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  • 1
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    Regulation of myeloid leukaemia by the cell-fate determinant Musashi (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-07-20
    Description: Chronic myelogenous leukaemia (CML) can progress from a slow growing chronic phase to an aggressive blast crisis phase, but the molecular basis of this transition remains poorly understood. Here we have used mouse models of CML to show that disease progression is regulated by the Musashi-Numb signalling axis. Specifically, we find that the chronic phase is marked by high levels of Numb expression whereas the blast crisis phase has low levels of Numb expression, and that ectopic expression of Numb promotes differentiation and impairs advanced-phase disease in vivo. As a possible explanation for the decreased levels of Numb in the blast crisis phase, we show that NUP98-HOXA9, an oncogene associated with blast crisis CML, can trigger expression of the RNA-binding protein Musashi2 (Msi2), which in turn represses Numb. Notably, loss of Msi2 restores Numb expression and significantly impairs the development and propagation of blast crisis CML in vitro and in vivo. Finally we show that Msi2 expression is not only highly upregulated during human CML progression but is also an early indicator of poorer prognosis. These data show that the Musashi-Numb pathway can control the differentiation of CML cells, and raise the possibility that targeting this pathway may provide a new strategy for the therapy of aggressive leukaemias.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918284/" 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/PMC2918284/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ito, Takahiro -- Kwon, Hyog Young -- Zimdahl, Bryan -- Congdon, Kendra L -- Blum, Jordan -- Lento, William E -- Zhao, Chen -- Lagoo, Anand -- Gerrard, Gareth -- Foroni, Letizia -- Goldman, John -- Goh, Harriet -- Kim, Soo-Hyun -- Kim, Dong-Wook -- Chuah, Charles -- Oehler, Vivian G -- Radich, Jerald P -- Jordan, Craig T -- Reya, Tannishtha -- AI067798/AI/NIAID NIH HHS/ -- CA122206/CA/NCI NIH HHS/ -- CA140371/CA/NCI NIH HHS/ -- CA18029/CA/NCI NIH HHS/ -- DK072234/DK/NIDDK NIH HHS/ -- DK63031/DK/NIDDK NIH HHS/ -- DP1 CA174422/CA/NCI NIH HHS/ -- DP1 OD006430/OD/NIH HHS/ -- DP1 OD006430-01/OD/NIH HHS/ -- DP1 OD006430-02/OD/NIH HHS/ -- DP1OD006430/OD/NIH HHS/ -- HL097767/HL/NHLBI NIH HHS/ -- P01 CA018029/CA/NCI NIH HHS/ -- R01 CA140371/CA/NCI NIH HHS/ -- R01 DK063031/DK/NIDDK NIH HHS/ -- R01 DK063031-01/DK/NIDDK NIH HHS/ -- R01 DK063031-01S1/DK/NIDDK NIH HHS/ -- R01 DK063031-02/DK/NIDDK NIH HHS/ -- R01 DK063031-03/DK/NIDDK NIH HHS/ -- R01 DK063031-04/DK/NIDDK NIH HHS/ -- R01 DK063031-05/DK/NIDDK NIH HHS/ -- R01 DK063031-06/DK/NIDDK NIH HHS/ -- R01 DK063031-07/DK/NIDDK NIH HHS/ -- R01 DK063031-07S1/DK/NIDDK NIH HHS/ -- R01 DK063031-08/DK/NIDDK NIH HHS/ -- R01 DK072234/DK/NIDDK NIH HHS/ -- R01 DK072234-01A1/DK/NIDDK NIH HHS/ -- R01 DK072234-02/DK/NIDDK NIH HHS/ -- R01 DK072234-03/DK/NIDDK NIH HHS/ -- R01 DK072234-04/DK/NIDDK NIH HHS/ -- R01 HL097767/HL/NHLBI NIH HHS/ -- R01 HL097767-01/HL/NHLBI NIH HHS/ -- R01 HL097767-02/HL/NHLBI NIH HHS/ -- T32 GM007184-33/GM/NIGMS NIH HHS/ -- U19 AI067798/AI/NIAID NIH HHS/ -- U19 AI067798-010006/AI/NIAID NIH HHS/ -- U19 AI067798-020006/AI/NIAID NIH HHS/ -- U19 AI067798-030006/AI/NIAID NIH HHS/ -- U19 AI067798-040006/AI/NIAID NIH HHS/ -- U19 AI067798-050006/AI/NIAID NIH HHS/ -- England -- Nature. 2010 Aug 5;466(7307):765-8. doi: 10.1038/nature09171. Epub 2010 Jul 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20639863" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blast Crisis/genetics/metabolism/pathology ; *Cell Differentiation/genetics ; Disease Progression ; Fusion Proteins, bcr-abl/genetics/metabolism ; Gene Expression Regulation, Neoplastic ; Homeodomain Proteins/genetics/metabolism ; Humans ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics/*metabolism/*pathology ; Membrane Proteins/biosynthesis/genetics/metabolism ; Mice ; Mice, Inbred C57BL ; Nerve Tissue Proteins/biosynthesis/genetics/metabolism ; Nuclear Pore Complex Proteins/genetics/metabolism ; Oncogene Proteins, Fusion/genetics/metabolism ; Prognosis ; RNA-Binding Proteins/biosynthesis/genetics/*metabolism ; Receptor, Notch1/metabolism ; Signal Transduction ; Tumor Suppressor Protein p53/metabolism ; Up-Regulation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
