male ; Mice ; Neocortex/anatomy & histology/cytology/metabolism ; Oligonucleotide Array Sequence Analysis ; Post-Synaptic Density/genetics ; RNA, Messenger/analysis/genetics ; S100 Calcium Binding Protein G/genetics ; Species Specificity ; Transcriptome/*genetics
    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: 2014-04-30
    Description: Pluripotent stem cells provide a potential solution to current epidemic rates of heart failure by providing human cardiomyocytes to support heart regeneration. Studies of human embryonic-stem-cell-derived cardiomyocytes (hESC-CMs) in small-animal models have shown favourable effects of this treatment. However, it remains unknown whether clinical-scale hESC-CM transplantation is feasible, safe or can provide sufficient myocardial regeneration. Here we show that hESC-CMs can be produced at a clinical scale (more than one billion cells per batch) and cryopreserved with good viability. Using a non-human primate model of myocardial ischaemia followed by reperfusion, we show that cryopreservation and intra-myocardial delivery of one billion hESC-CMs generates extensive remuscularization of the infarcted heart. The hESC-CMs showed progressive but incomplete maturation over a 3-month period. Grafts were perfused by host vasculature, and electromechanical junctions between graft and host myocytes were present within 2 weeks of engraftment. Importantly, grafts showed regular calcium transients that were synchronized to the host electrocardiogram, indicating electromechanical coupling. In contrast to small-animal models, non-fatal ventricular arrhythmias were observed in hESC-CM-engrafted primates. Thus, hESC-CMs can remuscularize substantial amounts of the infarcted monkey heart. Comparable remuscularization of a human heart should be possible, but potential arrhythmic complications need to be overcome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154594/" 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/PMC4154594/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chong, James J H -- Yang, Xiulan -- Don, Creighton W -- Minami, Elina -- Liu, Yen-Wen -- Weyers, Jill J -- Mahoney, William M -- Van Biber, Benjamin -- Cook, Savannah M -- Palpant, Nathan J -- Gantz, Jay A -- Fugate, James A -- Muskheli, Veronica -- Gough, G Michael -- Vogel, Keith W -- Astley, Cliff A -- Hotchkiss, Charlotte E -- Baldessari, Audrey -- Pabon, Lil -- Reinecke, Hans -- Gill, Edward A -- Nelson, Veronica -- Kiem, Hans-Peter -- Laflamme, Michael A -- Murry, Charles E -- P01 GM081619/GM/NIGMS NIH HHS/ -- P01 HL094374/HL/NHLBI NIH HHS/ -- P01GM081619/GM/NIGMS NIH HHS/ -- P01HL094374/HL/NHLBI NIH HHS/ -- P51 OD010425/OD/NIH HHS/ -- R01 HL084642/HL/NHLBI NIH HHS/ -- R01 HL117991/HL/NHLBI NIH HHS/ -- R01HL084642/HL/NHLBI NIH HHS/ -- T32 GM007266/GM/NIGMS NIH HHS/ -- U01 HL100405/HL/NHLBI NIH HHS/ -- U01HL100405/HL/NHLBI NIH HHS/ -- England -- Nature. 2014 Jun 12;510(7504):273-7. doi: 10.1038/nature13233. Epub 2014 Apr 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Center for Cardiovascular Biology, University of Washington, Seattle, Washington 98109, USA [2] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98109, USA [3] Department of Cardiology Westmead Hospital, Westmead, New South Wales 2145, Australia [4] School of Medicine, University of Sydney, Sydney, New South Wales 2006, Australia [5] Department of Pathology, University of Washington, Seattle, Washington 98195, USA [6] University of Sydney School of Medicine, Sydney, New South Wales 2006, Australia and Westmead Millennium Institute and Westmead Hospital, Westmead, New South Wales 2145, Australia. ; 1] Center for Cardiovascular Biology, University of Washington, Seattle, Washington 98109, USA [2] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98109, USA [3] Department of Pathology, University of Washington, Seattle, Washington 98195, USA. ; Department of Medicine/Cardiology, University of Washington, Seattle, Washington 98195, USA. ; 1] Center for Cardiovascular Biology, University of Washington, Seattle, Washington 98109, USA [2] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98109, USA [3] Department of Pathology, University of Washington, Seattle, Washington 98195, USA [4] Department of Medicine/Cardiology, University of Washington, Seattle, Washington 98195, USA. ; Department of Comparative Medicine, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98109, USA. ; 1] Center for Cardiovascular Biology, University of Washington, Seattle, Washington 98109, USA [2] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98109, USA [3] Department of Pathology, University of Washington, Seattle, Washington 98195, USA [4] Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA. ; Washington National Primate Research Center, University of Washington, Seattle, Washington 98195, USA. ; Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. ; 1] Department of Pathology, University of