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  • 1
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    Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-09
    Description: Shewanella putrefaciens CN-32 contains a single Type I-Fv CRISPR-Cas system which confers adaptive immunity against bacteriophage infection. Three Cas proteins (Cas6f, Cas7fv, Cas5fv) and mature CRISPR RNAs were shown to be required for the assembly of an interference complex termed Cascade. The Cas protein-CRISPR RNA interaction sites within this complex were identified via mass spectrometry. Additional Cas proteins, commonly described as large and small subunits, that are present in all other investigated Cascade structures, were not detected. We introduced this minimal Type I system in Escherichia coli and show that it provides heterologous protection against lambda phage. The absence of a large subunit suggests that the length of the crRNA might not be fixed and recombinant Cascade complexes with drastically shortened and elongated crRNAs were engineered. Size-exclusion chromatography and small-angle X-ray scattering analyses revealed that the number of Cas7fv backbone subunits is adjusted in these shortened and extended Cascade variants. Larger Cascade complexes can still confer immunity against lambda phage infection in E. coli . Minimized Type I CRISPR-Cas systems expand our understanding of the evolution of Cascade assembly and diversity. Their adjustable crRNA length opens the possibility for customizing target DNA specificity.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Fast, accurate, and reliable molecular docking with QuickVina 2 (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-27
    Description: Motivation: The need for efficient molecular docking tools for high-throughput screening is growing alongside the rapid growth of drug-fragment databases. AutoDock Vina (‘Vina’) is a widely used docking tool with parallelization for speed. QuickVina (‘QVina 1’) then further enhanced the speed via a heuristics, requiring high exhaustiveness. With low exhaustiveness, its accuracy was compromised. We present in this article the latest version of QuickVina (‘QVina 2’) that inherits both the speed of QVina 1 and the reliability of the original Vina. Results: We tested the efficacy of QVina 2 on the core set of PDBbind 2014. With the default exhaustiveness level of Vina ( i.e. 8), a maximum of 20.49-fold and an average of 2.30-fold acceleration with a correlation coefficient of 0.967 for the first mode and 0.911 for the sum of all modes were attained over the original Vina. A tendency for higher acceleration with increased number of rotatable bonds as the design variables was observed. On the accuracy, Vina wins over QVina 2 on 30% of the data with average energy difference of only 0.58 kcal/mol. On the same dataset, GOLD produced RMSD smaller than 2 Å on 56.9% of the data while QVina 2 attained 63.1%. Availability and implementation : The C++ source code of QVina 2 is available at ( www.qvina.org ). Contact: aalhossary@pmail.ntu.edu.sg 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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  • 3
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    Asymmetric structure in Sgr A* at 3 mm from closure phase measurements with VLBA, GBT and LMT (2016)
    Oxford University Press
    Details
    Publication Date: 2016-08-13
    Description: We present the results of a closure phase analysis of 3 mm very long baseline interferometry measurements performed on Sagittarius A* (Sgr A*). We have analysed observations made in 2015 May using the Very Long Baseline Array, the Robert C. Byrd Green Bank Telescope and the Large Millimeter Telescope Alfonso Serrano and obtained non-zero closure phase measurements on several station triangles – indicative of a non-point-symmetric source structure. The data are fitted with an asymmetric source structure model in Sgr A*, represented by a simple two-component model, which favours a fainter component due east of the main source. This result is discussed in light of a scattering screen with substructure or an intrinsically asymmetric source.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Reference genomes of two indica rice varieties [Genetics] (2016)
    National Academy of Sciences
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    Publication Date: 2016-08-31
    Description: Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica. Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 5
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    Role of PVDBP1 in Duffy-null Africans [Microbiology] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-06-01
    Description: The ability of the malaria parasite Plasmodium vivax to invade erythrocytes is dependent on the expression of the Duffy blood group antigen on erythrocytes. Consequently, Africans who are null for the Duffy antigen are not susceptible to P. vivax infections. Recently, P. vivax infections in Duffy-null Africans have been documented,...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Evidence for erythrocyte-binding antigen 175 as a component of a ligand-blocking blood-stage malaria vaccine [Microbiology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-05-04