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    Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-04-30
    Description: Monozygotic or 'identical' twins have been widely studied to dissect the relative contributions of genetics and environment in human diseases. In multiple sclerosis (MS), an autoimmune demyelinating disease and common cause of neurodegeneration and disability in young adults, disease discordance in monozygotic twins has been interpreted to indicate environmental importance in its pathogenesis. However, genetic and epigenetic differences between monozygotic twins have been described, challenging the accepted experimental model in disambiguating the effects of nature and nurture. Here we report the genome sequences of one MS-discordant monozygotic twin pair, and messenger RNA transcriptome and epigenome sequences of CD4(+) lymphocytes from three MS-discordant, monozygotic twin pairs. No reproducible differences were detected between co-twins among approximately 3.6 million single nucleotide polymorphisms (SNPs) or approximately 0.2 million insertion-deletion polymorphisms. Nor were any reproducible differences observed between siblings of the three twin pairs in HLA haplotypes, confirmed MS-susceptibility SNPs, copy number variations, mRNA and genomic SNP and insertion-deletion genotypes, or the expression of approximately 19,000 genes in CD4(+) T cells. Only 2 to 176 differences in the methylation of approximately 2 million CpG dinucleotides were detected between siblings of the three twin pairs, in contrast to approximately 800 methylation differences between T cells of unrelated individuals and several thousand differences between tissues or between normal and cancerous tissues. In the first systematic effort to estimate sequence variation among monozygotic co-twins, we did not find evidence for genetic, epigenetic or transcriptome differences that explained disease discordance. These are the first, to our knowledge, female, twin and autoimmune disease individual genome sequences reported.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862593/" 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/PMC2862593/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baranzini, Sergio E -- Mudge, Joann -- van Velkinburgh, Jennifer C -- Khankhanian, Pouya -- Khrebtukova, Irina -- Miller, Neil A -- Zhang, Lu -- Farmer, Andrew D -- Bell, Callum J -- Kim, Ryan W -- May, Gregory D -- Woodward, Jimmy E -- Caillier, Stacy J -- McElroy, Joseph P -- Gomez, Refujia -- Pando, Marcelo J -- Clendenen, Leonda E -- Ganusova, Elena E -- Schilkey, Faye D -- Ramaraj, Thiruvarangan -- Khan, Omar A -- Huntley, Jim J -- Luo, Shujun -- Kwok, Pui-Yan -- Wu, Thomas D -- Schroth, Gary P -- Oksenberg, Jorge R -- Hauser, Stephen L -- Kingsmore, Stephen F -- P20 RR016480/RR/NCRR NIH HHS/ -- P20 RR016480-09/RR/NCRR NIH HHS/ -- R01 NS026799/NS/NINDS NIH HHS/ -- R01 NS026799-20A1/NS/NINDS NIH HHS/ -- R01 NS046297/NS/NINDS NIH HHS/ -- R01 NS046297-06/NS/NINDS NIH HHS/ -- R01NS26799/NS/NINDS NIH HHS/ -- R01NS46297/NS/NINDS NIH HHS/ -- RR016480/RR/NCRR NIH HHS/ -- U01 AI066569/AI/NIAID NIH HHS/ -- U01 AI066569-05/AI/NIAID NIH HHS/ -- U19 HD077693/HD/NICHD NIH HHS/ -- England -- Nature. 2010 Apr 29;464(7293):1351-6. doi: 10.1038/nature08990.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurology, University of California at San Francisco, San Francisco, California 94143, USA. sebaran@cgl.