Washington, Seattle, Washington 98195, USA [2] Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. ; 1] Center for Cardiovascular Biology, University of Washington, Seattle, Washington 98109, USA [2] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98109, USA [3] Department of Pathology, University of Washington, Seattle, Washington 98195, USA [4] Department of Medicine/Cardiology, University of Washington, Seattle, Washington 98195, USA [5] Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24776797" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arrhythmias, Cardiac/physiopathology ; Calcium/metabolism ; Cell Survival ; Coronary Vessels/physiology ; Cryopreservation ; Disease Models, Animal ; Electrocardiography ; Embryonic Stem Cells/*cytology ; *Heart ; Humans ; Macaca nemestrina ; Male ; Mice ; Myocardial Infarction/*pathology/*therapy ; Myocytes, Cardiac/*cytology ; *Regeneration ; Regenerative Medicine/methods
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
  • 6
    Publication Date: 2014-07-29
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 7
    Publication Date: 2012-03-01
    Description: Motivation: Next-generation sequencing methods are generating increasingly massive datasets, yet still do not fully capture genetic diversity in the richest environments. To understand such complicated and elusive systems, effective tools are needed to assist with delineating the differences found in and between community datasets. Results: The Small Subunit Markov Modeler (SSuMMo) was developed to probabilistically assign SSU rRNA gene fragments from any sequence dataset to recognized taxonomic clades, producing consistent, comparable cladograms. Accuracy tests predicted 〉90% of genera correctly for sequences downloaded from public reference databases. Sequences from a next-generation sequence dataset, sampled from lean, overweight and obese individuals, were analysed to demonstrate parallel visualization of comparable datasets. SSuMMo shows potential as a valuable curatorial tool, as numerous incorrect and outdated taxonomic entries and annotations were identified in public databases. Availability and implementation: SSuMMo is GPLv3 open source Python software, available at http://code.google.com/p/ssummo/ . Taxonomy and HMM databases can be downloaded from http://bioltfws1.york.ac.uk/ssummo/ . Contact: albl500@york.ac.uk Supplementary information: Supplemental materials are available at Bioinformatics Online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 8
    Publication Date: 2014-11-05
    Description: Author(s): F. Li, C. Chong, J. Yang, P. G. Kevrekidis, and C. Daraio We present a dynamically tunable mechanism of wave transmission in one-dimensional helicoidal phononic crystals in a shape similar to DNA structures. These helicoidal architectures allow slanted nonlinear contact among cylindrical constituents, and the relative torsional movements can dynamically tu... [Phys. Rev. E 90, 053201] Published Tue Nov 04, 2014
    Keywords: Classical Physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
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  • 9
    Publication Date: 2014-05-20
    Description: The trigger loop (TL) of RNA polymerase II (Pol II) is a conserved structural motif that is crucial for Pol II catalytic activity and transcriptional fidelity. The TL remains in an inactive open conformation when the mismatched substrate is bound. In contrast, TL switches from an inactive open state to a closed active state to facilitate nucleotide addition upon the binding of the cognate substrate to the Pol II active site. However, a comprehensive understanding of the specific chemical interactions and substrate structural signatures that are essential to this TL conformational change remains elusive. Here we employed synthetic nucleotide analogues as ‘chemical mutation’ tools coupling with α-amanitin transcription inhibition assay to systematically dissect the key chemical interactions and structural signatures governing the substrate-coupled TL closure in Saccharomyces cerevisiae Pol II. This study reveals novel insights into understanding the molecular basis of TL conformational transition upon substrate binding during Pol II transcription. This synthetic chemical biology approach may be extended to understand the mechanisms of other RNA polymerases as well as other nucleic acid enzymes in future studies.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 10
    Publication Date: 2014-08-13
    Description: Nonenzymatic RNA polymerization in early life is likely to introduce backbone heterogeneity with a mixture of 2′–5′ and 3′–5′ linkages. On the other hand, modern nucleic acids are dominantly composed of 3′–5′ linkages. RNA polymerase II (pol II) is a key modern enzyme responsible for synthesizing 3′–5′–linked RNA with high...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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