    Description: The ligands that pathogens use to invade their target cells have often proven to be good targets for vaccine development. However, Plasmodium falciparum has redundant ligands that mediate invasion of erythrocytes. The first requirement for the development of a successful ligand-blocking malaria vaccine is the demonstration that antibodies induced to each ligand can block the erythrocyte invasion of parasites with polymorphic sequences. Because of P. falciparum’s redundancy in erythrocyte invasion, each ligand needs to be studied under artificial conditions in which parasite invasion is restricted in its use of alternative pathways. Here we investigate the role of erythrocyte-binding antigen 175 (EBA-175), a parasite ligand that binds to sialic acid on glycophorin A, in the invasion of erythrocytes by 10 P. falciparum clones under conditions in which invasion is partially limited to the EBA-175–glycophorin A pathway, using chymotrypsin-treated erythrocytes. We show that the ability to invade erythrocytes for both sialic acid–independent and sialic acid–dependent pathways requires the EBA-175–glycophorin A pathway for erythrocyte invasion. Importantly, antibodies against region II of EBA-175 from the 3D7 clone blocked invasion of chymotrypsin-treated erythrocytes by 〉50% by all parasite clones studied, including those with multiple different mutations described in the literature. The one exception was FCR3, which had a similar sequence to 3D7 but only 30% inhibition of invasion of chymotrypsin-treated erythrocytes, indicating alternative pathways for invasion of chymotrypsin-treated erythrocytes. Our findings suggest that antibodies to region II of EBA-175, as one component of a ligand-blocking malaria vaccine, are largely unaffected by polymorphism in EBA-175.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    Coexistence of Fermi arcs and Fermi pockets in a high-T(c) copper oxide superconductor (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-11-20
    Description: In the pseudogap state of the high-transition-temperature (high-T(c)) copper oxide superconductors, angle-resolved photoemission (ARPES) measurements have seen Fermi arcs-that is, open-ended gapless sections in the large Fermi surface-rather than a closed loop expected of an ordinary metal. This is all the more puzzling because Fermi pockets (small closed Fermi surface features) have been suggested by recent quantum oscillation measurements. The Fermi arcs cannot be understood in terms of existing theories, although there is a solution in the form of conventional Fermi surface pockets associated with competing order, but with a back side that is for detailed reasons invisible to photoemission probes. Here we report ARPES measurements of Bi(2)Sr(2-x)La(x)CuO(6+delta) (La-Bi2201) that reveal Fermi pockets. The charge carriers in the pockets are holes, and the pockets show an unusual dependence on doping: they exist in underdoped but not overdoped samples. A surprise is that these Fermi pockets appear to coexist with the Fermi arcs. This coexistence has not been expected theoretically.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meng, Jianqiao -- Liu, Guodong -- Zhang, Wentao -- Zhao, Lin -- Liu, Haiyun -- Jia, Xiaowen -- Mu, Daixiang -- Liu, Shanyu -- Dong, Xiaoli -- Zhang, Jun -- Lu, Wei -- Wang, Guiling -- Zhou, Yong -- Zhu, Yong -- Wang, Xiaoyang -- Xu, Zuyan -- Chen, Chuangtian -- Zhou, X J -- England -- Nature. 2009 Nov 19;462(7271):335-8. doi: 10.1038/nature08521.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Laboratory for Superconductivity, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19924210" target="_blank"〉PubMed〈/a〉
    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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  • 8
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    A new redox cofactor in eukaryotic enzymes: 6-hydroxydopa at the active site of bovine serum amine oxidase (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-05-25
    Description: An active site, cofactor-containing peptide has been obtained in high yield from bovine serum amine oxidase. Sequencing of this pentapeptide indicates: Leu-Asn-X-Asp-Tyr. Analysis of the peptide by mass spectrometry, ultraviolet-visible spectroscopy, and proton nuclear magnetic resonance leads to the identification of X as 6-hydroxydopa. This result indicates that, contrary to previous proposals, pyrroloquinoline quinone is not the active site cofactor in mammalian copper amine oxidases. Although 6-hydroxydopa has been implicated in neurotoxicity, the data presented suggest that this compound has a functional role at an enzyme active site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janes, S M -- Mu, D -- Wemmer, D -- Smith, A J -- Kaur, S -- Maltby, D -- Burlingame, A L -- Klinman, J P -- GM 39296/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 May 25;248(4958):981-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2111581" target="_blank"〉PubMed〈/a〉