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20428171" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Allelic Imbalance/genetics ; Breast/metabolism ; Breast Neoplasms/genetics ; CD4-Positive T-Lymphocytes/metabolism ; Case-Control Studies ; CpG Islands/genetics ; DNA Copy Number Variations/genetics ; DNA Methylation/genetics ; Epigenesis, Genetic/*genetics ; Female ; Genetic Predisposition to Disease/genetics ; Genome, Human/*genetics ; Haplotypes/genetics ; Heterozygote ; Humans ; INDEL Mutation/genetics ; Lung/metabolism ; Lung Neoplasms/genetics ; Male ; Multiple Sclerosis/*genetics ; Polymorphism, Genetic/genetics ; Quantitative Trait Loci/genetics ; RNA, Messenger/analysis/*genetics/metabolism ; Twins, Monozygotic/*genetics
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-07-31
    Description: Small (〈200 nucleotide) RNA (sRNA) profiling of human cells using various technologies demonstrates unexpected complexity of sRNAs with hundreds of thousands of sRNA species present. Genetic and in vitro studies show that these RNAs are not merely degradation products of longer transcripts but could indeed have a function. Furthermore, profiling of RNAs, including the sRNAs, can reveal not only novel transcripts, but also make clear predictions about the existence and properties of novel biochemical pathways operating in a cell. For example, sRNA profiling in human cells indicated the existence of an unknown capping mechanism operating on cleaved RNA, a biochemical component of which was later identified. Here we show that human cells contain a novel type of sRNA that has non-genomically encoded 5' poly(U) tails. The presence of these RNAs at the termini of genes, specifically at the very 3' ends of known mRNAs, strongly argues for the presence of a yet uncharacterized endogenous biochemical pathway in cells that can copy RNA. We show that this pathway can operate on multiple genes, with specific enrichment towards transcript-encoding components of the translational machinery. Finally, we show that genes are also flanked by sense, 3' polyadenylated sRNAs that are likely to be capped.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058539/" 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/PMC3058539/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kapranov, Philipp -- Ozsolak, Fatih -- Kim, Sang Woo -- Foissac, Sylvain -- Lipson, Doron -- Hart, Chris -- Roels, Steve -- Borel, Christelle -- Antonarakis, Stylianos E -- Monaghan, A Paula -- John, Bino -- Milos, Patrice M -- GM079756/GM/NIGMS NIH HHS/ -- MH60774/MH/NIMH NIH HHS/ -- R01 GM079756/GM/NIGMS NIH HHS/ -- R01 GM079756-01A1/GM/NIGMS NIH HHS/ -- R01 GM079756-02/GM/NIGMS NIH HHS/ -- R01 GM079756-03/GM/NIGMS NIH HHS/ -- R01 HG005230/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Jul 29;466(7306):642-6. doi: 10.1038/nature09190.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Helicos BioSciences Corporation, 1 Kendall Sq. Ste B7301 Cambridge, Massachusetts 02139-1671, USA. philippk08@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20671709" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Genes/*genetics ; HeLa Cells ; Humans ; Models, Genetic ; Nucleotides/genetics ; Poly A/genetics/metabolism ; Poly U/genetics/metabolism ; RNA/biosynthesis/*classification/genetics/*metabolism ; RNA, Antisense/classification/genetics/metabolism ; Templates, Genetic
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  • 4
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    High-harmonic generation by resonant plasmon field enhancement (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-06-06
    Description: High-harmonic generation by focusing a femtosecond laser onto a gas is a well-known method of producing coherent extreme-ultraviolet (EUV) light. This nonlinear conversion process requires high pulse intensities, greater than 10(13) W cm(-2), which are not directly attainable using only the output power of a femtosecond oscillator. Chirped-pulse amplification enables the pulse intensity to exceed this threshold by incorporating several regenerative and/or multi-pass amplifier cavities in tandem. Intracavity pulse amplification (designed not to reduce the pulse repetition rate) also requires a long cavity. Here we demonstrate a method of high-harmonic generation that requires no extra cavities. This is achieved by exploiting the local field enhancement induced by resonant plasmons within a metallic nanostructure consisting of bow-tie-shaped gold elements on a sapphire substrate. In our experiment, the output beam emitted from a modest femtosecond oscillator (100-kW peak power, 1.3-nJ pulse energy and 10-fs pulse duration) is directly focused onto the nanostructure with a pulse intensity of only 10(11) W cm(-2). The enhancement factor exceeds 20 dB, which is sufficient to produce EUV wavelengths down to 47 nm by injection with an argon gas jet. The method could form the basis for constructing laptop-sized EUV light sources for advanced lithography and high-resolution imaging applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Seungchul -- Jin, Jonghan -- Kim, Young-Jin -- Park, In-Yong -- Kim, Yunseok -- Kim, Seung-Woo -- England -- Nature. 2008 Jun 5;453(7196):757-60. doi: 10.1038/nature07012.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Billionth Uncertainty Precision Engineering Group, KAIST, Daedeok Science Town, Daejeon 305-701, South Korea.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18528390" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
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  • 5
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    A highly annotated whole-genome sequence of a Korean individual (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-07-10
    Description: Recent advances in sequencing technologies have initiated an era of personal genome sequences. To date, human genome sequences have been reported for individuals with ancestry in three distinct geographical regions: a Yoruba African, two individuals of northwest European origin, and a person from China. Here we provide a highly annotated, whole-genome sequence for a Korean individual, known as AK1. The genome of AK1 was determined by an exacting, combined approach that included whole-genome shotgun sequencing (27.8x coverage), targeted bacterial artificial chromosome sequencing, and high-resolution comparative genomic hybridization using custom microarrays featuring more than 24 million probes. Alignment to the NCBI reference, a composite of several ethnic clades, disclosed nearly 3.45 million single nucleotide polymorphisms (SNPs), including 10,162 non-synonymous SNPs, and 170,202 deletion or insertion polymorphisms (indels). SNP and indel densities were strongly correlated genome-wide. Applying very conservative criteria yielded highly reliable copy number variants for clinical considerations. Potential medical phenotypes were annotated for non-synonymous SNPs, coding domain indels, and structural variants. The integration of several human whole-genome sequences derived from several ethnic groups will assist in understanding genetic ancestry, migration patterns and population bottlenecks.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860965/" 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/PMC2860965/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Jong-Il -- Ju, Young Seok -- Park, Hansoo -- Kim, Sheehyun -- Lee, Seonwook -- Yi, Jae-Hyuk -- Mudge, Joann -- Miller, Neil A -- Hong, Dongwan -- Bell, Callum J -- Kim, Hye-Sun -- Chung, In-Soon -- Lee, Woo-Chung -- Lee, Ji-Sun -- Seo, Seung-Hyun -- Yun, Ji-Young -- Woo, Hyun Nyun -- Lee, Heewook -- Suh, Dongwhan -- Lee, Seungbok -- Kim, Hyun-Jin -- Yavartanoo, Maryam -- Kwak, Minhye -- Zheng, Ying -- Lee, Mi Kyeong -- Park, Hyunjun -- Kim, Jeong Yeon -- Gokcumen, Omer -- Mills, Ryan E -- Zaranek, Alexander Wait -- Thakuria, Joseph -- Wu, Xiaodi -- Kim, Ryan W -- Huntley, Jim J -- Luo, Shujun -- Schroth, Gary P -- Wu, Thomas D -- Kim, HyeRan -- Yang, Kap-Seok -- Park, Woong-Yang -- Kim, Hyungtae -- Church, George M -- Lee, Charles -- Kingsmore, Stephen F -- Seo, Jeong-Sun -- HG004221/HG/NHGRI NIH HHS/ -- P20 RR016480/RR/NCRR NIH HHS/ -- P20 RR016480-08/RR/NCRR NIH HHS/ -- RR016480/RR/NCRR NIH HHS/ -- U01 AI066569/AI/NIAID NIH HHS/ -- U01 AI066569-04/AI/NIAID NIH HHS/ -- U19 HD077693/HD/NICHD NIH HHS/ -- England -- Nature. 2009 Aug 20;460(7258):1011-5. doi: 10.1038/nature08211. Epub 2009 Jul 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, Korea.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19587683" target="_blank"〉PubMed〈/a〉