    Keywords: *Amine Oxidase (Copper-Containing) ; Amino Acid Sequence ; Animals ; Binding Sites ; Cattle ; Copper ; Dihydroxyphenylalanine/*analogs & derivatives/metabolism ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Molecular Sequence Data ; Oxidoreductases/metabolism ; Oxidoreductases Acting on CH-NH Group Donors/blood/*metabolism ; Peptide Fragments/analysis/chemical synthesis ; Quinones/metabolism ; Spectrophotometry, Ultraviolet
    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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  • 9
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    Genome sequence and analysis of the tuber crop potato (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-07-12
    Description: Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Potato Genome Sequencing Consortium -- Xu, Xun -- Pan, Shengkai -- Cheng, Shifeng -- Zhang, Bo -- Mu, Desheng -- Ni, Peixiang -- Zhang, Gengyun -- Yang, Shuang -- Li, Ruiqiang -- Wang, Jun -- Orjeda, Gisella -- Guzman, Frank -- Torres, Michael -- Lozano, Roberto -- Ponce, Olga -- Martinez, Diana -- De la Cruz, German -- Chakrabarti, S K -- Patil, Virupaksh U -- Skryabin, Konstantin G -- Kuznetsov, Boris B -- Ravin, Nikolai V -- Kolganova, Tatjana V -- Beletsky, Alexey V -- Mardanov, Andrei V -- Di Genova, Alex -- Bolser, Daniel M -- Martin, David M A -- Li, Guangcun -- Yang, Yu -- Kuang, Hanhui -- Hu, Qun -- Xiong, Xingyao -- Bishop, Gerard J -- Sagredo, Boris -- Mejia, Nilo -- Zagorski, Wlodzimierz -- Gromadka, Robert -- Gawor, Jan -- Szczesny, Pawel -- Huang, Sanwen -- Zhang, Zhonghua -- Liang, Chunbo -- He, Jun -- Li, Ying -- He, Ying -- Xu, Jianfei -- Zhang, Youjun -- Xie, Binyan -- Du, Yongchen -- Qu, Dongyu -- Bonierbale, Merideth -- Ghislain, Marc -- Herrera, Maria del Rosario -- Giuliano, Giovanni -- Pietrella, Marco -- Perrotta, Gaetano -- Facella, Paolo -- O'Brien, Kimberly -- Feingold, Sergio E -- Barreiro, Leandro E -- Massa, Gabriela A -- Diambra, Luis -- Whitty, Brett R -- Vaillancourt, Brieanne -- Lin, Haining -- Massa, Alicia N -- Geoffroy, Michael -- Lundback, Steven -- DellaPenna, Dean -- Buell, C Robin -- Sharma, Sanjeev Kumar -- Marshall, David F -- Waugh, Robbie -- Bryan, Glenn J -- Destefanis, Marialaura -- Nagy, Istvan -- Milbourne, Dan -- Thomson, Susan J -- Fiers, Mark -- Jacobs, Jeanne M E -- Nielsen, Kare L -- Sonderkaer, Mads -- Iovene, Marina -- Torres, Giovana A -- Jiang, Jiming -- Veilleux, Richard E -- Bachem, Christian W B -- de Boer, Jan -- Borm, Theo -- Kloosterman, Bjorn -- van Eck, Herman -- Datema, Erwin -- Hekkert, Bas te Lintel -- Goverse, Aska -- van Ham, Roeland C H J -- Visser, Richard G F -- BB/F012640/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F012640/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- WT 083481/Wellcome Trust/United Kingdom -- England -- Nature. 2011 Jul 10;475(7355):189-95. doi: 10.1038/nature10158.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BGI-Shenzhen, Chinese Ministry of Agricultural, Key Lab of Genomics, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21743474" target="_blank"〉PubMed〈/a〉
    Keywords: Evolution, Molecular ; Gene Duplication ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genetic Variation ; Genome, Plant/*genetics ; *Genomics ; Haplotypes/genetics ; Heterozygote ; Homozygote ; Immunity, Innate ; Inbreeding ; Molecular Sequence Annotation ; Molecular Sequence Data ; Plant Diseases/genetics ; Ploidies ; Solanum tuberosum/*genetics/physiology
    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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  • 10
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    Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences (2016)
    Oxford University Press
    Details
    Publication Date: 2016-10-08
    Description: Motivation: Next generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative datasets (e.g. physical, optical and genetic maps). To address this problem, we developed a semi-automated software tool—Genome Puzzle Master (GPM)—that enables the integration of additional genomic signposts to edit and build ‘new-gen-assemblies’ that result in high-quality ‘annotation-ready’ pseudomolecules. Results: With GPM, loaded datasets can be connected to each other via their logical relationships which accomplishes tasks to ‘group,’ ‘merge,’ ‘order and orient’ sequences in a draft assembly. Manual editing can also be performed with a user-friendly graphical interface. Final pseudomolecules reflect a user’s total data package and are available for long-term project management. GPM is a web-based pipeline and an important part of a Laboratory Information Management System (LIMS) which can be easily deployed on local servers for any genome research laboratory. Availability and Implementation: The GPM (with LIMS) package is available at https://github.com/Jianwei-Zhang/LIMS Contacts: jzhang@mail.hzau.edu.cn or rwing@mail.arizona.edu 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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