    Keywords: Asian Continental Ancestry Group/*genetics ; Chromosomes, Artificial, Bacterial/genetics ; Comparative Genomic Hybridization ; Computational Biology ; Genome, Human/*genetics ; Humans ; INDEL Mutation/genetics ; Korea ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA
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  • 6
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    Hexameric assembly of the proteasomal ATPases is templated through their C termini (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-05-05
    Description: Substrates of the proteasome are recognized and unfolded by the regulatory particle, and then translocated into the core particle (CP) to be degraded. A hetero-hexameric ATPase ring, containing subunits Rpt1-6, is situated within the base subassembly of the regulatory particle. The ATPase ring sits atop the CP, with the Rpt carboxy termini inserted into pockets in the CP. Here we identify a previously unknown function of the Rpt proteins in proteasome biogenesis through deleting the C-terminal residue from each Rpt in the yeast Saccharomyces cerevisiae. Our results indicate that assembly of the hexameric ATPase ring is templated on the CP. We have also identified an apparent intermediate in base assembly, BP1, which contains Rpn1, three Rpts and Hsm3, a chaperone for base assembly. The Rpt proteins with the strongest assembly phenotypes, Rpt4 and Rpt6, were absent from BP1. We propose that Rpt4 and Rpt6 form a nucleating complex to initiate base assembly, and that this complex is subsequently joined by BP1 to complete the Rpt ring. Our studies show that assembly of the proteasome base is a rapid yet highly orchestrated process.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2722381/" 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/PMC2722381/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Soyeon -- Roelofs, Jeroen -- Kim, Woong -- Robert, Jessica -- Schmidt, Marion -- Gygi, Steven P -- Finley, Daniel -- 5F32GM75737-2/GM/NIGMS NIH HHS/ -- F32 GM075737-01A2/GM/NIGMS NIH HHS/ -- GM043601/GM/NIGMS NIH HHS/ -- GM67945/GM/NIGMS NIH HHS/ -- R01 GM084228/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jun 11;459(7248):866-70. doi: 10.1038/nature08065.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19412160" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/genetics/*metabolism ; Molecular Chaperones/metabolism ; Proteasome Endopeptidase Complex/*biosynthesis/*chemistry/genetics/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism
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  • 7
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    A strong ferroelectric ferromagnet created by means of spin-lattice coupling (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-08-21
    Description: Ferroelectric ferromagnets are exceedingly rare, fundamentally interesting multiferroic materials that could give rise to new technologies in which the low power and high speed of field-effect electronics are combined with the permanence and routability of voltage-controlled ferromagnetism. Furthermore, the properties of the few compounds that simultaneously exhibit these phenomena are insignificant in comparison with those of useful ferroelectrics or ferromagnets: their spontaneous polarizations or magnetizations are smaller by a factor of 1,000 or more. The same holds for magnetic- or electric-field-induced multiferroics. Owing to the weak properties of single-phase multiferroics, composite and multilayer approaches involving strain-coupled piezoelectric and magnetostrictive components are the closest to application today. Recently, however, a new route to ferroelectric ferromagnets was proposed by which magnetically ordered insulators that are neither ferroelectric nor ferromagnetic are transformed into ferroelectric ferromagnets using a single control parameter, strain. The system targeted, EuTiO(3), was predicted to exhibit strong ferromagnetism (spontaneous magnetization, approximately 7 Bohr magnetons per Eu) and strong ferroelectricity (spontaneous polarization, approximately 10 microC cm(-2)) simultaneously under large biaxial compressive strain. These values are orders of magnitude higher than those of any known ferroelectric ferromagnet and rival the best materials that are solely ferroelectric or ferromagnetic. Hindered by the absence of an appropriate substrate to provide the desired compression we turned to tensile strain. Here we show both experimentally and theoretically the emergence of a multiferroic state under biaxial tension with the unexpected benefit that even lower strains are required, thereby allowing thicker high-quality crystalline films. This realization of a strong ferromagnetic ferroelectric points the way to high-temperature manifestations of this spin-lattice coupling mechanism. Our work demonstrates that a single experimental parameter, strain, simultaneously controls multiple order parameters and is a viable alternative tuning parameter to composition for creating multiferroics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, June Hyuk -- Fang, Lei -- Vlahos, Eftihia -- Ke, Xianglin -- Jung, Young Woo -- Kourkoutis, Lena Fitting -- Kim, Jong-Woo -- Ryan, Philip J -- Heeg, Tassilo -- Roeckerath, Martin -- Goian, Veronica -- Bernhagen, Margitta -- Uecker, Reinhard -- Hammel, P Chris -- Rabe, Karin M -- Kamba, Stanislav -- Schubert, Jurgen -- Freeland, John W -- Muller, David A -- Fennie, Craig J -- Schiffer, Peter -- Gopalan, Venkatraman -- Johnston-Halperin, Ezekiel -- Schlom, Darrell G -- England -- Nature. 2010 Aug 19;466(7309):954-8. doi: 10.1038/nature09331.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853-1501, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20725036" target="_blank"〉PubMed〈/a〉
    Keywords: Electric Capacitance ; *Electricity ; Europium/*chemistry ; *Magnetics ; Microscopy, Electron, Scanning Transmission ; Oxides/*chemistry ; Temperature ; Titanium/*chemistry ; X-Ray Diffraction
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  • 8
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    Direct observation of bond formation in solution with femtosecond X-ray scattering (2015)
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    Publication Date: 2015-02-20
    Description: The making and breaking of atomic bonds are essential processes in chemical reactions. Although the ultrafast dynamics of bond breaking have been studied intensively using time-resolved techniques, it is very difficult to study the structural dynamics of bond making, mainly because of its bimolecular nature. It is especially difficult to initiate and follow diffusion-limited bond formation in solution with ultrahigh time resolution. Here we use femtosecond time-resolved X-ray solution scattering to visualize the formation of a gold trimer complex, [Au(CN)2(-)]3 in real time without the limitation imposed by slow diffusion. This photoexcited gold trimer, which has weakly bound gold atoms in the ground state, undergoes a sequence of structural changes, and our experiments probe the dynamics of individual reaction steps, including covalent bond formation, the bent-to-linear transition, bond contraction and tetramer formation with a time resolution of approximately 500 femtoseconds. We also determined the three-dimensional structures of reaction intermediates with sub-angstrom spatial resolution. This work demonstrates that it is possible to track in detail and in real time the structural changes that occur during a chemical reaction in solution using X-ray free-electron lasers and advanced analysis of time-resolved solution scattering data.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Kyung Hwan -- Kim, Jong Goo -- Nozawa, Shunsuke -- Sato, Tokushi -- Oang, Key Young -- Kim, Tae Wu -- Ki, Hosung -- Jo, Junbeom -- Park, Sungjun -- Song, Changyong -- Sato, Takahiro -- Ogawa, Kanade -- Togashi, Tadashi -- Tono, Kensuke -- Yabashi, Makina -- Ishikawa, Tetsuya -- Kim, Joonghan -- Ryoo, Ryong -- Kim, Jeongho -- Ihee, Hyotcherl -- Adachi, Shin-ichi -- England -- Nature. 2015 Feb 19;518(7539):385-9. doi: 10.1038/nature14163.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, South Korea [2] Department of Chemistry, KAIST, Daejeon 305-701, South Korea. ; Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan. ; RIKEN SPring-8 Center, Kouto 1-1-1, Sayo, Hyogo 679-5148, Japan. ; Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan. ; Department of Chemistry, The Catholic University of Korea, Bucheon 420-743, South Korea. ; Department of Chemistry, Inha University, Incheon 402-751, South Korea. ; 1] Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan [2] Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25693570" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
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    Analyses of pig genomes provide insight into porcine demography and evolution (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-11-16
    Description: For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564/" 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/PMC3566564/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Groenen, Martien A M -- Archibald, Alan L -- Uenishi, Hirohide -- Tuggle, Christopher K -- Takeuchi, Yasuhiro -- Rothschild, Max F -- Rogel-Gaillard, Claire -- Park, Chankyu -- Milan, Denis -- Megens, Hendrik-Jan -- Li, Shengting -- Larkin, Denis M -- Kim, Heebal -- Frantz, Laurent A F -- Caccamo, Mario -- Ahn, Hyeonju -- Aken, Bronwen L -- Anselmo, Anna -- Anthon, Christian -- Auvil, Loretta -- Badaoui, Bouabid -- Beattie, Craig W -- Bendixen, Christian -- Berman, Daniel -- Blecha, Frank -- Blomberg, Jonas -- Bolund, Lars -- Bosse, Mirte -- Botti, Sara -- Bujie, Zhan -- Bystrom, Megan -- Capitanu, Boris -- Carvalho-Silva, Denise -- Chardon, Patrick -- Chen, Celine -- Cheng, Ryan -- Choi, Sang-Haeng -- Chow, William -- Clark, Richard C -- Clee, Christopher -- Crooijmans, Richard P M A -- Dawson, Harry D -- Dehais, Patrice -- De Sapio, Fioravante -- Dibbits, Bert -- Drou, Nizar -- Du, Zhi-Qiang -- Eversole, Kellye -- Fadista, Joao -- Fairley, Susan -- Faraut, Thomas -- Faulkner, Geoffrey J -- Fowler, Katie E -- Fredholm, Merete -- Fritz, Eric -- Gilbert, James G R -- Giuffra, Elisabetta -- Gorodkin, Jan -- Griffin, Darren K -- Harrow, Jennifer L -- Hayward, Alexander -- Howe, Kerstin -- Hu, Zhi-Liang -- Humphray, Sean J -- Hunt, Toby -- Hornshoj, Henrik -- Jeon, Jin-Tae -- Jern, Patric -- Jones, Matthew -- Jurka, Jerzy -- Kanamori, Hiroyuki -- Kapetanovic, Ronan -- Kim, Jaebum -- Kim, Jae-Hwan -- Kim, Kyu-Won -- Kim, Tae-Hun -- Larson, Greger -- Lee, Kyooyeol -- Lee, Kyung-Tai -- Leggett, Richard -- Lewin, Harris A -- Li, Yingrui -- Liu, Wansheng -- Loveland, Jane E -- Lu, Yao -- Lunney, Joan K -- Ma, Jian -- Madsen, Ole -- Mann, Katherine -- Matthews, Lucy -- McLaren, Stuart -- Morozumi, Takeya -- Murtaugh, Michael P -- Narayan, Jitendra -- Nguyen, Dinh Truong -- Ni, Peixiang -- Oh, Song-Jung -- Onteru, Suneel -- Panitz, Frank -- Park, Eung-Woo -- Park, Hong-Seog -- Pascal, Geraldine -- Paudel, Yogesh -- Perez-Enciso, Miguel -- Ramirez-Gonzalez, Ricardo -- Reecy, James M -- Rodriguez-Zas, Sandra -- Rohrer, Gary A -- Rund, Lauretta -- Sang, Yongming -- Schachtschneider, Kyle -- Schraiber, Joshua G -- Schwartz, John -- Scobie, Linda -- Scott, Carol -- Searle, Stephen -- Servin, Bertrand -- Southey, Bruce R -- Sperber, Goran -- Stadler, Peter -- Sweedler, Jonathan V -- Tafer, Hakim -- Thomsen, Bo -- Wali, Rashmi -- Wang, Jian -- Wang, Jun -- White, Simon -- Xu, Xun -- Yerle, Martine -- Zhang, Guojie -- Zhang, Jianguo -- Zhang, Jie -- Zhao, Shuhong -- Rogers, Jane -- Churcher, Carol -- Schook, Lawrence B -- 095908/Wellcome Trust/United Kingdom -- 249894/European Research Council/International -- 5 P41 LM006252/LM/NLM NIH HHS/ -- 5 P41LM006252/LM/NLM NIH HHS/ -- BB/E010520/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E010520/2/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E010768/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E011640/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G004013/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H005935/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/I025328/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0900950/Medical Research Council/United Kingdom -- P20-RR017686/RR/NCRR NIH HHS/ -- P30 DA018310/DA/NIDA NIH HHS/ -- R13 RR020283A/RR/NCRR NIH HHS/ -- R13 RR032267A/RR/NCRR NIH HHS/ -- R21 DA027548/DA/NIDA NIH HHS/ -- R21 HG006464/HG/NHGRI NIH HHS/ -- T32 AI083196/AI/NIAID NIH HHS/ -- England -- Nature. 2012 Nov 15;491(7424):393-8. doi: 10.1038/nature11622.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands. martien.groenen@wur.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23151582" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Demography ; Genome/*genetics ; Models, Animal ; Molecular Sequence Data ; *Phylogeny ; Population Dynamics ; Sus scrofa/*classification/*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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  • 10
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    Dicalcium nitride as a two-dimensional electride with an anionic electron layer (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-02-01
    Description: Recent studies suggest that electrides--ionic crystals in which electrons serve as anions--are not exceptional materials but rather a generalized form, particularly under high pressure. The topology of the cavities confining anionic electrons determines their physical properties. At present, reported confining sites consist only of zero-dimensional cavities or weakly linked channels. Here we report a layered-structure electride of dicalcium nitride, Ca(2)N, which possesses two-dimensionally confined anionic electrons whose concentration agrees well with that for the chemical formula of [Ca(2)N](+).e(-). Two-dimensional transport characteristics are demonstrated by a high electron mobility (520 cm(2) V(-1) s(-1)) and long mean scattering time (0.6 picoseconds) with a mean free path of 0.12 micrometres. The quadratic temperature dependence of the resistivity up to 120 Kelvin indicates the presence of an electron-electron interaction. A striking anisotropic magnetoresistance behaviour with respect to the direction of magnetic field (negative for the field perpendicular to the conducting plane and positive for the field parallel to it) is observed, confirming diffusive two-dimensional transport in dense electron layers. Additionally, band calculations support confinement of anionic electrons within the interlayer space, and photoemission measurements confirm anisotropic low work functions of 3.5 and 2.6 electronvolts, revealing the loosely bound nature of the anionic electrons. We conclude that Ca(2)N is a two-dimensional electride in terms of [Ca(2)N](+).e(-).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Kimoon -- Kim, Sung Wng -- Toda, Yoshitake -- Matsuishi, Satoru -- Hosono, Hideo -- England -- Nature. 2013 Feb 21;494(7437):336-40. doi: 10.1038/nature11812. Epub 2013 Jan 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Frontier Research Center, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23364689" 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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